WO2016075546A2 - Antibodies that neutralize ebola virus and uses thereof - Google Patents

Antibodies that neutralize ebola virus and uses thereof Download PDF

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Publication number
WO2016075546A2
WO2016075546A2 PCT/IB2015/002342 IB2015002342W WO2016075546A2 WO 2016075546 A2 WO2016075546 A2 WO 2016075546A2 IB 2015002342 W IB2015002342 W IB 2015002342W WO 2016075546 A2 WO2016075546 A2 WO 2016075546A2
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amino acid
antibody
seq
acid sequences
cdr2
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PCT/IB2015/002342
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French (fr)
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WO2016075546A3 (en
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Antonio Lanzavecchia
Davide Corti
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Antonio Lanzavecchia
Davide Corti
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Publication of WO2016075546A2 publication Critical patent/WO2016075546A2/en
Publication of WO2016075546A3 publication Critical patent/WO2016075546A3/en

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/08—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from viruses
    • C07K16/10—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from viruses from RNA viruses
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/20—Immunoglobulins specific features characterized by taxonomic origin
    • C07K2317/21—Immunoglobulins specific features characterized by taxonomic origin from primates, e.g. man
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
    • C07K2317/56—Immunoglobulins specific features characterized by immunoglobulin fragments variable (Fv) region, i.e. VH and/or VL
    • C07K2317/565—Complementarity determining region [CDR]

Definitions

  • Ebola virus is one of five known species within the genus Ebolavirus. There are five (5) EBOV species: Zaire (ZEBOV), Sudan (SEBOV), Bunbibugyo (BEBOV), Reston (REBOV), Cote d'lrium (CIEBOV).
  • Zaire Zaire
  • SEBOV Sudan
  • BEBOV Bunbibugyo
  • REBOV Reston
  • Ebola virus disease EVD
  • the virus was first recognized in 1976 during an outbreak in the Ebola River valley in Zaire (now the Democratic Republic of Congo). Ebola virus has caused the majority of human deaths from EVD, and ZEBOV is the cause of the 2014 Ebola virus epidemic in West Africa.
  • EBOV is an enveloped virus with a bacilliform to filamentous shape, with a diameter of approximately 80 nm and length between 800-1000 nm.
  • the viral glycoprotein projects from the viral lipid bilayer with spikes that are 7-10 nm in length.
  • the EBOV genome is a single-stranded RNA that is approximately 19,000 nucleotides long. It encodes seven structural proteins:
  • nucleoprotein NP
  • polymerase cofactor VP35
  • VP40 polymerase cofactor
  • glycoprotein GP
  • transcription activator VP30
  • VP24 RNA polymerase
  • GP is polypeptide with 676 amino acids (transcriptional editing is also responsible for the production of soluble GP, sGP, that is 364 amino acids in length). GP is post-translationally cleaved by furin to yield disulphide-linked GP1 and GP2 subunits. Soluble GP (sGP) and GP1 are identical in their first 295 NH2-terminal amino acids, whereas the remaining COOH-terminal 69 amino acids of sGP and 206 amino acids of GP1 are encoded by different reading frames. GP1 effects attachment to host cells, whereas GP2 mediates fusion of viral and host membranes. GP is the only target of EBOV neutralizing antibodies.
  • EBOV is thought to enter host cells by receptor-mediated endocytosis (two receptors have been suggested: cholesterol transporter protein, the host-encoded Niemann-Pick CI (NPC1), and TIM-1). GP is further processed by endosomal cathepsin, thus acquiring fusogenic activity.
  • Ebola virus (EBOV) infections cause severe illness in humans, and after an incubation period of 3 to 21 days, patients initially present with general flu-like symptoms before a rapid progression to advanced disease characterized by haemorrhage, multiple organ failure and a shock- like syndrome. In the spring of 2014, a new EBOV variant emerged in the West African country of Guinea, an area in which EBOV had not been previously reported.
  • chimeric or humanized monoclonal antibodies are immunogenic and could not be therefore considered for EBOV prophylaxis.
  • fully human antibodies, and even a single highly effective human monoclonal antibody are non- immunogenic or very poorly immunogenic and could be used as a prophylactic agent to prevent the infection in healthcare workers or in individuals at high risk of exposure.
  • a single administration of a fully human, potent EBOV neutralizing antibody, or combinations of 2 or more neutralizing antibodies targeting different sites on the virus could confer a highly effective sterilizing immunity lasting for weeks, if not months.
  • Passively administered monoclonal antibodies could confer rapid and specific immunity in all populations, including the young, the elderly and the immunocompromised individuals. In some instances monoclonal antibodies could confer passively higher- than-natural levels of immunity compared to vaccinations.
  • agents capable of preventing as well as treating or attenuating Ebola virus infection in high-risk patients with high potency and efficacy are important to have antibodies that target different epitopes and different antigenic sites on the various strains in order to avoid appearance of resistant virus strains and reducing the risk of selecting viral escape mutants.
  • the invention is based, in part, on the discovery, isolation and production of antibodies that specifically bind the Ebola virus GP protein or that potently neutralize infection of Ebola virus, as well as antigenic sites and epitopes to which the antibodies of the invention bind.
  • the invention comprises an isolated and/or purified, and/or recombinant antibody, for example a monoclonal antibody, a human antibody, a human monoclonal antibody, an antibody variant, or an antigen binding antibody fragment, that specifically binds the Ebola virus GP protein or neutralizes infection of Ebola virus.
  • a monoclonal antibody for example a monoclonal antibody, a human antibody, a human monoclonal antibody, an antibody variant, or an antigen binding antibody fragment, that specifically binds the Ebola virus GP protein or neutralizes infection of Ebola virus.
  • the invention comprises an isolated and/or purified, and/or recombinant human antibody, or an antigen binding fragment thereof, that specifically binds the Ebola virus GP protein.
  • the antibody, or antigen binding fragment thereof potently neutralizes infection of at least one strain of Ebola virus.
  • the invention comprises an isolated and/or purified, and/or recombinant antibody, or an antigen binding fragment thereof, that neutralizes infection of more than one strain of Ebola virus.
  • the antibody, or antigen binding fragment thereof neutralizes two (2) strains of Ebola virus.
  • the antibody, or antigen binding fragment thereof neutralizes three (3) or more, e.g., four or five strains of Ebola virus.
  • the invention comprises an isolated and/or purified, and/or recombinant antibody, or an antigen binding fragment thereof, that specifically binds the Ebola virus GP protein or neutralizes infection of Ebola virus and comprises a heavy chain comprising CDRl, CDR2 and CDR3 and a light chain comprising CDRl, CDR2 and CDR3, wherein the heavy chain CDR3 comprises the amino acid sequence of SEQ ID NOs: 3, 31, 47, 63 or 78.
  • the invention comprises an isolated and/or purified, and/or recombinant antibody or antigen binding fragment thereof, that specifically binds the Ebola virus GP protein or neutralizes infection of Ebola virus, comprising: (i) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences as set forth in SEQ ID NOs: 1-6, respectively; (ii) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences as set forth in SEQ ID NOs: 17, 2, 3, 18, 5, 6, respectively; (iii) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences as set forth in SEQ ID NOs: 1, 2, 3, 18, 5, 6, respectively; (iv) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain C
  • the invention comprises an isolated and/or purified, and/or recombinant antibody or antigen binding fragment thereof, that specifically binds the Ebola virus GP protein or neutralizes infection of Ebola Virus, comprising: (i) a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 13 and a light chain variable region comprising the amino acid sequence of SEQ ID NO: 14; or (ii) a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 25 and a light chain variable region comprising the amino acid sequence of SEQ ID NO: 26; (iii) or a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 13 and a light chain variable region comprising the amino acid sequence of SEQ ID NO: 26; or (iv) a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 25 and a light chain variable region comprising the amino acid sequence of SEQ ID NO: 14; or (v) a heavy chain variable region comprising the
  • the invention further comprises an isolated and/or purified, and/or recombinant antibody, or an antigen binding fragment thereof, described herein as EVB114 variant 1, EVB114 variant 2, EVB114 variant 3, EVB114 variant 4, EVB100, EVB166, EVB 165, EVB167 variant 1, or EVB167 variant 2.
  • the invention comprises an antibody, or antigen binding fragment thereof, that specifically binds the Ebola virus GP protein or neutralizes infection of Ebola virus, wherein the antibody or fragment thereof is expressed by an
  • the invention comprises a nucleic acid molecule comprising a polynucleotide encoding an antibody or antibody fragment of the invention.
  • the invention comprises a vector comprising a nucleic acid molecule of the invention.
  • the invention also comprises a cell comprising a vector of the invention or a cell that expresses an antibody of the invention or an antigen binding fragment thereof.
  • the invention comprises an isolated or purified immunogenic polypeptide comprising an epitope that binds to an antibody or antigen binding fragment of the invention.
  • the invention further comprises a pharmaceutical composition comprising an antibody of the invention or an antigen binding fragment thereof, a nucleic acid molecule of the invention, a vector comprising a nucleic acid molecule of the invention, a cell comprising a vector of the invention, a cell expressing an antibody or an antibody fragment of the invention, or an immunogenic polypeptide of the invention, and a pharmaceutically acceptable diluent or carrier.
  • the invention also comprises a pharmaceutical composition comprising a first antibody or an antigen binding fragment thereof, and a second antibody, or an antigen binding fragment thereof, wherein the first antibody is an antibody of the invention, and the second antibody is an antibody, or an antigen binding fragment thereof, that specifically binds the Ebola virus GP protein or neutralizes infection of Ebola virus.
  • an antibody of the invention or an antigen binding fragment thereof, a nucleic acid of the invention, a vector comprising a nucleic acid of the invention, a cell expressing a vector of the invention, an isolated or purified immunogenic polypeptide comprising an epitope that binds to an antibody or antibody fragment of the invention, or a pharmaceutical composition of the invention in the manufacture of a medicament for (i) the prevention, treatment or attenuation of Ebola virus infection, (ii) vaccination against Ebola virus infection, or
  • diagnosis of Ebola virus infection is also contemplated to be within the scope of the invention.
  • use of an antibody of the invention, or an antigen binding fragment thereof, for monitoring the quality of a vaccine against Ebola virus by checking that the antigen of said vaccine contains the specific epitope in the correct conformation is also contemplated to be within the scope of the invention.
  • the invention comprises a method of treating or attenuating Ebola virus infection or lowering the risk of Ebola virus infection comprising administering to a subject in need thereof, a therapeutically effective amount of an antibody or an antigen binding antibody fragment of the invention.
  • the invention comprises a polypeptide which specifically binds to an antibody of the invention, or an antigen binding fragment thereof, for use (i) in therapy, (ii) in the manufacture of a medicament for the treatment or attenuation of Ebola virus infection, (iii) as a vaccine, or (iv) in screening for ligands able to neutralise infection of Ebola virus.
  • Figure 1 shows the results of binding to ZEBOV GP and to an irrelevant antigen (Ctr. Ag.) by a panel of 52 human monoclonal antibodies as measured by ELISA.
  • Figure 2A shows the results of binding to ZEBOV GP by human monoclonal antibodies
  • FIG. 2B shows the results of binding to ZEBOV GP by human monoclonal antibodies EVB165, EVB166 and EVB167.
  • Figure 3 shows the results of a monoclonal antibody cross-competition assay performed by ELISA on the EVBIOO, EVBl 14 and EVB166 monoclonal antibodies. Shown is the binding of the biotinylated antibody EVBl 14 in the presence of ascending concentrations of unlabeled EVBIOO, EVBl 14 and EVB166 monoclonal antibodies.
  • Figure 4 shows the binding of serial dilutions of parental EVBl 14 antibody and three variants mutated in heavy chain (M36S/wt), light chain (wt/D36S) and heavy and light chain
  • FIG. 4A shows FACS dot plots of the antibody variants binding to the mixture of cells.
  • Figure 4B shows a plot of the binding of different concentration of the antibody variants (in ng/ml) expressed as mean fluorescence intensity (MFI).
  • Figure 5 shows the amino acid sequences for the two heavy chains of the variants of antibody EVB114 and the nucleic acid sequences that encode them (Figure 5A); as well as the amino acid sequences for the two light chains of the variants of antibody EVB114 and the nucleic acid sequences that encode them( Figure 5B).
  • Figure 5A shows the amino acid sequences of the CDRs and the nucleic acid sequences that encode the CDRs.
  • Figure 6 shows the amino acid sequences for the heavy and light chains of antibody EVB100 as well as the nucleic acid sequences that encode them.
  • the amino acid sequences of the CDRs and the nucleic acid sequences that encode the CDRs are provided in bold text.
  • Figure 7 shows the amino acid sequences for the heavy and light chains of antibody EVB166 as well as the nucleic acid sequences that encode them.
  • the amino acid sequences of the CDRs and the nucleic acid sequences that encode the CDRs are provided in bold text.
  • Figure 8 shows the amino acid sequences for the heavy and light chains of antibody
  • EVB165 as well as the nucleic acid sequences that encode them.
  • the amino acid sequences of the CDRs and the nucleic acid sequences that encode the CDRs are provided in bold text.
  • Figure 9 shows the amino acid sequences for the heavy chain and the two light chains of the variants of antibody EVB167 and the nucleic acid sequences that encode them.
  • the amino acid sequences of the CDRs and the nucleic acid sequences that encode the CDRs are provided in bold text.
  • the invention is based, in part, on the discovery and isolation or production of antibodies that are highly specific to the Ebola virus GP protein or are highly potent in neutralizing Ebola virus infection, as well as antigenic sites and epitopes to which the antibodies of the invention bind.
  • Such antibodies are desirable, as only small quantities of the antibodies are required in order to neutralize Ebola virus infection and are highly effective in preventing as well as treating or attenuating Ebola virus infection in high-risk patients. This reduces the costs of production of medicaments comprising the antibodies for the treatment of EBOV infection.
  • the antigenic sites or immunogenic polypeptides comprising epitopes recognized by the antibodies of the invention may be part of a vaccine capable of inducing protection against EBOV.
  • the invention provides an isolated and/or purified, and/or recombinant antibody, antibody variants and antigen binding fragments thereof, that specifically binds the Ebola virus GP protein.
  • the antibody is a monoclonal antibody, a human antibody, or a human monoclonal antibody.
  • the invention comprises an isolated and/or purified, and/or recombinant human antibody, or an antigen binding fragment thereof, that specifically binds the Ebola virus GP protein and neutralizes infection of at least one strain of Ebola virus.
  • the invention comprises an isolated and/or purified, and/or recombinant antibody, or an antigen binding fragment thereof, that specifically binds the Ebola virus GP protein and neutralizes infection of more than one strain of Ebola virus.
  • the antibody, or antigen binding fragment thereof neutralizes two (2) strains of Ebola virus.
  • the antibody, or antigen binding fragment thereof neutralizes three (3) or more, e.g., four or five strains of Ebola virus.
  • the antibody and antigen binding fragment of the invention have high neutralizing potency.
  • concentration of the antibody of the invention required for 50% neutralization of Ebola virus (IC50) is, for example, about 10 ⁇ g /ml or less. In one embodiment, the
  • concentration of the antibody of the invention required for 50% neutralization of EBOV is about 9 ⁇ g/ml to about 11 ⁇ g/ml. In other embodiments, the concentration of the antibody of the invention required for 50% neutralization of EBOV is about 11 ⁇ g/ml or less, or about 10 ⁇ g/ml or less, or about 9 ⁇ g/ml or less, or about 8 ⁇ g/ml or less, or about 7 ⁇ g/ml or less, or about 6 ⁇ g/ml or less, or about 5 ⁇ g/ml or less, or about 4 ⁇ g/ml or less, or about 3.5 ⁇ g/ml or less, or about 3 ⁇ g/ml or less, or about 2.5 ⁇ g/ml or less, or about 2 ⁇ g/ml or less, or about 1.5 ⁇ g/ml or less, or about 1,4 ⁇ g/ml or less, or about 1.3 ⁇ g/ml or less, or about 1.2 ⁇ g/ml or less, or
  • the concentration of the antibody of the invention required for 50% neutralization of EBOV is about 250 ng/ml or less, or about 200 ng/ml or less, or about 175 ng/ml or less, or about 150 ng/ml or less, or about 140 ng/ml or less, or about 130 ng/ml or less, or about 120 ng/ml or less, or about 110 ng/ml or less, or about 100 ng/ml or less, or about 90 ng/ml or less, or about 80 ng/ml or less, or about 70 ng/ml or less, or about 60 ng/ml or less, or about 50 ng/ml or less, or about 40 ng/ml or less, or about 30 ng/ml or less, or about 10 ng/ml or less.
  • the concentration of the antibody of the invention required for 50% neutralization of EBOV is about 20 ng/ml or about 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6 5, 4, 3, 2 or about 1 ng/ml or less. This means that only low concentrations of antibody are required for 50% neutralization of EBOV.
  • the antibodies of the invention may be human antibodies, monoclonal antibodies, human monoclonal antibodies, recombinant antibodies or purified antibodies.
  • the invention also provides fragments of the antibodies of the invention, particularly fragments that retain the antigen-binding activity of the antibodies. Such fragments include, but are not limited to, single chain antibodies, Fab, Fab', F(ab')2, Fv or scFv. Although the specification, including the claims, may, in some places, refer explicitly to antigen binding fragment(s), antibody
  • antibody or “antibody of the invention” includes all categories of antibodies, namely, antigen binding fragment(s), antibody fragment(s), variant(s) and derivative(s) of antibodies.
  • the sequences of the heavy chains and light chains of several antibodies of the invention, each comprising three CDRs on the heavy chain and three CDRs on the light chain have been determined.
  • the positions of the CDR amino acids are defined according to the EVIGT numbering system.
  • the sequences of the CDRs, heavy chains, light chains as well as the sequences of the nucleic acid molecules encoding the CDRs, heavy chains, and light chains of the antibodies of the invention are disclosed in the sequence listing.
  • the CDRs of the antibody heavy chains are referred to as CDRHl, CDRH2 and CDRH3, respectively.
  • CDRLl the CDRs of the antibody light chains
  • CDRL2 the CDRs of the antibody light chains
  • CDRL3 the CDRs of the antibody light chains
  • Table 1 provides the SEQ ID numbers for the amino acid sequences of the six CDRs of the heavy and light chains, respectively, of some examples of antibodies of the invention.
  • Table 1. SEQ ID Numbers for CDR polypeptides of antibodies that neutralize Ebola
  • an isolated and/or purified, and/or recombinant antibody or antibody fragment of the invention comprises at least one CDR with a sequence that has at least 95% sequence identity to any one of SEQ ID NOs: 1-6, 17, 18, 29-34, 45-50, 61-65 or 76-80.
  • the amino acid sequences of the heavy and light chain variable regions of the antibodies of the invention as well as the nucleic acid sequences that encode them are provided in Figures 5 A, 5B, 6, 7, 8 and 9.
  • the amino acid residues corresponding to the six CDRs and the nucleic acid residues that encode them are highlighted in bold text.
  • the invention provides an isolated and/or purified, and/or recombinant antibody or antigen binding fragment comprising a heavy chain comprising one or more (i.e., one, two or all three) heavy chain CDRs from EVB114 variant 1, EVB114 variant 2, EVB114 variant 3, EVB 114 variant 4, EVB100, EVB166, EVB165, EVB 167 variant 1, or EVB167 variant 2.
  • the isolated and/or purified, and/or recombinant antibody or antigen binding fragment of the invention comprises a heavy chain CDR1 with the amino acid sequence of SEQ ID NOs: 1, 17, 29, 45, 61 or 76; a heavy chain CDR2 with the amino acid sequence of SEQ ID NOs: 2, 30, 46, 62 or 77; and a heavy chain CDR3 with the amino acid sequence of SEQ ID NOs: 3, 31, 47, 63 or 78.
  • an antibody or antibody fragment as provided herein comprises a heavy chain comprising the amino acid sequence of (i) SEQ ID NO: 1 for CDRHl, SEQ ID NO: 2 for CDRH2 and SEQ ID NO: 3 for CDRH3; (ii) SEQ ID NO: 17 for CDRHl, SEQ ID NO: 2 for CDRH2, and SEQ ID NO: 3 for CDRH3; (iii) SEQ ID NO: 29 for CDRHl, SEQ ID NO: 30 for CDRH2, and SEQ ID NO: 31 for CDRH3; (iv) SEQ ID NO: 45 for CDRHl, SEQ ID NO: 46 for CDRH2, and SEQ ID NO: 47 for CDRH3; (v) or SEQ ID NO: 61 for CDRHl, SEQ ID NO: 62 for CDRH2, and SEQ ID NO: 63 for CDRH3; or (vi) SEQ ID NO: 76 for CDRHl, SEQ ID NO: 77 for CDRH3;
  • an isolated and/or purified, and/or recombinant antibody of the invention, or antigen binding fragment thereof, specifically binds the Ebola virus GP protein or neutralizes infection of EBOV and comprises a heavy chain comprising CDR1, CDR2 and CDR3 and a light chain comprising CDR1, CDR2 and CDR3, wherein the heavy chain CDR3 comprises an amino acid sequence that is at least 90%, for example, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical to SEQ ID NOs: 3, 31, 47, 63 or 78.
  • an isolated and/or purified, and/or recombinant antibody or antigen binding fragment that neutralizes infection of Ebola virus and comprises a light chain comprising one or more (i.e. one, two or all three) light chain CDRs from EVB114 variant 1, EVB114 variant 2, EVB114 variant 3, EVB114 variant 4, EVB100, EVB166, EVB 165, EVB167 variant 1, or EVB167 variant 2.
  • the antibody or antigen binding fragment of the invention comprises a light chain CDR1 with the amino acid sequence of SEQ ID NOs: 4, 18, 32, 48, 64 or 79; a light chain CDR2 with the amino acid sequence of SEQ ID NOs: 5, 33 or 49; and a light chain CDR3 with the amino acid sequence of SEQ ID NO: 6, 34, 50, 65 or 80.
  • an antibody or antibody fragment as provided herein comprises a light chain comprising the amino acid sequence of (i) SEQ ID NO: 4 for CDRL1, SEQ ID NO: 5 for CDRL2, and SEQ ID NO: 6 for CDRL3; (ii) SEQ ID NO: 18 for CDRL1, SEQ ID NO: 5 for CDRL2, and SEQ ID NO: 6 for CDRL3; (iii) SEQ ID NO: 32 for CDRL1, SEQ ID NO: 33 for CDRL2, and SEQ ID NO: 34 for CDRL3; (iv) SEQ ID NO: 48 for CDRL1, SEQ ID NO: 49 for CDRL2, and SEQ ID NO: 50 for CDRL3; (v) SEQ ID NO: 64 for CDRL1, SEQ ID NO: 5 for CDRL2, and SEQ ID NO: 65 for CDRL3; or (vi) SEQ ID NO: 79 for CDRL1, SEQ ID NO; 49 for CDRL2, and SEQ ID NO: 80 for CDRL3.
  • an isolated and/or purified, and/or recombinant antibody of the invention, or antigen binding fragment thereof comprises all six of the CDRs of antibody EVBl 14 variant 1 as listed in Table 1, and specifically binds the Ebola virus GP protein or neutralizes infection of EBOV.
  • an antibody of the invention, or antigen binding fragment thereof comprises all six of the CDRs of antibody EVBl 14 variant 2 as listed in Table 1, and specifically binds the Ebola virus GP protein or neutralizes infection of EBOV.
  • an antibody of the invention, or antigen binding fragment thereof comprises all six of the CDRs of antibody EVBl 14 variant 3 as listed in Table 1, and specifically binds the Ebola virus GP protein or neutralizes infection of EBOV.
  • an antibody of the invention, or antigen binding fragment thereof comprises all six of the CDRs of antibody EVBl 14 variant 4 as listed in Table 1, and specifically binds the Ebola virus GP protein or neutralizes infection of EBOV.
  • an antibody of the invention, or antigen binding fragment thereof comprises all six of the CDRs of antibody EVBl 00 as listed in Table 1, and specifically binds the Ebola virus GP protein or neutralizes infection of EBOV.
  • an antibody of the invention, or antigen binding fragment thereof comprises all six of the CDRs of antibody EVBl 66 as listed in Table 1, and specifically binds the Ebola virus GP protein or neutralizes infection of EBOV.
  • an antibody of the invention, or antigen binding fragment thereof comprises all six of the CDRs of antibody EVBl 65 as listed in Table 1, and specifically binds the Ebola virus GP protein or neutralizes infection of EBOV.
  • an antibody of the invention, or antigen binding fragment thereof comprises all six of the CDRs of antibody EVBl 67 variant 1 as listed in Table 1, and specifically binds the Ebola virus GP protein or neutralizes infection of EBOV.
  • an antibody of the invention, or antigen binding fragment thereof comprises all six of the CDRs of antibody EVBl 67 variant 2 as listed in Table 1, and specifically binds the Ebola virus GP protein or neutralizes infection of EBOV.
  • the invention comprises an isolated and/or purified, and/or recombinant antibody or antigen binding fragment thereof, comprising heavy chain CDRl, CDR2 and CDR3 and light chain CDRl, CDR2, and CDR3 amino acid sequences that are at least 90%, for example, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical to the amino acid sequences of the CDR sequences provided in Table 1, wherein the antibody specifically binds the Ebola virus GP protein or neutralizes infection of EBOV.
  • the invention comprises an isolated and/or purified, and/or recombinant antibody or antigen binding fragment thereof, that specifically binds the Ebola virus GP protein or neutralizes infection of EBOV, comprising: (i) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences that are at least 90% identical to the amino acid sequences of SEQ ID NOs: 1-6, respectively; (ii) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences that are at least 90% identical to the amino acid sequences of SEQ ID NOs: 17, 2, 3, 18, 5, 6, respectively; (iii) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences that are at least 90% identical to the amino acid sequences of SEQ ID NOs: 1, 2, 3, 18, 5, 6, respectively; (iv) heavy chain
  • the invention comprises an isolated and/or purified, and/or recombinant antibody or antigen binding fragment thereof, that specifically binds the Ebola virus GP protein or neutralizes infection of EBOV, comprising: (i) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences as set forth in SEQ ID NOs: 1-6, respectively; (ii) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences as set forth in SEQ ID NOs: 17, 2, 3, 18, 5, 6, respectively; (iii) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences as set forth in SEQ ID NOs: 1, 2, 3, 18, 5, 6, respectively; (iv) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDR
  • an antibody or antibody fragment of the invention specifically binds the Ebola virus GP protein or neutralizes infection of EBOV and comprises a heavy chain variable region having an amino acid sequence that is about 70%, 75%, 80%, 85%, 88%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical to the sequence recited in any one of SEQ ID NOs: 13, 25, 41, 57, 72 or 87.
  • the antibody or antibody fragment comprises a light chain variable region having an amino acid sequence that is about 70%, 75%, 80%, 85%, 90%, 85%, 88%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical to the sequence recited in SEQ ID NOs: 14, 26, 42, 58, 73 or 88.
  • the antibody or antibody fragment comprises a heavy chain or a light chain variable region having an amino acid sequence that is about 70%, 75%, 80%, 85%, 88%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical to the sequences provided in Figures 5A, 5B, 6, 7, 8 or 9.
  • Figures 5A, 5B, 6, 7, 8 and 9 show the amino acid sequences for the heavy and light chains of antibodies EVB 114 variant 1 , EVB 114 variant 2, EVB 114 variant 3 , EVB 114 variant 4, EVB100, EVB166, EVB165, EVB167 variant 1, or EVB167 variant 2, as well as for the nucleic acid sequences that encode them.
  • the amino acid sequences of the CDRs and the nucleic acid sequences that encode the CDRs are in bold text whereas the amino acid sequences of the framework region and the nucleic acid sequences that encode the framework region are in plain text.
  • the invention comprises an isolated and/or purified, and/or recombinant antibody, or an antigen binding fragment thereof, that specifically binds the Ebola virus GP protein or neutralizes infection of EBOV and comprises (i) a heavy chain variable region having at least 80%, for example, 85%, 88%, 90%, 92%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to the amino acid sequence of SEQ ID NO: 13 and a light chain variable region having at least 80%, for example, 85%, 88%, 90%, 92%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to the amino acid sequence of SEQ ID NO: 14; or (ii) a heavy chain variable region having at least 80%, for example, 85%, 88%, 90%, 92%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to the amino acid sequence of SEQ ID NO: 25 and a light chain variable region having at least 80%, for example, 85%, 88%, 90%
  • the invention comprises an antibody, or an antigen binding fragment thereof, that specifically binds the Ebola virus GP protein or neutralizes infection of EBOV and comprises a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 13 and a light chain variable region comprising the amino acid sequence of SEQ ID NO: 14; or a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 25 and a light chain variable region comprising the amino acid sequence of SEQ ID NO: 26; or a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 13 and a light chain variable region comprising the amino acid sequence of SEQ ID NO: 26; or a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 25 and a light chain variable region comprising the amino acid sequence of SEQ ID NO: 14; or a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 41 and a light chain variable region comprising the amino acid sequence of SEQ ID NO: 42; or a heavy chain variable region
  • antibodies of the invention include, but are not limited to, EVB114 variant 1, EVB114 variant 2, EVB114 variant 3, EVB114 variant 4, EVB 100, EVB166, EVB165, EVB167 variant 1, or EVB167 variant 2 as characterized by the sequences provided in Tables 1 and 2.
  • the invention further comprises an antibody, or fragment thereof, that binds to the same epitope as an antibody or antigen binding fragment of the invention, or an antibody that competes with an antibody or antigen binding fragment of the invention.
  • Antibodies of the invention also include hybrid antibody molecules that specifically bind the Ebola virus GP protein or neutralize infection of Ebola virus and that comprise one or more CDRs from an antibody of the invention and one or more CDRs from another antibody to the same epitope.
  • hybrid antibodies comprise three CDRs from an antibody of the invention and three CDRs from another antibody to the same epitope.
  • hybrid antibodies comprise (i) the three heavy chain CDRs from an antibody of the invention and the three light chain CDRs from another antibody to the same epitope, or (ii) the three light chain CDRs from an antibody of the invention and the three heavy chain CDRs from another antibody to the same epitope or (iii) heavy chain CDR3 from an antibody of the invention and one or more heavy or light chain CDRs from another antibody to the same epitope.
  • variants of the sequences recited in the application are also included within the scope of the invention.
  • variants include natural variants generated by somatic mutation in vivo during the immune response or in vitro upon culture of immortalized B cell clones.
  • variants may arise due to the degeneracy of the genetic code or may be produced due to errors in transcription or translation.
  • Further variants of the antibody sequences having improved affinity and/or potency may be obtained using methods known in the art and are included within the scope of the invention.
  • amino acid substitutions may be used to obtain antibodies with further improved affinity.
  • codon optimization of the nucleotide sequence may be used to improve the efficiency of translation in expression systems for the production of the antibody.
  • polynucleotides comprising a sequence optimized for antibody specificity or neutralizing activity by the application of a directed evolution method to any of the nucleic acid sequences of the invention are also within the scope of the invention.
  • variant antibody sequences may share 70% or more (i.e. 75%, 80%, 85%, 88%, 90%, 92%, 95%, 96%, 97%, 98%, 99% or more) amino acid sequence identity with the sequences recited in the application.
  • Such variants in general, have a greater homology to the sequences listed herein in the CDRs of the V H and V L than in the framework region.
  • mutations are more tolerated, i.e., there is limited or no loss of function (e.g., specificity or neutralization ability) in the framework regions than in the CDRs.
  • the invention comprises an antibody, or an antigen binding fragment thereof, wherein the variation from the sequences provided herein is in the framework region(s) of the antibody or in the nucleic acid residues that encode the framework region(s) of the antibody.
  • sequence identity is calculated with regard to the full length of the reference sequence (i.e., the sequence recited in the application).
  • the invention also includes nucleic acid sequences encoding part or all of the light and heavy chains and CDRs of the antibodies of the present invention.
  • nucleic acid sequences encoding part or all of the light and heavy chains and CDRs of examples of antibodies of the invention are provided herein.
  • Table 2 provides the SEQ ID numbers for the nucleic acid sequences encoding the heavy chain and light chain variable regions of some examples of antibodies of the invention.
  • Table 3 provides the SEQ ID numbers for the nucleic acid sequences encoding the CDRs of some examples of the antibodies of the invention. Due to the redundancy of the genetic code, variants of these nucleic acid sequences will exist that encode the same amino acid sequences.
  • nucleic acid sequences according to the invention include nucleic acid sequences having at least 70%, at least 75%, at least 80%, at least 85%, at least 88%, at least 90%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% identity to the nucleic acid encoding the variable region of a heavy or light chain of an antibody of the invention.
  • a nucleic acid sequence of the invention has the sequence of a nucleic acid encoding a heavy or light chain CDR of an antibody of the invention.
  • a nucleic acid sequence according to the invention comprises a sequence that is at least 75%, at least 80%, at least 85%, at least 88%, at least 90%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% identical to the nucleic acid sequences of SEQ ID NOs: 7-12, 15, 16, 19-24, 27, 28, 35-40, 43, 44, 51-56, 59, 60, 66-71, 74, 75, 81-86, 89, 90 or 91.
  • nucleic acid sequences according to the invention include nucleic acid sequences having at least 70%, at least 75%, at least 80%, at least 85%, at least 88%, at least 90%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% identity to the nucleic acid encoding a heavy or light chain of an antibody of the invention as provided in Figures 5A, 5B, 6, 7, 8 or 9.
  • vectors for example, expression vectors, comprising a nucleic acid sequence according to the invention.
  • Cells transformed with such vectors are also included within the scope of the invention. Examples of such cells include but are not limited to, eukaryotic cells, e.g., yeast cells, animal cells or plant cells.
  • the cells are mammalian, e.g., human, CHO, HEK293T, PER.C6, NS0, myeloma or hybridoma cells.
  • the invention also relates to monoclonal antibodies that bind to an epitope capable of binding the antibodies or antigen binding fragments of the invention.
  • Monoclonal and recombinant antibodies are particularly useful in identification and purification of the individual polypeptides or other antigens against which they are directed.
  • the antibodies of the invention have additional utility in that they may be employed as reagents in immunoassays, radioimmunoassays (RIA) or enzyme-linked immunosorbent assays (ELISA).
  • the antibodies can be labeled with an analytically-detectable reagent such as a radioisotope, a fluorescent molecule or an enzyme.
  • the antibodies may also be used for the molecular identification and characterization (epitope mapping) of antigens.
  • Antibodies of the invention can be coupled to a drug for delivery to a treatment site or coupled to a detectable label to facilitate imaging of a site comprising cells of interest, such as cells infected with Ebola virus.
  • Methods for coupling antibodies to drugs and detectable labels are well known in the art, as are methods for imaging using detectable labels.
  • Labeled antibodies may be employed in a wide variety of assays, employing a wide variety of labels. Detection of the formation of an antibody-antigen complex between an antibody of the invention and an epitope of interest (e.g., EBOV) can be facilitated by attaching a detectable substance to the antibody.
  • an epitope of interest e.g., EBOV
  • Suitable detection means include the use of labels such as radionuclides, enzymes, coenzymes, fluorescers, chemiluminescers, chromogens, enzyme substrates or co-factors, enzyme inhibitors, prosthetic group complexes, free radicals, particles, dyes, and the like.
  • labels such as radionuclides, enzymes, coenzymes, fluorescers, chemiluminescers, chromogens, enzyme substrates or co-factors, enzyme inhibitors, prosthetic group complexes, free radicals, particles, dyes, and the like.
  • suitable enzymes include horseradish peroxidase, alkaline phosphatase, ⁇ - galactosidase, or acetylcholinesterase;
  • suitable prosthetic group complexes include streptavidin/biotin and avidin/biotin;
  • suitable fluorescent materials include umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin; an example of a luminescent material is luminol;
  • examples of bioluminescent materials include luciferase, luciferin, and aequorin; and
  • suitable radioactive material include 1251, 1311, 35S, or 3H.
  • Such labeled reagents may be used in a variety of well-known assays, such as radioimmunoassays, enzyme immunoassays, e.g., ELISA, fluorescent immunoassays, and the like. (See US 3,766,162; US 3,791,932; US 3,817,837; and US 4,233,402 for example).
  • An antibody according to the invention may be conjugated to a therapeutic moiety such as a cytotoxin, a therapeutic agent, or a radioactive metal ion or radioisotope.
  • a therapeutic moiety such as a cytotoxin, a therapeutic agent, or a radioactive metal ion or radioisotope.
  • radioisotopes include, but are not limited to, 1-131 , 1- 123, 1- 125, Y-90, Re- 188, Re-186, At-211, Cu-67, Bi-212, Bi-213, Pd- 109, Tc-99, In-I l l, and the like.
  • Such antibody conjugates can be used for modifying a given biological response; the drug moiety is not to be construed as limited to classical chemical therapeutic agents.
  • the drug moiety may be a protein or polypeptide possessing a desired biological activity.
  • Such proteins may include, for example, a toxin such as abrin, ricin A, pseudomonas exotoxin, or diphtheria toxin.
  • Techniques for conjugating such therapeutic moiety to antibodies are well known. See, for example, Arnon et al. (1985) "Monoclonal Antibodies for Immunotargeting of Drugs in Cancer Therapy," in Monoclonal Antibodies and Cancer Therapy, ed. Reisfeld et al. (Alan R. Liss, Inc.), pp. 243-256; ed. Hellstrom et al. (1987) "Antibodies for Drug Delivery," in
  • an antibody, or antibody fragment thereof can be conjugated to a second antibody, or antibody fragment thereof, to form an antibody heteroconjugate as described in US 4,676,980.
  • linkers may be used between the labels and the antibodies of the invention (e.g., US 4,831,175).
  • Antibodies or, antigen-binding fragments thereof may be directly labeled with radioactive iodine, indium, yttrium, or other radioactive particle known in the art (e.g., US 5,595,721). Treatment may consist of a combination of treatment with conjugated and non-conjugated antibodies administered simultaneously or subsequently
  • Antibodies of the invention may also be attached to a solid support. Additionally, antibodies of the invention, or functional antibody fragments thereof, can be chemically modified by covalent conjugation to a polymer to, for example, increase their circulating half-life.
  • the polymers may be selected from polyoxyethylated polyols and polyethylene glycol (PEG).
  • PEG is soluble in water at room temperature and has the general formula: R(0— CH2— CH2)n O— R where R can be hydrogen, or a protective group such as an alkyl or alkanol group.
  • the protective group may have between 1 and 8 carbons.
  • the protective group is methyl.
  • n is a positive integer. In one embodiment n is between 1 and 1,000. In another embodiment n is between 2 and 500.
  • the PEG has an average molecular weight between 1,000 and 40,000.
  • the PEG has a molecular weight between 2,000 and 20,000. In yet a further embodiment the PEG has a molecular weight between 3,000 and 12,000. In one embodiment PEG has at least one hydroxy group. In another embodiment the PEG has a terminal hydroxy group. In yet another embodiment it is the terminal hydroxy group which is activated to react with a free amino group on the inhibitor. However, it will be understood that the type and amount of the reactive groups may be varied to achieve a covalently conjugated PEG/antibody of the present invention.
  • Water-soluble polyoxyethylated polyols are also useful in the present invention. They include polyoxyethylated sorbitol, polyoxyethylated glucose, polyoxyethylated glycerol (POG), and the like. In one embodiment, POG is used. Without being bound by any theory, because the glycerol backbone of polyoxyethylated glycerol is the same backbone occurring naturally in, for example, animals and humans in mono-, di-, triglycerides, this branching would not necessarily be seen as a foreign agent in the body. In some embodiments POG has a molecular weight in the same range as PEG. Another drug delivery system that can be used for increasing circulatory half-life is the liposome. Methods of preparing liposome delivery systems are known to one of skill in the art. Other drug delivery systems are known in the art and are described in, for example, referenced in Poznansky et al. (1980) and Poznansky (1984).
  • Antibodies of the invention may be provided in purified form. Typically, the antibody will be present in a composition that is substantially free of other polypeptides e.g., where less than 90% (by weight), usually less than 60% and more usually less than 50% of the composition is made up of other polypeptides.
  • Antibodies of the invention may be immunogenic in non-human (or heterologous) hosts e.g., in mice.
  • the antibodies may have an idiotope that is immunogenic in non-human hosts, but not in a human host.
  • Antibodies of the invention for human use include those that cannot be easily isolated from hosts such as mice, goats, rabbits, rats, non-primate mammals, etc. and cannot generally be obtained by humanization or from xeno-mice.
  • Antibodies of the invention can be of any isotype (e.g., IgA, IgG, IgM i.e. an ⁇ , ⁇ or ⁇ heavy chain), but will generally be IgG. Within the IgG isotype, antibodies may be IgGl, IgG2, IgG3 or IgG4 subclass. Antibodies of the invention may have a ⁇ or a ⁇ light chain.
  • Antibodies according to the invention can be made by any method known in the art.
  • the general methodology for making monoclonal antibodies using hybridoma technology is well known (Kohler, G. and Milstein, C,. 1975; Kozbar et al. 1983).
  • the alternative EBV immortalization method described in WO2004/076677 is used.
  • B cells producing the antibody of the invention can be transformed with EBV and a polyclonal B cell activator. Additional stimulants of cellular growth and differentiation may optionally be added during the transformation step to further enhance the efficiency. These stimulants may be cytokines such as IL-2 and IL- 15. In one aspect, IL-2 is added during the immortalization step to further improve the efficiency of immortalization, but its use is not essential.
  • the immortalized B cells produced using these methods can then be cultured using methods known in the art and antibodies isolated therefrom.
  • plasma cells can be cultured in limited numbers, or as single plasma cells in microwell culture plates.
  • Antibodies can be isolated from the plasma cell cultures. Further, from the plasma cell cultures, RNA can be extracted and PCR can be performed using methods known in the art. The VH and VL regions of the antibodies can be amplified by RT-PCR, sequenced and cloned into an expression vector that is then transfected into HEK293T cells or other host cells. The cloning of nucleic acid in expression vectors, the transfection of host cells, the culture of the transfected host cells and the isolation of the produced antibody can be done using any methods known to one of skill in the art.
  • the antibodies may be further purified, if desired, using filtration, centrifugation and various chromatographic methods such as HPLC or affinity chromatography. Techniques for purification of antibodies, e.g., monoclonal antibodies, including techniques for producing pharmaceutical-grade antibodies, are well known in the art.
  • antibodies In general currently marketed antibodies have a pi between 7.4 and 8.6 and are formulated in the pH range of 5.0 to 7.2, with most of the antibodies being formulated at slightly acidic pH.
  • the antibodies provided herein as examples of antibodies of the invention have a pi between about 8.1 and 8.5, making them excellent candidates for production and formulation in marketable quantities.
  • Fragments of the antibodies of the invention can be obtained from the antibodies by methods that include digestion with enzymes, such as pepsin or papain, and/or by cleavage of disulfide bonds by chemical reduction.
  • fragments of the antibodies can be obtained by cloning and expression of part of the sequences of the heavy or light chains.
  • Antibody "fragments” include Fab, Fab', F(ab')2 and Fv fragments.
  • the invention also encompasses single-chain Fv fragments (scFv) derived from the heavy and light chains of an antibody of the invention.
  • scFv single-chain Fv fragments
  • the invention includes a scFv comprising the CDRs from an antibody of the invention.
  • heavy or light chain monomers and dimers single domain heavy chain antibodies, single domain light chain antibodies, as well as single chain antibodies, e.g., single chain Fv in which the heavy and light chain variable domains are joined by a peptide linker.
  • Antibody fragments of the invention may impart monovalent or multivalent interactions and be contained in a variety of structures as described above.
  • scFv molecules may be synthesized to create a trivalent "triabody” or a tetravalent "tetrabody.”
  • the scFv molecules may include a domain of the Fc region resulting in bivalent minibodies.
  • the sequences of the invention may be a component of multispecific molecules in which the sequences of the invention target the epitopes of the invention and other regions of the molecule bind to other targets.
  • Exemplary molecules include, but are not limited to, bispecific Fab2, trispecific Fab3, bispecific scFv, and diabodies (Holliger and Hudson, 2005, Nature
  • Any suitable host cell/vector system may be used for expression of the DNA sequences encoding the antibody molecules of the present invention or fragments thereof.
  • Bacterial, for example E. coli, and other microbial systems may be used, in part, for expression of antibody fragments such as Fab and F(ab')2 fragments, and especially Fv fragments and single chain antibody fragments, for example, single chain Fvs.
  • Eukaryotic, e.g., mammalian, host cell expression systems may be used for production of larger antibody molecules, including complete antibody molecules.
  • Suitable mammalian host cells include, but are not limited to, CHO, HEK293T, PER.C6, NSO, myeloma or hybridoma cells.
  • the present invention also provides a process for the production of an antibody molecule according to the present invention comprising culturing a host cell comprising a vector encoding a nucleic acid of the present invention under conditions suitable for expression of protein from DNA encoding the antibody molecule of the present invention, and isolating the antibody molecule.
  • the antibody molecule may comprise only a heavy or light chain polypeptide, in which case only a heavy chain or light chain polypeptide coding sequence needs to be used to transfect the host cells.
  • the cell line may be transfected with two vectors, a first vector encoding a light chain polypeptide and a second vector encoding a heavy chain polypeptide.
  • a single vector may be used, the vector including sequences encoding light chain and heavy chain polypeptides.
  • antibodies according to the invention may be produced by (i) expressing a nucleic acid sequence according to the invention in a host cell, and (ii) isolating the expressed antibody product. Additionally, the method may include (iii) purifying the isolated antibody.
  • Transformed B cells and cultured plasma cells may be screened for those producing antibodies of the desired specificity or function.
  • the screening step may be carried out by any immunoassay, e.g., ELISA, by staining of tissues or cells (including transfected cells), by neutralization assay or by one of a number of other methods known in the art for identifying desired specificity or function.
  • the assay may select on the basis of simple recognition of one or more antigens, or may select on the additional basis of a desired function e.g., to select neutralizing antibodies rather than just antigen-binding antibodies, to select antibodies that can change characteristics of targeted cells, such as their signaling cascades, their shape, their growth rate, their capability of influencing other cells, their response to the influence by other cells or by other reagents or by a change in conditions, their differentiation status, etc.
  • Individual transformed B cell clones may then be produced from the positive transformed
  • the cloning step for separating individual clones from the mixture of positive cells may be carried out using limiting dilution, micromanipulation, single cell deposition by cell sorting or another method known in the art.
  • Nucleic acid from the cultured plasma cells can be isolated, cloned and expressed in HEK293T cells or other known host cells using methods known in the art.
  • the immortalized B cell clones or the transfected host-cells of the invention can be used in various ways e.g., as a source of monoclonal antibodies, as a source of nucleic acid (DNA or mRNA) encoding a monoclonal antibody of interest, for research, etc.
  • the invention provides a composition comprising immortalized B memory cells or transfected host cells that produce antibodies that specifically bind the Ebola virus GP protein or neutralize infection of EBOV.
  • the immortalized B cell clone or the cultured plasma cells of the invention may also be used as a source of nucleic acid for the cloning of antibody genes for subsequent recombinant expression.
  • Expression from recombinant sources is more common for pharmaceutical purposes than expression from B cells or hybridomas e.g., for reasons of stability, reproducibility, culture ease, etc.
  • the invention provides a method for preparing a recombinant cell, comprising the steps of: (i) obtaining one or more nucleic acids (e.g., heavy and/or light chain mRNAs) from the B cell clone or the cultured plasma cells that encodes the antibody of interest; (ii) inserting the nucleic acid into an expression vector and (iii) transfecting the vector into a host cell in order to permit expression of the antibody of interest in that host cell.
  • nucleic acids e.g., heavy and/or light chain mRNAs
  • the invention provides a method for preparing a recombinant cell, comprising the steps of: (i) sequencing nucleic acid(s) from the B cell clone or the cultured plasma cells that encodes the antibody of interest; and (ii) using the sequence information from step (i) to prepare nucleic acid(s) for insertion into a host cell in order to permit expression of the antibody of interest in that host cell.
  • the nucleic acid may, but need not, be manipulated between steps (i) and (ii) to introduce restriction sites, to change codon usage, and/or to optimize transcription and/or translation regulatory sequences.
  • the invention also provides a method of preparing a transfected host cell, comprising the step of transfecting a host cell with one or more nucleic acids that encode an antibody of interest, wherein the nucleic acids are nucleic acids that were derived from an immortalized B cell clone or a cultured plasma cell of the invention.
  • the procedures for first preparing the nucleic acid(s) and then using it to transfect a host cell can be performed at different times by different people in different places (e.g., in different countries).
  • recombinant cells of the invention can then be used for expression and culture purposes. They are particularly useful for expression of antibodies for large-scale
  • Any suitable culture technique can be used, including but not limited to static culture, roller bottle culture, ascites fluid, hollow-fiber type bioreactor cartridge, modular minifermenter, stirred tank, microcarrier culture, ceramic core perfusion, etc.
  • the transfected host cell may be a eukaryotic cell, including yeast and animal cells, particularly mammalian cells (e.g., CHO cells, NS0 cells, human cells such as PER.C6 or
  • transfected host cell may be able to grow in serum-free media.
  • transfected host cell may be able to grow in culture without the presence of animal-derived products.
  • the transfected host cell may also be cultured to give a cell line.
  • the invention also provides a method for preparing one or more nucleic acid molecules (e.g., heavy and light chain genes) that encode an antibody of interest, comprising the steps of: (i) preparing an immortalized B cell clone or culturing plasma cells according to the invention; (ii) obtaining from the B cell clone or the cultured plasma cells nucleic acid that encodes the antibody of interest. Further, the invention provides a method for obtaining a nucleic acid sequence that encodes an antibody of interest, comprising the steps of: (i) preparing an immortalized B cell clone or culturing plasma cells according to the invention; (ii) sequencing nucleic acid from the B cell clone or the cultured plasma cells that encodes the antibody of interest.
  • nucleic acid molecules e.g., heavy and light chain genes
  • the invention also provides a method of preparing nucleic acid molecule(s) that encode an antibody of interest, comprising the step of obtaining the nucleic acid that was obtained from a transformed B cell clone or cultured plasma cells of the invention.
  • a method of preparing nucleic acid molecule(s) that encode an antibody of interest comprising the step of obtaining the nucleic acid that was obtained from a transformed B cell clone or cultured plasma cells of the invention.
  • the procedures for first obtaining the B cell clone or the cultured plasma cell, and then obtaining nucleic acid(s) from the B cell clone or the cultured plasma cells can be performed at different times by different people in different places (e.g., in different countries).
  • the invention provides a method for preparing an antibody (e.g., for pharmaceutical use), comprising the steps of: (i) obtaining and/or sequencing one or more nucleic acids (e.g., heavy and light chain genes) from the selected B cell clone or the cultured plasma cells expressing the antibody of interest; (ii) inserting the nucleic acid(s) into or using the nucleic acid(s) sequence(s) to prepare an expression vector; (iii) transfecting a host cell that can express the antibody of interest; (iv) culturing or sub-culturing the transfected host cells under conditions where the antibody of interest is expressed; and, optionally, (v) purifying the antibody of interest.
  • nucleic acids e.g., heavy and light chain genes
  • the invention also provides a method of preparing an antibody comprising the steps of: culturing or sub-culturing a transfected host cell population under conditions where the antibody of interest is expressed and, optionally, purifying the antibody of interest, wherein said transfected host cell population has been prepared by (i) providing nucleic acid(s) encoding a selected antibody of interest that is produced by a B cell clone or cultured plasma cells prepared as described above, (ii) inserting the nucleic acid(s) into an expression vector, (iii) transfecting the vector in a host cell that can express the antibody of interest, and (iv) culturing or sub- culturing the transfected host cell comprising the inserted nucleic acids to produce the antibody of interest.
  • the procedures for first preparing the recombinant host cell and then culturing it to express antibody can be performed at very different times by different people in different places (e.g., in different countries).
  • the antibodies of the invention can be used to map the epitopes to which they bind.
  • the invention provides novel epitopes to which the neutralizing antibodies of the invention bind. These epitopes are found on the Ebola virus glycoprotein.
  • the antibodies, or antigen binding fragments thereof bind Ebola virus soluble glycoprotein (sGP).
  • sGP Ebola virus soluble glycoprotein
  • the epitopes to which the antibodies of the invention bind may be linear (continuous) or conformational (discontinuous).
  • the antibodies and antibody fragments of the invention bind a conformational epitope.
  • the conformational epitope is present only under non-reducing conditions.
  • the polypeptides that bind to the antibodies of the present invention may have a number of uses.
  • the polypeptides and polypeptide variants thereof in purified or synthetic form can be used to raise immune responses (i.e., as a vaccine, or for the production of antibodies for other uses) or for screening sera for antibodies that immunoreact with the epitope or mimotopes thereof.
  • such polypeptides or polypeptide variants, or antigen comprising such a polypeptides or polypeptide variants may be used as a vaccine for raising an immune response that comprises antibodies of the same quality as those described in the present invention.
  • the antibodies and antibody fragments of the invention can also be used in a method of monitoring the quality of vaccines.
  • the antibodies can be used to check that the antigen in a vaccine contains the correct immunogenic epitope in the correct conformation.
  • the use of an antibody of the invention, or an antigen binding fragment thereof, for monitoring the quality of a vaccine against Ebola virus by, for example, checking that the antigen of said vaccine contains the specific epitope in the correct conformation, is also contemplated to be within the scope of the invention.
  • the polypeptides that bind to the antibodies of the present invention may also be useful in screening for ligands that bind to said polypeptides.
  • Such ligands include but are not limited to antibodies; including those from camels, sharks and other species, fragments of antibodies, peptides, phage display technology products, aptamers, adnectins or fragments of other viral or cellular proteins, may block the epitope and so prevent infection.
  • Such ligands are encompassed within the scope of the invention.
  • the invention provides a pharmaceutical composition
  • a pharmaceutical composition comprising one or more of: the antibodies or antibody fragments of the invention; nucleic acid encoding such antibodies or fragments; vectors encoding the nucleic acids; or polypeptides recognized by the antibodies or antigen binding fragment of the invention.
  • the pharmaceutical composition may also contain a pharmaceutically acceptable carrier or excipient. Although the carrier or excipient may facilitate administration, it should not itself induce the production of antibodies harmful to the individual receiving the composition. Nor should it be toxic. Suitable carriers may be large, slowly metabolized macromolecules such as proteins, polypeptides, liposomes, polysaccharides, polylactic acids, polyglycolic acids, polymeric amino acids, amino acid copolymers and inactive virus particles.
  • salts can be used, for example mineral acid salts, such as hydrochlorides, hydrobromides, phosphates and sulphates, or salts of organic acids, such as acetates, propionates, malonates and benzoates. 4
  • Pharmaceutically acceptable carriers in therapeutic compositions may additionally contain liquids such as water, saline, glycerol and ethanol. Additionally, auxiliary substances, such as wetting or emulsifying agents or pH buffering substances, may be present in such compositions. Such carriers enable the pharmaceutical compositions to be formulated as tablets, pills, dragees, capsules, liquids, gels, syrups, slurries and suspensions, for ingestion by the subject.
  • compositions present in several forms of administration include, but are not limited to, those forms suitable for parenteral administration, e.g., by injection or infusion, for example by bolus injection or continuous infusion.
  • parenteral administration e.g., by injection or infusion, for example by bolus injection or continuous infusion.
  • the product may take the form of a suspension, solution or emulsion in an oily or aqueous vehicle and it may contain formulatory agents, such as suspending, preservative, stabilizing and/or dispersing agents.
  • the antibody molecule may be in dry form, for reconstitution before use with an appropriate sterile liquid.
  • compositions of the invention can be administered directly to the subject.
  • the compositions are adapted for administration to mammalian, e.g., human subjects.
  • compositions of this invention may be administered by any number of routes including, but not limited to, oral, intravenous, intramuscular, intra-arterial,
  • the therapeutic compositions may be prepared as injectables, either as liquid solutions or
  • compositions Solid forms suitable for solution in, or suspension in, liquid vehicles prior to injection may also be prepared.
  • Direct delivery of the compositions will generally be accomplished by injection, subcutaneously, intraperitoneally, intravenously or intramuscularly, or delivered to the interstitial space of a tissue.
  • the compositions can also be administered into a lesion. Dosage treatment may be a single dose schedule or a multiple dose schedule.
  • compositions provide guidance relating to frequency of administration e.g., whether a pharmaceutical should be delivered daily, weekly, monthly, etc. Frequency and dosage may also depend on the severity of symptoms.
  • compositions of the invention may be prepared in various forms.
  • the compositions may be prepared as injectables, either as liquid solutions or suspensions.
  • Solid forms suitable for solution in, or suspension in, liquid vehicles prior to injection can also be prepared (e.g., a lyophilized composition, like SynagisTM and HerceptinTM, for reconstitution with sterile water containing a preservative).
  • the composition may be prepared for topical administration e.g., as an ointment, cream or powder.
  • the composition may be prepared for oral administration e.g., as a tablet or capsule, as a spray, or as a syrup (optionally flavored).
  • the composition may be prepared for pulmonary administration e.g., as an inhaler, using a fine powder or a spray.
  • the composition may be prepared as a suppository or pessary.
  • the composition may be prepared for nasal, aural or ocular administration e.g., as drops.
  • the composition may be in kit form, designed such that a combined composition is reconstituted just prior to administration to a subject.
  • a lyophilized antibody can be provided in kit form with sterile water or a sterile buffer.
  • the active ingredient in the composition will be an antibody molecule, an antibody fragment or variants and derivatives thereof. As such, it will be susceptible to degradation in the gastrointestinal tract.
  • the composition will need to contain agents which protect the antibody from degradation but which release the antibody once it has been absorbed from the gastrointestinal tract.
  • compositions of the invention generally have a pH between 5.5 and 8.5, in some embodiments this may be between 6 and 8, and in other embodiments about 7.
  • the pH may be maintained by the use of a buffer.
  • the composition may be sterile and/or pyrogen free.
  • the composition may be isotonic with respect to humans.
  • pharmaceutical compositions of the invention are supplied in hermetically- sealed containers.
  • compositions will include an effective amount of one or more antibodies of the invention and/or a polypeptide comprising an epitope that binds an antibody of the invention i.e., an amount that is sufficient to treat, ameliorate, attenuate or prevent a desired disease or condition, or to exhibit a detectable therapeutic effect.
  • Therapeutic effects also include reduction or attenuation in pathogenic potency or physical symptoms.
  • the precise effective amount for any particular subject will depend upon their size, weight, and health, the nature and extent of the condition, and the therapeutics or combination of therapeutics selected for administration. The effective amount for a given situation is determined by routine experimentation and is within the judgment of a clinician.
  • an effective dose will generally be from about O.Olmg/kg to about 50 mg/kg, or about
  • HerceptinTM is administered by intravenous infusion of a 21 mg/ml solution, with an initial loading dose of 4 mg/kg body weight and a weekly maintenance dose of 2 mg/kg body weight; RituxanTM is administered weekly at 375 mg/m 2 ; etc.
  • compositions can include one or more (e.g., 2, 3, etc.) antibodies of the invention to provide an additive or synergistic therapeutic effect.
  • the composition may comprise one or more (e.g., 2, 3, etc.) antibodies of the invention and one or more (e.g., 2, 3, etc.) additional antibodies against Ebola virus.
  • the administration of antibodies of the invention together with antibodies specific to other pathogens, for example, influenza A or influenza B virus, are within the scope of the invention.
  • the antibodies of the invention can be administered either combined/simultaneously or at separate times from antibodies specific to pathogens other than Ebola virus.
  • the invention provides a pharmaceutical composition comprising two or more antibodies, wherein the first antibody is an antibody of the invention as described herein and the second antibody is specific for EBOV or a different pathogen that may have co- infected the subject to whom the pharmaceutical composition is being administered.
  • antibodies of the invention specific for, and that specifically bind the Ebola virus GP protein or neutralize infection of EBOV include, but are not limited to, EVB l 14 variant 1, EVB 114 variant 2, EVB 114 variant 3, EVB 114 variant 4, EVB 100, EVB 166,
  • EVB 165 EVB 167 variant 1
  • EVB 167 variant 2 EVB 167 variant 2.
  • the invention provides a pharmaceutical composition comprising the antibody EVB l 14 variant 1 or an antigen binding fragment thereof, and a pharmaceutically acceptable carrier. In another embodiment, the invention provides a pharmaceutical composition comprising the antibody EVB l 14 variant 2 or an antigen binding fragment thereof, and a pharmaceutically acceptable carrier. In another embodiment, the invention provides a pharmaceutical composition comprising the antibody EVB l 14 variant 3 or an antigen binding fragment thereof, and a pharmaceutically acceptable carrier. In another embodiment, the invention provides a pharmaceutical composition comprising the antibody EVB l 14 variant 4 or an antigen binding fragment thereof, and a pharmaceutically acceptable carrier. In another embodiment, the invention provides a pharmaceutical composition comprising the antibody EVB l 00 or an antigen binding fragment thereof, and a pharmaceutically acceptable carrier.
  • the invention provides a pharmaceutical composition comprising the antibody EVB 166 or an antigen binding fragment thereof, and a pharmaceutically acceptable carrier. In another embodiment, the invention provides a pharmaceutical composition comprising the antibody EVB 167 variant 1 or an antigen binding fragment thereof, and a pharmaceutically acceptable carrier. In another embodiment, the invention provides a pharmaceutical composition comprising the antibody EVB 167 variant 2 or an antigen binding fragment thereof, and a pharmaceutically acceptable carrier.
  • Antibodies of the invention may be administered (either combined or separately) with other therapeutics e.g., with chemotherapeutic compounds, with radiotherapy, etc.
  • the therapeutic compounds include anti-viral compounds such as TamifluTM.
  • Such combination therapy provides an additive or synergistic improvement in therapeutic efficacy relative to the individual therapeutic agents when administered alone.
  • the term "synergy” is used to describe a combined effect of two or more active agents that is greater than the sum of the individual effects of each respective active agent. Thus, where the combined effect of two or more agents results in "synergistic inhibition" of an activity or process, it is intended that the inhibition of the activity or process is greater than the sum of the inhibitory effects of each respective active agent.
  • the term "synergistic therapeutic effect” refers to a therapeutic effect observed with a combination of two or more therapies wherein the therapeutic effect (as measured by any of a number of parameters) is greater than the sum of the individual therapeutic effects observed with the respective individual therapies.
  • Antibodies may be administered to those subjects who have previously shown no response, i.e., have been shown to be refractive to treatment for EBOV infection.
  • the invention provides a pharmaceutical composition comprising one or more antibodies of the invention, or antigen binding fragments thereof and an anti- viral agent effective against Ebola virus.
  • the anti-viral agent may be an agent now known to one of skill in the art, or a later discovered or invented agent.
  • a composition of the invention may include antibodies of the invention, wherein the antibodies may make up at least 50% by weight (e.g., 60%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99% or more) of the total protein in the composition.
  • the antibodies are in purified form.
  • the invention provides a method of preparing a pharmaceutical composition comprising the steps of: (i) preparing an antibody of the invention; and (ii) admixing the purified antibody with one or more pharmaceutically-acceptable carriers.
  • a method of preparing a pharmaceutical composition comprises the step of: admixing an antibody with one or more pharmaceutically-acceptable carriers, wherein the antibody is a monoclonal antibody that was obtained from a transformed B cell or a cultured plasma cell of the invention.
  • the procedures for first obtaining the monoclonal antibody and then preparing the pharmaceutical can be performed at very different times by different people in different places (e.g., in different countries).
  • compositions of the invention may be immunogenic compositions, and in some embodiments may be vaccine compositions comprising an antigen comprising an epitope recognized by an antibody of the invention or an antigen binding fragment thereof.
  • Vaccines according to the invention may either be prophylactic (i.e., prevent infection) or therapeutic (i.e., treat or ameliorate infection).
  • Compositions may include an antimicrobial, particularly if packaged in a multiple dose format. They may comprise detergent e.g., a Tween (polysorbate), such as Tween 80.
  • compositions may also include sodium salts (e.g., sodium chloride) to give tonicity. A concentration of 10+2mg/ml NaCl is typical. Further, compositions may comprise a sugar alcohol (e.g., mannitol) or a disaccharide
  • compositions of the invention may also comprise one or more immunoregulatory agents.
  • one or more of the immunoregulatory agents include(s) an adjuvant.
  • the epitope compositions of the invention may elicit both a cell mediated immune response as well as a humoral immune response in order to effectively address Ebola virus infection.
  • This immune response may induce long lasting (e.g., neutralizing) antibodies and a cell mediated immunity that can quickly respond upon exposure to EBOV.
  • the antibodies and antibody fragments of the invention or derivatives and variants thereof may be used for the treatment of EBOV infection; for the prevention of infection of Ebola virus; or for the diagnosis of Ebola virus infection.
  • the methods of the invention provide for the administration of an antibody of the invention or a fragment thereof for the treatment of Ebola virus infection.
  • the invention provides a method of treating or reducing Ebola virus infection, or lowering the risk of Ebola virus infection, comprising: administering to a subject in need thereof, a therapeutically effective amount of an antibody of the invention, or an antigen binding fragment thereof.
  • the invention provides an antibody of the invention, or an antigen binding fragment thereof, for use as a medicament.
  • the invention provides an antibody of the invention, or an antigen binding fragment thereof, for use as a medicament in the treatment of Ebola virus infection.
  • the invention provides the use of an antibody of the invention, or an antigen binding fragment thereof, for the manufacturing of a medicament.
  • the invention provides the use of an antibody of the invention, or an antigen binding fragment thereof, for the manufacturing of a medicament for the treatment of a disease or disorder, including, but not limited to, the treatment of Ebola virus infection.
  • Methods of diagnosis may include contacting an antibody or an antibody fragment with a sample.
  • samples may be tissue samples taken from, for example, nasal passages, sinus cavities, salivary glands, lung, liver, pancreas, kidney, ear, eye, placenta, alimentary tract, heart, ovaries, pituitary, adrenals, thyroid, brain or skin.
  • the methods of diagnosis may also include the detection of an antigen/antibody complex.
  • the invention therefore provides (i) an antibody, an antibody fragment, or variants and derivatives thereof according to the invention, (ii) an immortalized B cell clone according to the invention, (iii) an epitope capable of binding an antibody of the invention or (iv) a ligand, preferably an antibody, capable of binding an epitope that binds an antibody of the invention for use in therapy.
  • the invention also provides a method of treating a subject comprising administering to the subject an antibody, an antibody fragment, or variants and derivatives thereof according to the invention, or, a ligand, preferably an antibody, capable of binding an epitope that binds an antibody of the invention.
  • the method results in reduced Ebola virus infection in the subject.
  • the method prevents, reduces the risk if EBOV infection or delays the onset of EBOV infection in the subject.
  • the invention also provides the use of (i) an antibody, an antibody fragment, or variants and derivatives thereof according to the invention, (ii) an immortalized B cell clone according to the invention, (iii) an epitope capable of binding an antibody of the invention, (iv) a ligand, preferably an antibody, that binds to an epitope capable of binding an antibody of the invention, or (v) a pharmaceutical composition of the invention in the manufacture of a medicament for the treatment or attenuation of infection by Ebola virus and/or in the manufacture of a medicament for prevention of Ebola virus infection, i.e., a vaccine, and/or in the manufacture of a medicament for the diagnosis of Ebola virus infection.
  • the invention provides a composition of the invention for use as a medicament for the prevention or treatment of EBOV infection. It also provides the use of an antibody of the invention and/or a protein comprising an epitope to which such an antibody binds in the manufacture of a medicament for treatment of a subject and/or diagnosis in a subject. It also provides a method for treating a subject, comprising the step of administering to the subject a composition of the invention. In some embodiments the subject may be a human.
  • One way of checking efficacy of therapeutic treatment involves monitoring disease symptoms after administration of the composition of the invention. Treatment can be a single dose schedule or a multiple dose schedule.
  • an antibody or antibody fragment including, but not limited to, a recombinant antibody or fragment thereof, immortalized B cell clone, epitope or composition according to the invention is administered to a subject in need of such treatment.
  • a subject includes, but is not limited to, one who is particularly at risk of or susceptible to Ebola virus infection, including, for example, an immunocompromised subject.
  • the antibody or antibody fragment of the invention can also be used in passive immunization or active vaccination.
  • Antibodies and fragments thereof as described in the present invention may also be used in a kit for the diagnosis of EBOV infection. Further, epitopes capable of binding an antibody of the invention may be used in a kit for monitoring the efficacy of vaccination procedures by detecting the presence of protective anti-EBOV antibodies. Antibodies, antibody fragment, or variants and derivatives thereof, as described in the present invention may also be used in a kit for monitoring vaccine manufacture with the desired immunogenicity.
  • the invention also provides an epitope that specifically binds to an antibody of the invention or an antigen binding fragment thereof, for use (i) in therapy, (ii) in the manufacture of a medicament for the prevention, treatment or attenuation of EBOV infection, (iii) as a vaccine, or (iv) in screening for ligands able to neutralize EBOV infection.
  • the invention also provides a method of preparing a pharmaceutical, comprising the step of admixing a monoclonal antibody with one or more pharmaceutically-acceptable carriers, wherein the monoclonal antibody is a monoclonal antibody that was obtained from a transfected host cell of the invention.
  • the pharmaceutical carrier(s) e.g., expressing it and/or purifying it
  • admixing it with the pharmaceutical carrier(s) can be performed at very different times by different people in different places (e.g., in different countries).
  • various steps of culturing, sub-culturing, cloning, sub-cloning, sequencing, nucleic acid preparation etc. can be performed in order to perpetuate the antibody expressed by the transformed B cell or the cultured plasma cell, with optional optimization at each step.
  • the above methods further comprise techniques of optimization (e.g., affinity maturation or optimization) applied to the nucleic acids encoding the antibody.
  • the invention encompasses all cells, nucleic acids, vectors, sequences, antibodies etc. used and prepared during such steps. In all these methods, the nucleic acid used in the expression host may be manipulated to insert, delete or alter certain nucleic acid sequences.
  • Changes from such manipulation include, but are not limited to, changes to introduce restriction sites, to amend codon usage, to add or optimize transcription and/or translation regulatory sequences, etc. It is also possible to change the nucleic acid to alter the encoded amino acids. For example, it may be useful to introduce one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, etc.) amino acid substitutions, deletions and/or insertions into the antibody' s amino acid sequence. Such point mutations can modify effector functions, antigen-binding affinity, post-translational modifications, immunogenicity, etc., can introduce amino acids for the attachment of covalent groups (e.g., labels) or can introduce tags (e.g., for purification purposes).
  • covalent groups e.g., labels
  • tags e.g., for purification purposes.
  • Mutations can be introduced in specific sites or can be introduced at random, followed by selection (e.g., molecular evolution).
  • one or more nucleic acids encoding any of the CDR regions, heavy chain variable regions or light chain variable regions of antibodies of the invention can be randomly or directionally mutated to introduce different properties in the encoded amino acids.
  • Such changes can be the result of an iterative process wherein initial changes are retained and new changes at other nucleotide positions are introduced. Further, changes achieved in independent steps may be combined.
  • Different properties introduced into the encoded amino acids may include, but are not limited to, enhanced affinity.
  • antibody fragment As used herein, the terms “antigen binding fragment,” “fragment,” and “antibody fragment” are used interchangeably to refer to any fragment of an antibody of the invention that retains the antigen-binding activity of the antibody. Examples of antibody fragments include, but are not limited to, a single chain antibody, Fab, Fab' , F(ab') 2 , Fv or scFv. Further, the term “antibody” as used herein includes both antibodies and antigen binding fragments thereof. As used herein, a “neutralizing antibody” is one that can neutralize, i.e. , prevent, inhibit, reduce, impede or interfere with, the ability of a pathogen to initiate and/or perpetuate an infection in a host.
  • neutralizing antibody and "an antibody that neutralizes” or “antibodies that neutralize” are used interchangeably herein. These antibodies can be used alone, or in combination, as prophylactic or therapeutic agents upon appropriate formulation, in association with active vaccination, as a diagnostic tool, or as a production tool as described herein.
  • composition “comprising” encompasses “including” as well as “consisting” e.g., a composition “comprising” X may consist exclusively of X or may include something additional e.g., X + Y.
  • disease as used herein is intended to be generally synonymous, and is used interchangeably with, the terms “disorder” and “condition” (as in medical condition), in that all reflect an abnormal condition of the human or animal body or of one of its parts that impairs normal functioning, is typically manifested by distinguishing signs and symptoms, and causes the human or animal to have a reduced duration or quality of life.
  • treatment of a subject or patient is intended to include prevention, prophylaxis, attenuation, amelioration and therapy.
  • subject or patient are used interchangeably herein to mean all mammals including humans. Examples of subjects include humans, cows, dogs, cats, horses, goats, sheep, pigs, and rabbits. In one embodiment, the patient is a human.
  • Example 1 Isolation of fully human EBOV neutralizing antibodies.
  • IgG Memory B cells from two individuals who recoverd from EBOV infection were immortalized with EBV and CpG as previously described (Traggiai et al., Nat. Med. 2004) and supernatants were then tested in a primary screening for binding to ZEBOV GP protein by ELISA. Positive supernatants were then tested for binding to EBOV GP and to an irrelevant antigen. From the results of these assays, 52 antibodies were selected that showed specificity for EBOV GP ( Figure 1). Titration experiments showed that the antibodies bound with sometimes different binding profiles.
  • EVBl 00 binds to GP with OD values lower than EVBl 14, EVB166, and EVB165, thus suggesting that EVB100 might recognize a particular conformation of the GP protein that is not efficiently exposed when coated on a solid surface ( Figure 2).
  • Example 2 Antigenic sites recognized by the isolated EBOV-neutralizing human monoclonal antibodies.
  • EVB 114 has a methionine residue in the CDR1 of the heavy chain (M36 according to IMGT numbering) that represents a medium-scoring sequence liability issue.
  • M36 is introduced by a somatic mutation, and the corresponding germline residue is serine (S36).
  • S36 serine
  • the CDR1 of the light chain contains the DN motif (residues 36 and 37 according to IMGT numbering) which represents a low risk site for acidic cleavage.
  • EVBl 14 to remove M36 in HCDRl by mutating it to S36 (SEQ ID 17 and 25) and to remove D36 in LCDRl by mutating it to S36 (SEQ ID 18 and 26).
  • EVBl 14 carrying M36S mutation in HCDRl
  • EVBl 14 carrying D36S in LCDRl EVBl 14 carrying both M36S in HCDRl and D36S in LCDRl.

Abstract

The invention relates to antibodies, and antigen binding fragments thereof, that specifically bind to the Ebola virus GP protein or neutralize infection of Ebola virus. The invention also relates to antigenic sites to which the antibodies and antigen binding fragments bind, as well as to nucleic acids that encode, and immortalized B cells and cultured plasma cells that produce, such antibodies and antibody fragments. In addition, the invention relates to the use of the antibodies, antibody fragments, and polypeptides recognized by the antibodies of the invention in screening methods as well as in the diagnosis, treatment and prevention of Ebola virus infection.

Description

ANTIBODIES THAT NEUTRALIZE EBOLA VIRUS AND USES THEREOF
This application claims the benefit of priority of United States provisional Application No. 62/080,094, filed November 14, 2014, the disclosure of which is hereby incorporated by reference, as if written herein, in its entirety. BACKGROUND
Ebola virus (EBOV) is one of five known species within the genus Ebolavirus. There are five (5) EBOV species: Zaire (ZEBOV), Sudan (SEBOV), Bunbibugyo (BEBOV), Reston (REBOV), Cote d'lvoire (CIEBOV). Four of the five known Ebola species cause a severe, and often fatal, hemorrhagic fever in humans and other mammals known as Ebola virus disease (EVD). The virus was first recognized in 1976 during an outbreak in the Ebola River valley in Zaire (now the Democratic Republic of Congo). Ebola virus has caused the majority of human deaths from EVD, and ZEBOV is the cause of the 2014 Ebola virus epidemic in West Africa. EBOV is an enveloped virus with a bacilliform to filamentous shape, with a diameter of approximately 80 nm and length between 800-1000 nm. The viral glycoprotein projects from the viral lipid bilayer with spikes that are 7-10 nm in length. The EBOV genome is a single-stranded RNA that is approximately 19,000 nucleotides long. It encodes seven structural proteins:
nucleoprotein (NP), polymerase cofactor (VP35), (VP40), glycoprotein (GP), transcription activator (VP30), (VP24), and RNA polymerase (L).
GP is polypeptide with 676 amino acids (transcriptional editing is also responsible for the production of soluble GP, sGP, that is 364 amino acids in length). GP is post-translationally cleaved by furin to yield disulphide-linked GP1 and GP2 subunits. Soluble GP (sGP) and GP1 are identical in their first 295 NH2-terminal amino acids, whereas the remaining COOH-terminal 69 amino acids of sGP and 206 amino acids of GP1 are encoded by different reading frames. GP1 effects attachment to host cells, whereas GP2 mediates fusion of viral and host membranes. GP is the only target of EBOV neutralizing antibodies. EBOV is thought to enter host cells by receptor-mediated endocytosis (two receptors have been suggested: cholesterol transporter protein, the host-encoded Niemann-Pick CI (NPC1), and TIM-1). GP is further processed by endosomal cathepsin, thus acquiring fusogenic activity. Ebola virus (EBOV) infections cause severe illness in humans, and after an incubation period of 3 to 21 days, patients initially present with general flu-like symptoms before a rapid progression to advanced disease characterized by haemorrhage, multiple organ failure and a shock- like syndrome. In the spring of 2014, a new EBOV variant emerged in the West African country of Guinea, an area in which EBOV had not been previously reported. Despite a sustained international response from local and international authorities since March 2014, the outbreak has yet to be brought to an end after eight months. As of 7 November 2014, there are 13,042 total cases and 4,818 deaths spanning Guinea, Sierra Leone, Liberia, Mali, Nigeria, Senegal, Spain and US. Controlling an EBOV outbreak of this magnitude has proven to be a challenge and the outbreak is predicted to last for at least several more months, with a risk that EBOV will become endemic in those areas. In the absence of licensed vaccines and therapeutics against EBOV, there is little that can be done for infected patients outside of supportive care, which includes fluid replenishment, administration of generic antivirals, and management of secondary symptoms. Over the past decade, several experimental strategies have shown promise in treating
EBOV-challenged nonhuman primates (NHPs) after infection. Several previous studies have showed that antibodies are crucial for host survival from EBOV. Prior NHP studies have also demonstrated that the cocktail of chimeric monoclonal antibodies could protect or partially protect animals when dosing was initiated 1 or 2 days post infection (dpi). Before the success with monoclonal-antibody-based therapies, other candidate therapeutics had only demonstrated efficacy when given within 60 minutes of EBOV exposure.
Clinical studies in patients with severe pneumonia have shown that convalescent sera from patients who have recovered from infections can have a therapeutic benefit. This has been demonstrated for several viral infections, for example, Spanish influenza pneumonia during 1918-1919, (Luke et al, Ann Intern Med. 2006); SARS-CoV (Cheng et al, EJMID 2005); H5N1 influenza virus (Zhou et al, NEJM 2007) and HlNl severe influenza infection (Hung et al. CID 2009); Ebola 1995 outbreak in Kikwit and the current outbreak. These studies demonstrate that the therapeutic use of convalescent sera has the potential to significantly reduce morbidity and mortality associated with severe respiratory virus infections. The therapeutic effect has been attributed to the presence of virus neutralizing antibodies in the convalescent sera. However, the availability of convalescent sera can significantly limit the implementation and utility of this approach.
Isolation, purification and production of specific human neutralizing monoclonal antibodies represents a safe, controlled, affordable and unlimited source of the most "active" ingredient present in convalescent sera, overcoming the limitations of patient-derived
convalescent sera. The safety of monoclonal antibody therapy is well documented, with generally low rates of adverse reactions, that is particularly true for fully human monoclonal antibodies.
In this regard a limitation of chimeric or humanized monoclonal antibodies (such as those composing the Zmapp cocktail reported by Qiu et al., Nature 2014) is that they are immunogenic and could not be therefore considered for EBOV prophylaxis. Conversely, fully human antibodies, and even a single highly effective human monoclonal antibody, are non- immunogenic or very poorly immunogenic and could be used as a prophylactic agent to prevent the infection in healthcare workers or in individuals at high risk of exposure. A single administration of a fully human, potent EBOV neutralizing antibody, or combinations of 2 or more neutralizing antibodies targeting different sites on the virus, could confer a highly effective sterilizing immunity lasting for weeks, if not months. Passively administered monoclonal antibodies could confer rapid and specific immunity in all populations, including the young, the elderly and the immunocompromised individuals. In some instances monoclonal antibodies could confer passively higher- than-natural levels of immunity compared to vaccinations.
Accordingly, there is a need for agents capable of preventing as well as treating or attenuating Ebola virus infection in high-risk patients with high potency and efficacy. Further, it is important to have antibodies that target different epitopes and different antigenic sites on the various strains in order to avoid appearance of resistant virus strains and reducing the risk of selecting viral escape mutants.
SUMMARY
The invention is based, in part, on the discovery, isolation and production of antibodies that specifically bind the Ebola virus GP protein or that potently neutralize infection of Ebola virus, as well as antigenic sites and epitopes to which the antibodies of the invention bind.
Accordingly, in one aspect of the invention, the invention comprises an isolated and/or purified, and/or recombinant antibody, for example a monoclonal antibody, a human antibody, a human monoclonal antibody, an antibody variant, or an antigen binding antibody fragment, that specifically binds the Ebola virus GP protein or neutralizes infection of Ebola virus.
In one embodiment of the invention, the invention comprises an isolated and/or purified, and/or recombinant human antibody, or an antigen binding fragment thereof, that specifically binds the Ebola virus GP protein. The antibody, or antigen binding fragment thereof, potently neutralizes infection of at least one strain of Ebola virus.
In another embodiment of the invention, the invention comprises an isolated and/or purified, and/or recombinant antibody, or an antigen binding fragment thereof, that neutralizes infection of more than one strain of Ebola virus. In one embodiment, the antibody, or antigen binding fragment thereof, neutralizes two (2) strains of Ebola virus. In another embodiment, the antibody, or antigen binding fragment thereof, neutralizes three (3) or more, e.g., four or five strains of Ebola virus.
In yet another embodiment of the invention, the invention comprises an isolated and/or purified, and/or recombinant antibody, or an antigen binding fragment thereof, that specifically binds the Ebola virus GP protein or neutralizes infection of Ebola virus and comprises a heavy chain comprising CDRl, CDR2 and CDR3 and a light chain comprising CDRl, CDR2 and CDR3, wherein the heavy chain CDR3 comprises the amino acid sequence of SEQ ID NOs: 3, 31, 47, 63 or 78. In yet another embodiment of the invention, the invention comprises an isolated and/or purified, and/or recombinant antibody or antigen binding fragment thereof, that specifically binds the Ebola virus GP protein or neutralizes infection of Ebola virus, comprising: (i) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences as set forth in SEQ ID NOs: 1-6, respectively; (ii) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences as set forth in SEQ ID NOs: 17, 2, 3, 18, 5, 6, respectively; (iii) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences as set forth in SEQ ID NOs: 1, 2, 3, 18, 5, 6, respectively; (iv) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences as set forth in SEQ ID NOs: 17, 2, 3, 4, 5, 6, respectively; (v) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences as set forth in SEQ ID NOs: 29-34, respectively; (vi) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences as set forth in SEQ ID NOs: 45-50, respectively; (vii) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences as set forth in SEQ ID NOs: 61-64, 5, 65, respectively; or (viii) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences as set forth in SEQ ID NOs: 76-79, 49, 80, respectively.
In still another embodiment of the invention, the invention comprises an isolated and/or purified, and/or recombinant antibody or antigen binding fragment thereof, that specifically binds the Ebola virus GP protein or neutralizes infection of Ebola Virus, comprising: (i) a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 13 and a light chain variable region comprising the amino acid sequence of SEQ ID NO: 14; or (ii) a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 25 and a light chain variable region comprising the amino acid sequence of SEQ ID NO: 26; (iii) or a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 13 and a light chain variable region comprising the amino acid sequence of SEQ ID NO: 26; or (iv) a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 25 and a light chain variable region comprising the amino acid sequence of SEQ ID NO: 14; or (v) a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 41 and a light chain variable region comprising the amino acid sequence of SEQ ID NO: 42; or (vi) a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 57 and a light chain variable region comprising the amino acid sequence of SEQ ID NO: 58; or (vii) a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 72 and a light chain variable region comprising the amino acid sequence of SEQ ID NO: 73; or (viii) a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 87 and a light chain variable region comprising the amino acid sequence of SEQ ID NO: 88.
The invention further comprises an isolated and/or purified, and/or recombinant antibody, or an antigen binding fragment thereof, described herein as EVB114 variant 1, EVB114 variant 2, EVB114 variant 3, EVB114 variant 4, EVB100, EVB166, EVB 165, EVB167 variant 1, or EVB167 variant 2. In another embodiment, the invention comprises an antibody, or antigen binding fragment thereof, that specifically binds the Ebola virus GP protein or neutralizes infection of Ebola virus, wherein the antibody or fragment thereof is expressed by an
immortalized B cell clone that produces EVB114 variant 1, EVB114 variant 2, EVB114 variant 3, EVB114 variant 4, EVB100, EVB166, EVB165, EVB167 variant 1, or EVB167 variant 2. In another aspect, the invention comprises a nucleic acid molecule comprising a polynucleotide encoding an antibody or antibody fragment of the invention. In yet another aspect, the invention comprises a vector comprising a nucleic acid molecule of the invention. The invention also comprises a cell comprising a vector of the invention or a cell that expresses an antibody of the invention or an antigen binding fragment thereof. In still another aspect, the invention comprises an isolated or purified immunogenic polypeptide comprising an epitope that binds to an antibody or antigen binding fragment of the invention.
The invention further comprises a pharmaceutical composition comprising an antibody of the invention or an antigen binding fragment thereof, a nucleic acid molecule of the invention, a vector comprising a nucleic acid molecule of the invention, a cell comprising a vector of the invention, a cell expressing an antibody or an antibody fragment of the invention, or an immunogenic polypeptide of the invention, and a pharmaceutically acceptable diluent or carrier. The invention also comprises a pharmaceutical composition comprising a first antibody or an antigen binding fragment thereof, and a second antibody, or an antigen binding fragment thereof, wherein the first antibody is an antibody of the invention, and the second antibody is an antibody, or an antigen binding fragment thereof, that specifically binds the Ebola virus GP protein or neutralizes infection of Ebola virus.
Use of an antibody of the invention, or an antigen binding fragment thereof, a nucleic acid of the invention, a vector comprising a nucleic acid of the invention, a cell expressing a vector of the invention, an isolated or purified immunogenic polypeptide comprising an epitope that binds to an antibody or antibody fragment of the invention, or a pharmaceutical composition of the invention in the manufacture of a medicament for (i) the prevention, treatment or attenuation of Ebola virus infection, (ii) vaccination against Ebola virus infection, or
(iii) diagnosis of Ebola virus infection is also contemplated to be within the scope of the invention. Further, use of an antibody of the invention, or an antigen binding fragment thereof, for monitoring the quality of a vaccine against Ebola virus by checking that the antigen of said vaccine contains the specific epitope in the correct conformation is also contemplated to be within the scope of the invention.
In another aspect of the invention, the invention comprises a method of treating or attenuating Ebola virus infection or lowering the risk of Ebola virus infection comprising administering to a subject in need thereof, a therapeutically effective amount of an antibody or an antigen binding antibody fragment of the invention.
In yet another aspect of the invention, the invention comprises a polypeptide which specifically binds to an antibody of the invention, or an antigen binding fragment thereof, for use (i) in therapy, (ii) in the manufacture of a medicament for the treatment or attenuation of Ebola virus infection, (iii) as a vaccine, or (iv) in screening for ligands able to neutralise infection of Ebola virus.
DESCRIPTION OF FIGURES
Figure 1 shows the results of binding to ZEBOV GP and to an irrelevant antigen (Ctr. Ag.) by a panel of 52 human monoclonal antibodies as measured by ELISA. Figure 2A shows the results of binding to ZEBOV GP by human monoclonal antibodies
EVBIOO, EVBl 14 and a negative control monoclonal antibody. Figure 2B shows the results of binding to ZEBOV GP by human monoclonal antibodies EVB165, EVB166 and EVB167.
Figure 3 shows the results of a monoclonal antibody cross-competition assay performed by ELISA on the EVBIOO, EVBl 14 and EVB166 monoclonal antibodies. Shown is the binding of the biotinylated antibody EVBl 14 in the presence of ascending concentrations of unlabeled EVBIOO, EVBl 14 and EVB166 monoclonal antibodies.
Figure 4 shows the binding of serial dilutions of parental EVBl 14 antibody and three variants mutated in heavy chain (M36S/wt), light chain (wt/D36S) and heavy and light chain
(M36S/D36S) to EBOV GP expressed on the surface of MDCK-SIAT cells by FACS analysis. Parental MDCK-SIAT cells were labeled with CFSE dye (y-axis) and mixed with unlabelled MDCK-SIAT EBOV GP cells. The binding of human antibodies was detected with a fluorophore- (APC, x axis) conjugated anti-human antibody. Figure 4A shows FACS dot plots of the antibody variants binding to the mixture of cells. Figure 4B shows a plot of the binding of different concentration of the antibody variants (in ng/ml) expressed as mean fluorescence intensity (MFI).
Figure 5 shows the amino acid sequences for the two heavy chains of the variants of antibody EVB114 and the nucleic acid sequences that encode them (Figure 5A); as well as the amino acid sequences for the two light chains of the variants of antibody EVB114 and the nucleic acid sequences that encode them(Figure 5B). In both Figures 5 A and 5B the amino acid sequences of the CDRs and the nucleic acid sequences that encode the CDRs are provided in bold text.
Figure 6 shows the amino acid sequences for the heavy and light chains of antibody EVB100 as well as the nucleic acid sequences that encode them. The amino acid sequences of the CDRs and the nucleic acid sequences that encode the CDRs are provided in bold text.
Figure 7 shows the amino acid sequences for the heavy and light chains of antibody EVB166 as well as the nucleic acid sequences that encode them. The amino acid sequences of the CDRs and the nucleic acid sequences that encode the CDRs are provided in bold text. Figure 8 shows the amino acid sequences for the heavy and light chains of antibody
EVB165 as well as the nucleic acid sequences that encode them. The amino acid sequences of the CDRs and the nucleic acid sequences that encode the CDRs are provided in bold text.
Figure 9 shows the amino acid sequences for the heavy chain and the two light chains of the variants of antibody EVB167 and the nucleic acid sequences that encode them. The amino acid sequences of the CDRs and the nucleic acid sequences that encode the CDRs are provided in bold text.
DETAILED DESCRIPTION
The invention is based, in part, on the discovery and isolation or production of antibodies that are highly specific to the Ebola virus GP protein or are highly potent in neutralizing Ebola virus infection, as well as antigenic sites and epitopes to which the antibodies of the invention bind. Such antibodies are desirable, as only small quantities of the antibodies are required in order to neutralize Ebola virus infection and are highly effective in preventing as well as treating or attenuating Ebola virus infection in high-risk patients. This reduces the costs of production of medicaments comprising the antibodies for the treatment of EBOV infection. In addition, the antigenic sites or immunogenic polypeptides comprising epitopes recognized by the antibodies of the invention may be part of a vaccine capable of inducing protection against EBOV.
In one aspect of the invention, the invention provides an isolated and/or purified, and/or recombinant antibody, antibody variants and antigen binding fragments thereof, that specifically binds the Ebola virus GP protein. In some embodiments, the antibody is a monoclonal antibody, a human antibody, or a human monoclonal antibody.
In one embodiment of the invention, the invention comprises an isolated and/or purified, and/or recombinant human antibody, or an antigen binding fragment thereof, that specifically binds the Ebola virus GP protein and neutralizes infection of at least one strain of Ebola virus. In another embodiment of the invention, the invention comprises an isolated and/or purified, and/or recombinant antibody, or an antigen binding fragment thereof, that specifically binds the Ebola virus GP protein and neutralizes infection of more than one strain of Ebola virus. In one embodiment, the antibody, or antigen binding fragment thereof, neutralizes two (2) strains of Ebola virus. In another embodiment, the antibody, or antigen binding fragment thereof, neutralizes three (3) or more, e.g., four or five strains of Ebola virus.
The antibody and antigen binding fragment of the invention have high neutralizing potency. The concentration of the antibody of the invention required for 50% neutralization of Ebola virus (IC50) is, for example, about 10 μg /ml or less. In one embodiment, the
concentration of the antibody of the invention required for 50% neutralization of EBOV is about 9 μg/ml to about 11 μg/ml. In other embodiments, the concentration of the antibody of the invention required for 50% neutralization of EBOV is about 11 μg/ml or less, or about 10 μg/ml or less, or about 9 μg/ml or less, or about 8 μg/ml or less, or about 7 μg/ml or less, or about 6 μg/ml or less, or about 5 μg/ml or less, or about 4 μg/ml or less, or about 3.5 μg/ml or less, or about 3 μg/ml or less, or about 2.5 μg/ml or less, or about 2 μg/ml or less, or about 1.5 μg/ml or less, or about 1,4 μg/ml or less, or about 1.3 μg/ml or less, or about 1.2 μg/ml or less, or about 1.1 μg/ml or less, or about 1 μg/ml or less, or about 0.9 μg/ml or less, or about 0.8 μg/ml or less, or about 0.7 μg/ml or less, or about 0.6 μg/ml or less, or about 0.5 μg/ml or less, or about 0.4 μg/ml or less, or about 0.3 μg/ml or less, or about 0.25 μg/ml or less, or about 0.2 μg/ml or less, or about 0.15 μg/ml or less, or about 0.1 μg/ml or less. In some embodiments, the concentration of the antibody of the invention required for 50% neutralization of EBOV is about 250 ng/ml or less, or about 200 ng/ml or less, or about 175 ng/ml or less, or about 150 ng/ml or less, or about 140 ng/ml or less, or about 130 ng/ml or less, or about 120 ng/ml or less, or about 110 ng/ml or less, or about 100 ng/ml or less, or about 90 ng/ml or less, or about 80 ng/ml or less, or about 70 ng/ml or less, or about 60 ng/ml or less, or about 50 ng/ml or less, or about 40 ng/ml or less, or about 30 ng/ml or less, or about 10 ng/ml or less. In other embodiments, the concentration of the antibody of the invention required for 50% neutralization of EBOV is about 20 ng/ml or about 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6 5, 4, 3, 2 or about 1 ng/ml or less. This means that only low concentrations of antibody are required for 50% neutralization of EBOV.
Specificity and potency can be measured using standard assays as known to one of skill in the art.
The antibodies of the invention may be human antibodies, monoclonal antibodies, human monoclonal antibodies, recombinant antibodies or purified antibodies. The invention also provides fragments of the antibodies of the invention, particularly fragments that retain the antigen-binding activity of the antibodies. Such fragments include, but are not limited to, single chain antibodies, Fab, Fab', F(ab')2, Fv or scFv. Although the specification, including the claims, may, in some places, refer explicitly to antigen binding fragment(s), antibody
fragment(s), variant(s) and/or derivative(s) of antibodies, it is understood that the term
"antibody" or "antibody of the invention" includes all categories of antibodies, namely, antigen binding fragment(s), antibody fragment(s), variant(s) and derivative(s) of antibodies. The sequences of the heavy chains and light chains of several antibodies of the invention, each comprising three CDRs on the heavy chain and three CDRs on the light chain have been determined. The positions of the CDR amino acids are defined according to the EVIGT numbering system. The sequences of the CDRs, heavy chains, light chains as well as the sequences of the nucleic acid molecules encoding the CDRs, heavy chains, and light chains of the antibodies of the invention are disclosed in the sequence listing. The CDRs of the antibody heavy chains are referred to as CDRHl, CDRH2 and CDRH3, respectively. Similarly, the CDRs of the antibody light chains are referred to as CDRLl, CDRL2 and CDRL3, respectively. Table 1 provides the SEQ ID numbers for the amino acid sequences of the six CDRs of the heavy and light chains, respectively, of some examples of antibodies of the invention. Table 1. SEQ ID Numbers for CDR polypeptides of antibodies that neutralize Ebola
Figure imgf000012_0001
In one embodiment, an isolated and/or purified, and/or recombinant antibody or antibody fragment of the invention comprises at least one CDR with a sequence that has at least 95% sequence identity to any one of SEQ ID NOs: 1-6, 17, 18, 29-34, 45-50, 61-65 or 76-80. The amino acid sequences of the heavy and light chain variable regions of the antibodies of the invention as well as the nucleic acid sequences that encode them are provided in Figures 5 A, 5B, 6, 7, 8 and 9. The amino acid residues corresponding to the six CDRs and the nucleic acid residues that encode them are highlighted in bold text.
In another embodiment, the invention provides an isolated and/or purified, and/or recombinant antibody or antigen binding fragment comprising a heavy chain comprising one or more (i.e., one, two or all three) heavy chain CDRs from EVB114 variant 1, EVB114 variant 2, EVB114 variant 3, EVB 114 variant 4, EVB100, EVB166, EVB165, EVB 167 variant 1, or EVB167 variant 2. In yet another embodiment, the isolated and/or purified, and/or recombinant antibody or antigen binding fragment of the invention comprises a heavy chain CDR1 with the amino acid sequence of SEQ ID NOs: 1, 17, 29, 45, 61 or 76; a heavy chain CDR2 with the amino acid sequence of SEQ ID NOs: 2, 30, 46, 62 or 77; and a heavy chain CDR3 with the amino acid sequence of SEQ ID NOs: 3, 31, 47, 63 or 78. In certain embodiments, an antibody or antibody fragment as provided herein comprises a heavy chain comprising the amino acid sequence of (i) SEQ ID NO: 1 for CDRHl, SEQ ID NO: 2 for CDRH2 and SEQ ID NO: 3 for CDRH3; (ii) SEQ ID NO: 17 for CDRHl, SEQ ID NO: 2 for CDRH2, and SEQ ID NO: 3 for CDRH3; (iii) SEQ ID NO: 29 for CDRHl, SEQ ID NO: 30 for CDRH2, and SEQ ID NO: 31 for CDRH3; (iv) SEQ ID NO: 45 for CDRHl, SEQ ID NO: 46 for CDRH2, and SEQ ID NO: 47 for CDRH3; (v) or SEQ ID NO: 61 for CDRHl, SEQ ID NO: 62 for CDRH2, and SEQ ID NO: 63 for CDRH3; or (vi) SEQ ID NO: 76 for CDRHl, SEQ ID NO: 77 for CDRH2, and SEQ ID NO: 78 for CDRH3.
In one embodiment, an isolated and/or purified, and/or recombinant antibody of the invention, or antigen binding fragment thereof, specifically binds the Ebola virus GP protein or neutralizes infection of EBOV and comprises a heavy chain comprising CDR1, CDR2 and CDR3 and a light chain comprising CDR1, CDR2 and CDR3, wherein the heavy chain CDR3 comprises an amino acid sequence that is at least 90%, for example, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical to SEQ ID NOs: 3, 31, 47, 63 or 78. Also provided is an isolated and/or purified, and/or recombinant antibody or antigen binding fragment that neutralizes infection of Ebola virus and comprises a light chain comprising one or more (i.e. one, two or all three) light chain CDRs from EVB114 variant 1, EVB114 variant 2, EVB114 variant 3, EVB114 variant 4, EVB100, EVB166, EVB 165, EVB167 variant 1, or EVB167 variant 2. In one embodiment, the antibody or antigen binding fragment of the invention comprises a light chain CDR1 with the amino acid sequence of SEQ ID NOs: 4, 18, 32, 48, 64 or 79; a light chain CDR2 with the amino acid sequence of SEQ ID NOs: 5, 33 or 49; and a light chain CDR3 with the amino acid sequence of SEQ ID NO: 6, 34, 50, 65 or 80. In certain embodiments, an antibody or antibody fragment as provided herein comprises a light chain comprising the amino acid sequence of (i) SEQ ID NO: 4 for CDRL1, SEQ ID NO: 5 for CDRL2, and SEQ ID NO: 6 for CDRL3; (ii) SEQ ID NO: 18 for CDRL1, SEQ ID NO: 5 for CDRL2, and SEQ ID NO: 6 for CDRL3; (iii) SEQ ID NO: 32 for CDRL1, SEQ ID NO: 33 for CDRL2, and SEQ ID NO: 34 for CDRL3; (iv) SEQ ID NO: 48 for CDRL1, SEQ ID NO: 49 for CDRL2, and SEQ ID NO: 50 for CDRL3; (v) SEQ ID NO: 64 for CDRL1, SEQ ID NO: 5 for CDRL2, and SEQ ID NO: 65 for CDRL3; or (vi) SEQ ID NO: 79 for CDRL1, SEQ ID NO; 49 for CDRL2, and SEQ ID NO: 80 for CDRL3. In one embodiment, an isolated and/or purified, and/or recombinant antibody of the invention, or antigen binding fragment thereof, comprises all six of the CDRs of antibody EVBl 14 variant 1 as listed in Table 1, and specifically binds the Ebola virus GP protein or neutralizes infection of EBOV. In another embodiment, an antibody of the invention, or antigen binding fragment thereof, comprises all six of the CDRs of antibody EVBl 14 variant 2 as listed in Table 1, and specifically binds the Ebola virus GP protein or neutralizes infection of EBOV. In another embodiment, an antibody of the invention, or antigen binding fragment thereof, comprises all six of the CDRs of antibody EVBl 14 variant 3 as listed in Table 1, and specifically binds the Ebola virus GP protein or neutralizes infection of EBOV. In another embodiment, an antibody of the invention, or antigen binding fragment thereof, comprises all six of the CDRs of antibody EVBl 14 variant 4 as listed in Table 1, and specifically binds the Ebola virus GP protein or neutralizes infection of EBOV.
In another embodiment, an antibody of the invention, or antigen binding fragment thereof, comprises all six of the CDRs of antibody EVBl 00 as listed in Table 1, and specifically binds the Ebola virus GP protein or neutralizes infection of EBOV. In another embodiment, an antibody of the invention, or antigen binding fragment thereof, comprises all six of the CDRs of antibody EVBl 66 as listed in Table 1, and specifically binds the Ebola virus GP protein or neutralizes infection of EBOV. In another embodiment, an antibody of the invention, or antigen binding fragment thereof, comprises all six of the CDRs of antibody EVBl 65 as listed in Table 1, and specifically binds the Ebola virus GP protein or neutralizes infection of EBOV. In another embodiment, an antibody of the invention, or antigen binding fragment thereof, comprises all six of the CDRs of antibody EVBl 67 variant 1 as listed in Table 1, and specifically binds the Ebola virus GP protein or neutralizes infection of EBOV. In another embodiment, an antibody of the invention, or antigen binding fragment thereof, comprises all six of the CDRs of antibody EVBl 67 variant 2 as listed in Table 1, and specifically binds the Ebola virus GP protein or neutralizes infection of EBOV. In another embodiment of the invention, the invention comprises an isolated and/or purified, and/or recombinant antibody or antigen binding fragment thereof, comprising heavy chain CDRl, CDR2 and CDR3 and light chain CDRl, CDR2, and CDR3 amino acid sequences that are at least 90%, for example, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical to the amino acid sequences of the CDR sequences provided in Table 1, wherein the antibody specifically binds the Ebola virus GP protein or neutralizes infection of EBOV.
In another embodiment, the invention comprises an isolated and/or purified, and/or recombinant antibody or antigen binding fragment thereof, that specifically binds the Ebola virus GP protein or neutralizes infection of EBOV, comprising: (i) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences that are at least 90% identical to the amino acid sequences of SEQ ID NOs: 1-6, respectively; (ii) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences that are at least 90% identical to the amino acid sequences of SEQ ID NOs: 17, 2, 3, 18, 5, 6, respectively; (iii) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences that are at least 90% identical to the amino acid sequences of SEQ ID NOs: 1, 2, 3, 18, 5, 6, respectively; (iv) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences that are at least 90% identical to the amino acid sequences of SEQ ID NOs: 17, 2, 3, 4, 5, 6, respectively; (v) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences that are at least 90% identical to the amino acid sequences of SEQ ID NOs: 29-34, respectively; (vi) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences that are at least 90% identical to the amino acid sequences of SEQ ID
NOs: 45-50, respectively; (vii) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences that are at least 90% identical to the amino acid sequences of SEQ ID NOs: 61-64, 5, 65, respectively; or (viii) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences that are at least 90% identical to the amino acid sequences of SEQ ID NOs: 76-79, 49, 80, respectively. In yet another embodiment of the invention, the invention comprises an isolated and/or purified, and/or recombinant antibody or antigen binding fragment thereof, that specifically binds the Ebola virus GP protein or neutralizes infection of EBOV, comprising: (i) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences as set forth in SEQ ID NOs: 1-6, respectively; (ii) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences as set forth in SEQ ID NOs: 17, 2, 3, 18, 5, 6, respectively; (iii) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences as set forth in SEQ ID NOs: 1, 2, 3, 18, 5, 6, respectively; (iv) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences as set forth in SEQ ID NOs: 17, 2, 3, 4, 5, 6, respectively; (v) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences as set forth in SEQ ID NOs: 29-34, respectively; (vi) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences as set forth in SEQ ID NOs: 45-50, respectively; (vii) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences as set forth in SEQ ID NOs: 61-64, 5, 65, respectively; or (viii) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences as set forth in SEQ ID NOs: 76-79, 49, 80, respectively.
The SEQ ID numbers for the amino acid sequence for the heavy chain variable region (VH) and the light chain variable region (VL) of some examples of antibodies of the invention as well as the SEQ ID numbers for the nucleic acid sequences encoding them are listed in Table 2.
Table 2. SEQ ID Numbers for VH and VL amino acid and nucleic acid residues for antibodies that neutralize Ebola virus.
Figure imgf000016_0001
EVB100 41 42 43 44
EVB166 57 58 59 60
EVB165 72 73 74 75
EVB167
87 88 89 90
variant 1
EVB167
87 88 89 91
variant 2
In one embodiment, an antibody or antibody fragment of the invention specifically binds the Ebola virus GP protein or neutralizes infection of EBOV and comprises a heavy chain variable region having an amino acid sequence that is about 70%, 75%, 80%, 85%, 88%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical to the sequence recited in any one of SEQ ID NOs: 13, 25, 41, 57, 72 or 87. In another embodiment, the antibody or antibody fragment comprises a light chain variable region having an amino acid sequence that is about 70%, 75%, 80%, 85%, 90%, 85%, 88%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical to the sequence recited in SEQ ID NOs: 14, 26, 42, 58, 73 or 88. In yet another embodiment, the antibody or antibody fragment comprises a heavy chain or a light chain variable region having an amino acid sequence that is about 70%, 75%, 80%, 85%, 88%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical to the sequences provided in Figures 5A, 5B, 6, 7, 8 or 9.
Figures 5A, 5B, 6, 7, 8 and 9 show the amino acid sequences for the heavy and light chains of antibodies EVB 114 variant 1 , EVB 114 variant 2, EVB 114 variant 3 , EVB 114 variant 4, EVB100, EVB166, EVB165, EVB167 variant 1, or EVB167 variant 2, as well as for the nucleic acid sequences that encode them. The amino acid sequences of the CDRs and the nucleic acid sequences that encode the CDRs are in bold text whereas the amino acid sequences of the framework region and the nucleic acid sequences that encode the framework region are in plain text.
In one embodiment, the invention comprises an isolated and/or purified, and/or recombinant antibody, or an antigen binding fragment thereof, that specifically binds the Ebola virus GP protein or neutralizes infection of EBOV and comprises (i) a heavy chain variable region having at least 80%, for example, 85%, 88%, 90%, 92%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to the amino acid sequence of SEQ ID NO: 13 and a light chain variable region having at least 80%, for example, 85%, 88%, 90%, 92%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to the amino acid sequence of SEQ ID NO: 14; or (ii) a heavy chain variable region having at least 80%, for example, 85%, 88%, 90%, 92%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to the amino acid sequence of SEQ ID NO: 25 and a light chain variable region having at least 80%, for example, 85%, 88%, 90%, 92%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to the amino acid sequence of SEQ ID NO: 26; or (iii) or a heavy chain variable region having at least 80%, for example, 85%, 88%, 90%, 92%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to the amino acid sequence of SEQ ID NO: 13 and a light chain variable region having at least 80%, for example, 85%, 88%, 90%, 92%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to the amino acid sequence of SEQ ID NO: 26; or (iv) a heavy chain variable region having at least 80%, for example, 85%, 88%, 90%, 92%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to the amino acid sequence of SEQ ID NO: 25 and a light chain variable region having at least 80%, for example, 85%, 88%, 90%, 92%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to the amino acid sequence of SEQ ID NO: 14; or (v) a heavy chain variable region having at least 80%, for example, 85%, 88%, 90%, 92%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to the amino acid sequence of SEQ ID NO: 41 and a light chain variable region having at least 80%, for example, 85%, 88%, 90%, 92%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to the amino acid sequence of SEQ ID NO: 42; or (vi) a heavy chain variable region having at least 80%, for example, 85%, 88%,
90%, 92%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to the amino acid sequence of SEQ ID NO: 57 and a light chain variable region having at least 80%, for example, 85%, 88%, 90%, 92%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to the amino acid sequence of SEQ ID NO: 58; or (vii) a heavy chain variable region having at least 80%, for example, 85%, 88%, 90%, 92%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to the amino acid sequence of SEQ ID NO: 72 and a light chain variable region having at least 80%, for example, 85%, 88%, 90%, 92%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to the amino acid sequence of SEQ ID NO: 73; or (viii) a heavy chain variable region having at least 80%, for example, 85%, 88%, 90%, 92%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to the amino acid sequence of SEQ ID NO: 87 and a light chain variable region having at least 80%, for example, 85%, 88%, 90%, 92%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to the amino acid sequence of SEQ ID NO: 88.
In another embodiment of the invention, the invention comprises an antibody, or an antigen binding fragment thereof, that specifically binds the Ebola virus GP protein or neutralizes infection of EBOV and comprises a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 13 and a light chain variable region comprising the amino acid sequence of SEQ ID NO: 14; or a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 25 and a light chain variable region comprising the amino acid sequence of SEQ ID NO: 26; or a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 13 and a light chain variable region comprising the amino acid sequence of SEQ ID NO: 26; or a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 25 and a light chain variable region comprising the amino acid sequence of SEQ ID NO: 14; or a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 41 and a light chain variable region comprising the amino acid sequence of SEQ ID NO: 42; or a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 57 and a light chain variable region comprising the amino acid sequence of SEQ ID NO: 58; or a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 72 and a light chain variable region comprising the amino acid sequence of SEQ ID NO: 73; or a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 87 and a light chain variable region comprising the amino acid sequence of SEQ ID NO: 88.
Examples of antibodies of the invention include, but are not limited to, EVB114 variant 1, EVB114 variant 2, EVB114 variant 3, EVB114 variant 4, EVB 100, EVB166, EVB165, EVB167 variant 1, or EVB167 variant 2 as characterized by the sequences provided in Tables 1 and 2.
The invention further comprises an antibody, or fragment thereof, that binds to the same epitope as an antibody or antigen binding fragment of the invention, or an antibody that competes with an antibody or antigen binding fragment of the invention.
Antibodies of the invention also include hybrid antibody molecules that specifically bind the Ebola virus GP protein or neutralize infection of Ebola virus and that comprise one or more CDRs from an antibody of the invention and one or more CDRs from another antibody to the same epitope. In one embodiment, such hybrid antibodies comprise three CDRs from an antibody of the invention and three CDRs from another antibody to the same epitope. Examples of hybrid antibodies comprise (i) the three heavy chain CDRs from an antibody of the invention and the three light chain CDRs from another antibody to the same epitope, or (ii) the three light chain CDRs from an antibody of the invention and the three heavy chain CDRs from another antibody to the same epitope or (iii) heavy chain CDR3 from an antibody of the invention and one or more heavy or light chain CDRs from another antibody to the same epitope.
Variant antibodies are also included within the scope of the invention. Thus, variants of the sequences recited in the application are also included within the scope of the invention. Such variants include natural variants generated by somatic mutation in vivo during the immune response or in vitro upon culture of immortalized B cell clones. Alternatively, variants may arise due to the degeneracy of the genetic code or may be produced due to errors in transcription or translation. Further variants of the antibody sequences having improved affinity and/or potency may be obtained using methods known in the art and are included within the scope of the invention. For example, amino acid substitutions may be used to obtain antibodies with further improved affinity. Alternatively, codon optimization of the nucleotide sequence may be used to improve the efficiency of translation in expression systems for the production of the antibody. Further, polynucleotides comprising a sequence optimized for antibody specificity or neutralizing activity by the application of a directed evolution method to any of the nucleic acid sequences of the invention are also within the scope of the invention.
In one embodiment variant antibody sequences may share 70% or more (i.e. 75%, 80%, 85%, 88%, 90%, 92%, 95%, 96%, 97%, 98%, 99% or more) amino acid sequence identity with the sequences recited in the application. Such variants, in general, have a greater homology to the sequences listed herein in the CDRs of the VH and VL than in the framework region. As is known to one of skill in the art, mutations are more tolerated, i.e., there is limited or no loss of function (e.g., specificity or neutralization ability) in the framework regions than in the CDRs. In one embodiment, the invention comprises an antibody, or an antigen binding fragment thereof, wherein the variation from the sequences provided herein is in the framework region(s) of the antibody or in the nucleic acid residues that encode the framework region(s) of the antibody.
In some embodiments such sequence identity is calculated with regard to the full length of the reference sequence (i.e., the sequence recited in the application). In some further embodiments, percentage identity, as referred to herein, is as determined using BLAST version 2.1.3 using the default parameters specified by the NCBI (the National Center for Biotechnology Information; http://www.ncbi.nlm.nih.gov/) [Blosum 62 matrix; gap open penalty=l l and gap extension penalty= 1 ] .
In another aspect, the invention also includes nucleic acid sequences encoding part or all of the light and heavy chains and CDRs of the antibodies of the present invention. Provided herein are nucleic acid sequences encoding part or all of the light and heavy chains and CDRs of examples of antibodies of the invention. Table 2 provides the SEQ ID numbers for the nucleic acid sequences encoding the heavy chain and light chain variable regions of some examples of antibodies of the invention. Table 3 provides the SEQ ID numbers for the nucleic acid sequences encoding the CDRs of some examples of the antibodies of the invention. Due to the redundancy of the genetic code, variants of these nucleic acid sequences will exist that encode the same amino acid sequences.
Table 3. SEQ ID Numbers for CDR Polynucleotides of Antibodies that Neutralize Ebola virus.
Figure imgf000021_0001
EVB165 66 67 68 69 70 71
EVB167
81 82 83 84 85 86 variant 1
EVB167
81 82 83 84 85 86 variant 2
In one embodiment, nucleic acid sequences according to the invention include nucleic acid sequences having at least 70%, at least 75%, at least 80%, at least 85%, at least 88%, at least 90%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% identity to the nucleic acid encoding the variable region of a heavy or light chain of an antibody of the invention. In another embodiment, a nucleic acid sequence of the invention has the sequence of a nucleic acid encoding a heavy or light chain CDR of an antibody of the invention. For example, a nucleic acid sequence according to the invention comprises a sequence that is at least 75%, at least 80%, at least 85%, at least 88%, at least 90%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% identical to the nucleic acid sequences of SEQ ID NOs: 7-12, 15, 16, 19-24, 27, 28, 35-40, 43, 44, 51-56, 59, 60, 66-71, 74, 75, 81-86, 89, 90 or 91.
In yet another embodiment, nucleic acid sequences according to the invention include nucleic acid sequences having at least 70%, at least 75%, at least 80%, at least 85%, at least 88%, at least 90%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% identity to the nucleic acid encoding a heavy or light chain of an antibody of the invention as provided in Figures 5A, 5B, 6, 7, 8 or 9.
Further included within the scope of the invention are vectors, for example, expression vectors, comprising a nucleic acid sequence according to the invention. Cells transformed with such vectors are also included within the scope of the invention. Examples of such cells include but are not limited to, eukaryotic cells, e.g., yeast cells, animal cells or plant cells. In one embodiment the cells are mammalian, e.g., human, CHO, HEK293T, PER.C6, NS0, myeloma or hybridoma cells.
The invention also relates to monoclonal antibodies that bind to an epitope capable of binding the antibodies or antigen binding fragments of the invention. Monoclonal and recombinant antibodies are particularly useful in identification and purification of the individual polypeptides or other antigens against which they are directed. The antibodies of the invention have additional utility in that they may be employed as reagents in immunoassays, radioimmunoassays (RIA) or enzyme-linked immunosorbent assays (ELISA). In these applications, the antibodies can be labeled with an analytically-detectable reagent such as a radioisotope, a fluorescent molecule or an enzyme. The antibodies may also be used for the molecular identification and characterization (epitope mapping) of antigens.
Antibodies of the invention can be coupled to a drug for delivery to a treatment site or coupled to a detectable label to facilitate imaging of a site comprising cells of interest, such as cells infected with Ebola virus. Methods for coupling antibodies to drugs and detectable labels are well known in the art, as are methods for imaging using detectable labels. Labeled antibodies may be employed in a wide variety of assays, employing a wide variety of labels. Detection of the formation of an antibody-antigen complex between an antibody of the invention and an epitope of interest (e.g., EBOV) can be facilitated by attaching a detectable substance to the antibody. Suitable detection means include the use of labels such as radionuclides, enzymes, coenzymes, fluorescers, chemiluminescers, chromogens, enzyme substrates or co-factors, enzyme inhibitors, prosthetic group complexes, free radicals, particles, dyes, and the like.
Examples of suitable enzymes include horseradish peroxidase, alkaline phosphatase, β- galactosidase, or acetylcholinesterase; examples of suitable prosthetic group complexes include streptavidin/biotin and avidin/biotin; examples of suitable fluorescent materials include umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin; an example of a luminescent material is luminol; examples of bioluminescent materials include luciferase, luciferin, and aequorin; and examples of suitable radioactive material include 1251, 1311, 35S, or 3H. Such labeled reagents may be used in a variety of well-known assays, such as radioimmunoassays, enzyme immunoassays, e.g., ELISA, fluorescent immunoassays, and the like. (See US 3,766,162; US 3,791,932; US 3,817,837; and US 4,233,402 for example).
An antibody according to the invention may be conjugated to a therapeutic moiety such as a cytotoxin, a therapeutic agent, or a radioactive metal ion or radioisotope. Examples of radioisotopes include, but are not limited to, 1-131 , 1- 123, 1- 125, Y-90, Re- 188, Re-186, At-211, Cu-67, Bi-212, Bi-213, Pd- 109, Tc-99, In-I l l, and the like. Such antibody conjugates can be used for modifying a given biological response; the drug moiety is not to be construed as limited to classical chemical therapeutic agents. For example, the drug moiety may be a protein or polypeptide possessing a desired biological activity. Such proteins may include, for example, a toxin such as abrin, ricin A, pseudomonas exotoxin, or diphtheria toxin. Techniques for conjugating such therapeutic moiety to antibodies are well known. See, for example, Arnon et al. (1985) "Monoclonal Antibodies for Immunotargeting of Drugs in Cancer Therapy," in Monoclonal Antibodies and Cancer Therapy, ed. Reisfeld et al. (Alan R. Liss, Inc.), pp. 243-256; ed. Hellstrom et al. (1987) "Antibodies for Drug Delivery," in
Controlled Drug Delivery, ed. Robinson et al. (2d ed; Marcel Dekker, Inc.), pp. 623-653; Thorpe (1985) "Antibody Carriers of Cytotoxic Agents in Cancer Therapy: A Review," in Monoclonal Antibodies '84: Biological and Clinical Applications, ed. Pinchera et al. pp. 475-506 (Editrice Kurtis, Milano, Italy, 1985); "Analysis, Results, and Future Prospective of the Therapeutic Use of Radiolabeled Antibody in Cancer Therapy," in Monoclonal Antibodies for Cancer Detection and Therapy, ed. Baldwin et al. (Academic Press, New York, 1985), pp. 303-316; and Thorpe et al. (1982) Immunol. Rev. 62: 119-158.
Alternatively, an antibody, or antibody fragment thereof, can be conjugated to a second antibody, or antibody fragment thereof, to form an antibody heteroconjugate as described in US 4,676,980. In addition, linkers may be used between the labels and the antibodies of the invention (e.g., US 4,831,175). Antibodies or, antigen-binding fragments thereof may be directly labeled with radioactive iodine, indium, yttrium, or other radioactive particle known in the art (e.g., US 5,595,721). Treatment may consist of a combination of treatment with conjugated and non-conjugated antibodies administered simultaneously or subsequently
(e.g., WO00/52031 ; WO00/52473).
Antibodies of the invention may also be attached to a solid support. Additionally, antibodies of the invention, or functional antibody fragments thereof, can be chemically modified by covalent conjugation to a polymer to, for example, increase their circulating half-life.
Examples of polymers, and methods to attach them to peptides, are shown in US 4,766, 106;
US 4, 179,337; US 4,495,285 and US 4,609,546. In some embodiments the polymers may be selected from polyoxyethylated polyols and polyethylene glycol (PEG). PEG is soluble in water at room temperature and has the general formula: R(0— CH2— CH2)n O— R where R can be hydrogen, or a protective group such as an alkyl or alkanol group. In one embodiment the protective group may have between 1 and 8 carbons. In a further embodiment the protective group is methyl. The symbol n is a positive integer. In one embodiment n is between 1 and 1,000. In another embodiment n is between 2 and 500. In one embodiment the PEG has an average molecular weight between 1,000 and 40,000. In a further embodiment the PEG has a molecular weight between 2,000 and 20,000. In yet a further embodiment the PEG has a molecular weight between 3,000 and 12,000. In one embodiment PEG has at least one hydroxy group. In another embodiment the PEG has a terminal hydroxy group. In yet another embodiment it is the terminal hydroxy group which is activated to react with a free amino group on the inhibitor. However, it will be understood that the type and amount of the reactive groups may be varied to achieve a covalently conjugated PEG/antibody of the present invention.
Water-soluble polyoxyethylated polyols are also useful in the present invention. They include polyoxyethylated sorbitol, polyoxyethylated glucose, polyoxyethylated glycerol (POG), and the like. In one embodiment, POG is used. Without being bound by any theory, because the glycerol backbone of polyoxyethylated glycerol is the same backbone occurring naturally in, for example, animals and humans in mono-, di-, triglycerides, this branching would not necessarily be seen as a foreign agent in the body. In some embodiments POG has a molecular weight in the same range as PEG. Another drug delivery system that can be used for increasing circulatory half-life is the liposome. Methods of preparing liposome delivery systems are known to one of skill in the art. Other drug delivery systems are known in the art and are described in, for example, referenced in Poznansky et al. (1980) and Poznansky (1984).
Antibodies of the invention may be provided in purified form. Typically, the antibody will be present in a composition that is substantially free of other polypeptides e.g., where less than 90% (by weight), usually less than 60% and more usually less than 50% of the composition is made up of other polypeptides.
Antibodies of the invention may be immunogenic in non-human (or heterologous) hosts e.g., in mice. In particular, the antibodies may have an idiotope that is immunogenic in non-human hosts, but not in a human host. Antibodies of the invention for human use include those that cannot be easily isolated from hosts such as mice, goats, rabbits, rats, non-primate mammals, etc. and cannot generally be obtained by humanization or from xeno-mice. Antibodies of the invention can be of any isotype (e.g., IgA, IgG, IgM i.e. an α, γ or μ heavy chain), but will generally be IgG. Within the IgG isotype, antibodies may be IgGl, IgG2, IgG3 or IgG4 subclass. Antibodies of the invention may have a κ or a λ light chain.
Production of Antibodies
Antibodies according to the invention can be made by any method known in the art. For example, the general methodology for making monoclonal antibodies using hybridoma technology is well known (Kohler, G. and Milstein, C,. 1975; Kozbar et al. 1983). In one embodiment, the alternative EBV immortalization method described in WO2004/076677 is used.
Using the method described in WO 2004/076677, B cells producing the antibody of the invention can be transformed with EBV and a polyclonal B cell activator. Additional stimulants of cellular growth and differentiation may optionally be added during the transformation step to further enhance the efficiency. These stimulants may be cytokines such as IL-2 and IL- 15. In one aspect, IL-2 is added during the immortalization step to further improve the efficiency of immortalization, but its use is not essential. The immortalized B cells produced using these methods can then be cultured using methods known in the art and antibodies isolated therefrom.
Using the method described in WO 2010/046775, plasma cells can be cultured in limited numbers, or as single plasma cells in microwell culture plates. Antibodies can be isolated from the plasma cell cultures. Further, from the plasma cell cultures, RNA can be extracted and PCR can be performed using methods known in the art. The VH and VL regions of the antibodies can be amplified by RT-PCR, sequenced and cloned into an expression vector that is then transfected into HEK293T cells or other host cells. The cloning of nucleic acid in expression vectors, the transfection of host cells, the culture of the transfected host cells and the isolation of the produced antibody can be done using any methods known to one of skill in the art.
The antibodies may be further purified, if desired, using filtration, centrifugation and various chromatographic methods such as HPLC or affinity chromatography. Techniques for purification of antibodies, e.g., monoclonal antibodies, including techniques for producing pharmaceutical-grade antibodies, are well known in the art.
It is known in the art that physical aggregation of monoclonal antibodies is pH
dependent, since pH has an impact on the tertiary structure conformation as well as the net charge of the protein, thus affecting net protein-protein interactions (Ejima et al., 2007, Proteins Structural Function Bioinformatics, 66, 954-962). Aggregation of monoclonal antibodies is favored when the working pH is near to the isoelectric point of the antibody. While solution environment higher than pH 7.0 can promote deamidation of the asparagine residues, disulphide exchange and aggregation, lower pH values (pH 4 and below) can promote isomerization, hydrolysis and fragmentation (Zheng et al., 2006, Internal Journal of Pharmacology, 308,
46-51). In general currently marketed antibodies have a pi between 7.4 and 8.6 and are formulated in the pH range of 5.0 to 7.2, with most of the antibodies being formulated at slightly acidic pH. The antibodies provided herein as examples of antibodies of the invention have a pi between about 8.1 and 8.5, making them excellent candidates for production and formulation in marketable quantities.
Fragments of the antibodies of the invention can be obtained from the antibodies by methods that include digestion with enzymes, such as pepsin or papain, and/or by cleavage of disulfide bonds by chemical reduction. Alternatively, fragments of the antibodies can be obtained by cloning and expression of part of the sequences of the heavy or light chains.
Antibody "fragments" include Fab, Fab', F(ab')2 and Fv fragments. The invention also encompasses single-chain Fv fragments (scFv) derived from the heavy and light chains of an antibody of the invention. For example, the invention includes a scFv comprising the CDRs from an antibody of the invention. Also included are heavy or light chain monomers and dimers, single domain heavy chain antibodies, single domain light chain antibodies, as well as single chain antibodies, e.g., single chain Fv in which the heavy and light chain variable domains are joined by a peptide linker.
Antibody fragments of the invention may impart monovalent or multivalent interactions and be contained in a variety of structures as described above. For instance, scFv molecules may be synthesized to create a trivalent "triabody" or a tetravalent "tetrabody." The scFv molecules may include a domain of the Fc region resulting in bivalent minibodies. In addition, the sequences of the invention may be a component of multispecific molecules in which the sequences of the invention target the epitopes of the invention and other regions of the molecule bind to other targets. Exemplary molecules include, but are not limited to, bispecific Fab2, trispecific Fab3, bispecific scFv, and diabodies (Holliger and Hudson, 2005, Nature
Biotechnology 9: 1126-1136). Standard techniques of molecular biology may be used to prepare DNA sequences encoding the antibodies or antibody fragments of the present invention. Desired DNA sequences may be synthesized completely or in part using oligonucleotide synthesis techniques. Site- directed mutagenesis and polymerase chain reaction (PCR) techniques may be used as appropriate.
Any suitable host cell/vector system may be used for expression of the DNA sequences encoding the antibody molecules of the present invention or fragments thereof. Bacterial, for example E. coli, and other microbial systems may be used, in part, for expression of antibody fragments such as Fab and F(ab')2 fragments, and especially Fv fragments and single chain antibody fragments, for example, single chain Fvs. Eukaryotic, e.g., mammalian, host cell expression systems may be used for production of larger antibody molecules, including complete antibody molecules. Suitable mammalian host cells include, but are not limited to, CHO, HEK293T, PER.C6, NSO, myeloma or hybridoma cells.
The present invention also provides a process for the production of an antibody molecule according to the present invention comprising culturing a host cell comprising a vector encoding a nucleic acid of the present invention under conditions suitable for expression of protein from DNA encoding the antibody molecule of the present invention, and isolating the antibody molecule.
The antibody molecule may comprise only a heavy or light chain polypeptide, in which case only a heavy chain or light chain polypeptide coding sequence needs to be used to transfect the host cells. For production of products comprising both heavy and light chains, the cell line may be transfected with two vectors, a first vector encoding a light chain polypeptide and a second vector encoding a heavy chain polypeptide. Alternatively, a single vector may be used, the vector including sequences encoding light chain and heavy chain polypeptides. Alternatively, antibodies according to the invention may be produced by (i) expressing a nucleic acid sequence according to the invention in a host cell, and (ii) isolating the expressed antibody product. Additionally, the method may include (iii) purifying the isolated antibody.
Transformed B cells and cultured plasma cells may be screened for those producing antibodies of the desired specificity or function. The screening step may be carried out by any immunoassay, e.g., ELISA, by staining of tissues or cells (including transfected cells), by neutralization assay or by one of a number of other methods known in the art for identifying desired specificity or function. The assay may select on the basis of simple recognition of one or more antigens, or may select on the additional basis of a desired function e.g., to select neutralizing antibodies rather than just antigen-binding antibodies, to select antibodies that can change characteristics of targeted cells, such as their signaling cascades, their shape, their growth rate, their capability of influencing other cells, their response to the influence by other cells or by other reagents or by a change in conditions, their differentiation status, etc. Individual transformed B cell clones may then be produced from the positive transformed
B cell culture. The cloning step for separating individual clones from the mixture of positive cells may be carried out using limiting dilution, micromanipulation, single cell deposition by cell sorting or another method known in the art.
Nucleic acid from the cultured plasma cells can be isolated, cloned and expressed in HEK293T cells or other known host cells using methods known in the art.
The immortalized B cell clones or the transfected host-cells of the invention can be used in various ways e.g., as a source of monoclonal antibodies, as a source of nucleic acid (DNA or mRNA) encoding a monoclonal antibody of interest, for research, etc.
The invention provides a composition comprising immortalized B memory cells or transfected host cells that produce antibodies that specifically bind the Ebola virus GP protein or neutralize infection of EBOV.
The immortalized B cell clone or the cultured plasma cells of the invention may also be used as a source of nucleic acid for the cloning of antibody genes for subsequent recombinant expression. Expression from recombinant sources is more common for pharmaceutical purposes than expression from B cells or hybridomas e.g., for reasons of stability, reproducibility, culture ease, etc.
Thus the invention provides a method for preparing a recombinant cell, comprising the steps of: (i) obtaining one or more nucleic acids (e.g., heavy and/or light chain mRNAs) from the B cell clone or the cultured plasma cells that encodes the antibody of interest; (ii) inserting the nucleic acid into an expression vector and (iii) transfecting the vector into a host cell in order to permit expression of the antibody of interest in that host cell.
Similarly, the invention provides a method for preparing a recombinant cell, comprising the steps of: (i) sequencing nucleic acid(s) from the B cell clone or the cultured plasma cells that encodes the antibody of interest; and (ii) using the sequence information from step (i) to prepare nucleic acid(s) for insertion into a host cell in order to permit expression of the antibody of interest in that host cell. The nucleic acid may, but need not, be manipulated between steps (i) and (ii) to introduce restriction sites, to change codon usage, and/or to optimize transcription and/or translation regulatory sequences. The invention also provides a method of preparing a transfected host cell, comprising the step of transfecting a host cell with one or more nucleic acids that encode an antibody of interest, wherein the nucleic acids are nucleic acids that were derived from an immortalized B cell clone or a cultured plasma cell of the invention. Thus the procedures for first preparing the nucleic acid(s) and then using it to transfect a host cell can be performed at different times by different people in different places (e.g., in different countries).
These recombinant cells of the invention can then be used for expression and culture purposes. They are particularly useful for expression of antibodies for large-scale
pharmaceutical production. They can also be used as the active ingredient of a pharmaceutical composition. Any suitable culture technique can be used, including but not limited to static culture, roller bottle culture, ascites fluid, hollow-fiber type bioreactor cartridge, modular minifermenter, stirred tank, microcarrier culture, ceramic core perfusion, etc.
Methods for obtaining and sequencing immunoglobulin genes from B cells or plasma cells are well known in the art (e.g., see Chapter 4 of Kuby Immunology, 4th edition, 2000).
The transfected host cell may be a eukaryotic cell, including yeast and animal cells, particularly mammalian cells (e.g., CHO cells, NS0 cells, human cells such as PER.C6 or
HKB-11 cells, myeloma cells), as well as plant cells. Preferred expression hosts can glycosylate the antibody of the invention, particularly with carbohydrate structures that are not themselves immunogenic in humans. In one embodiment the transfected host cell may be able to grow in serum-free media. In a further embodiment the transfected host cell may be able to grow in culture without the presence of animal-derived products. The transfected host cell may also be cultured to give a cell line.
The invention also provides a method for preparing one or more nucleic acid molecules (e.g., heavy and light chain genes) that encode an antibody of interest, comprising the steps of: (i) preparing an immortalized B cell clone or culturing plasma cells according to the invention; (ii) obtaining from the B cell clone or the cultured plasma cells nucleic acid that encodes the antibody of interest. Further, the invention provides a method for obtaining a nucleic acid sequence that encodes an antibody of interest, comprising the steps of: (i) preparing an immortalized B cell clone or culturing plasma cells according to the invention; (ii) sequencing nucleic acid from the B cell clone or the cultured plasma cells that encodes the antibody of interest.
The invention also provides a method of preparing nucleic acid molecule(s) that encode an antibody of interest, comprising the step of obtaining the nucleic acid that was obtained from a transformed B cell clone or cultured plasma cells of the invention. Thus the procedures for first obtaining the B cell clone or the cultured plasma cell, and then obtaining nucleic acid(s) from the B cell clone or the cultured plasma cells can be performed at different times by different people in different places (e.g., in different countries).
The invention provides a method for preparing an antibody (e.g., for pharmaceutical use), comprising the steps of: (i) obtaining and/or sequencing one or more nucleic acids (e.g., heavy and light chain genes) from the selected B cell clone or the cultured plasma cells expressing the antibody of interest; (ii) inserting the nucleic acid(s) into or using the nucleic acid(s) sequence(s) to prepare an expression vector; (iii) transfecting a host cell that can express the antibody of interest; (iv) culturing or sub-culturing the transfected host cells under conditions where the antibody of interest is expressed; and, optionally, (v) purifying the antibody of interest. The invention also provides a method of preparing an antibody comprising the steps of: culturing or sub-culturing a transfected host cell population under conditions where the antibody of interest is expressed and, optionally, purifying the antibody of interest, wherein said transfected host cell population has been prepared by (i) providing nucleic acid(s) encoding a selected antibody of interest that is produced by a B cell clone or cultured plasma cells prepared as described above, (ii) inserting the nucleic acid(s) into an expression vector, (iii) transfecting the vector in a host cell that can express the antibody of interest, and (iv) culturing or sub- culturing the transfected host cell comprising the inserted nucleic acids to produce the antibody of interest. Thus the procedures for first preparing the recombinant host cell and then culturing it to express antibody can be performed at very different times by different people in different places (e.g., in different countries).
Epitopes
As mentioned above, the antibodies of the invention can be used to map the epitopes to which they bind. The invention provides novel epitopes to which the neutralizing antibodies of the invention bind. These epitopes are found on the Ebola virus glycoprotein. In one
embodiment, the antibodies, or antigen binding fragments thereof, bind Ebola virus soluble glycoprotein (sGP).
The epitopes to which the antibodies of the invention bind may be linear (continuous) or conformational (discontinuous). In one embodiment, the antibodies and antibody fragments of the invention bind a conformational epitope. In another embodiment, the conformational epitope is present only under non-reducing conditions.
The polypeptides that bind to the antibodies of the present invention may have a number of uses. The polypeptides and polypeptide variants thereof in purified or synthetic form can be used to raise immune responses (i.e., as a vaccine, or for the production of antibodies for other uses) or for screening sera for antibodies that immunoreact with the epitope or mimotopes thereof. In one embodiment such polypeptides or polypeptide variants, or antigen comprising such a polypeptides or polypeptide variants may be used as a vaccine for raising an immune response that comprises antibodies of the same quality as those described in the present invention. The antibodies and antibody fragments of the invention can also be used in a method of monitoring the quality of vaccines. In particular the antibodies can be used to check that the antigen in a vaccine contains the correct immunogenic epitope in the correct conformation. The use of an antibody of the invention, or an antigen binding fragment thereof, for monitoring the quality of a vaccine against Ebola virus by, for example, checking that the antigen of said vaccine contains the specific epitope in the correct conformation, is also contemplated to be within the scope of the invention. The polypeptides that bind to the antibodies of the present invention may also be useful in screening for ligands that bind to said polypeptides. Such ligands, include but are not limited to antibodies; including those from camels, sharks and other species, fragments of antibodies, peptides, phage display technology products, aptamers, adnectins or fragments of other viral or cellular proteins, may block the epitope and so prevent infection. Such ligands are encompassed within the scope of the invention.
Pharmaceutical Compositions
The invention provides a pharmaceutical composition comprising one or more of: the antibodies or antibody fragments of the invention; nucleic acid encoding such antibodies or fragments; vectors encoding the nucleic acids; or polypeptides recognized by the antibodies or antigen binding fragment of the invention. The pharmaceutical composition may also contain a pharmaceutically acceptable carrier or excipient. Although the carrier or excipient may facilitate administration, it should not itself induce the production of antibodies harmful to the individual receiving the composition. Nor should it be toxic. Suitable carriers may be large, slowly metabolized macromolecules such as proteins, polypeptides, liposomes, polysaccharides, polylactic acids, polyglycolic acids, polymeric amino acids, amino acid copolymers and inactive virus particles.
Pharmaceutically acceptable salts can be used, for example mineral acid salts, such as hydrochlorides, hydrobromides, phosphates and sulphates, or salts of organic acids, such as acetates, propionates, malonates and benzoates. 4
Pharmaceutically acceptable carriers in therapeutic compositions may additionally contain liquids such as water, saline, glycerol and ethanol. Additionally, auxiliary substances, such as wetting or emulsifying agents or pH buffering substances, may be present in such compositions. Such carriers enable the pharmaceutical compositions to be formulated as tablets, pills, dragees, capsules, liquids, gels, syrups, slurries and suspensions, for ingestion by the subject.
Within the scope of the invention are compositions present in several forms of administration; the forms include, but are not limited to, those forms suitable for parenteral administration, e.g., by injection or infusion, for example by bolus injection or continuous infusion. Where the product is for injection or infusion, it may take the form of a suspension, solution or emulsion in an oily or aqueous vehicle and it may contain formulatory agents, such as suspending, preservative, stabilizing and/or dispersing agents. Alternatively, the antibody molecule may be in dry form, for reconstitution before use with an appropriate sterile liquid.
Once formulated, the compositions of the invention can be administered directly to the subject. In one embodiment the compositions are adapted for administration to mammalian, e.g., human subjects.
The pharmaceutical compositions of this invention may be administered by any number of routes including, but not limited to, oral, intravenous, intramuscular, intra-arterial,
intramedullary, intraperitoneal, intrathecal, intraventricular, transdermal, transcutaneous, topical, subcutaneous, intranasal, enteral, sublingual, intravaginal or rectal routes. Hyposprays may also be used to administer the pharmaceutical compositions of the invention. Typically, the therapeutic compositions may be prepared as injectables, either as liquid solutions or
suspensions. Solid forms suitable for solution in, or suspension in, liquid vehicles prior to injection may also be prepared. Direct delivery of the compositions will generally be accomplished by injection, subcutaneously, intraperitoneally, intravenously or intramuscularly, or delivered to the interstitial space of a tissue. The compositions can also be administered into a lesion. Dosage treatment may be a single dose schedule or a multiple dose schedule. Known antibody-based
pharmaceuticals provide guidance relating to frequency of administration e.g., whether a pharmaceutical should be delivered daily, weekly, monthly, etc. Frequency and dosage may also depend on the severity of symptoms.
Compositions of the invention may be prepared in various forms. For example, the compositions may be prepared as injectables, either as liquid solutions or suspensions. Solid forms suitable for solution in, or suspension in, liquid vehicles prior to injection can also be prepared (e.g., a lyophilized composition, like Synagis™ and Herceptin™, for reconstitution with sterile water containing a preservative). The composition may be prepared for topical administration e.g., as an ointment, cream or powder. The composition may be prepared for oral administration e.g., as a tablet or capsule, as a spray, or as a syrup (optionally flavored). The composition may be prepared for pulmonary administration e.g., as an inhaler, using a fine powder or a spray. The composition may be prepared as a suppository or pessary. The composition may be prepared for nasal, aural or ocular administration e.g., as drops. The composition may be in kit form, designed such that a combined composition is reconstituted just prior to administration to a subject. For example, a lyophilized antibody can be provided in kit form with sterile water or a sterile buffer. It will be appreciated that the active ingredient in the composition will be an antibody molecule, an antibody fragment or variants and derivatives thereof. As such, it will be susceptible to degradation in the gastrointestinal tract. Thus, if the composition is to be administered by a route using the gastrointestinal tract, the composition will need to contain agents which protect the antibody from degradation but which release the antibody once it has been absorbed from the gastrointestinal tract.
A thorough discussion of pharmaceutically acceptable carriers is available in Gennaro (2000) Remington: The Science and Practice of Pharmacy, 20th edition, ISBN: 0683306472.
Pharmaceutical compositions of the invention generally have a pH between 5.5 and 8.5, in some embodiments this may be between 6 and 8, and in other embodiments about 7. The pH may be maintained by the use of a buffer. The composition may be sterile and/or pyrogen free. The composition may be isotonic with respect to humans. In one embodiment pharmaceutical compositions of the invention are supplied in hermetically- sealed containers.
Pharmaceutical compositions will include an effective amount of one or more antibodies of the invention and/or a polypeptide comprising an epitope that binds an antibody of the invention i.e., an amount that is sufficient to treat, ameliorate, attenuate or prevent a desired disease or condition, or to exhibit a detectable therapeutic effect. Therapeutic effects also include reduction or attenuation in pathogenic potency or physical symptoms. The precise effective amount for any particular subject will depend upon their size, weight, and health, the nature and extent of the condition, and the therapeutics or combination of therapeutics selected for administration. The effective amount for a given situation is determined by routine experimentation and is within the judgment of a clinician. For purposes of the present invention, an effective dose will generally be from about O.Olmg/kg to about 50 mg/kg, or about
0.05 mg/kg to about 10 mg/kg of the compositions of the present invention in the individual to which it is administered. Known antibody-based pharmaceuticals provide guidance in this respect e.g., Herceptin™ is administered by intravenous infusion of a 21 mg/ml solution, with an initial loading dose of 4 mg/kg body weight and a weekly maintenance dose of 2 mg/kg body weight; Rituxan™ is administered weekly at 375 mg/m2; etc.
In one embodiment compositions can include one or more (e.g., 2, 3, etc.) antibodies of the invention to provide an additive or synergistic therapeutic effect. In another embodiment, the composition may comprise one or more (e.g., 2, 3, etc.) antibodies of the invention and one or more (e.g., 2, 3, etc.) additional antibodies against Ebola virus. Further, the administration of antibodies of the invention together with antibodies specific to other pathogens, for example, influenza A or influenza B virus, are within the scope of the invention. The antibodies of the invention can be administered either combined/simultaneously or at separate times from antibodies specific to pathogens other than Ebola virus.
In another embodiment, the invention provides a pharmaceutical composition comprising two or more antibodies, wherein the first antibody is an antibody of the invention as described herein and the second antibody is specific for EBOV or a different pathogen that may have co- infected the subject to whom the pharmaceutical composition is being administered. Examples of antibodies of the invention specific for, and that specifically bind the Ebola virus GP protein or neutralize infection of EBOV include, but are not limited to, EVB l 14 variant 1, EVB 114 variant 2, EVB 114 variant 3, EVB 114 variant 4, EVB 100, EVB 166,
EVB 165, EVB 167 variant 1, or EVB 167 variant 2.
In one embodiment, the invention provides a pharmaceutical composition comprising the antibody EVB l 14 variant 1 or an antigen binding fragment thereof, and a pharmaceutically acceptable carrier. In another embodiment, the invention provides a pharmaceutical composition comprising the antibody EVB l 14 variant 2 or an antigen binding fragment thereof, and a pharmaceutically acceptable carrier. In another embodiment, the invention provides a pharmaceutical composition comprising the antibody EVB l 14 variant 3 or an antigen binding fragment thereof, and a pharmaceutically acceptable carrier. In another embodiment, the invention provides a pharmaceutical composition comprising the antibody EVB l 14 variant 4 or an antigen binding fragment thereof, and a pharmaceutically acceptable carrier. In another embodiment, the invention provides a pharmaceutical composition comprising the antibody EVB l 00 or an antigen binding fragment thereof, and a pharmaceutically acceptable carrier. In another embodiment, the invention provides a pharmaceutical composition comprising the antibody EVB 166 or an antigen binding fragment thereof, and a pharmaceutically acceptable carrier. In another embodiment, the invention provides a pharmaceutical composition comprising the antibody EVB 167 variant 1 or an antigen binding fragment thereof, and a pharmaceutically acceptable carrier. In another embodiment, the invention provides a pharmaceutical composition comprising the antibody EVB 167 variant 2 or an antigen binding fragment thereof, and a pharmaceutically acceptable carrier.
Antibodies of the invention may be administered (either combined or separately) with other therapeutics e.g., with chemotherapeutic compounds, with radiotherapy, etc. In one embodiment, the therapeutic compounds include anti-viral compounds such as Tamiflu™. Such combination therapy provides an additive or synergistic improvement in therapeutic efficacy relative to the individual therapeutic agents when administered alone. The term "synergy" is used to describe a combined effect of two or more active agents that is greater than the sum of the individual effects of each respective active agent. Thus, where the combined effect of two or more agents results in "synergistic inhibition" of an activity or process, it is intended that the inhibition of the activity or process is greater than the sum of the inhibitory effects of each respective active agent. The term "synergistic therapeutic effect" refers to a therapeutic effect observed with a combination of two or more therapies wherein the therapeutic effect (as measured by any of a number of parameters) is greater than the sum of the individual therapeutic effects observed with the respective individual therapies. Antibodies may be administered to those subjects who have previously shown no response, i.e., have been shown to be refractive to treatment for EBOV infection.
In one embodiment, the invention provides a pharmaceutical composition comprising one or more antibodies of the invention, or antigen binding fragments thereof and an anti- viral agent effective against Ebola virus. The anti-viral agent may be an agent now known to one of skill in the art, or a later discovered or invented agent.
In one embodiment, a composition of the invention may include antibodies of the invention, wherein the antibodies may make up at least 50% by weight (e.g., 60%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99% or more) of the total protein in the composition. In such a composition, the antibodies are in purified form. The invention provides a method of preparing a pharmaceutical composition comprising the steps of: (i) preparing an antibody of the invention; and (ii) admixing the purified antibody with one or more pharmaceutically-acceptable carriers.
In another embodiment, a method of preparing a pharmaceutical composition comprises the step of: admixing an antibody with one or more pharmaceutically-acceptable carriers, wherein the antibody is a monoclonal antibody that was obtained from a transformed B cell or a cultured plasma cell of the invention. Thus the procedures for first obtaining the monoclonal antibody and then preparing the pharmaceutical can be performed at very different times by different people in different places (e.g., in different countries). As an alternative to delivering antibodies or B cells for therapeutic purposes, it is possible to deliver nucleic acid (typically DNA) that encodes the monoclonal antibody (or active fragment thereof) of interest derived from the B cell or the cultured plasma cells to a subject, such that the nucleic acid can be expressed in the subject in situ to provide a desired therapeutic effect. Suitable gene therapy and nucleic acid delivery vectors are known in the art. Compositions of the invention may be immunogenic compositions, and in some embodiments may be vaccine compositions comprising an antigen comprising an epitope recognized by an antibody of the invention or an antigen binding fragment thereof. Vaccines according to the invention may either be prophylactic (i.e., prevent infection) or therapeutic (i.e., treat or ameliorate infection). Compositions may include an antimicrobial, particularly if packaged in a multiple dose format. They may comprise detergent e.g., a Tween (polysorbate), such as Tween 80.
Detergents are generally present at low levels e.g., less than 0.01%. Compositions may also include sodium salts (e.g., sodium chloride) to give tonicity. A concentration of 10+2mg/ml NaCl is typical. Further, compositions may comprise a sugar alcohol (e.g., mannitol) or a disaccharide
(e.g., sucrose or trehalose) e.g., at around 15-30 mg/ml (e.g., 25 mg/ml), particularly if they are to be lyophilized or if they include material which has been reconstituted from lyophilized material. The pH of a composition for lyophilisation may be adjusted to between 5 and 8, or between 5.5 and 7, or around 6.1 prior to lyophilisation. The compositions of the invention may also comprise one or more immunoregulatory agents. In one embodiment, one or more of the immunoregulatory agents include(s) an adjuvant.
The epitope compositions of the invention may elicit both a cell mediated immune response as well as a humoral immune response in order to effectively address Ebola virus infection. This immune response may induce long lasting (e.g., neutralizing) antibodies and a cell mediated immunity that can quickly respond upon exposure to EBOV.
Medical Treatments and Uses
The antibodies and antibody fragments of the invention or derivatives and variants thereof may be used for the treatment of EBOV infection; for the prevention of infection of Ebola virus; or for the diagnosis of Ebola virus infection.
The methods of the invention provide for the administration of an antibody of the invention or a fragment thereof for the treatment of Ebola virus infection.
In one embodiment, the invention provides a method of treating or reducing Ebola virus infection, or lowering the risk of Ebola virus infection, comprising: administering to a subject in need thereof, a therapeutically effective amount of an antibody of the invention, or an antigen binding fragment thereof.
In another embodiment, the invention provides an antibody of the invention, or an antigen binding fragment thereof, for use as a medicament. For example, the invention provides an antibody of the invention, or an antigen binding fragment thereof, for use as a medicament in the treatment of Ebola virus infection.
In yet another embodiment, the invention provides the use of an antibody of the invention, or an antigen binding fragment thereof, for the manufacturing of a medicament. For example, the invention provides the use of an antibody of the invention, or an antigen binding fragment thereof, for the manufacturing of a medicament for the treatment of a disease or disorder, including, but not limited to, the treatment of Ebola virus infection.
Methods of diagnosis may include contacting an antibody or an antibody fragment with a sample. Such samples may be tissue samples taken from, for example, nasal passages, sinus cavities, salivary glands, lung, liver, pancreas, kidney, ear, eye, placenta, alimentary tract, heart, ovaries, pituitary, adrenals, thyroid, brain or skin. The methods of diagnosis may also include the detection of an antigen/antibody complex.
The invention therefore provides (i) an antibody, an antibody fragment, or variants and derivatives thereof according to the invention, (ii) an immortalized B cell clone according to the invention, (iii) an epitope capable of binding an antibody of the invention or (iv) a ligand, preferably an antibody, capable of binding an epitope that binds an antibody of the invention for use in therapy.
The invention also provides a method of treating a subject comprising administering to the subject an antibody, an antibody fragment, or variants and derivatives thereof according to the invention, or, a ligand, preferably an antibody, capable of binding an epitope that binds an antibody of the invention. In one embodiment, the method results in reduced Ebola virus infection in the subject. In another embodiment, the method prevents, reduces the risk if EBOV infection or delays the onset of EBOV infection in the subject.
The invention also provides the use of (i) an antibody, an antibody fragment, or variants and derivatives thereof according to the invention, (ii) an immortalized B cell clone according to the invention, (iii) an epitope capable of binding an antibody of the invention, (iv) a ligand, preferably an antibody, that binds to an epitope capable of binding an antibody of the invention, or (v) a pharmaceutical composition of the invention in the manufacture of a medicament for the treatment or attenuation of infection by Ebola virus and/or in the manufacture of a medicament for prevention of Ebola virus infection, i.e., a vaccine, and/or in the manufacture of a medicament for the diagnosis of Ebola virus infection.
The invention provides a composition of the invention for use as a medicament for the prevention or treatment of EBOV infection. It also provides the use of an antibody of the invention and/or a protein comprising an epitope to which such an antibody binds in the manufacture of a medicament for treatment of a subject and/or diagnosis in a subject. It also provides a method for treating a subject, comprising the step of administering to the subject a composition of the invention. In some embodiments the subject may be a human. One way of checking efficacy of therapeutic treatment involves monitoring disease symptoms after administration of the composition of the invention. Treatment can be a single dose schedule or a multiple dose schedule. In one embodiment, an antibody or antibody fragment, including, but not limited to, a recombinant antibody or fragment thereof, immortalized B cell clone, epitope or composition according to the invention is administered to a subject in need of such treatment. Such a subject includes, but is not limited to, one who is particularly at risk of or susceptible to Ebola virus infection, including, for example, an immunocompromised subject. The antibody or antibody fragment of the invention can also be used in passive immunization or active vaccination.
Antibodies and fragments thereof as described in the present invention may also be used in a kit for the diagnosis of EBOV infection. Further, epitopes capable of binding an antibody of the invention may be used in a kit for monitoring the efficacy of vaccination procedures by detecting the presence of protective anti-EBOV antibodies. Antibodies, antibody fragment, or variants and derivatives thereof, as described in the present invention may also be used in a kit for monitoring vaccine manufacture with the desired immunogenicity.
The invention also provides an epitope that specifically binds to an antibody of the invention or an antigen binding fragment thereof, for use (i) in therapy, (ii) in the manufacture of a medicament for the prevention, treatment or attenuation of EBOV infection, (iii) as a vaccine, or (iv) in screening for ligands able to neutralize EBOV infection.
The invention also provides a method of preparing a pharmaceutical, comprising the step of admixing a monoclonal antibody with one or more pharmaceutically-acceptable carriers, wherein the monoclonal antibody is a monoclonal antibody that was obtained from a transfected host cell of the invention. Thus the procedures for first obtaining the monoclonal antibody
(e.g., expressing it and/or purifying it) and then admixing it with the pharmaceutical carrier(s) can be performed at very different times by different people in different places (e.g., in different countries).
Starting with a transformed B cell or a cultured plasma cell of the invention, various steps of culturing, sub-culturing, cloning, sub-cloning, sequencing, nucleic acid preparation etc. can be performed in order to perpetuate the antibody expressed by the transformed B cell or the cultured plasma cell, with optional optimization at each step. In one embodiment, the above methods further comprise techniques of optimization (e.g., affinity maturation or optimization) applied to the nucleic acids encoding the antibody. The invention encompasses all cells, nucleic acids, vectors, sequences, antibodies etc. used and prepared during such steps. In all these methods, the nucleic acid used in the expression host may be manipulated to insert, delete or alter certain nucleic acid sequences. Changes from such manipulation include, but are not limited to, changes to introduce restriction sites, to amend codon usage, to add or optimize transcription and/or translation regulatory sequences, etc. It is also possible to change the nucleic acid to alter the encoded amino acids. For example, it may be useful to introduce one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, etc.) amino acid substitutions, deletions and/or insertions into the antibody' s amino acid sequence. Such point mutations can modify effector functions, antigen-binding affinity, post-translational modifications, immunogenicity, etc., can introduce amino acids for the attachment of covalent groups (e.g., labels) or can introduce tags (e.g., for purification purposes). Mutations can be introduced in specific sites or can be introduced at random, followed by selection (e.g., molecular evolution). For instance, one or more nucleic acids encoding any of the CDR regions, heavy chain variable regions or light chain variable regions of antibodies of the invention can be randomly or directionally mutated to introduce different properties in the encoded amino acids. Such changes can be the result of an iterative process wherein initial changes are retained and new changes at other nucleotide positions are introduced. Further, changes achieved in independent steps may be combined. Different properties introduced into the encoded amino acids may include, but are not limited to, enhanced affinity.
General
As used herein, the terms "antigen binding fragment," "fragment," and "antibody fragment" are used interchangeably to refer to any fragment of an antibody of the invention that retains the antigen-binding activity of the antibody. Examples of antibody fragments include, but are not limited to, a single chain antibody, Fab, Fab' , F(ab')2, Fv or scFv. Further, the term "antibody" as used herein includes both antibodies and antigen binding fragments thereof. As used herein, a "neutralizing antibody" is one that can neutralize, i.e. , prevent, inhibit, reduce, impede or interfere with, the ability of a pathogen to initiate and/or perpetuate an infection in a host. The terms "neutralizing antibody" and "an antibody that neutralizes" or "antibodies that neutralize" are used interchangeably herein. These antibodies can be used alone, or in combination, as prophylactic or therapeutic agents upon appropriate formulation, in association with active vaccination, as a diagnostic tool, or as a production tool as described herein.
The term "comprising" encompasses "including" as well as "consisting" e.g., a composition "comprising" X may consist exclusively of X or may include something additional e.g., X + Y.
The word "substantially" does not exclude "completely" e.g., a composition which is "substantially free" from Y may be completely free from Y. Where necessary, the word
"substantially" may be omitted from the definition of the invention.
The term "about" in relation to a numerical value x means x + 10%.
The term "disease" as used herein is intended to be generally synonymous, and is used interchangeably with, the terms "disorder" and "condition" (as in medical condition), in that all reflect an abnormal condition of the human or animal body or of one of its parts that impairs normal functioning, is typically manifested by distinguishing signs and symptoms, and causes the human or animal to have a reduced duration or quality of life.
As used herein, reference to "treatment" of a subject or patient is intended to include prevention, prophylaxis, attenuation, amelioration and therapy. The terms "subject" or "patient" are used interchangeably herein to mean all mammals including humans. Examples of subjects include humans, cows, dogs, cats, horses, goats, sheep, pigs, and rabbits. In one embodiment, the patient is a human.
EXAMPLES
Examples of embodiments of the present invention are provided in the following examples. The following examples are presented only by way of illustration and to assist one of ordinary skill in using the invention. The examples are not intended in any way to otherwise limit the scope of the invention.
Example 1. Isolation of fully human EBOV neutralizing antibodies.
IgG Memory B cells from two individuals who recoverd from EBOV infection (EVA and EVB) were immortalized with EBV and CpG as previously described (Traggiai et al., Nat. Med. 2004) and supernatants were then tested in a primary screening for binding to ZEBOV GP protein by ELISA. Positive supernatants were then tested for binding to EBOV GP and to an irrelevant antigen. From the results of these assays, 52 antibodies were selected that showed specificity for EBOV GP (Figure 1). Titration experiments showed that the antibodies bound with sometimes different binding profiles. In particular, EVBl 00 binds to GP with OD values lower than EVBl 14, EVB166, and EVB165, thus suggesting that EVB100 might recognize a particular conformation of the GP protein that is not efficiently exposed when coated on a solid surface (Figure 2).
Example 2. Antigenic sites recognized by the isolated EBOV-neutralizing human monoclonal antibodies.
In order to understand if the three best EBOV-neutralizing antibodies, EVB 100, EVBl 14 and EVB166, bind to distinct antigenic sites on GP the antibodies were tested in an ELISA cross- competition assay on GP-coated ELISA plates. The results of this analysis showed that the three EBOV-neutralizing antibodies bind to distinct sites on GP (Figure 3). These results, in addition to the finding that EVBl 00 does not bind to sGP, suggest that these three antibodies can be combined in a cocktail in EBOV therapy to reduce the risk of selecting viral escape mutants and to potentially target multiple steps of viral entry and replication.
Example 3. EVB114 sequence engineering to improve its development.
The analysis of the EVBl 14 antibody sequence presented some amino acid sequenced that posed potential risks for antibody development. In particular, EVB 114 has a methionine residue in the CDR1 of the heavy chain (M36 according to IMGT numbering) that represents a medium-scoring sequence liability issue. Of note, M36 is introduced by a somatic mutation, and the corresponding germline residue is serine (S36). Similarly, the CDR1 of the light chain contains the DN motif (residues 36 and 37 according to IMGT numbering) which represents a low risk site for acidic cleavage. In this case, as observed in the case of the M in HCDRl, the D36 residue is also introduced by a somatic mutation, and the corresponding germline residue is serine (S36). We therefore engineered EVBl 14 to remove M36 in HCDRl by mutating it to S36 (SEQ ID 17 and 25) and to remove D36 in LCDRl by mutating it to S36 (SEQ ID 18 and 26). We therefore produced three more variants of EVBl 14: EVBl 14 carrying M36S mutation in HCDRl, EVBl 14 carrying D36S in LCDRl and EVBl 14 carrying both M36S in HCDRl and D36S in LCDRl. These three new engineered variants of EVBl 14 were produced recombinantly and serial dilutions of each variant were tested, in parallel with the parental EVBl 14 antibody, for binding to EBOV GP expressed on the surface of MDCK-SIAT cells by FACS analysis (Figure 4). All 3 EVBl 14 variants bound to surface expressed GP similarly to parental EVBl 14 antibody. These results indicate that variants of EVBl 14 antibody bind to membrane-expressed EBOV GP similarly to the parental EVBl 14 antibody.
Other Embodiments
The detailed description set-forth above is provided to aid those skilled in the art in practicing the present disclosure. However, the disclosure described and claimed herein is not to be limited in scope by the specific embodiments herein disclosed because these embodiments are intended as illustration of several aspects of the disclosure. Any equivalent embodiments are intended to be within the scope of this disclosure. Indeed, various modifications of the disclosure in addition to those shown and described herein will become apparent to those skilled in the art from the foregoing description, which do not depart from the spirit or scope of the present inventive discovery. Such modifications are also intended to fall within the scope of the appended claims.

Claims

1. An isolated or purified human antibody or a recombinant antibody, or an antigen binding fragment thereof, that specifically binds the Ebola virus GP protein.
2. The antibody of claim 1, or an antigen binding fragment thereof, wherein the antibody or antigen binding fragment comprises a heavy chain comprising CDRl, CDR2 and CDR3 and a light chain comprising CDRl, CDR2 and CDR3, wherein the heavy chain CDR3 comprises an amino acid sequence that is at least 90% identical to SEQ ID NOs: 3, 31, 47, 63 or 78.
3. The antibody of claim 1, or an antigen binding fragment thereof, wherein the antibody or antigen binding fragment comprises a heavy chain comprising CDRl, CDR2 and CDR3 and a light chain comprising CDRl, CDR2 and CDR3, wherein the heavy chain CDR3 comprises the amino acid sequence of SEQ ID NOs: 3, 31, 47, 63 or 78.
4. The antibody of claim 1, or an antigen binding fragment thereof, wherein the antibody or antigen binding fragment comprises: (i) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences that are at least 90% identical to the amino acid sequences of SEQ ID NOs: 1-6, respectively; (ii) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences that are at least 90% identical to the amino acid sequences of SEQ ID NOs: 17, 2, 3, 18, 5, 6, respectively; (iii) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences that are at least 90% identical to the amino acid sequences of SEQ ID NOs: 1, 2, 3, 18, 5, 6, respectively; (iv) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences that are at least 90% identical to the amino acid sequences of SEQ ID NOs: 17, 2, 3, 4, 5, 6, respectively; (v) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences that are at least 90% identical to the amino acid sequences of SEQ ID NOs: 29-34, respectively; (vi) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences that are at least 90% identical to the amino acid sequences of SEQ ID NOs: 45-50, respectively; (vii) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences that are at least 90% identical to the amino acid sequences of SEQ ID NOs: 61-64, 5, 65, respectively; or (viii) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences that are at least 90% identical to the amino acid sequences of SEQ ID NOs: 76-79, 49, 80, respectively.
5. The antibody of claim 1, or an antigen binding fragment thereof, wherein the antibody or antigen binding fragment comprises: (i) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences as set forth in SEQ ID NOs: 1-6, respectively; (ii) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences as set forth in SEQ ID NOs: 17, 2, 3, 18, 5, 6, respectively; (iii) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences as set forth in SEQ ID NOs: 1, 2, 3, 18, 5, 6, respectively; (iv) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences as set forth in SEQ ID NOs: 17, 2, 3, 4, 5, 6, respectively; (v) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences as set forth in SEQ ID NOs: 29-34, respectively; (vi) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences as set forth in SEQ ID NOs: 45-50, respectively; (vii) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences as set forth in SEQ ID NOs: 61-64, 5, 65, respectively; or
(viii) heavy chain CDRl, CDR2, and CDR3 amino acid sequences and light chain CDRl, CDR2, and CDR3 amino acid sequences as set forth in SEQ ID NOs: 76-79, 49, 80, respectively.
6. The antibody of claim 1, or an antigen binding fragment thereof, comprising: (i) a heavy chain variable region having at least 80% sequence identity to the amino acid sequence of SEQ ID NO: 13 and a light chain variable region having at least 80% sequence identity to the amino acid sequence of SEQ ID NO: 14; or (ii) a heavy chain variable region having at least 80% sequence identity to the amino acid sequence of SEQ ID NO: 25 and a light chain variable region having at least 80% sequence identity to the amino acid sequence of SEQ ID NO: 26; or (iii) a heavy chain variable region having at least 80% sequence identity to the amino acid sequence of SEQ ID NO: 13 and a light chain variable region having at least 80% sequence identity to the amino acid sequence of SEQ ID NO: 26; or (iv) a heavy chain variable region having at least 80% sequence identity to the amino acid sequence of SEQ ID NO: 25 and a light chain variable region having at least 80% sequence identity to the amino acid sequence of SEQ ID NO: 14; or (v) a heavy chain variable region having at least 80% sequence identity to the amino acid sequence of SEQ ID NO: 41 and a light chain variable region having at least 80% sequence identity to the amino acid sequence of SEQ ID NO: 42; or (vi) a heavy chain variable region having at least 80% sequence identity to the amino acid sequence of SEQ ID NO: 57 and a light chain variable region having at least 80% sequence identity to the amino acid sequence of SEQ ID NO: 58; or (vii) a heavy chain variable region having at least 80% sequence identity to the amino acid sequence of SEQ ID NO: 72 and a light chain variable region having at least 80% sequence identity to the amino acid sequence of SEQ ID NO: 73; or (viii) a heavy chain variable region having at least 80% sequence identity to the amino acid sequence of SEQ ID NO: 87 and a light chain variable region having at least 80% sequence identity to the amino acid sequence of SEQ ID NO: 88.
7. The antibody of claim 1, or an antigen binding fragment thereof, comprising: (i) a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 13 and a light chain variable region comprising the amino acid sequence of SEQ ID NO: 14; or (ii) a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 25 and a light chain variable region comprising the amino acid sequence of SEQ ID NO: 26; or (iii) a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 13 and a light chain variable region comprising the amino acid sequence of SEQ ID NO: 26; or (iv) a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 25 and a light chain variable region comprising the amino acid sequence of SEQ ID NO: 14; or (v) a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 41 and a light chain variable region comprising the amino acid sequence of SEQ ID NO: 42; or (vi) a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 57 and a light chain variable region comprising the amino acid sequence of SEQ ID NO: 58; or (vii) a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 72 and a light chain variable region comprising the amino acid sequence of SEQ ID NO: 73; or (viii) a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 87 and a light chain variable region comprising the amino acid sequence of SEQ ID NO: 88.
8. The antibody of claim 1, or an antigen binding fragment thereof, wherein the antibody is EVB114 variant 1, EVB 114 variant 2, EVB114 variant 3, EVB114 variant 4, EVB100, EVB166, EVB165, EVB 167 variant 1, or EVB167 variant 2.
9. The antibody of any one of the above claims, or an antigen binding fragment thereof,
wherein the antibody is a monoclonal antibody, a human monoclonal antibody, a purified antibody, a single chain antibody, Fab, Fab', F(ab')2, Fv or scFv.
10. An antibody, or an antigen binding fragment thereof, that binds to the same epitope as the antibody of any one of the previous claims, wherein the antibody or antigen binding fragment thereof neutralizes infection of Ebola virus.
11. The antibody of any one of the previous claims, or an antigen binding fragment thereof, for use in the prevention, treatment or attenuation of infection by Ebola virus.
12. A nucleic acid molecule comprising a polynucleotide encoding the antibody, or an antigen binding fragment thereof, of any one of the previous claims.
13. The nucleic acid molecule of claim 12, wherein the polynucleotide sequence is at least 75% identical to the nucleic acid sequence of any one of SEQ ID NOs: 7-12, 15, 16, 19-24, 27, 28, 35-40, 43, 44, 51-56, 59, 60, 66-71, 74, 75, 81-86, 88, 89 or 91.
14. A vector comprising the nucleic acid molecule of claim 12 or claim 13.
15. A cell expressing the antibody of any one of claims 1-11, or an antigen binding fragment thereof; or comprising the vector of claim 14.
16. An isolated or purified immunogenic polypeptide comprising an epitope that specifically binds to the antibody of any one of claims 1-11, or an antigen binding fragment thereof.
17. A pharmaceutical composition comprising the antibody of any one of claims 1-11, or an antigen binding fragment thereof, the nucleic acid of claim 12 or claim 13, the vector of claim 14, the cell of claim 15, or the immunogenic polypeptide of claim 16, and a pharmaceutically acceptable excipient, diluent or carrier.
18. A pharmaceutical composition comprising a first antibody or an antigen binding fragment thereof, and a second antibody, or an antigen binding fragment thereof, wherein the first antibody is an antibody of any one of claims 1-11, and the second antibody neutralizes infection of Ebola virus.
19. Use of the antibody of any one of claims 1-11, or an antigen binding fragment thereof, the nucleic acid of claim 12 or claim 13, the vector of claim 14, the cell of claim 15, or the immunogenic polypeptide of claim 16, or the pharmaceutical composition of claim 17 or claim 18 in the manufacture of a medicament (i) for the prevention, treatment or attenuation of Ebola virus infection; (ii) for vaccination against Ebola virus infection; or (iii) for diagnosis of Ebola virus infection.
20. Use of the antibody of any one of claims 1-11, or an antigen binding fragment thereof, for monitoring the quality of anti-Ebola virus vaccines by checking that the antigen of said vaccine contains the specific epitope in the correct conformation.
21. A method of reducing Ebola virus infection, or lowering the risk of Ebola virus infection, comprising: administering to a subject in need thereof, a therapeutically effective amount of the antibody of any one of claims 1-11, or an antigen binding fragment thereof.
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US10160795B2 (en) 2014-11-14 2018-12-25 The United States Of America, As Represented By The Secretary, Department Of Health And Human Services Neutralizing antibodies to Ebola virus glycoprotein and their use
WO2019136029A1 (en) * 2018-01-02 2019-07-11 The United States Of America, As Represented By The Secretary, Department Of Health And Human Services Neutralizing antibodies to ebola virus glycoprotein and their use
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