WO2020061159A1 - Human antibodies to zika virus - Google Patents

Human antibodies to zika virus Download PDF

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Publication number
WO2020061159A1
WO2020061159A1 PCT/US2019/051677 US2019051677W WO2020061159A1 WO 2020061159 A1 WO2020061159 A1 WO 2020061159A1 US 2019051677 W US2019051677 W US 2019051677W WO 2020061159 A1 WO2020061159 A1 WO 2020061159A1
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Prior art keywords
antibody
fragment
antibodies
zikv
antigen
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PCT/US2019/051677
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French (fr)
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Jr. James E. Crowe
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Vanderbilt University
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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/12—Antivirals
    • A61P31/14—Antivirals for RNA viruses
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/005—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from viruses
    • 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
    • C07K16/1081—Togaviridae, e.g. flavivirus, rubella virus, hog cholera virus
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/569—Immunoassay; Biospecific binding assay; Materials therefor for microorganisms, e.g. protozoa, bacteria, viruses
    • G01N33/56983—Viruses
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/505—Medicinal preparations containing antigens or antibodies comprising antibodies
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/545—Medicinal preparations containing antigens or antibodies characterised by the dose, timing or administration schedule
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/55—Medicinal preparations containing antigens or antibodies characterised by the host/recipient, e.g. newborn with maternal antibodies
    • 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
    • C07K2317/30—Immunoglobulins specific features characterized by aspects of specificity or valency
    • C07K2317/32—Immunoglobulins specific features characterized by aspects of specificity or valency specific for a neo-epitope on a complex, e.g. antibody-antigen or ligand-receptor
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/30—Immunoglobulins specific features characterized by aspects of specificity or valency
    • C07K2317/34—Identification of a linear epitope shorter than 20 amino acid residues or of a conformational epitope defined by amino acid residues
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/70—Immunoglobulins specific features characterized by effect upon binding to a cell or to an antigen
    • C07K2317/76—Antagonist effect on antigen, e.g. neutralization or inhibition of binding
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2770/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssRNA viruses positive-sense
    • C12N2770/00011—Details
    • C12N2770/24011—Flaviviridae
    • C12N2770/24111—Flavivirus, e.g. yellow fever virus, dengue, JEV
    • C12N2770/24122—New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2333/00—Assays involving biological materials from specific organisms or of a specific nature
    • G01N2333/005—Assays involving biological materials from specific organisms or of a specific nature from viruses
    • G01N2333/08—RNA viruses
    • G01N2333/18—Togaviridae; Flaviviridae
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A50/00—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE in human health protection, e.g. against extreme weather
    • Y02A50/30—Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change

Definitions

  • the present disclosure relates generally to the fields of medicine, infectious disease, and immunology. More particular, the disclosure relates to human antibodies binding to Zika virus.
  • ZIKV Zika virus
  • Aedes species mosquitoes which are global in distribution, countries in which these vectors are present could be sites for future epidemics.
  • specific treatments or vaccines for ZIKV are not available, leaving a considerable unmet need in the field.
  • a method of detecting a Zika virus infection in a subject comprising (a) contacting a sample from said subject with an antibody or antibody fragment having clone-paired heavy and light chain sequences from Table 2; and (b) detecting Zika virus in said sample by binding of said antibody or antibody fragment to a Zika virus antigen in said sample.
  • the sample may be a body fluid, such as blood, sputum, tears, saliva, mucous or serum, semen, cervical or vaginal secretions, amniotic fluid, placental tissues, urine, exudate, transudate, tissue scrapings or feces.
  • Detection may comprise ELISA, RIA, lateral flow assay or Western blot.
  • the method may further comprise performing steps (a) and (b) a second time and determining a change in Zika virus antigen levels as compared to the first assay.
  • the antibody or antibody fragment may be encoded by clone- paired variable sequences as set forth in Table 1.
  • the antibody fragment may be a recombinant scFv (single chain fragment variable) antibody, Fab fragment, F(ab')2 fragment, or Fv fragment.
  • the antibody or antibody fragment may be encoded by clone-paired light and heavy chain variable sequences as set forth in Table 1.
  • the antibody fragment may be a recombinant scFv (single chain fragment variable) antibody, Fab fragment, F(ab')2 fragment, or Fv fragment.
  • the antibody may be an IgG, or a recombinant IgG antibody or antibody fragment comprising an Fc portion mutated to alter (eliminate or enhance) FcR interactions, to increase half-life and/or increase therapeutic efficacy, such as a LALA, N297, GASD/ALIE, YTE or LS mutation or glycan modified to alter (eliminate or enhance) FcR interactions such as enzymatic or chemical addition or removal of glycans or expression in a cell line engineered with a defined glycosylating pattern.
  • the antibody or antibody fragment comprises both LALA and YTE mutations.
  • the antibody may be a chimeric antibody or a bispecific antibody.
  • the antibody or antibody fragment may be administered prior to infection or after infection.
  • the subject may be a pregnant female, a sexually active female, or a female undergoing fertility treatments.
  • Delivering comprises antibody or antibody fragment administration, or genetic delivery with an RNA or DNA sequence or vector encoding the antibody or antibody fragment.
  • a monoclonal antibody wherein the antibody or antibody fragment is characterized by clone-paired heavy and light chain sequences from Table 2.
  • the antibody or antibody fragment may be encoded by clone-paired light and heavy chain variable sequences as set forth in Table 1.
  • the antibody fragment may be a recombinant scFv (single chain fragment variable) antibody, Fab fragment, F(ab')2 fragment, or Fv fragment.
  • the antibody may be an IgG, or a recombinant IgG antibody or antibody fragment comprising an Fc portion mutated to alter (eliminate or enhance) FcR interactions, to increase half-life and/or increase therapeutic efficacy, such as a LALA, N297, GASD/ALIE, YTE or LS mutation or glycan modified to alter (eliminate or enhance) FcR interactions such as enzymatic or chemical addition or removal of glycans or expression in a cell line engineered with a defined glycosylating pattern.
  • the antibody or antibody fragment comprises both LALA and YTE mutations.
  • the antibody may bea chimeric antibody or a bispecific antibody.
  • the antibody or antibody fragment may further comprise a cell penetrating peptide and/or is an intrabody.
  • a hybridoma or engineered cell encoding an antibody or antibody fragment wherein the antibody or antibody fragment is characterized by clone-paired heavy and light chain sequences from Table 2.
  • the antibody or antibody fragment may be encoded by clone-paired light and heavy chain variable sequences as set forth in Table 1.
  • the antibody fragment may be a recombinant scFv (single chain fragment variable) antibody, Fab fragment, F(ab')2 fragment, or Fv fragment.
  • the antibody may be an IgG, or a recombinant IgG antibody or antibody fragment comprising an Fc portion mutated to alter (eliminate or enhance) FcR interactions, to increase half-life and/or increase therapeutic efficacy, such as a LALA, N297, GASD/ALIE, YTE or LS mutation or glycan modified to alter (eliminate or enhance) FcR interactions such as enzymatic or chemical addition or removal of glycans or expression in a cell line engineered with a defined glycosylating pattern.
  • the antibody may bea chimeric antibody or a bispecific antibody.
  • the antibody or antibody fragment comprises both LALA and YTE mutations.
  • the antibody or antibody fragment may further comprise a cell penetrating peptide and/or is an intrabody.
  • a vaccine formulation comprising one or more antibodies or antibody fragments characterized by clone-paired heavy and light chain sequences from Table 2.
  • the antibody or antibody fragment may be encoded by clone-paired light and heavy chain variable sequences as set forth in Table 1.
  • the antibody fragment may be a recombinant scFv (single chain fragment variable) antibody, Fab fragment, F(ab')2 fragment, or Fv fragment.
  • the antibody may be an IgG, or a recombinant IgG antibody or antibody fragment comprising an Fc portion mutated to alter (eliminate or enhance) FcR interactions, to increase half-life and/or increase therapeutic efficacy, such as a LALA, N297, GASD/ALIE, YTE or LS mutation or glycan modified to alter (eliminate or enhance) FcR interactions such as enzymatic or chemical addition or removal of glycans or expression in a cell line engineered with a defined glycosylating pattern.
  • the antibody or antibody fragment comprises both LALA and YTE mutations.
  • the antibody may be a chimeric antibody or abispecific antibody.
  • the antibody or antibody fragment may further comprise a cell penetrating peptide and/or is an intrabody.
  • vaccine formulation comprising one or more expression vectors encoding a first antibody or antibody fragment as described above.
  • the expression vector(s) may be Sindbis virus or VEE vector(s).
  • the formulation may be formulated for delivery by needle injection, jet injection, or electroporation.
  • the vaccine formulation may further comprise one or more expression vectors encoding for a second antibody or antibody fragment, such as a defined above.
  • An additional embodiment comprises a method of protecting the health of a placenta and/or fetus of a pregnant a subject infected with or at risk of infection with Zika virus comprising delivering to said subject an antibody or antibody fragment having clone-paired heavy and light chain sequences from Table 2.
  • the antibody or antibody fragment may be encoded by clone-paired light and heavy chain variable sequences as set forth in Table 1.
  • the antibody fragment may be a recombinant scFv (single chain fragment variable) antibody, Fab fragment, F(ab')2 fragment, or Fv fragment.
  • the antibody may be an IgG, or a recombinant IgG antibody or antibody fragment comprising an Fc portion mutated to alter (eliminate or enhance) FcR interactions, to increase half-life and/or increase therapeutic efficacy, such as a LALA, N297, GASD/ALIE, YTE or LS mutation or glycan modified to alter (eliminate or enhance) FcR interactions such as enzymatic or chemical addition or removal of glycans or expression in a cell line engineered with a defined glycosylating pattern.
  • the antibody or antibody fragment comprises both LALA and YTE mutations.
  • the antibody may bea chimeric antibody or a bispecific antibody.
  • the antibody or antibody fragment may further comprise a cell penetrating peptide and/or is an intrabody.
  • the subject may be a pregnant female, a sexually active female, or a female undergoing fertility treatments.
  • Delivering may comprise antibody or antibody fragment administration, or genetic delivery with an RNA or DNA sequence or vector encoding the antibody or antibody fragment.
  • the antibody or antibody fragment may increase the size of the placenta as compared to an untreated control.
  • the antibody or antibody fragment may reduce viral load and/or pathology of the fetus as compared to an untreated control.
  • a further embodiment comprises a method of determining the antigenic integrity, correct conformation and/or correct sequence of a Zika virus antigen comprising (a) contacting a sample comprising said antigen with a first antibody or antibody fragment having clone- paired heavy and light chain sequences from Table 2; and (b) determining antigenic integrity, correct conformation and/or correct sequence of said antigen by detectable binding of said first antibody or antibody fragment to said antigen.
  • the sample may comprise recombinantly produced antigen, or the sample may comprise a vaccine formulation or vaccine production batch.
  • Detection may comprise ELISA, RIA, western blot, a biosensor using surface plasmon resonance or biolayer interferometry, or flow cytometric staining.
  • the first antibody or antibody fragment may be encoded by clone-paired variable sequences as set forth in Table 1.
  • the first antibody fragment may be a recombinant scFv (single chain fragment variable) antibody, Fab fragment, F(ab')2 fragment, or Fv fragment.
  • the method may further comprise performing steps (a) and (b) a second time to determine the antigenic stability of the antigen over time.
  • the method may further comprise (c) contacting a sample comprising said antigen with a second antibody or antibody fragment having clone- paired heavy and light chain sequences from Table 2; and (d) determining antigenic integrity of said antigen by detectable binding of said second antibody or antibody fragment to said antigen.
  • the second antibody or antibody fragment may beencoded by clone-paired variable sequences as set forth in Table 1.
  • the second antibody fragment may be a recombinant ScFv (single chain fragment variable) antibody, Fab fragment, F(ab')2 fragment, or Fv fragment.
  • the method may further comprise performing steps (c) and (d) a second time to determine the antigenic stability of the antigen over time.
  • FIGS. 1A-D Human antibody and B cell response to ZIKV infection. Serum samples from humans with a previous diagnosis of ZIKV infection were tested for (FIG.
  • FIG. 1 A binding to ZIKV E protein in ELISA (with two technical replicates) and (FIG. 1B) neutralization of ZIKV in a FRNT assay (performed with at least two independent repeats in triplicate). Subjects 973 and 972 sera were tested from two separate time points with similar results - these data were combined). Subject 1001 had the highest endpoint titer in the binding assay and displayed potent neutralizing activity. Subject 657 was a control without history of exposure to ZIKV.
  • FIG. 1C Supernatants of EBV -transformed B cell cultures from Subject 1001 were tested for binding to ZIKV E or Dill of ZIKV E or related flavivirus E proteins to assess the specificity of the immune response.
  • the frequency of antigen-specific cells against each viral protein was determined with a threshold optical density (OD) of 1.5; with alternate lower OD thresholds of 1.0 or 0.5, the frequency was 0.69% or 0.97% for ZIKV E, respectively.
  • OD optical density
  • FIG. 1D In four additional separate B cell transformation experiments, the frequency of B cells reactive with intact ZIKV E or E-FLM was determined.
  • FIG. 2A-E Characterization of anti-ZIKV mAbs.
  • FIG. 2A 29 mAbs were tested in binding, neutralization, and competition binding assays. The half-maximal binding concentration (EC50) against ZIKV E and the IC50 (by focus reduction neutralization test) against H/PF/2013 strain for neutralizing antibodies (highlighted in blue) are shown. The mAbs are displayed in four groups (A, B, C, or D) based on a competition binding assay. The values are the percent of binding that occurred during competition compared to uncompeted binding, which was normalized to 100% and the range of competition is indicated by the box colors.
  • FIG. 2B A ribbon diagram of three protomers of ZIKV E (DI in red, DII in yellow and Dill in blue) is shown with critical residues highlighted as spheres from epitope mapping experiments for representative antibodies in each of the competition binding groups. The colors of the critical residues correspond to the competition group designation as in FIG. 2A.
  • FIG. 2C Representative mAbs from each competition binding group are listed with the domains and residues critical for binding.
  • FIG. 2D Two mAbs were tested for neutralization of five strains of ZIKV. The concentrations at which 50% or 90% neutralization occurred are listed in (FIG. 2E). The neutralization data are pooled from at least three independent experiments performed in triplicate.
  • FIGS. 3A-F Protective activity of ZIKV-117 in adult male and pregnant female mice.
  • FIG. 3D-E PBS, (FIGS. 3D-F) 250 pg of hCHK-l52 isotype control mAh, (FIGS. 3D-F) 250 pg of ZIKV- 117, or (FIG. 3F) 250 pg of ZIKV-117 LALA.
  • dams were inoculated with 10 3 FFU of ZIKV-Dakar.
  • FIGS. 4A-E Effect of ZIKV-117 treatment on the placenta and the fetus.
  • FIG. 4A Cartoon depicting murine placental structures and zones.
  • FIG. 4B-E Pregnant dams were treated with PBS, hCHK-l52, or ZIKV-117 as described in (FIG. 4D-F) prior to infection with ZIKV-Dakar or mock-infected.
  • FIG. 4C Measurements of thickness and indicated areas of placenta and fetus body size. Each symbol represents data from an individual placenta or fetus. Significance was analyzed by ANOVA with a Dunn’s multiple comparison test (*, P ⁇ 0.05; **, P ⁇ 0.01, ***, P ⁇ 0.001; ****, p ⁇ 0.0001, n.s.; not significant, P > 0.05).
  • FIG. 4D In situ hybridization (ISH).
  • FIG. 5 Binding of human mAbs to Zika E protein, E Dill, or E fusion loop mutant (FLM). MAbs are organized by competition binding groups A to D.
  • FIGS. 6A-C High resolution epitope mapping of ZIKV mAbs.
  • FIG. 6A An alanine scanning mutation library for ZIKV envelope protein was constructed where each amino acid of prM/E was mutated individually to alanine (and alanine to serine) and expression constructs arrayed into 384-well plates, one mutation per well. Each clone in the ZIKV prM/E mutation library, expressed in HEK-293T cells, was tested for immunoreactivity with five mAbs from competition groups A-D, measured using an Intellicyt high-throughput flow cytometer.
  • Dill LR mutant was compared with mouse mAbs ZV-2 and ZV-54. Binding of ZIKV-116 and ZIKV-161 was decreased by mutations in Dill LR (ZIK-l 17 is the lowest). The order (from left to right) for each mutation in FIG. 6A is ZIK-l 2, ZIK-l 5, ZIK-l 6, ZIK-l 9 and ZIK-l 17.
  • FIG. 7 Binding of human mAbs to permeabilized DENV-infected C6/36 cells.
  • C6/36 cells were infected with DENV-l, DENV-2, DENV-3, DENV-4 or mock- infected.
  • Cells were stained with the indicated anti-ZIKV mAbs, an isotype control (a humanized antibody to chikungunya virus; hCHK-l52), or a positive control (a cross reactive antibody to DENV; chimeric human E60 [chE60]) and processed by flow cytometry.
  • the data are representative of two independent experiments. The numbers in the box indicate the fraction of cells that stained positively.
  • FIG. 8 Detection of human IgG in placenta or fetal head tissues after treatment of dams with ZIKV-117 or PBS treated pregnant mice.
  • WT female mice were mated with WT sires and monitored for pregnancy.
  • dams were treated with anti-Ifnarl mAh and PBS or 250 pg of ZIKV-l 17.
  • dams were infected with 10 3 FFU of ZIKV-Dakar.
  • FIGS. 9A-B Comparison of WT and LALA mutated antibodies.
  • FIG. 9A Binding to recombinant human FcvRl. The functional abrogation of the binding of the LALA variant IgG was confirmed in an ELISA binding assay with recombinant human FcyRI. ZIKV-l 17 WT bound to FcyRI, whereas the ZIKV-l 17 LALA antibody did not. WT and LALA versions of another human mAh, CKV063, were used as controls.
  • FIG. 9B Neutralization. ZIKV-l 17 WT and LALA antibodies exhibited equivalent neutralizing activity in vitro to each other and to the hybridoma-derived antibody.
  • FIG. 10 Effect of ZIKV-117 in NHP challenge studies.
  • Rhesus macaques were protected against viremia by ZIKV-l 17 at 10 mg/kg compared to the unrelated control mAh (10 mg/kg) after ZIKV challenge 1 day later (10 3 PFU ZIKV-Brazil) (left hand panels.
  • Rhesus macaques were rescued from ZIKV viremia by administration of ZIKV - 117 (10 mg/kg) on day +2 after ZIKV challenge (10 3 PFU ZIKV-Brazil) (right hand panels).
  • DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS
  • ZIKV infection causes systemic and central nervous system pathology or disease, with congenital birth defects linked to infection during pregnancy (Coyne et ah, 2016).
  • mAbs human monoclonal antibodies
  • E envelope
  • ZIKV- 117 broadly neutralized infection of ZIKV strains corresponding to African, Asian, and American lineages.
  • Zika virus Zika virus (ZIKV) is a member of the virus family Flaviviridae. It is spread by daytime- active Aedes mosquitoes, such as A. aegypti and A. albopictus. Its name comes from the Zika Forest of Kenya, where the virus was first isolated in 1947. Zika virus is related to the dengue, yellow fever, Japanese encephalitis, and West Nile viruses. Since the l950s, it has been known to occur within a narrow equatorial belt from Africa to Asia. From 2007 to 2016, the virus spread eastward, across the Pacific Ocean to the Americas, leading to the 2015-16 Zika virus epidemic.
  • Zika fever The infection, known as Zika fever or Zika virus disease, often causes no or only mild symptoms, similar to a very mild form of dengue fever. While there is no specific treatment, paracetamol (acetaminophen) and rest may help with the symptoms. As of 2016, the illness cannot be prevented by medications or vaccines. Zika can also spread from a pregnant woman to her fetus. This can result in microcephaly, severe brain malformations, and other birth defects. Zika infections in adults may result rarely in Guillain-Barre syndrome. In January 2016, the United States Centers for Disease Control and Prevention (CDC) issued travel guidance on affected countries, including the use of enhanced precautions, and guidelines for pregnant women including considering postponing travel. Other governments or health agencies also issued similar travel warnings, while Colombia, the Dominican Republic, Puerto Rico, Ecuador, El Salvador, and Jamaica advised women to postpone getting pregnant until more is known about the risks.
  • CDC United States Centers for Disease Control and Prevention
  • Zika virus belongs to the Flaviviridae family and the Flavivirus genus, and is thus related to the dengue, yellow fever, Japanese encephalitis, and West Nile viruses. Like other flaviviruses, Zika virus is enveloped and icosahedral and has a nonsegmented, single-stranded, 10 kb positive-sense RNA genome. It is most closely related to the Spondweni virus and is one of the two known viruses in the Spondweni virus clade.
  • a positive-sense RNA genome can be directly translated into viral proteins.
  • the RNA genome encodes seven nonstructural proteins and three structural proteins. One of the structural proteins encapsulates the virus.
  • the RNA genome forms a nucleocapsid along with copies of the l2-kDa capsid protein.
  • the nucleocapsid is enveloped within a host-derived membrane modified with two viral glycoproteins.
  • Viral genome replication depends on the synthesis of double sided RNA from the single stranded positive sense RNA (ssRNA(+)) genome followed by transcription and replication to provide viral mRNAs and new ssRNA(+) genomes.
  • Zika lineages There are two Zika lineages: the African lineage and the Asian lineage. Phylogenetic studies indicate that the virus spreading in the Americas is 89% identical to African genotypes but is most closely related to the Asian strain that circulated in French Polynesia during the 2013-2014 outbreak.
  • the vertebrate hosts of the virus were primarily monkeys in a so-called enzootic mosquito-monkey-mosquito cycle, with only occasional transmission to humans.
  • arboviruses have become established as a human disease and spread in a mosquito-human-mosquito cycle, like the yellow fever virus and the dengue fever virus (both flaviviruses), and the chikungunya virus (a togavirus).
  • Zika is primarily spread by Aedes aegypti mosquitoes and can also be transmitted through sexual contact or blood transfusions.
  • the basic reproduction number Ro a measure of transmissibility
  • Zika is primarily spread by the femal Q Aedes aegypti mosquito, which is active mostly in the daytime, although researchers have found the virus in common Culex house mosquitoes as well.
  • the mosquitos must feed on blood in order to lay eggs.
  • the virus has also been isolated from a number of arboreal mosquito species in the Aedes genus, such as A. africanus, A. apicoargenteus , A. furcifer, A. hensilli, A. luteocephalus and A. vittatus, with an extrinsic incubation period in mosquitoes of about 10 days.
  • Zika has been detected in many more species of Aedes, along with Anopheles coustani, Mansonia uniformis, and Culex perfuscus, although this alone does not incriminate them as a vector.
  • the potential societal risk of Zika can be delimited by the distribution of the mosquito species that transmit it.
  • the global distribution of the most cited carrier of Zika, A. aegypti, is expanding due to global trade and travel.
  • A. aegypti distribution is now the most extensive ever recorded - across all continents including North America and even the European periphery (Madeira, the Netherlands, and the northeastern Black Sea coast).
  • a mosquito population capable of carrying Zika has been found in a Capitol Hill neighborhood of Washington, D.C., and genetic evidence suggests they survived at least four consecutive winters in the region.
  • the Zika virus appears to be contagious via mosquitoes for around a week after infection. The virus is thought to be infectious for a longer period of time after infection (at least 2 weeks) when transmitted via semen.
  • Zika may be influenced to a greater degree by changes in precipitation and temperature than Dengue, making it more likely to be confined to tropical areas.
  • rising global temperatures would allow for the disease vector to expand their range further north, allowing Zika to follow.
  • Zika can be transmitted from men and women to their sexual partners. As of April 2016, sexual transmission of Zika has been documented in six countries - Argentina, Chile, France, Italy, New Zealand and the United States - during the 2015 outbreak.
  • the Zika virus can spread from an infected mother to her fetus during pregnancy or at delivery.
  • FDA US Food and Drug Administration
  • a potential risk had been suspected based on a blood-donor screening study during the French Polynesian Zika outbreak, in which 2.8% (42) of donors from November 2013 and February 2014 tested positive for Zika RNA and were all asymptomatic at the time of blood donation.
  • Eleven of the positive donors reported symptoms of Zika fever after their donation, but only three of 34 samples grew in culture.
  • Zika virus replicates in the mosquito's midgut epithelial cells and then its salivary gland cells. After 5-10 days, the virus can be found in the mosquito’s saliva. If the mosquito’s saliva is inoculated into human skin, the virus can infect epidermal keratinocytes, skin fibroblasts in the skin and the Langerhans cells. The pathogenesis of the virus is hypothesized to continue with a spread to lymph nodes and the bloodstream. Flaviviruses generally replicate in the cytoplasm, but Zika antigens have been found in infected cell nuclei.
  • Zika fever also known as Zika virus disease
  • Zika virus disease is an illness caused by the Zika virus. Most cases have no symptoms, but when present they are usually mild and can resemble dengue fever. Symptoms may include fever, red eyes, joint pain, headache, and a maculopapular rash. Symptoms generally last less than seven days. It has not caused any reported deaths during the initial infection. Infection during pregnancy causes microcephaly and other brain malformations in some babies. Infection in adults has been linked to Guillain-Barre syndrome (GBS). Diagnosis is by testing the blood, urine, or saliva for the presence of Zika virus RNA when the person is sick.
  • GBS Guillain-Barre syndrome
  • the virus was first isolated in April 1947 from a rhesus macaque monkey that had been placed in a cage in the Zika Forest of Kenya, near Lake Victoria, by the scientists of the Yellow Fever Research Institute. A second isolation from the mosquito A. africanus followed at the same site in January 1948. When the monkey developed a fever, researchers isolated from its serum a "filterable transmissible agent" that was named Zika in 1948.
  • Zika had been known to infect humans from the results of serological surveys in Kenya and Nigeria, published in 1952: Among 84 people of all ages, 50 individuals had antibodies to Zika, and all above 40 years of age were immune. A 1952 research study conducted in India had shown a "significant number" of Indians tested for Zika had exhibited an immune response to the virus, suggesting it had long been widespread within human populations.
  • an "isolated antibody” is one that has been separated and/or recovered from a component of its natural environment. Contaminant components of its natural environment are materials that would interfere with diagnostic or therapeutic uses for the antibody, and may include enzymes, hormones, and other proteinaceous or non-proteinaceous solutes.
  • the antibody is purified: (1) to greater than 95% by weight of antibody as determined by the Lowry method, and most particularly more than 99% by weight; (2) to a degree sufficient to obtain at least 15 residues of N-terminal or internal amino acid sequence by use of a spinning cup sequenator; or (3) to homogeneity by SDS-PAGE under reducing or non-reducing conditions using Coomassie blue or silver stain.
  • Isolated antibody includes the antibody in situ within recombinant cells since at least one component of the antibody's natural environment will not be present. Ordinarily, however, isolated antibody will be prepared by at least one purification step.
  • the basic four-chain antibody unit is a heterotetrameric glycoprotein composed of two identical light (L) chains and two identical heavy (H) chains.
  • An IgM antibody consists of 5 basic heterotetramer units along with an additional polypeptide called J chain, and therefore contain 10 antigen binding sites, while secreted IgA antibodies can polymerize to form polyvalent assemblages comprising 2-5 of the basic 4-chain units along with J chain.
  • the 4-chain unit is generally about 150,000 daltons.
  • Each L chain is linked to an H chain by one covalent disulfide bond, while the two H chains are linked to each other by one or more disulfide bonds depending on the H chain isotype.
  • Each H and L chain also has regularly spaced intrachain disulfide bridges.
  • Each H chain has at the N-terminus, a variable region (VH) followed by three constant domains (CH) for each of the alpha and gamma chains and four CH domains for mu and isotypes.
  • Each L chain has at the N-terminus, a variable region (VL) followed by a constant domain (CL) at its other end.
  • the VL is aligned with the VH and the CL is aligned with the first constant domain of the heavy chain (CHI).
  • Particular amino acid residues are believed to form an interface between the light chain and heavy chain variable regions.
  • the pairing of a VH and VL together forms a single antigen-binding site.
  • immunoglobulins can be assigned to different classes or isotypes. There are five classes of immunoglobulins: IgA, IgD, IgE, IgG, and IgM, having heavy chains designated alpha, delta, epsilon, gamma and mu, respectively.
  • gamma and alpha classes are further divided into subclasses on the basis of relatively minor differences in CH sequence and function, humans express the following subclasses: IgGl, IgG2, IgG3, IgG4, IgAl, and IgA2.
  • variable refers to the fact that certain segments of the V domains differ extensively in sequence among antibodies.
  • the V domain mediates antigen binding and defines specificity of a particular antibody for its particular antigen.
  • variability is not evenly distributed across the 110-amino acid span of the variable regions.
  • the V regions consist of relatively invariant stretches called framework regions (FRs) of 15-30 amino acids separated by shorter regions of extreme variability called “hypervariable regions” that are each 9-12 amino acids long.
  • FRs framework regions
  • hypervariable regions that are each 9-12 amino acids long.
  • the variable regions of native heavy and light chains each comprise four FRs, largely adopting a beta-sheet configuration, connected by three hypervariable regions, which form loops connecting, and in some cases forming part of, the beta-sheet structure.
  • the hypervariable regions in each chain are held together in close proximity by the FRs and, with the hypervariable regions from the other chain, contribute to the formation of the antigen-binding site of antibodies (see Rabat et al., Sequences of Proteins of Immunological Interest, 5th Ed. Public Health Service, National Institutes of Health, Bethesda, Md. (1991)).
  • the constant domains are not involved directly in binding an antibody to an antigen, but exhibit various effector functions, such as participation of the antibody in antibody dependent cellular cytotoxicity (ADCC), antibody-dependent cellular phagocytosis (ADCP), antibody-dependent neutrophil phagocytosis (ADNP), and antibody-dependent complement deposition (ADCD).
  • hypervariable region when used herein refers to the amino acid residues of an antibody that are responsible for antigen binding.
  • the hypervariable region generally comprises amino acid residues from a "complementarity determining region" or "CDR" (e.g., around about residues 24-34 (Ll), 50-56 (L2) and 89-97 (L3) in the VL, and around about 31- 35 (Hl), 50-65 (H2) and 95-102 (H3) in the VH when numbered in accordance with the Rabat numbering system; Rabat et al, Sequences of Proteins of Immunological Interest, 5th Ed. Public Health Service, National Institutes of Health, Bethesda, Md.
  • CDR complementarity determining region
  • residues from a "hypervariable loop” e.g., residues 24-34 (Ll), 50-56 (L2) and 89-97 (L3) in the VL, and 26-32 (Hl), 52-56 (H2) and 95-101 (H3) in the VH when numbered in accordance with the Chothia numbering system; Chothia and Lesk, J. Mol. Biol.
  • residues from a "hypervariable loop'VCDR e.g., residues 27-38 (Ll), 56-65 (L2) and 105-120 (L3) in the VL, and 27-38 (Hl), 56-65 (H2) and 105-120 (H3) in the VH when numbered in accordance with the IMGT numbering system; Lefranc, M. P. et al. Nucl. Acids Res. 27:209-212 (1999), Ruiz, M. et al. Nucl. Acids Res. 28:219-221 (2000)).
  • a "hypervariable loop'VCDR e.g., residues 27-38 (Ll), 56-65 (L2) and 105-120 (L3) in the VL, and 27-38 (Hl), 56-65 (H2) and 105-120 (H3) in the VH when numbered in accordance with the IMGT numbering system; Lefranc, M. P. et al. Nucl. Acids
  • the antibody has symmetrical insertions at one or more of the following points 28, 36 (Ll), 63, 74- 75 (L2) and 123 (L3) in the VL, and 28, 36 (Hl), 63, 74-75 (H2) and 123 (H3) in the V sub H when numbered in accordance with AHo; Honneger, A. and Plunkthun, A. J. Mol. Biol. 309:657-670 (2001)).
  • germline nucleic acid residue is meant the nucleic acid residue that naturally occurs in a germline gene encoding a constant or variable region.
  • Germline gene is the DNA found in a germ cell (i.e., a cell destined to become an egg or in the sperm).
  • a “germline mutation” refers to a heritable change in a particular DNA that has occurred in a germ cell or the zygote at the single-cell stage, and when transmitted to offspring, such a mutation is incorporated in every cell of the body.
  • a germline mutation is in contrast to a somatic mutation which is acquired in a single body cell.
  • nucleotides in a germline DNA sequence encoding for a variable region are mutated (i.e.. a somatic mutation) and replaced with a different nucleotide.
  • the term "monoclonal antibody” as used herein refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e., the individual antibodies comprising the population are identical except for possible naturally occurring mutations that may be present in minor amounts. Monoclonal antibodies are highly specific, being directed against a single antigenic site. Furthermore, in contrast to polyclonal antibody preparations that include different antibodies directed against different determinants (epitopes), each monoclonal antibody is directed against a single determinant on the antigen. In addition to their specificity, the monoclonal antibodies are advantageous in that they may be synthesized uncontaminated by other antibodies. The modifier "monoclonal" is not to be construed as requiring production of the antibody by any particular method.
  • the monoclonal antibodies useful in the present disclosure may be prepared by the hybridoma methodology first described by Kohler et al, Nature, 256:495 (1975), or may be made using recombinant DNA methods in bacterial, eukaryotic animal or plant cells (see, e.g., U.S. Pat. No. 4,816,567) after single cell sorting of an antigen specific B cell, an antigen specific plasmablast responding to an infection or immunization, or capture of linked heavy and light chains from single cells in a bulk sorted antigen specific collection.
  • the "monoclonal antibodies” may also be isolated from phage antibody libraries using the techniques described in Clackson et al, Nature, 352:624-628 (1991) and Marks et al, J. Mol. Biol., 222:581-597 (1991), for example.
  • monoclonal antibodies binding to Zika virus will have several applications. These include the production of diagnostic kits for use in detecting and diagnosing Zika virus infection, as well as for treating the same. In these contexts, one may link such antibodies to diagnostic or therapeutic agents, use them as capture agents or competitors in competitive assays, or use them individually without additional agents being attached thereto. The antibodies may be mutated or modified, as discussed further below. Methods for preparing and characterizing antibodies are well known in the art (see, e.g., Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, 1988; U.S. Patent 4,196,265). The methods for generating monoclonal antibodies (MAbs) generally begin along the same lines as those for preparing polyclonal antibodies.
  • the first step for both these methods is immunization of an appropriate host or identification of subjects who are immune due to prior natural infection or vaccination with a licensed or experimental vaccine.
  • a given composition for immunization may vary in its immunogenicity. It is often necessary therefore to boost the host immune system, as may be achieved by coupling a peptide or polypeptide immunogen to a carrier.
  • exemplary and preferred carriers are keyhole limpet hemocyanin (KLH) and bovine serum albumin (BSA).
  • KLH keyhole limpet hemocyanin
  • BSA bovine serum albumin
  • Other albumins such as ovalbumin, mouse serum albumin or rabbit serum albumin can also be used as carriers.
  • Means for conjugating a polypeptide to a carrier protein are well known in the art and include glutaraldehyde, m-maleimidobencoyl-N-hydroxysuccinimide ester, carbodiimyde and bis- biazotized benzidine.
  • the immunogenicity of a particular immunogen composition can be enhanced by the use of non-specific stimulators of the immune response, known as adjuvants.
  • Exemplary and preferred adjuvants in animals include complete Freund’s adjuvant (a non-specific stimulator of the immune response containing killed Mycobacterium tuberculosis), incomplete Freund’s adjuvants and aluminum hydroxide adjuvant and in humans include alum, CpG, MFP59 and combinations of immunostimulatory molecules (“Adjuvant Systems”, such as AS01 or AS03).
  • Additional experimental forms of inoculation to induce Zika virus-specific B cells is possible, including nanoparticle vaccines, or gene-encoded antigens delivered as DNA or RNA genes in a physical delivery system (such as lipid nanoparticle or on a gold biolistic bead), and delivered with needle, gene gun, transcutaneous electroporation device.
  • the antigen gene also can be carried as encoded by a replication competent or defective viral vector such as adenovirus, adeno-associated virus, poxvirus, herpesvirus, or alphavirus replicon, or alternatively a virus like particle.
  • a suitable approach is to identify subjects that have been exposed to the pathogens, such as those who have been diagnosed as having contracted the disease, or those who have been vaccinated to generate protective immunity against the pathogen or to test the safety or efficacy of an experimental vaccine. Circulating anti-pathogen antibodies can be detected, and antibody encoding or producing B cells from the antibody-positive subject may then be obtained.
  • the amount of immunogen composition used in the production of polyclonal antibodies varies upon the nature of the immunogen as well as the animal used for immunization.
  • a variety of routes can be used to administer the immunogen (subcutaneous, intramuscular, intradermal, intravenous and intraperitoneal).
  • the production of polyclonal antibodies may be monitored by sampling blood of the immunized animal at various points following immunization. A second, booster injection, also may be given. The process of boosting and titering is repeated until a suitable titer is achieved.
  • the immunized animal can be bled and the serum isolated and stored, and/or the animal can be used to generate MAbs.
  • somatic cells with the potential for producing antibodies, specifically B lymphocytes (B cells), are selected for use in the MAb generating protocol. These cells may be obtained from biopsied spleens, lymph nodes, tonsils or adenoids, bone marrow aspirates or biopsies, tissue biopsies from mucosal organs like lung or GI tract, or from circulating blood.
  • the antibody-producing B lymphocytes from the immunized animal or immune human are then fused with cells of an immortal myeloma cell, generally one of the same species as the animal that was immunized or human or human/mouse chimeric cells.
  • Myeloma cell lines suited for use in hybridoma-producing fusion procedures preferably are non-antibody-producing, have high fusion efficiency, and enzyme deficiencies that render then incapable of growing in certain selective media which support the growth of only the desired fused cells (hybridomas). Any one of a number of myeloma cells may be used, as are known to those of skill in the art (Goding, pp. 65-66, 1986; Campbell, pp. 75-83, 1984). HMMA2.5 cells or MFP-2 cells are particularly useful examples of such cells.
  • Methods for generating hybrids of antibody -producing spleen or lymph node cells and myeloma cells usually comprise mixing somatic cells with myeloma cells in a 2: 1 proportion, though the proportion may vary from about 20: 1 to about 1 : 1, respectively, in the presence of an agent or agents (chemical or electrical) that promote the fusion of cell membranes.
  • transformation of human B cells with Epstein Barr virus (EBV) as an initial step increases the size of the B cells, enhancing fusion with the relatively large-sized myeloma cells. Transformation efficiency by EBV is enhanced by using CpG and a Chk2 inhibitor drug in the transforming medium.
  • EBV Epstein Barr virus
  • human B cells can be activated by co-culture with transfected cell lines expressing CD40 Ligand (CD 154) in medium containing additional soluble factors, such as IL-21 and human B cell Activating Factor (BAFF), a Type II member of the TNF superfamily.
  • CD40 Ligand CD 1414
  • BAFF human B cell Activating Factor
  • Fusion methods using Sendai virus have been described by Kohler and Milstein (1975; 1976), and those using polyethylene glycol (PEG), such as 37% (v/v) PEG, by Gefter el al. (1977).
  • PEG polyethylene glycol
  • the use of electrically induced fusion methods also is appropriate (Goding, pp. 71-74, 1986) and there are processes for better efficiency (Yu et al, 2008).
  • Fusion procedures usually produce viable hybrids at low frequencies, about 1 x 10 6 to 1 x 10 8 , but with optimized procedures one can achieve fusion efficiencies close to 1 in 200 (Yu et al. , 2008).
  • relatively low efficiency of fusion does not pose a problem, as the viable, fused hybrids are differentiated from the parental, infused cells (particularly the infused myeloma cells that would normally continue to divide indefinitely) by culturing in a selective medium.
  • the selective medium is generally one that contains an agent that blocks the de novo synthesis of nucleotides in the tissue culture medium.
  • Exemplary and preferred agents are aminopterin, methotrexate, and azaserine.
  • Aminopterin and methotrexate block de novo synthesis of both purines and pyrimidines, whereas azaserine blocks only purine synthesis.
  • the medium is supplemented with hypoxanthine and thymidine as a source of nucleotides (HAT medium).
  • HAT medium Hypoxanthine
  • azaserine the medium is supplemented with hypoxanthine.
  • Ouabain is added if the B cell source is an EBV- transformed human B cell line, in order to eliminate EBV -transformed lines that have not fused to the myeloma.
  • the preferred selection medium is HAT or HAT with ouabain. Only cells capable of operating nucleotide salvage pathways are able to survive in HAT medium.
  • the myeloma cells are defective in key enzymes of the salvage pathway, e.g., hypoxanthine phosphoribosyl transferase (HPRT), and they cannot survive.
  • HPRT hypoxanthine phosphoribosyl transferase
  • the B cells can operate this pathway, but they have a limited life span in culture and generally die within about two weeks. Therefore, the only cells that can survive in the selective media are those hybrids formed from myeloma and B cells.
  • ouabain may also be used for drug selection of hybrids as EBV-transformed B cells are susceptible to drug killing, whereas the myeloma partner used is chosen to be ouabain resistant.
  • Culturing provides a population of hybridomas from which specific hybridomas are selected. Typically, selection of hybridomas is performed by culturing the cells by single-clone dilution in microtiter plates, followed by testing the individual clonal supernatants (after about two to three weeks) for the desired reactivity.
  • the assay should be sensitive, simple and rapid, such as radioimmunoassays, enzyme immunoassays, cytotoxicity assays, plaque assays dot immunobinding assays, and the like.
  • the selected hybridomas are then serially diluted or single-cell sorted by flow cytometric sorting and cloned into individual antibody-producing cell lines, which clones can then be propagated indefinitely to provide mAbs.
  • the cell lines may be exploited for MAb production in two basic ways.
  • a sample of the hybridoma can be injected (often into the peritoneal cavity) into an animal (e.g. , a mouse).
  • the animals are primed with a hydrocarbon, especially oils such as pristane (tetramethylpentadecane) prior to injection.
  • pristane tetramethylpentadecane
  • the injected animal develops tumors secreting the specific monoclonal antibody produced by the fused cell hybrid.
  • the body fluids of the animal such as serum or ascites fluid, can then be tapped to provide MAbs in high concentration.
  • the individual cell lines could also be cultured in vitro, where the MAbs are naturally secreted into the culture medium from which they can be readily obtained in high concentrations.
  • human hybridoma cells lines can be used in vitro to produce immunoglobulins in cell supernatant.
  • the cell lines can be adapted for growth in serum-free medium to optimize the ability to recover human monoclonal immunoglobulins of high purity.
  • MAbs produced by either means may be further purified, if desired, using filtration, centrifugation and various chromatographic methods such as FPLC or affinity chromatography.
  • Fragments of the monoclonal antibodies of the disclosure can be obtained from the purified monoclonal antibodies by methods which include digestion with enzymes, such as pepsin or papain, and/or by cleavage of disulfide bonds by chemical reduction.
  • monoclonal antibody fragments encompassed by the present disclosure can be synthesized using an automated peptide synthesizer.
  • RNA can be isolated from the single cells and antibody genes amplified by RT-PCR.
  • antigen-specific bulk sorted populations of cells can be segregated into microvesicles and the matched heavy and light chain variable genes recovered from single cells using physical linkage of heavy and light chain amplicons, or common barcoding of heavy and light chain genes from a vesicle.
  • Matched heavy and light chain genes form single cells also can be obtained from populations of antigen specific B cells by treating cells with cell-penetrating nanoparticles bearing RT-PCR primers and barcodes for marking transcripts with one barcode per cell.
  • the antibody variable genes also can be isolated by RNA extraction of a hybridoma line and the antibody genes obtained by RT-PCR and cloned into an immunoglobulin expression vector.
  • combinatorial immunoglobulin phagemid libraries are prepared from RNA isolated from the cell lines and phagemids expressing appropriate antibodies are selected by panning using viral antigens.
  • Antibodies according to the present disclosure may be defined, in the first instance, by their binding specificity. Those of skill in the art, by assessing the binding specificity/affmity of a given antibody using techniques well known to those of skill in the art, can determine whether such antibodies fall within the scope of the instant claims.
  • the epitope to which a given antibody bind may consist of a single contiguous sequence of 3 or more (e.g., 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20) amino acids located within the antigen molecule (e.g., a linear epitope in a domain).
  • the epitope may consist of a plurality of non-contiguous amino acids (or amino acid sequences) located within the antigen molecule (e.g., a conformational epitope).
  • Various techniques known to persons of ordinary skill in the art can be used to determine whether an antibody“interacts with one or more amino acids” within a polypeptide or protein.
  • Exemplary techniques include, for example, routine cross-blocking assays, such as that described in Antibodies, Harlow and Lane (Cold Spring Harbor Press, Cold Spring Harbor, N.Y.). Cross-blocking can be measured in various binding assays such as ELISA, biolayer interferometry, or surface plasmon resonance. Other methods include alanine scanning mutational analysis, peptide blot analysis (Reineke (2004) Methods Mol. Biol.
  • peptide cleavage analysis high-resolution electron microscopy techniques using single particle reconstruction, cryoEM, or tomography, crystallographic studies and NMR analysis.
  • methods such as epitope excision, epitope extraction and chemical modification of antigens can be employed (Tomer (2000) Prot. Sci. 9: 487-496).
  • Another method that can be used to identify the amino acids within a polypeptide with which an antibody interacts is hydrogen/deuterium exchange detected by mass spectrometry.
  • the hydrogen/deuterium exchange method involves deuterium-labeling the protein of interest, followed by binding the antibody to the deuterium-labeled protein.
  • the protein/antibody complex is transferred to water and exchangeable protons within amino acids that are protected by the antibody complex undergo deuterium-to-hydrogen back-exchange at a slower rate than exchangeable protons within amino acids that are not part of the interface.
  • amino acids that form part of the protein/antibody interface may retain deuterium and therefore exhibit relatively higher mass compared to amino acids not included in the interface.
  • the target protein is subjected to protease cleavage and mass spectrometry analysis, thereby revealing the deuterium-labeled residues which correspond to the specific amino acids with which the antibody interacts.
  • antibody escape mutant variant organisms can be isolated by propagating Zika virus in vitro or in animal models in the presence of high concentrations of the antibody. Sequence analysis of the Zika virus gene encoding the antigen targeted by the antibody reveals the mutation(s) conferring antibody escape, indicating residues in the epitope or that affect the structure of the epitope allosterically.
  • epitope refers to a site on an antigen to which B and/or T cells respond.
  • B- cell epitopes can be formed both from contiguous amino acids or noncontiguous amino acids juxtaposed by tertiary folding of a protein. Epitopes formed from contiguous amino acids are typically retained on exposure to denaturing solvents, whereas epitopes formed by tertiary folding are typically lost on treatment with denaturing solvents.
  • An epitope typically includes at least 3, and more usually, at least 5 or 8-10 amino acids in a unique spatial conformation.
  • MAP Modification-Assisted Profiling
  • SAP Antigen Structure-based Antibody Profiling
  • mAbs monoclonal antibodies
  • Each category may reflect a unique epitope either distinctly different from or partially overlapping with epitope represented by another category. This technology allows rapid filtering of genetically identical antibodies, such that characterization can be focused on genetically distinct antibodies.
  • MAP may facilitate identification of rare hybridoma clones that produce mAbs having the desired characteristics.
  • MAP may be used to sort the antibodies of the disclosure into groups of antibodies binding different epitopes.
  • the present disclosure includes antibodies that may bind to the same epitope, or a portion of the epitope. Likewise, the present disclosure also includes antibodies that compete for binding to a target or a fragment thereof with any of the specific exemplary antibodies described herein.
  • test antibody If the test antibody is able to bind to the target molecule following saturation binding with the reference antibody, it can be concluded that the test antibody binds to a different epitope than the reference antibody. On the other hand, if the test antibody is not able to bind to the target molecule following saturation binding with the reference antibody, then the test antibody may bind to the same epitope as the epitope bound by the reference antibody.
  • the above-described binding methodology is performed in two orientations: In a first orientation, the reference antibody is allowed to bind to the Zika virus antigen under saturating conditions followed by assessment of binding of the test antibody to the Zika virus antigen. In a second orientation, the test antibody is allowed to bind to the Zika virus antigen molecule under saturating conditions followed by assessment of binding of the reference antibody to the Zika virus antigen. If, in both orientations, only the first (saturating) antibody is capable of binding to the Zika virus antigen, then it is concluded that the test antibody and the reference antibody compete for binding to the Zika virus antigen.
  • an antibody that competes for binding with a reference antibody may not necessarily bind to the identical epitope as the reference antibody but may sterically block binding of the reference antibody by binding an overlapping or adjacent epitope.
  • Two antibodies bind to the same or overlapping epitope if each competitively inhibits (blocks) binding of the other to the antigen. That is, a 1-, 5-, 10-, 20- or lOO-fold excess of one antibody inhibits binding of the other by at least 50% but preferably 75%, 90% or even 99% as measured in a competitive binding assay (see, e.g., Junghans el al, Cancer Res. 1990 50: 1495-1502).
  • two antibodies have the same epitope if essentially all amino acid mutations in the antigen that reduce or eliminate binding of one antibody reduce or eliminate binding of the other.
  • Two antibodies have overlapping epitopes if some amino acid mutations that reduce or eliminate binding of one antibody reduce or eliminate binding of the other.
  • Additional routine experimentation e.g., peptide mutation and binding analyses
  • peptide mutation and binding analyses can then be carried out to confirm whether the observed lack of binding of the test antibody is in fact due to binding to the same epitope as the reference antibody or if steric blocking (or another phenomenon) is responsible for the lack of observed binding.
  • steric blocking or another phenomenon
  • Structural studies with EM or crystallography also can demonstrate whether or not two antibodies that compete for binding recognize the same epitope.
  • monoclonal antibodies having clone-paired CDRs from the heavy and light chains as illustrated in Tables 3 and 4, respectively.
  • Such antibodies may be produced by the clones discussed below in the Examples section using methods described herein.
  • the antibodies may be defined by their variable sequence, which include additional“framework” regions. These are provided in Tables 1 and 2 that encode or represent full variable regions.
  • the antibodies sequences may vary from these sequences, optionally using methods discussed in greater detail below.
  • nucleic acid sequences may vary from those set out above in that (a) the variable regions may be segregated away from the constant domains of the light and heavy chains, (b) the nucleic acids may vary from those set out above while not affecting the residues encoded thereby, (c) the nucleic acids may vary from those set out above by a given percentage, e.g., 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% homology, (d) the nucleic acids may vary from those set out above by virtue of the ability to hybridize under high stringency conditions, as exemplified by low salt and/or high temperature conditions, such as provided by about 0.02 M to
  • two sequences are said to be “identical” if the sequence of nucleotides or amino acids in the two sequences is the same when aligned for maximum correspondence, as described below. Comparisons between two sequences are typically performed by comparing the sequences over a comparison window to identify and compare local regions of sequence similarity.
  • a “comparison window” as used herein refers to a segment of at least about 20 contiguous positions, usually 30 to about 75, 40 to about 50, in which a sequence may be compared to a reference sequence of the same number of contiguous positions after the two sequences are optimally aligned.
  • Optimal alignment of sequences for comparison may be conducted using the Megalign program in the Lasergene suite of bioinformatics software (DNASTAR, Inc., Madison, Wis.), using default parameters.
  • This program embodies several alignment schemes described in the following references: Dayhoff, M. O. (1978) A model of evolutionary change in proteins- Matrices for detecting distant relationships. In Dayhoff, M. O. (ed.) Atlas of Protein Sequence and Structure, National Biomedical Research Foundation, Washington D.C. Vol. 5, Suppl. 3, pp. 345-358; Hein J. (1990) Unified Approach to Alignment and Phylogeny pp. 626-645 Methods in Enzymology vol.
  • optimal alignment of sequences for comparison may be conducted by the local identity algorithm of Smith and Waterman (1981) Add. APL. Math 2:482, by the identity alignment algorithm of Needleman and Wunsch (1970) J. Mol. Biol. 48:443, by the search for similarity methods of Pearson and Lipman (1988) Proc. Natl. Acad. Sci. USA 85: 2444, by computerized implementations of these algorithms (GAP, BESTFIT, BLAST, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group (GCG), 575 Science Dr., Madison, Wis.), or by inspection.
  • BLAST and BLAST 2.0 are described in Altschul et al. (1977) Nucl. Acids Res. 25:3389-3402 and Altschul et al. (1990) J. Mol. Biol. 215:403-410, respectively.
  • BLAST and BLAST 2.0 can be used, for example with the parameters described herein, to determine percent sequence identity for the polynucleotides and polypeptides of the disclosure.
  • Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information. The rearranged nature of an antibody sequence and the variable length of each gene requires multiple rounds of BLAST searches for a single antibody sequence.
  • IgBLAST (world-wide-web at ncbi.nlm.nih.gov/igblast/) identifies matches to the germline V, D and J genes, details at rearrangement junctions, the delineation of Ig V domain framework regions and complementarity determining regions.
  • IgBLAST can analyze nucleotide or protein sequences and can process sequences in batches and allows searches against the germline gene databases and other sequence databases simultaneously to minimize the chance of missing possibly the best matching germline V gene.
  • cumulative scores can be calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always >0) and N (penalty score for mismatching residues; always ⁇ 0). Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached.
  • the BLAST algorithm parameters W, T and X determine the sensitivity and speed of the alignment.
  • a scoring matrix can be used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached.
  • the BLAST algorithm parameters W, T and X determine the sensitivity and speed of the alignment.
  • the "percentage of sequence identity” is determined by comparing two optimally aligned sequences over a window of comparison of at least 20 positions, wherein the portion of the polynucleotide or polypeptide sequence in the comparison window may comprise additions or deletions (i.e., gaps) of 20 percent or less, usually 5 to 15 percent, or 10 to 12 percent, as compared to the reference sequences (which does not comprise additions or deletions) for optimal alignment of the two sequences.
  • the percentage is calculated by determining the number of positions at which the identical nucleic acid bases or amino acid residues occur in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the reference sequence (i.e., the window size) and multiplying the results by 100 to yield the percentage of sequence identity.
  • an antibody is as a“derivative” of any of the below- described antibodies and their antigen-binding fragments.
  • the term“derivative” refers to an antibody or antigen-binding fragment thereof that immunospecifically binds to an antigen but which comprises, one, two, three, four, five or more amino acid substitutions, additions, deletions or modifications relative to a“parental” (or wild-type) molecule. Such amino acid substitutions or additions may introduce naturally occurring (i.e., DNA-encoded) or non- naturally occurring amino acid residues.
  • the term“derivative” encompasses, for example, as variants having altered CH1, hinge, CH2, CH3 or CH4 regions, so as to form, for example antibodies, etc.
  • derivative additionally encompasses non-amino acid modifications, for example, amino acids that may be glycosylated (e.g., have altered mannose, 2-N- acetylglucosamine, galactose, fucose, glucose, sialic acid, 5-N-acetylneuraminic acid, 5- glycolneuraminic acid, etc. content), acetylated, pegylated, phosphorylated, amidated, derivatized by known protecting/blocking groups, proteolytic cleavage, linked to a cellular ligand or other protein, etc.
  • non-amino acid modifications for example, amino acids that may be glycosylated (e.g., have altered mannose, 2-N- acetylglucosamine, galactose, fucose, glucose, sialic acid, 5-N-acetylneuraminic acid, 5- glycolneuraminic acid, etc. content), acetylated, pegylated,
  • the altered carbohydrate modifications modulate one or more of the following: solubilization of the antibody, facilitation of subcellular transport and secretion of the antibody, promotion of antibody assembly, conformational integrity, and antibody-mediated effector function.
  • the altered carbohydrate modifications enhance antibody mediated effector function relative to the antibody lacking the carbohydrate modification.
  • Carbohydrate modifications that lead to altered antibody mediated effector function are well known in the art (for example, see Shields, R. L. et al. (2002)“ Lack Of Fucose On Human IgG N-Linked Oligosaccharide Improves Binding To Human Fcgamma RIII And Antibody-Dependent Cellular Toxicity ,” J. Biol. Chem.
  • a derivative antibody or antibody fragment can be generated with an engineered sequence or glycosylation state to confer preferred levels of activity in antibody dependent cellular cytotoxicity (ADCC), antibody-dependent cellular phagocytosis (ADCP), antibody-dependent neutrophil phagocytosis (ADNP), or antibody-dependent complement deposition (ADCD) functions as measured by bead-based or cell-based assays or in vivo studies in animal models.
  • ADCC antibody dependent cellular cytotoxicity
  • ADCP antibody-dependent cellular phagocytosis
  • ADNP antibody-dependent neutrophil phagocytosis
  • ADCD antibody-dependent complement deposition
  • a derivative antibody or antibody fragment may be modified by chemical modifications using techniques known to those of skill in the art, including, but not limited to, specific chemical cleavage, acetylation, formulation, metabolic synthesis of tunicamycin, etc.
  • an antibody derivative will possess a similar or identical function as the parental antibody.
  • an antibody derivative will exhibit an altered activity relative to the parental antibody.
  • a derivative antibody (or fragment thereof) can bind to its epitope more tightly or be more resistant to proteolysis than the parental antibody.
  • Modified antibodies may be made by any technique known to those of skill in the art, including expression through standard molecular biological techniques, or the chemical synthesis of polypeptides. Methods for recombinant expression are addressed elsewhere in this document. The following is a general discussion of relevant goals techniques for antibody engineering.
  • Hybridomas may be cultured, then cells lysed, and total RNA extracted. Random hexamers may be used with RT to generate cDNA copies of RNA, and then PCR performed using a multiplex mixture of PCR primers expected to amplify all human variable gene sequences. PCR product can be cloned into pGEM-T Easy vector, then sequenced by automated DNA sequencing using standard vector primers. Assay of binding and neutralization may be performed using antibodies collected from hybridoma supernatants and purified by FPLC, using Protein G columns.
  • Recombinant full-length IgG antibodies can be generated by subcloning heavy and light chain Fv DNAs from the cloning vector into an IgG plasmid vector, transfected into 293 (e.g., Freestyle) cells or CHO cells, and antibodies can be collected and purified from the 293 or CHO cell supernatant.
  • 293 e.g., Freestyle
  • Other appropriate host cells systems include bacteria, such as E. coli, insect cells (S2, Sf9, Sf29, High Five), plant cells (e.g., tobacco, with or without engineering for human-like glycans), algae, or in a variety of non-human transgenic contexts, such as mice, rats, goats or cows.
  • Antibody coding sequences can be RNA, such as native RNA or modified RNA.
  • Modified RNA contemplates certain chemical modifications that confer increased stability and low immunogenicity to mRNAs, thereby facilitating expression of therapeutically important proteins. For instance, Nl -methyl-pseudouridine (N 1 hiY) outperforms several other nucleoside modifications and their combinations in terms of translation capacity.
  • RNA may be delivered as naked RNA or in a delivery vehicle, such as a lipid nanoparticle.
  • DNA encoding the antibody may be employed for the same purposes.
  • the DNA is included in an expression cassette comprising a promoter active in the host cell for which it is designed.
  • the expression cassette is advantageously included in a replicable vector, such as a conventional plasmid or minivector.
  • Vectors include viral vectors, such as poxviruses, adenoviruses, herpesviruses, adeno-associated viruses, and lentiviruses are contemplated.
  • Replicons encoding antibody genes such as alphavirus replicons based on VEE virus or Sindbis virus are also contemplated. Delivery of such vectors can be performed by needle through intramuscular, subcutaneous, or intradermal routes, or by transcutaneous electroporation when in vivo expression is desired.
  • Lonza has developed a generic method using pooled transfectants grown in CDACF medium, for the rapid production of small quantities (up to 50 g) of antibodies in CHO cells. Although slightly slower than a true transient system, the advantages include a higher product concentration and use of the same host and process as the production cell line.
  • Antibody molecules will comprise fragments (such as F(ab'), F(ab')2) that are produced, for example, by the proteolytic cleavage of the mAbs, or single-chain immunoglobulins producible, for example, via recombinant means.
  • F(ab') antibody derivatives are monovalent, while F(ab')2 antibody derivatives are bivalent.
  • fragments can be combined with one another, or with other antibody fragments or receptor ligands to form “chimeric” binding molecules.
  • such chimeric molecules may contain substituents capable of binding to different epitopes of the same molecule.
  • the antibody is a derivative of the disclosed antibodies, e.g., an antibody comprising the CDR sequences identical to those in the disclosed antibodies (e.g., a chimeric, or CDR-grafted antibody).
  • an antibody comprising the CDR sequences identical to those in the disclosed antibodies (e.g., a chimeric, or CDR-grafted antibody).
  • modifications such as introducing conservative changes into an antibody molecule.
  • the hydropathic index of amino acids may be considered.
  • the importance of the hydropathic amino acid index in conferring interactive biologic function on a protein is generally understood in the art (Kyte and Doolittle, 1982). It is accepted that the relative hydropathic character of the amino acid contributes to the secondary structure of the resultant protein, which in turn defines the interaction of the protein with other molecules, for example, enzymes, substrates, receptors, DNA, antibodies, antigens, and the like.
  • Patent 4,554,101 the following hydrophilicity values have been assigned to amino acid residues: basic amino acids: arginine (+3.0), lysine (+3.0), and histidine (-0.5); acidic amino acids: aspartate (+3.0 ⁇ 1), glutamate (+3.0 ⁇ 1), asparagine (+0.2), and glutamine (+0.2); hydrophilic, nonionic amino acids: serine (+0.3), asparagine (+0.2), glutamine (+0.2), and threonine (-0.4), sulfur containing amino acids: cysteine (-1.0) and methionine (-1.3); hydrophobic, nonaromatic amino acids: valine (-1.5), leucine (-1.8), isoleucine (-1.8), proline (-0.5 ⁇ 1), alanine (-0.5), and glycine (0); hydrophobic, aromatic amino acids: tryptophan (- 3.4), phenylalanine (-2.5), and tyrosine (-2.3).
  • an amino acid can be substituted for another having a similar hydrophilicity and produce a biologically or immunologically modified protein.
  • substitution of amino acids whose hydrophilicity values are within ⁇ 2 is preferred, those that are within ⁇ 1 are particularly preferred, and those within ⁇ 0.5 are even more particularly preferred.
  • amino acid substitutions generally are based on the relative similarity of the amino acid side-chain substituents, for example, their hydrophobicity, hydrophilicity, charge, size, and the like.
  • Exemplary substitutions that take into consideration the various foregoing characteristics are well known to those of skill in the art and include: arginine and lysine; glutamate and aspartate; serine and threonine; glutamine and asparagine; and valine, leucine and isoleucine.
  • the present disclosure also contemplates isotype modification.
  • isotype modification By modifying the Fc region to have a different isotype, different functionalities can be achieved. For example, changing to IgGi can increase antibody dependent cell cytotoxicity, switching to class A can improve tissue distribution, and switching to class M can improve valency.
  • binding polypeptide of particular interest may be one that binds to Clq and displays complement dependent cytotoxicity.
  • Polypeptides with pre-existing Clq binding activity, optionally further having the ability to mediate CDC may be modified such that one or both of these activities are enhanced.
  • Amino acid modifications that alter Clq and/or modify its complement dependent cytotoxicity function are described, for example, in WO/0042072, which is hereby incorporated by reference.
  • effector functions are responsible for activating or diminishing a biological activity (e.g., in a subject).
  • effector functions include, but are not limited to: Clq binding; complement dependent cytotoxicity (CDC); Fc receptor binding; antibody-dependent cell- mediated cytotoxicity (ADCC); phagocytosis; down regulation of cell surface receptors (e.g., B cell receptor; BCR), etc.
  • Such effector functions may require the Fc region to be combined with a binding domain (e.g., an antibody variable domain) and can be assessed using various assays (e.g., Fc binding assays, ADCC assays, CDC assays, etc.).
  • a binding domain e.g., an antibody variable domain
  • assays e.g., Fc binding assays, ADCC assays, CDC assays, etc.
  • a variant Fc region of an antibody with improved Clq binding and improved FcyRIII binding e.g., having both improved ADCC activity and improved CDC activity.
  • a variant Fc region can be engineered with reduced CDC activity and/or reduced ADCC activity.
  • only one of these activities may be increased, and, optionally, also the other activity reduced (e.g., to generate an Fc region variant with improved ADCC activity, but reduced CDC activity and vice versa).
  • FcRn binding Fc mutations can also be introduced and engineered to alter their interaction with the neonatal Fc receptor (FcRn) and improve their pharmacokinetic properties.
  • FcRn neonatal Fc receptor
  • a collection of human Fc variants with improved binding to the FcRn have been described (Shields et al., (2001). High resolution mapping of the binding site on human IgGl for FcyRI, FcyRII, FcyRIII, and FcRn and design of IgGl variants with improved binding to the FcyR, (J. Biol. Chem. 276:6591-6604).
  • amino acid modifications may be generated through techniques including alanine scanning mutagenesis, random mutagenesis and screening to assess the binding to the neonatal Fc receptor (FcRn) and/or the in vivo behavior.
  • Computational strategies followed by mutagenesis may also be used to select one of amino acid mutations to mutate.
  • the present disclosure therefore provides a variant of an antigen binding protein with optimized binding to FcRn.
  • the said variant of an antigen binding protein comprises at least one amino acid modification in the Fc region of said antigen binding protein, wherein said modification is selected from the group consisting of 226, 227, 228, 230, 231, 233, 234, 239, 241, 243, 246, 250, 252, 256, 259, 264, 265, 267, 269, 270, 276, 284, 285,
  • the modifications are M252Y/S254T/T256E.
  • Derivatized antibodies may be used to alter the half-lives (e.g., serum half-lives) of parental antibodies in a mammal, particularly a human. Such alterations may result in a half- life of greater than 15 days, preferably greater than 20 days, greater than 25 days, greater than 30 days, greater than 35 days, greater than 40 days, greater than 45 days, greater than 2 months, greater than 3 months, greater than 4 months, or greater than 5 months.
  • half-lives e.g., serum half-lives
  • Antibodies or fragments thereof having increased in vivo half-lives can be generated by techniques known to those of skill in the art. For example, antibodies or fragments thereof with increased in vivo half-lives can be generated by modifying (e.g., substituting, deleting or adding) amino acid residues identified as involved in the interaction between the Fc domain and the FcRn receptor.
  • a particular embodiment of the present disclosure is an isolated monoclonal antibody, or antigen binding fragment thereof, containing a substantially homogeneous glycan without sialic acid, galactose, or fucose.
  • the monoclonal antibody comprises a heavy chain variable region and a light chain variable region, both of which may be attached to heavy chain or light chain constant regions respectively.
  • the aforementioned substantially homogeneous glycan may be covalently attached to the heavy chain constant region.
  • Another embodiment of the present disclosure comprises a mAh with a novel Fc glycosylation pattern.
  • the isolated monoclonal antibody, or antigen binding fragment thereof is present in a substantially homogenous composition represented by the GNGN or G1/G2 gly coform.
  • Fc glycosylation plays a significant role in anti-viral and anti-cancer properties of therapeutic mAbs.
  • the disclosure is in line with a recent study that shows increased anti- lentivirus cell-mediated viral inhibition of a fucose free anti-HIV mAh in vitro.
  • This embodiment of the present disclosure with homogenous glycans lacking a core fucose showed increased protection against specific viruses by a factor greater than two-fold. Elimination of core fucose dramatically improves the ADCC activity of mAbs mediated by natural killer (NK) cells but appears to have the opposite effect on the ADCC activity of polymorphonuclear cells (PMNs).
  • NK natural killer
  • the isolated monoclonal antibody, or antigen binding fragment thereof, comprising a substantially homogenous composition represented by the GNGN or G1/G2 gly coform exhibits increased binding affinity for Fc gamma RI and Fc gamma RIII compared to the same antibody without the substantially homogeneous GNGN glycoform and with GO, G1F, G2F, GNF, GNGNF or GNGNFX containing glycoforms.
  • the antibody dissociates from Fc gamma RI with a Kd of 1 x 10 8 M or less and from Fc gamma RIII with a Kd of 1 x 10 7 M or less.
  • N-linked refers to the attachment of the carbohydrate moiety to the side chain of an asparagine residue.
  • O- linked glycosylation refers to the attachment of one of the sugars N-acetylgalactosamine, galactose, or xylose to a hydroxyamino acid, most commonly serine or threonine, although 5- hydroxyproline or 5-hydroxylysine may also be used.
  • the recognition sequences for enzymatic attachment of the carbohydrate moiety to the asparagine side chain peptide sequences are asparagine-X-serine and asparagine-X-threonine, where X is any amino acid except proline.
  • the glycosylation pattern may be altered, for example, by deleting one or more glycosylation site(s) found in the polypeptide, and/or adding one or more glycosylation site(s) that are not present in the polypeptide.
  • Addition of glycosylation sites to the Fc region of an antibody is conveniently accomplished by altering the amino acid sequence such that it contains one or more of the above-described tripeptide sequences (for N-linked glycosylation sites).
  • An exemplary glycosylation variant has an amino acid substitution of residue Asn 297 of the heavy chain.
  • the alteration may also be made by the addition of, or substitution by, one or more serine or threonine residues to the sequence of the original polypeptide (for O-linked glycosylation sites). Additionally, a change of Asn 297 to Ala can remove one of the glycosylation sites.
  • the antibody is expressed in cells that express beta (l,4)-N- acetylglucosaminyltransferase III (GnT III), such that GnT III adds GlcNAc to the IL-23pl9 antibody.
  • GnT III beta (l,4)-N- acetylglucosaminyltransferase III
  • Methods for producing antibodies in such a fashion are provided in WO/9954342, WO/03011878, patent publication 20030003097A1, and Umana et al., Nature Biotechnology, 17: 176-180, February 1999.
  • Cell lines can be altered to enhance or reduce or eliminate certain post-translational modifications, such as glycosylation, using genome editing technology such as Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR).
  • CRISPR technology can be used to eliminate genes encoding glycosylating enzymes in 293 or CHO cells used to express recombinant monoclonal antibodies
  • Such motifs can be eliminated by altering the synthetic gene for the cDNA encoding recombinant antibodies.
  • Antibodies can be engineered for enhanced biophysical properties.
  • Differential Scanning Calorimetry (DSC) measures the heat capacity, C P , of a molecule (the heat required to warm it, per degree) as a function of temperature.
  • DSC Differential Scanning Calorimetry
  • C P the heat capacity of a molecule (the heat required to warm it, per degree) as a function of temperature.
  • DSC data for mAbs is particularly interesting because it sometimes resolves the unfolding of individual domains within the mAh structure, producing up to three peaks in the thermogram (from unfolding of the Fab, CH2, and CH3 domains). Typically unfolding of the Fab domain produces the strongest peak.
  • the DSC profiles and relative stability of the Fc portion show characteristic differences for the human IgGi, IgG 2 , IgGv and IgGr subclasses (Garber and Demarest, Biochem. Biophys. Res. Commun. 355, 751-757, 2007).
  • CD circular dichroism
  • Far-UV CD spectra will be measured for antibodies in the range of 200 to 260 nm at increments of 0.5 nm. The final spectra can be determined as averages of 20 accumulations. Residue ellipticity values can be calculated after background subtraction.
  • DLS dynamic light scattering
  • DLS measurements of a sample can show whether the particles aggregate over time or with temperature variation by determining whether the hydrodynamic radius of the particle increases. If particles aggregate, one can see a larger population of particles with a larger radius. Stability depending on temperature can be analyzed by controlling the temperature in situ.
  • Capillary electrophoresis (CE) techniques include proven methodologies for determining features of antibody stability. One can use an iCE approach to resolve antibody protein charge variants due to deamidation, C-terminal lysines, sialylation, oxidation, glycosylation, and any other change to the protein that can result in a change in pi of the protein.
  • Each of the expressed antibody proteins can be evaluated by high throughput, free solution isoelectric focusing (IEF) in a capillary column (cIEF), using a Protein Simple Maurice instrument.
  • IEF free solution isoelectric focusing
  • cIEF capillary column
  • Whole-column UV absorption detection can be performed every 30 seconds for real time monitoring of molecules focusing at the isoelectric points (pis).
  • This approach combines the high resolution of traditional gel IEF with the advantages of quantitation and automation found in column-based separations while eliminating the need for a mobilization step.
  • the technique yields reproducible, quantitative analysis of identity, purity, and heterogeneity profiles for the expressed antibodies.
  • the results identify charge heterogeneity and molecular sizing on the antibodies, with both absorbance and native fluorescence detection modes and with sensitivity of detection down to 0.7 pg/mL.
  • Solubility One can determine the intrinsic solubility score of antibody sequences.
  • the intrinsic solubility scores can be calculated using CamSol Intrinsic (Sormanni el al. , JMol Biol 427, 478-490, 2015).
  • the amino acid sequences for residues 95-102 (Kabat numbering) in HCDR3 of each antibody fragment such as a scFv can be evaluated via the online program to calculate the solubility scores.
  • autoreactivity Generally, it is thought that autoreactive clones should be eliminated during ontogeny by negative selection, however it has become clear that many human naturally occurring antibodies with autoreactive properties persist in adult mature repertoires, and the autoreactivity may enhance the antiviral function of many antibodies to pathogens. It has been noted that HCDR3 loops in antibodies during early B cell development are often rich in positive charge and exhibit autoreactive patterns (Wardemann et al, Science 301, 1374-1377, 2003). One can test a given antibody for autoreactivity by assessing the level of binding to human origin cells in microscopy (using adherent HeLa or HEp-2 epithelial cells) and flow cytometric cell surface staining (using suspension Jurkat T cells and 293 S human embryonic kidney cells). Autoreactivity also can be surveyed using assessment of binding to tissues in tissue arrays.
  • Human Likeness B cell repertoire deep sequencing of human B cells from blood donors is being performed on a wide scale in many recent studies. Sequence information about a significant portion of the human antibody repertoire facilitates statistical assessment of antibody sequence features common in healthy humans. With knowledge about the antibody sequence features in a human recombined antibody variable gene reference database, the position specific degree of“Human Likeness” (HL) of an antibody sequence can be estimated. HL has been shown to be useful for the development of antibodies in clinical use, like therapeutic antibodies or antibodies as vaccines. The goal is to increase the human likeness of antibodies to reduce potential adverse effects and anti-antibody immune responses that will lead to significantly decreased efficacy of the antibody drug or can induce serious health implications.
  • HL Human Likeness
  • rHL Relative Human Likeness
  • a single chain variable fragment is a fusion of the variable regions of the heavy and light chains of immunoglobulins, linked together with a short (usually serine, glycine) linker.
  • This chimeric molecule retains the specificity of the original immunoglobulin, despite removal of the constant regions and the introduction of a linker peptide. This modification usually leaves the specificity unaltered.
  • These molecules were created historically to facilitate phage display where it is highly convenient to express the antigen binding domain as a single peptide.
  • scFv can be created directly from subcloned heavy and light chains derived from a hybridoma or B cell.
  • Single chain variable fragments lack the constant F c region found in complete antibody molecules, and thus, the common binding sites (e.g., protein A/G) used to purify antibodies. These fragments can often be purified/immobilized using Protein L since Protein L interacts with the variable region of kappa light chains.
  • Flexible linkers generally are comprised of helix- and turn-promoting amino acid residues such as alanine, serine and glycine. However, other residues can function as well.
  • Tang et al. (1996) used phage display as a means of rapidly selecting tailored linkers for single chain antibodies (scFvs) from protein linker libraries.
  • a random linker library was constructed in which the genes for the heavy and light chain variable domains were linked by a segment encoding an 18-amino acid polypeptide of variable composition.
  • the scFv repertoire (approx. 5 x 10 6 different members) was displayed on filamentous phage and subjected to affinity selection with hapten. The population of selected variants exhibited significant increases in binding activity but retained considerable sequence diversity.
  • the recombinant antibodies of the present disclosure may also involve sequences or moieties that permit dimerization or multimerization of the receptors.
  • sequences include those derived from IgA, which permit formation of multimers in conjunction with the J-chain.
  • Another multimerization domain is the Gal4 dimerization domain.
  • the chains may be modified with agents such as biotin/avidin, which permit the combination of two antibodies.
  • a single-chain antibody can be created by joining receptor light and heavy chains using a non-peptide linker or chemical unit.
  • the light and heavy chains will be produced in distinct cells, purified, and subsequently linked together in an appropriate fashion (/. e. , the N-terminus of the heavy chain being attached to the C-terminus of the light chain via an appropriate chemical bridge).
  • Cross-linking reagents are used to form molecular bridges that tie functional groups of two different molecules, e.g., a stabilizing and coagulating agent.
  • a stabilizing and coagulating agent e.g., a stabilizing and coagulating agent.
  • dimers or multimers of the same analog or heteromeric complexes comprised of different analogs can be created.
  • hetero- bifunctional cross-linkers can be used that eliminate unwanted homopolymer formation.
  • An exemplary hetero-bifunctional cross-linker contains two reactive groups: one reacting with primary amine group (e.g., N-hydroxy succinimide) and the other reacting with a thiol group (e.g., pyridyl disulfide, maleimides, halogens, etc.).
  • primary amine group e.g., N-hydroxy succinimide
  • a thiol group e.g., pyridyl disulfide, maleimides, halogens, etc.
  • the cross-linker may react with the lysine residue(s) of one protein (e.g., the selected antibody or fragment) and through the thiol reactive group, the cross-linker, already tied up to the first protein, reacts with the cysteine residue (free sulfhydryl group) of the other protein (e.g., the selective agent).
  • cross-linker having reasonable stability in blood will be employed.
  • Numerous types of disulfide-bond containing linkers are known that can be successfully employed to conjugate targeting and therapeutic/preventative agents. Linkers that contain a disulfide bond that is sterically hindered may prove to give greater stability in vivo, preventing release of the targeting peptide prior to reaching the site of action. These linkers are thus one group of linking agents.
  • Another cross-linking reagent is SMPT, which is a bifunctional cross-linker containing a disulfide bond that is“sterically hindered” by an adjacent benzene ring and methyl groups.
  • steric hindrance of the disulfide bond serves a function of protecting the bond from attack by thiolate anions such as glutathione which can be present in tissues and blood, and thereby help in preventing decoupling of the conjugate prior to the delivery of the attached agent to the target site.
  • the SMPT cross-linking reagent lends the ability to cross-link functional groups such as the SH of cysteine or primary amines (e.g., the epsilon amino group of lysine).
  • Another possible type of cross-linker includes the hetero-bifunctional photoreactive phenylazides containing a cleavable disulfide bond such as sulfosuccinimidyl-2-(p-azido salicylamido) ethyl-l,3'-dithiopropionate.
  • the N-hydroxy- succinimidyl group reacts with primary amino groups and the phenylazide (upon photolysis) reacts non-selectively with any amino acid residue.
  • non-hindered linkers also can be employed in accordance herewith.
  • Other useful cross-linkers include SATA, SPDP and 2-iminothiolane (Wawrzynczak & Thorpe, 1987). The use of such cross-linkers is well understood in the art. Another embodiment involves the use of flexible linkers.
  • U.S. Patent 4,680,338 describes bifunctional linkers useful for producing conjugates of ligands with amine-containing polymers and/or proteins, especially for forming antibody conjugates with chelators, drugs, enzymes, detectable labels and the like.
  • U.S. Patents 5,141,648 and 5,563,250 disclose cleavable conjugates containing a labile bond that is cleavable under a variety of mild conditions. This linker is particularly useful in that the agent of interest may be bonded directly to the linker, with cleavage resulting in release of the active agent. Particular uses include adding a free amino or free sulfhydryl group to a protein, such as an antibody, or a drug.
  • U.S. Patent 5,856,456 provides peptide linkers for use in connecting polypeptide constituents to make fusion proteins, e.g., single chain antibodies.
  • the linker is up to about 50 amino acids in length, contains at least one occurrence of a charged amino acid (preferably arginine or lysine) followed by a proline, and is characterized by greater stability and reduced aggregation.
  • U.S. Patent 5,880,270 discloses aminooxy-containing linkers useful in a variety of immunodiagnostic and separative techniques.
  • antibodies of the present disclosure are bispecific or multispecific.
  • Bispecific antibodies are antibodies that have binding specificities for at least two different epitopes.
  • Exemplary bispecific antibodies may bind to two different epitopes of a single antigen.
  • Other such antibodies may combine a first antigen binding site with a binding site for a second antigen.
  • an anti-pathogen arm may be combined with an arm that binds to a triggering molecule on a leukocyte, such as a T-cell receptor molecule (e.g., CD3), or Fc receptors for IgG (FcyR), such as FcyRI (CD64), FcyRII (CD32) and Fc gamma RIII (CD 16), so as to focus and localize cellular defense mechanisms to the infected cell.
  • a triggering molecule on a leukocyte such as a T-cell receptor molecule (e.g., CD3), or Fc receptors for IgG (FcyR), such as FcyRI (CD64), FcyRII (CD32) and Fc gamma RIII (CD 16), so as to focus and localize cellular defense mechanisms to the infected cell.
  • Bispecific antibodies may also be used to localize cytotoxic agents to infected cells.
  • bispecific antibodies possess a pathogen-binding arm and an arm that binds the cytotoxic agent (e.g., saporin, anti-interferon-a, vinca alkaloid, ricin A chain, methotrexate or radioactive isotope hapten).
  • Bispecific antibodies can be prepared as full-length antibodies or antibody fragments (e.g., F(ab') 2 bispecific antibodies).
  • WO 96/16673 describes a bispecific anti-ErbB2/anti-Fc gamma RIII antibody and U.S. Pat. No. 5,837,234 discloses a bispecific anti-ErbB2/anti-Fc gamma RI antibody.
  • a bispecific anti-ErbB2/Fc alpha antibody is shown in WO98/02463.
  • U.S. Pat. No. 5,821,337 teaches a bispecific anti-ErbB2/anti-CD3 antibody.
  • bispecific antibodies are known in the art. Traditional production of full-length bispecific antibodies is based on the co-expression of two immunoglobulin heavy chain-light chain pairs, where the two chains have different specificities (Millstein et al, Nature, 305:537-539 (1983)). Because of the random assortment of immunoglobulin heavy and light chains, these hybridomas (quadromas) produce a potential mixture of ten different antibody molecules, of which only one has the correct bispecific structure. Purification of the correct molecule, which is usually done by affinity chromatography steps, is rather cumbersome, and the product yields are low. Similar procedures are disclosed in WO 93/08829, and in Traunecker et al, EMBO J., 10:3655-3659 (1991).
  • antibody variable regions with the desired binding specificities are fused to immunoglobulin constant domain sequences.
  • the fusion is with an Ig heavy chain constant domain, comprising at least part of the hinge, Cm, and Cm regions. It is preferred to have the first heavy-chain constant region (Cm) containing the site necessary for light chain bonding, present in at least one of the fusions.
  • DNAs encoding the immunoglobulin heavy chain fusions and, if desired, the immunoglobulin light chain are inserted into separate expression vectors, and are co- transfected into a suitable host cell.
  • the bispecific antibodies are composed of a hybrid immunoglobulin heavy chain with a first binding specificity in one arm, and a hybrid immunoglobulin heavy chain-light chain pair (providing a second binding specificity) in the other arm. It was found that this asymmetric structure facilitates the separation of the desired bispecific compound from unwanted immunoglobulin chain combinations, as the presence of an immunoglobulin light chain in only one half of the bispecific molecule provides for a facile way of separation. This approach is disclosed in WO 94/04690. For further details of generating bispecific antibodies see, for example, Suresh etal., Methods in Enzymology, 121 :210 (1986).
  • the interface between a pair of antibody molecules can be engineered to maximize the percentage of heterodimers that are recovered from recombinant cell culture.
  • the preferred interface comprises at least a part of the Cro domain.
  • one or more small amino acid side chains from the interface of the first antibody molecule are replaced with larger side chains (e.g., tyrosine or tryptophan).
  • Compensatory "cavities" of identical or similar size to the large side chain(s) are created on the interface of the second antibody molecule by replacing large amino acid side chains with smaller ones (e.g., alanine or threonine). This provides a mechanism for increasing the yield of the heterodimer over other unwanted end-products such as homodimers.
  • Bispecific antibodies include cross-linked or "heteroconjugate" antibodies.
  • one of the antibodies in the heteroconjugate can be coupled to avidin, the other to biotin.
  • Such antibodies have, for example, been proposed to target immune system cells to unwanted cells (U.S. Pat. No. 4,676,980), and for treatment of HIV infection (WO 91/00360, WO 92/200373, and EP 03089).
  • Heteroconjugate antibodies may be made using any convenient cross-linking methods. Suitable cross-linking agents are well known in the art, and are disclosed in U.S. Pat. No. 4,676,980, along with a number of cross-linking techniques.
  • bispecific antibodies can be prepared using chemical linkage.
  • Brennan et al., Science, 229: 81 (1985) describe a procedure wherein intact antibodies are proteolytically cleaved to generate F(ab')2 fragments. These fragments are reduced in the presence of the dithiol complexing agent, sodium arsenite, to stabilize vicinal dithiols and prevent intermolecular disulfide formation.
  • the Fab' fragments generated are then converted to thionitrobenzoate (TNB) derivatives.
  • One of the Fab'-TNB derivatives is then reconverted to the Fab'-thiol by reduction with mercaptoethylamine and is mixed with an equimolar amount of the other Fab'-TNB derivative to form the bispecific antibody.
  • the bispecific antibodies produced can be used as agents for the selective immobilization of enzymes.
  • bispecific antibodies have been produced using leucine zippers (Kostelny et al. , J. Immunol., 148(5): 1547-1553, 1992).
  • the leucine zipper peptides from the Fos and Jun proteins were linked to the Fab' portions of two different antibodies by gene fusion.
  • the antibody homodimers were reduced at the hinge region to form monomers and then re-oxidized to form the antibody heterodimers.
  • This method can also be utilized for the production of antibody homodimers.
  • the "diabody” technology described by Hollinger et al. , Proc. Natl. Acad. Sci. USA, 90:6444-6448 (1993) has provided an alternative mechanism for making bispecific antibody fragments.
  • the fragments comprise a VH connected to a VL by a linker that is too short to allow pairing between the two domains on the same chain. Accordingly, the VH and VL domains of one fragment are forced to pair with the complementary VL and VH domains of another fragment, thereby forming two antigen-binding sites.
  • Another strategy for making bispecific antibody fragments by the use of single-chain Fv (sFv) dimers has also been reported. See Gruber et al, J. Immunol., 152:5368 (1994).
  • a bispecific or multispecific antibody may be formed as a DOCK-AND-LOCKTM (DNLTM) complex
  • DOCK-AND-LOCKTM DOCK-AND-LOCKTM
  • DDD dimerization and docking domain
  • R regulatory
  • AD anchor domain
  • the DDD and AD peptides may be attached to any protein, peptide or other molecule. Because the DDD sequences spontaneously dimerize and bind to the AD sequence, the technique allows the formation of complexes between any selected molecules that may be attached to DDD or AD sequences.
  • Antibodies with more than two valencies are contemplated.
  • trispecific antibodies can be prepared (Tutt et al, J. Immunol. 147: 60, 1991; Xu et al, Science, 358(6359):85-90, 2017).
  • a multivalent antibody may be internalized (and/or catabolized) faster than a bivalent antibody by a cell expressing an antigen to which the antibodies bind.
  • the antibodies of the present disclosure can be multivalent antibodies with three or more antigen binding sites (e.g., tetravalent antibodies), which can be readily produced by recombinant expression of nucleic acid encoding the polypeptide chains of the antibody.
  • the multivalent antibody can comprise a dimerization domain and three or more antigen binding sites.
  • the preferred dimerization domain comprises (or consists of) an Fc region or a hinge region.
  • the antibody will comprise an Fc region and three or more antigen binding sites amino-terminal to the Fc region.
  • the preferred multivalent antibody herein comprises (or consists of) three to about eight, but preferably four, antigen binding sites.
  • the multivalent antibody comprises at least one polypeptide chain (and preferably two polypeptide chains), wherein the polypeptide chain(s) comprise two or more variable regions.
  • the polypeptide chain(s) may comprise VDl-(Xl).sub.n-VD2-(X2) n -Fc, wherein VD1 is a first variable region, VD2 is a second variable region, Fc is one polypeptide chain of an Fc region, XI and X2 represent an amino acid or polypeptide, and n is 0 or 1.
  • the polypeptide chain(s) may comprise: VH-CH1 -flexible linker-VH-CHl-Fc region chain; or VH-CH1-VH- CHl-Fc region chain.
  • the multivalent antibody herein preferably further comprises at least two (and preferably four) light chain variable region polypeptides.
  • the multivalent antibody herein may, for instance, comprise from about two to about eight light chain variable region polypeptides.
  • the light chain variable region polypeptides contemplated here comprise a light chain variable region and, optionally, further comprise a CL domain.
  • Charge modifications are particularly useful in the context of a multispecific antibody, where amino acid substitutions in Fab molecules result in reducing the mispairing of light chains with non-matching heavy chains (Bence-Jones-type side products), which can occur in the production of Fab-based bi-/multispecific antigen binding molecules with a VH/VL exchange in one (or more, in case of molecules comprising more than two antigen-binding Fab molecules) of their binding arms (see also PCT publication no. WO 2015/150447, particularly the examples therein, incorporated herein by reference in its entirety).
  • an antibody comprised in the therapeutic agent comprises
  • the first antigen is an activating T cell antigen and the second antigen is a target cell antigen, or the first antigen is a target cell antigen and the second antigen is an activating T cell antigen;
  • the amino acid at position 124 is substituted by a positively charged amino acid (numbering according to Kabat), and wherein in the constant domain CH1 of the first Fab molecule under a) the amino acid at position 147 or the amino acid at position 213 is substituted by a negatively charged amino acid (numbering according to Kabat EU index); or ii) in the constant domain CL of the second Fab molecule under b) the amino acid at position 124 is substituted by a positively charged amino acid (numbering according to Kabat), and wherein in the constant domain CH1 of the second Fab molecule under b) the amino acid at position 147 or the amino acid at position 213 is substituted by a negatively charged amino acid (numbering according to Kabat EU index).
  • the antibody may not comprise both modifications mentioned under i) and ii).
  • the constant domains CL and CH1 of the second Fab molecule are not replaced by each other (i.e., remain unexchanged).
  • the amino acid at position 124 is substituted independently by lysine (K), arginine (R) or histidine (H) (numbering according to Rabat) (in one preferred embodiment independently by lysine (K) or arginine (R)), and in the constant domain CH1 of the first Fab molecule under a) the amino acid at position 147 or the amino acid at position 213 is substituted independently by glutamic acid (E), or aspartic acid (D) (numbering according to Rabat EU index).
  • the amino acid at position 124 is substituted independently by lysine (R), arginine (R) or histidine (H) (numbering according to Rabat), and in the constant domain CH1 of the first Fab molecule under a) the amino acid at position 147 is substituted independently by glutamic acid (E), or aspartic acid (D) (numbering according to Rabat EU index).
  • the amino acid at position 124 is substituted independently by lysine (R), arginine (R) or histidine (H) (numbering according to Rabat) (in one preferred embodiment independently by lysine (R) or arginine (R)) and the amino acid at position 123 is substituted independently by lysine (R), arginine (R) or histidine (H) (numbering according to Rabat) (in one preferred embodiment independently by lysine (R) or arginine (R)), and in the constant domain CH1 of the first Fab molecule under a) the amino acid at position 147 is substituted independently by glutamic acid (E), or aspartic acid (D) (numbering according to Rabat EU index) and the amino acid at position 213 is substituted independently by glutamic acid (E), or aspartic acid (D) (numbering according to Rabat EU index).
  • the amino acid at position 124 is substituted by lysine (R) (numbering according to Rabat) and the amino acid at position 123 is substituted by lysine (R) or arginine (R) (numbering according to Rabat), and in the constant domain CH1 of the first Fab molecule under a) the amino acid at position 147 is substituted by glutamic acid (E) (numbering according to Rabat EU index) and the amino acid at position 213 is substituted by glutamic acid (E) (numbering according to Rabat EU index).
  • the amino acid at position 124 is substituted by lysine (R) (numbering according to Rabat) and the amino acid at position 123 is substituted by arginine (R) (numbering according to Rabat), and in the constant domain CH1 of the first Fab molecule under a) the amino acid at position 147 is substituted by glutamic acid (E) (numbering according to Rabat EU index) and the amino acid at position 213 is substituted by glutamic acid (E) (numbering according to Rabat EU index).
  • T cell receptors also known as chimeric T cell receptors, chimeric immunoreceptors, chimeric antigen receptors (CARs)
  • CARs chimeric antigen receptors
  • these receptors are used to graft the specificity of a monoclonal antibody onto a T cell, with transfer of their coding sequence facilitated by retroviral vectors. In this way, a large number of target-specific T cells can be generated for adoptive cell transfer. Phase I clinical studies of this approach show efficacy.
  • scFv single-chain variable fragments
  • CD3-zeta transmembrane and endodomain Such molecules result in the transmission of a zeta signal in response to recognition by the scFv of its target.
  • An example of such a construct is l4g2a-Zeta, which is a fusion of a scFv derived from hybridoma l4g2a (which recognizes disialoganglioside GD2).
  • T cells express this molecule (usually achieved by oncoretroviral vector transduction), they recognize and kill target cells that express GD2 (e.g., neuroblastoma cells).
  • GD2 e.g., neuroblastoma cells
  • variable portions of an immunoglobulin heavy and light chain are fused by a flexible linker to form a scFv.
  • This scFv is preceded by a signal peptide to direct the nascent protein to the endoplasmic reticulum and subsequent surface expression (this is cleaved).
  • a flexible spacer allows to the scFv to orient in different directions to enable antigen binding.
  • the transmembrane domain is a typical hydrophobic alpha helix usually derived from the original molecule of the signaling endodomain which protrudes into the cell and transmits the desired signal.
  • Type I proteins are in fact two protein domains linked by a transmembrane alpha helix in between.
  • Ectodomain A signal peptide directs the nascent protein into the endoplasmic reticulum. This is essential if the receptor is to be glycosylated and anchored in the cell membrane. Any eukaryotic signal peptide sequence usually works fine. Generally, the signal peptide natively attached to the amino-terminal most component is used (e.g., in a scFv with orientation light chain - linker - heavy chain, the native signal of the light-chain is used
  • the antigen recognition domain is usually an scFv.
  • An antigen recognition domain from native T-cell receptor (TCR) alpha and beta single chains have been described, as have simple ectodomains (e.g., CD4 ectodomain to recognize HIV infected cells) and more exotic recognition components such as a linked cytokine (which leads to recognition of cells bearing the cytokine receptor).
  • TCR T-cell receptor
  • ectodomains e.g., CD4 ectodomain to recognize HIV infected cells
  • a linked cytokine which leads to recognition of cells bearing the cytokine receptor
  • a spacer region links the antigen binding domain to the transmembrane domain. It should be flexible enough to allow the antigen binding domain to orient in different directions to facilitate antigen recognition.
  • the simplest form is the hinge region from IgGl . Alternatives include the CH2CH3 region of immunoglobulin and portions of CD3. For most scFv based constructs, the IgGl hinge suffices. However, the best spacer often has to be determined empirically.
  • the transmembrane domain is a hydrophobic alpha helix that spans the membrane. Generally, the transmembrane domain from the most membrane proximal component of the endodomain is used. Interestingly, using the CD3-zeta transmembrane domain may result in incorporation of the artificial TCR into the native TCR a factor that is dependent on the presence of the native CD3-zeta transmembrane charged aspartic acid residue. Different transmembrane domains result in different receptor stability. The CD28 transmembrane domain results in a brightly expressed, stable receptor.
  • Endodomain This is the "business-end” of the receptor. After antigen recognition, receptors cluster and a signal is transmitted to the cell.
  • the most commonly used endodomain component is CD3-zeta which contains 3 ITAMs. This transmits an activation signal to the T cell after antigen is bound. CD3-zeta may not provide a fully competent activation signal and additional co-stimulatory signaling is needed.
  • First-generation CARs typically had the intracellular domain from the CD3 x- chain, which is the primary transmitter of signals from endogenous TCRs.
  • “Second-generation” CARs add intracellular signaling domains from various costimulatory protein receptors (e.g., CD28, 41BB, ICOS) to the cytoplasmic tail of the CAR to provide additional signals to the T cell.
  • costimulatory protein receptors e.g., CD28, 41BB, ICOS
  • Preclinical studies have indicated that the second generation of CAR designs improves the antitumor activity of T cells.
  • “third-generation” CARs combine multiple signaling domains, such as CD3z-CD28-4lBB or CD3z-CD28-OX40, to further augment potency.
  • Antibody Drug Conjugates or ADCs are a new class of highly potent biopharmaceutical drugs designed as a targeted therapy for the treatment of people with infectious disease.
  • ADCs are complex molecules composed of an antibody (a whole mAh or an antibody fragment such as a single-chain variable fragment, or scFv) linked, via a stable chemical linker with labile bonds, to a biological active cytotoxic/anti-viral payload or drug.
  • Antibody Drug Conjugates are examples of bioconjugates and immunoconjugates.
  • antibody-drug conjugates allow sensitive discrimination between healthy and diseased tissue. This means that, in contrast to traditional systemic approaches, antibody-drug conjugates target and attack the infected cell so that healthy cells are less severely affected.
  • an anti cancer drug e.g., a cell toxin or cytotoxin
  • an antibody that specifically targets a certain cell marker (e.g., a protein that, ideally, is only to be found in or on infected cells).
  • a certain cell marker e.g., a protein that, ideally, is only to be found in or on infected cells.
  • Antibodies track these proteins down in the body and attach themselves to the surface of cancer cells.
  • the biochemical reaction between the antibody and the target protein (antigen) triggers a signal in the tumor cell, which then absorbs or internalizes the antibody together with the cytotoxin.
  • the cytotoxic drug is released and kills the cell or impairs viral replication. Due to this targeting, ideally the drug has lower side effects and gives a wider therapeutic window than other agents.
  • a stable link between the antibody and cytotoxic/anti-viral agent is a crucial aspect of an ADC.
  • Linkers are based on chemical motifs including disulfides, hydrazones or peptides (cleavable), or thioethers (noncleavable) and control the distribution and delivery of the cytotoxic agent to the target cell. Cleavable and noncleavable types of linkers have been proven to be safe in preclinical and clinical trials.
  • Brentuximab vedotin includes an enzyme-sensitive cleavable linker that delivers the potent and highly toxic antimicrotubule agent Monomethyl auristatin E or MMAE, a synthetic antineoplastic agent, to human specific CD30-positive malignant cells.
  • MMAE which inhibits cell division by blocking the polymerization of tubulin, cannot be used as a single-agent chemotherapeutic drug.
  • cAClO a cell membrane protein of the tumor necrosis factor or TNF receptor
  • Trastuzumab emtansine is a combination of the microtubule-formation inhibitor mertansine (DM- 1), a derivative of the Maytansine, and antibody trastuzumab (Herceptin®/Genentech/Roche) atached by a stable, non-cleavable linker.
  • DM-1 microtubule-formation inhibitor mertansine
  • Herceptin®/Genentech/Roche antibody trastuzumab
  • the availability of better and more stable linkers has changed the function of the chemical bond.
  • the type of linker, cleavable or noncleavable lends specific properties to the cytotoxic (anti-cancer) drug. For example, a non-cleavable linker keeps the drug within the cell.
  • cleavable linker Another type of cleavable linker, currently in development, adds an extra molecule between the cytotoxic/anti-viral drug and the cleavage site. This linker technology allows researchers to create ADCs with more flexibility without worrying about changing cleavage kinetics. researchers are also developing a new method of peptide cleavage based on Edman degradation, a method of sequencing amino acids in a peptide. Future direction in the development of ADCs also include the development of site-specific conjugation (TDCs) to further improve stability and therapeutic index and a emiting immunoconjugates and antibody-conjugated nanoparticles.
  • TDCs site-specific conjugation
  • Bi-specific T-cell engagers are a class of artificial bispecific monoclonal antibodies that are investigated for the use as anti-cancer drugs. They direct a host's immune system, more specifically the T cells' cytotoxic activity, against infected cells. BiTE is a registered trademark of Micromet AG.
  • BiTEs are fusion proteins consisting of two single-chain variable fragments (scFvs) of different antibodies, or amino acid sequences from four different genes, on a single peptide chain of about 55 kilodaltons.
  • scFvs single-chain variable fragments
  • One of the scFvs binds to T cells via the CD3 receptor, and the other to an infected cell via a specific molecule.
  • BiTEs form a link between T cells and target cells. This causes T cells to exert cytotoxic/anti-viral activity on infected cells by producing proteins like perforin and granzymes, independently of the presence of MHC I or co-stimulatory molecules. These proteins enter infected cells and initiate the cell's apoptosis. This action mimics physiological processes observed during T cell attacks against infected cells.
  • the antibody is a recombinant antibody that is suitable for action inside of a cell - such antibodies are known as“intrabodies.” These antibodies may interfere with target function by a variety of mechanism, such as by altering intracellular protein trafficking, interfering with enzymatic function, and blocking protein-protein or protein-DNA interactions. In many ways, their structures mimic or parallel those of single chain and single domain antibodies, discussed above. Indeed, single-transcript/single-chain is an important feature that permits intracellular expression in a target cell, and also makes protein transit across cell membranes more feasible. However, additional features are required.
  • the two major issues impacting the implementation of intrabody therapeutic are delivery, including cell/tissue targeting, and stability.
  • delivery a variety of approaches have been employed, such as tissue-directed delivery, use of cell-type specific promoters, viral-based delivery and use of cell-permeability/membrane translocating peptides.
  • the approach is generally to either screen by brute force, including methods that involve phage display and may include sequence maturation or development of consensus sequences, or more directed modifications such as insertion stabilizing sequences (e.g., Fc regions, chaperone protein sequences, leucine zippers) and disulfide replacement/modification.
  • insertion stabilizing sequences e.g., Fc regions, chaperone protein sequences, leucine zippers
  • intrabodies may require is a signal for intracellular targeting.
  • Vectors that can target intrabodies (or other proteins) to subcellular regions such as the cytoplasm, nucleus, mitochondria and ER have been designed and are commercially available (Invitrogen Corp.; Persic et al, 1997).
  • intrabodies By virtue of their ability to enter cells, intrabodies have additional uses that other types of antibodies may not achieve.
  • the ability to interact with the MUC1 cytoplasmic domain in a living cell may interfere with functions associated with the MUC1 CD, such as signaling functions (binding to other molecules) or oligomer formation.
  • functions associated with the MUC1 CD such as signaling functions (binding to other molecules) or oligomer formation.
  • such antibodies can be used to inhibit MUC1 dimer formation.
  • the antibodies of the present disclosure may be purified.
  • the term“purified,” as used herein, is intended to refer to a composition, isolatable from other components, wherein the protein is purified to any degree relative to its naturally-obtainable state.
  • a purified protein therefore also refers to a protein, free from the environment in which it may naturally occur.
  • this designation will refer to a composition in which the protein or peptide forms the major component of the composition, such as constituting about 50%, about 60%, about 70%, about 80%, about 90%, about 95% or more of the proteins in the composition.
  • Protein purification techniques are well known to those of skill in the art. These techniques involve, at one level, the crude fractionation of the cellular milieu to polypeptide and non-polypeptide fractions. Having separated the polypeptide from other proteins, the polypeptide of interest may be further purified using chromatographic and electrophoretic techniques to achieve partial or complete purification (or purification to homogeneity). Analytical methods particularly suited to the preparation of a pure peptide are ion-exchange chromatography, exclusion chromatography; polyacrylamide gel electrophoresis; isoelectric focusing.
  • protein purification include, precipitation with ammonium sulfate, PEG, antibodies and the like or by heat denaturation, followed by centrifugation; gel filtration, reverse phase, hydroxylapatite and affinity chromatography; and combinations of such and other techniques.
  • polypeptide In purifying an antibody of the present disclosure, it may be desirable to express the polypeptide in a prokaryotic or eukaryotic expression system and extract the protein using denaturing conditions.
  • the polypeptide may be purified from other cellular components using an affinity column, which binds to a tagged portion of the polypeptide.
  • affinity column which binds to a tagged portion of the polypeptide.
  • antibodies are fractionated utilizing agents (i.e.. protein A) that bind the Fc portion of the antibody.
  • agents i.e.. protein A
  • antigens may be used to simultaneously purify and select appropriate antibodies.
  • Such methods often utilize the selection agent bound to a support, such as a column, filter or bead.
  • the antibodies are bound to a support, contaminants removed (e.g., washed away), and the antibodies released by applying conditions (salt, heat, etc.).
  • compositions comprising anti-Zika virus antibodies and antigens for generating the same.
  • Such compositions comprise a prophylactically or therapeutically effective amount of an antibody or a fragment thereof, or a peptide immunogen, and a pharmaceutically acceptable carrier.
  • pharmaceutically acceptable means approved by a regulatory agency of the Federal or a state government or listed in the U.S. Pharmacopeia or other generally recognized pharmacopeia for use in animals, and more particularly in humans.
  • carrier refers to a diluent, excipient, or vehicle with which the therapeutic is administered.
  • Such pharmaceutical carriers can be sterile liquids, such as water and oils, including those of petroleum, animal, vegetable or synthetic origin, such as peanut oil, soybean oil, mineral oil, sesame oil and the like. Water is a particular carrier when the pharmaceutical composition is administered intravenously. Saline solutions and aqueous dextrose and glycerol solutions can also be employed as liquid carriers, particularly for injectable solutions.
  • suitable pharmaceutical excipients include starch, glucose, lactose, sucrose, gelatin, malt, rice, flour, chalk, silica gel, sodium stearate, glycerol monostearate, talc, sodium chloride, dried skim milk, glycerol, propylene, glycol, water, ethanol and the like.
  • compositions can also contain minor amounts of wetting or emulsifying agents, or pH buffering agents.
  • These compositions can take the form of solutions, suspensions, emulsion, tablets, pills, capsules, powders, sustained-release formulations and the like.
  • Oral formulations can include standard carriers such as pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharine, cellulose, magnesium carbonate, etc. Examples of suitable pharmaceutical agents are described in“Remington's Pharmaceutical Sciences.” Such compositions will contain a prophylactically or therapeutically effective amount of the antibody or fragment thereof, preferably in purified form, together with a suitable amount of carrier so as to provide the form for proper administration to the patient.
  • the formulation should suit the mode of administration, which can be oral, intravenous, intraarterial, intrabuccal, intranasal, nebulized, bronchial inhalation, intra-rectal, vaginal, topical or delivered by mechanical ventilation.
  • Active vaccines are also envisioned where antibodies like those disclosed are produced in vivo in a subject at risk of Zika virus infection.
  • Such vaccines can be formulated for parenteral administration, e.g., formulated for injection via the intradermal, intravenous, intramuscular, subcutaneous, or even intraperitoneal routes. Administration by intradermal and intramuscular routes are contemplated.
  • the vaccine could alternatively be administered by a topical route directly to the mucosa, for example by nasal drops, inhalation, by nebulizer, or via intrarectal or vaginal delivery.
  • Pharmaceutically-acceptable salts include the acid salts and those which are formed with inorganic acids such as, for example, hydrochloric or phosphoric acids, or such organic acids as acetic, oxalic, tartaric, mandelic, and the like. Salts formed with the free carboxyl groups may also be derived from inorganic bases such as, for example, sodium, potassium, ammonium, calcium, or ferric hydroxides, and such organic bases as isopropylamine, trimethylamine, 2-ethylamino ethanol, histidine, procaine, and the like.
  • inorganic acids such as, for example, hydrochloric or phosphoric acids, or such organic acids as acetic, oxalic, tartaric, mandelic, and the like.
  • Salts formed with the free carboxyl groups may also be derived from inorganic bases such as, for example, sodium, potassium, ammonium, calcium, or ferric hydroxides, and such organic bases as isopropylamine, trimethyl
  • Passive transfer of antibodies generally will involve the use of intravenous or intramuscular injections.
  • the forms of antibody can be human or animal blood plasma or serum, as pooled human immunoglobulin for intravenous (IVIG) or intramuscular (IG) use, as high-titer human IVIG or IG from immunized or from donors recovering from disease, and as monoclonal antibodies (MAb).
  • IVIG intravenous
  • IG intramuscular
  • MAb monoclonal antibodies
  • Such immunity generally lasts for only a short period of time, and there is also a potential risk for hypersensitivity reactions, and serum sickness, especially from gamma globulin of non-human origin.
  • passive immunity provides immediate protection.
  • the antibodies will be formulated in a carrier suitable for injection, /. e.. sterile and syringeable.
  • compositions of the disclosure are supplied either separately or mixed together in unit dosage form, for example, as a dry lyophilized powder or water-free concentrate in a hermetically sealed container such as an ampoule or sachette indicating the quantity of active agent.
  • a hermetically sealed container such as an ampoule or sachette indicating the quantity of active agent.
  • the composition is to be administered by infusion, it can be dispensed with an infusion bottle containing sterile pharmaceutical grade water or saline.
  • an ampoule of sterile water for injection or saline can be provided so that the ingredients may be mixed prior to administration.
  • compositions of the disclosure can be formulated as neutral or salt forms.
  • Pharmaceutically acceptable salts include those formed with anions such as those derived from hydrochloric, phosphoric, acetic, oxalic, tartaric acids, etc., and those formed with cations such as those derived from sodium, potassium, ammonium, calcium, ferric hydroxides, isopropylamine, triethylamine, 2-ethylamino ethanol, histidine, procaine, etc.
  • Antibody-dependent cell-mediated cytotoxicity is an immune mechanism leading to the lysis of antibody-coated target cells by immune effector cells.
  • the target cells are cells to which antibodies or fragments thereof comprising an Fc region specifically bind, generally via the protein part that is N-terminal to the Fc region.
  • antibody having increased/reduced antibody dependent cell-mediated cytotoxicity is meant an antibody having increased/reduced ADCC as determined by any suitable method known to those of ordinary skill in the art.
  • the term “increased/reduced ADCC” is defined as either an increase/reduction in the number of target cells that are lysed in a given time, at a given concentration of antibody in the medium surrounding the target cells, by the mechanism of ADCC defined above, and/or a reduction/increase in the concentration of antibody, in the medium surrounding the target cells, required to achieve the lysis of a given number of target cells in a given time, by the mechanism of ADCC.
  • the increase/reduction in ADCC is relative to the ADCC mediated by the same antibody produced by the same type of host cells, using the same standard production, purification, formulation and storage methods (which are known to those skilled in the art), but that has not been engineered.
  • the increase in ADCC mediated by an antibody produced by host cells engineered to have an altered pattern of glycosylation is relative to the ADCC mediated by the same antibody produced by the same type of non-engineered host cells.
  • CDC Complement-dependent cytotoxicity
  • MAC membrane attack complexes
  • Antibodies of the present disclosure may be linked to at least one agent to form an antibody conjugate.
  • it is conventional to link or covalently bind or complex at least one desired molecule or moiety.
  • a molecule or moiety may be, but is not limited to, at least one effector or reporter molecule.
  • Effector molecules comprise molecules having a desired activity, e.g. , cytotoxic activity.
  • Non-limiting examples of effector molecules which have been attached to antibodies include toxins, anti-tumor agents, therapeutic enzymes, radionuclides, antiviral agents, chelating agents, cytokines, growth factors, and oligo- or polynucleotides.
  • reporter molecule is defined as any moiety which may be detected using an assay.
  • reporter molecules which have been conjugated to antibodies include enzymes, radiolabels, haptens, fluorescent labels, phosphorescent molecules, chemiluminescent molecules, chromophores, photoaffmity molecules, colored particles or ligands, such as biotin.
  • Antibody conjugates are generally preferred for use as diagnostic agents.
  • Antibody diagnostics generally fall within two classes, those for use in in vitro diagnostics, such as in a variety of immunoassays, and those for use in vivo diagnostic protocols, generally known as "antibody-directed imaging.”
  • Many appropriate imaging agents are known in the art, as are methods for their attachment to antibodies (see, for e.g. , U.S. Patents 5,021,236, 4,938,948, and 4,472,509).
  • the imaging moieties used can be paramagnetic ions, radioactive isotopes, fluorochromes, NMR-detectable substances, and X-ray imaging agents.
  • paramagnetic ions such as chromium (III), manganese (II), iron (III), iron (II), cobalt (II), nickel (II), copper (II), neodymium (III), samarium (III), ytterbium (III), gadolinium (III), vanadium (II), terbium (III), dysprosium (III), holmium (III) and/or erbium (III), with gadolinium being particularly preferred.
  • Ions useful in other contexts, such as X-ray imaging include but are not limited to lanthanum (III), gold (III), lead (II), and especially bismuth (III).
  • radioactive isotopes for therapeutic and/or diagnostic application, one might mention astatine 211 , 14 carbon, 51 chromium, 36 chlorine, 57 cobalt, 58 cobalt, copper 67 , 152 Eu, gallium 67 , 3 hydrogen, iodine 123 , iodine 125 , iodine 131 , indium 111 , 59 iron, 32 phosphorus, rhenium 186 , rhenium 188 , 75 selenium, 35 sulphur, technicium 99 " 1 and/or yttrium 90 .
  • Radioactively labeled monoclonal antibodies of the present disclosure may be produced according to well-known methods in the art. For instance, monoclonal antibodies can be iodinated by contact with sodium and/or potassium iodide and a chemical oxidizing agent such as sodium hypochlorite, or an enzymatic oxidizing agent, such as lactoperoxidase.
  • Monoclonal antibodies according to the disclosure may be labeled with technetium 99 " 1 by ligand exchange process, for example, by reducing pertechnate with stannous solution, chelating the reduced technetium onto a Sephadex column and applying the antibody to this column.
  • direct labeling techniques may be used, e.g. , by incubating pertechnate, a reducing agent such as SNCh. a buffer solution such as sodium-potassium phthalate solution, and the antibody.
  • Intermediary functional groups which are often used to bind radioisotopes which exist as metallic ions to antibody are diethylenetriaminepentaacetic acid (DTP A) or ethylene diaminetetracetic acid (EDTA).
  • DTP A diethylenetriaminepentaacetic acid
  • EDTA ethylene diaminetetracetic acid
  • fluorescent labels contemplated for use as conjugates include Alexa 350, Alexa 430, AMCA, BODIPY 630/650, BODIPY 650/665, BODIPY-FL, BODIPY-R6G, BODIPY-TMR, BODIPY-TRX, Cascade Blue, Cy3, Cy5,6-FAM, Fluorescein Isothiocyanate, HEX, 6-JOE, Oregon Green 488, Oregon Green 500, Oregon Green 514, Pacific Blue, REG, Rhodamine Green, Rhodamine Red, Renographin, ROX, TAMRA, TET, Tetramethylrhodamine, and/or Texas Red.
  • antibodies contemplated in the present disclosure are those intended primarily for use in vitro, where the antibody is linked to a secondary binding ligand and/or to an enzyme (an enzyme tag) that will generate a colored product upon contact with a chromogenic substrate.
  • suitable enzymes include urease, alkaline phosphatase, (horseradish) hydrogen peroxidase or glucose oxidase.
  • Preferred secondary binding ligands are biotin and avidin and streptavidin compounds. The use of such labels is well known to those of skill in the art and are described, for example, in U.S. Patents 3,817,837, 3,850,752, 3,939,350, 3,996,345, 4,277,437, 4,275,149 and 4,366,241.
  • hapten-based affinity labels react with amino acids in the antigen binding site, thereby destroying this site and blocking specific antigen reaction.
  • this may not be advantageous since it results in loss of antigen binding by the antibody conjugate.
  • Molecules containing azido groups may also be used to form covalent bonds to proteins through reactive nitrene intermediates that are generated by low intensity ultraviolet light (Potter and Haley, 1983).
  • 2- and 8-azido analogues of purine nucleotides have been used as site-directed photoprobes to identify nucleotide binding proteins in crude cell extracts (Owens & Haley, 1987; Atherton et al, 1985).
  • the 2- and 8-azido nucleotides have also been used to map nucleotide binding domains of purified proteins (Khatoon et al, 1989; King et al, 1989; Dholakia et al, 1989) and may be used as antibody binding agents.
  • Some attachment methods involve the use of a metal chelate complex employing, for example, an organic chelating agent such as a diethylenetriaminepentaacetic acid anhydride (DTP A); ethylenetriaminetetraacetic acid; N-chloro-p-toluenesulfonamide; and/or tetrachloro-3a-6a-diphenylglycouril-3 attached to the antibody (U.S. Patents 4,472,509 and 4,938,948).
  • DTP A diethylenetriaminepentaacetic acid anhydride
  • ethylenetriaminetetraacetic acid N-chloro-p-toluenesulfonamide
  • tetrachloro-3a-6a-diphenylglycouril-3 attached to the antibody
  • Monoclonal antibodies may also be reacted with an enzyme in the presence of a coupling agent such as glutaraldehyde or periodate.
  • Conjugates with fluorescein markers are prepared in the presence of these coupling agents or by reaction with an isothiocyanate.
  • imaging of breast tumors is achieved using monoclonal antibodies and the detectable imaging moieties are bound to the antibody using linkers such as methyl-p- hydroxybenzimidate or N-succinimidyl-3-(4-hydroxyphenyl)propionate.
  • derivatization of immunoglobulins by selectively introducing sulfhydryl groups in the Fc region of an immunoglobulin, using reaction conditions that do not alter the antibody combining site are contemplated.
  • Antibody conjugates produced according to this methodology are disclosed to exhibit improved longevity, specificity and sensitivity (U.S. Patent 5,196,066, incorporated herein by reference).
  • Site-specific attachment of effector or reporter molecules, wherein the reporter or effector molecule is conjugated to a carbohydrate residue in the Fc region have also been disclosed in the literature (O’Shannessy et al, 1987). This approach has been reported to produce diagnostically and therapeutically promising antibodies which are currently in clinical evaluation.
  • the present disclosure concerns immunodetection methods for binding, purifying, removing, quantifying and otherwise generally detecting Zika virus and its associated antigens. While such methods can be applied in a traditional sense, another use will be in quality control and monitoring of vaccine and other virus stocks, where antibodies according to the present disclosure can be used to assess the amount or integrity (/. e. , long term stability) of antigens in viruses. Alternatively, the methods may be used to screen various antibodies for appropriate/desired reactivity profiles.
  • immunodetection methods include specific assays for determining the presence of Zika virus in a subject.
  • a wide variety of assay formats are contemplated, but specifically those that would be used to detect Zika virus in a fluid obtained from a subject, such as saliva, blood, plasma, sputum, semen or urine.
  • semen has been demonstrated as a viable sample for detecting Zika virus (Purpura et al. , 2016; Mansuy et al., 2016; Barzon et al., 2016; Gomet etal., 2016; Duffy etal. , 2009; CDC, 2016; Halfon etal., 2010; Elder etal. 2005).
  • the assays may be advantageously formatted for non-healthcare (home) use, including lateral flow assays (see below) analogous to home pregnancy tests.
  • These assays may be packaged in the form of a kit with appropriate reagents and instructions to permit use by the subject of a family member.
  • Some immunodetection methods include enzyme linked immunosorbent assay (ELISA), radioimmunoassay (RIA), immunoradiometric assay, fluoroimmunoassay, chemiluminescent assay, bioluminescent assay, and Western blot to mention a few.
  • ELISA enzyme linked immunosorbent assay
  • RIA radioimmunoassay
  • immunoradiometric assay fluoroimmunoassay
  • fluoroimmunoassay chemiluminescent assay
  • bioluminescent assay bioluminescent assay
  • Western blot to mention a few.
  • a competitive assay for the detection and quantitation of Zika virus antibodies directed to specific parasite epitopes in samples also is provided.
  • the steps of various useful immunodetection methods have been described in the scientific literature, such as, e.g., Doolittle and Ben-Zeev (1999), Gulbis and Galand (1993), De Jager e
  • These methods include methods for purifying Zika virus or related antigens from a sample.
  • the antibody will preferably be linked to a solid support, such as in the form of a column matrix, and the sample suspected of containing the Zika virus or antigenic component will be applied to the immobilized antibody. The unwanted components will be washed from the column, leaving the Zika virus antigen immunocomplexed to the immobilized antibody, which is then collected by removing the organism or antigen from the column.
  • the immunobinding methods also include methods for detecting and quantifying the amount of Zika virus or related components in a sample and the detection and quantification of any immune complexes formed during the binding process.
  • a sample suspected of containing Zika virus or its antigens and contact the sample with an antibody that binds Zika virus or components thereof, followed by detecting and quantifying the amount of immune complexes formed under the specific conditions.
  • the biological sample analyzed may be any sample that is suspected of containing Zika virus or Zika virus antigen, such as a tissue section or specimen, a homogenized tissue extract, a biological fluid, including blood and serum, or a secretion, such as feces or urine.
  • the chosen biological sample with the antibody under effective conditions and for a period of time sufficient to allow the formation of immune complexes is generally a matter of simply adding the antibody composition to the sample and incubating the mixture for a period of time long enough for the antibodies to form immune complexes with, i.e., to bind to Zika virus or antigens present.
  • the sample-antibody composition such as a tissue section, ELISA plate, dot blot or Western blot, will generally be washed to remove any non-specifically bound antibody species, allowing only those antibodies specifically bound within the primary immune complexes to be detected.
  • the antibody employed in the detection may itself be linked to a detectable label, wherein one would then simply detect this label, thereby allowing the amount of the primary immune complexes in the composition to be determined.
  • the first antibody that becomes bound within the primary immune complexes may be detected by means of a second binding ligand that has binding affinity for the antibody.
  • the second binding ligand may be linked to a detectable label.
  • the second binding ligand is itself often an antibody, which may thus be termed a“secondary” antibody.
  • the primary immune complexes are contacted with the labeled, secondary binding ligand, or antibody, under effective conditions and for a period of time sufficient to allow the formation of secondary immune complexes.
  • the secondary immune complexes are then generally washed to remove any non-specifically bound labeled secondary antibodies or ligands, and the remaining label in the secondary immune complexes is then detected.
  • Further methods include the detection of primary immune complexes by a two-step approach.
  • a second binding ligand such as an antibody that has binding affinity for the antibody, is used to form secondary immune complexes, as described above.
  • the secondary immune complexes are contacted with a third binding ligand or antibody that has binding affinity for the second antibody, again under effective conditions and for a period of time sufficient to allow the formation of immune complexes (tertiary immune complexes).
  • the third ligand or antibody is linked to a detectable label, allowing detection of the tertiary immune complexes thus formed. This system may provide for signal amplification if this is desired.
  • One method of immunodetection uses two different antibodies.
  • a first biotinylated antibody is used to detect the target antigen, and a second antibody is then used to detect the biotin attached to the complexed biotin.
  • the sample to be tested is first incubated in a solution containing the first step antibody. If the target antigen is present, some of the antibody binds to the antigen to form a biotinylated antibody/antigen complex.
  • the antibody/antigen complex is then amplified by incubation in successive solutions of streptavidin (or avidin), biotinylated DNA, and/or complementary biotinylated DNA, with each step adding additional biotin sites to the antibody/antigen complex.
  • the amplification steps are repeated until a suitable level of amplification is achieved, at which point the sample is incubated in a solution containing the second step antibody against biotin.
  • This second step antibody is labeled, as for example with an enzyme that can be used to detect the presence of the antibody/antigen complex by histoenzymology using a chromogen substrate.
  • a conjugate can be produced which is macroscopically visible.
  • PCR Polymerase Chain Reaction
  • the PCR method is similar to the Cantor method up to the incubation with biotinylated DNA, however, instead of using multiple rounds of streptavidin and biotinylated DNA incubation, the DNA/biotin/streptavidin/antibody complex is washed out with a low pH or high salt buffer that releases the antibody. The resulting wash solution is then used to carry out a PCR reaction with suitable primers with appropriate controls.
  • the enormous amplification capability and specificity of PCR can be utilized to detect a single antigen molecule.
  • Immunoassays in their most simple and direct sense, are binding assays. Certain preferred immunoassays are the various types of enzyme linked immunosorbent assays (ELISAs) and radioimmunoassays (RIA) known in the art. Immunohistochemical detection using tissue sections is also particularly useful. However, it will be readily appreciated that detection is not limited to such techniques, and western blotting, dot blotting, FACS analyses, and the like may also be used.
  • the antibodies of the disclosure are immobilized onto a selected surface exhibiting protein affinity, such as a well in a polystyrene microtiter plate. Then, a test composition suspected of containing the Zika virus or Zika virus antigen is added to the wells. After binding and washing to remove non-specifically bound immune complexes, the bound antigen may be detected. Detection may be achieved by the addition of another anti-Zika virus antibody that is linked to a detectable label.
  • ELISA is a simple “sandwich ELISA.” Detection may also be achieved by the addition of a second anti-Zika virus antibody, followed by the addition of a third antibody that has binding affinity for the second antibody, with the third antibody being linked to a detectable label.
  • the samples suspected of containing the Zika virus or Zika virus antigen are immobilized onto the well surface and then contacted with the anti-Zika virus antibodies of the disclosure. After binding and washing to remove non-specifically bound immune complexes, the bound anti-Zika virus antibodies are detected. Where the initial anti- Zika virus antibodies are linked to a detectable label, the immune complexes may be detected directly. Again, the immune complexes may be detected using a second antibody that has binding affinity for the first anti-Zika virus antibody, with the second antibody being linked to a detectable label.
  • ELIS As have certain features in common, such as coating, incubating and binding, washing to remove non-specifically bound species, and detecting the bound immune complexes. These are described below.
  • a plate with either antigen or antibody In coating a plate with either antigen or antibody, one will generally incubate the wells of the plate with a solution of the antigen or antibody, either overnight or for a specified period of hours. The wells of the plate will then be washed to remove incompletely adsorbed material. Any remaining available surfaces of the wells are then“coated” with a nonspecific protein that is antigenically neutral with regard to the test antisera. These include bovine serum albumin (BSA), casein or solutions of milk powder.
  • BSA bovine serum albumin
  • the coating allows for blocking of nonspecific adsorption sites on the immobilizing surface and thus reduces the background caused by nonspecific binding of antisera onto the surface.
  • a secondary or tertiary detection means rather than a direct procedure.
  • the immobilizing surface is contacted with the biological sample to be tested under conditions effective to allow immune complex (antigen/antibody) formation. Detection of the immune complex then requires a labeled secondary binding ligand or antibody, and a secondary binding ligand or antibody in conjunction with a labeled tertiary antibody or a third binding ligand.
  • Under conditions effective to allow immune complex (antigen/antibody) formation means that the conditions preferably include diluting the antigens and/or antibodies with solutions such as BSA, bovine gamma globulin (BGG) or phosphate buffered saline (PBS)/Tween. These added agents also tend to assist in the reduction of nonspecific background.
  • The“suitable” conditions also mean that the incubation is at a temperature or for a period of time sufficient to allow effective binding. Incubation steps are typically from about 1 to 2 to 4 hours or so, at temperatures preferably on the order of 25°C to 27°C, or may be overnight at about 4°C or so.
  • the contacted surface is washed so as to remove non-complexed material.
  • a preferred washing procedure includes washing with a solution such as PBS/Tween, or borate buffer. Following the formation of specific immune complexes between the test sample and the originally bound material, and subsequent washing, the occurrence of even minute amounts of immune complexes may be determined.
  • the second or third antibody will have an associated label to allow detection.
  • this will be an enzyme that will generate color development upon incubating with an appropriate chromogenic substrate.
  • a urease, glucose oxidase, alkaline phosphatase or hydrogen peroxidase-conjugated antibody for a period of time and under conditions that favor the development of further immune complex formation (e.g., incubation for 2 hours at room temperature in a PBS-containing solution such as PBS-Tween).
  • the amount of label is quantified, e.g., by incubation with a chromogenic substrate such as urea, or bromocresol purple, or 2,2'-azino-di-(3-ethyl-benzthiazoline-6- sulfonic acid (ABTS), or H2O2, in the case of peroxidase as the enzyme label. Quantification is then achieved by measuring the degree of color generated, e.g., using a visible spectra spectrophotometer.
  • a chromogenic substrate such as urea, or bromocresol purple, or 2,2'-azino-di-(3-ethyl-benzthiazoline-6- sulfonic acid (ABTS), or H2O2
  • Quantification is then achieved by measuring the degree of color generated, e.g., using a visible spectra spectrophotometer.
  • the present disclosure contemplates the use of competitive formats. This is particularly useful in the detection of Zika virus antibodies in sample.
  • competition-based assays an unknown amount of analyte or antibody is determined by its ability to displace a known amount of labeled antibody or analyte.
  • the quantifiable loss of a signal is an indication of the amount of unknown antibody or analyte in a sample.
  • the inventor proposes the use of labeled Zika virus monoclonal antibodies to determine the amount of Zika virus antibodies in a sample.
  • the basic format would include contacting a known amount of Zika virus monoclonal antibody (linked to a detectable label) with Zika virus antigen or particle.
  • the Zika virus antigen or organism is preferably attached to a support. After binding of the labeled monoclonal antibody to the support, the sample is added and incubated under conditions permitting any unlabeled antibody in the sample to compete with, and hence displace, the labeled monoclonal antibody.
  • the Western blot is an analytical technique used to detect specific proteins in a given sample of tissue homogenate or extract. It uses gel electrophoresis to separate native or denatured proteins by the length of the polypeptide (denaturing conditions) or by the 3-D structure of the protein (native/ non-denaturing conditions). The proteins are then transferred to a membrane (typically nitrocellulose or PVDF), where they are probed (detected) using antibodies specific to the target protein.
  • a membrane typically nitrocellulose or PVDF
  • Samples may be taken from whole tissue or from cell culture. In most cases, solid tissues are first broken down mechanically using a blender (for larger sample volumes), using a homogenizer (smaller volumes), or by sonication. Cells may also be broken open by one of the above mechanical methods. However, it should be noted that bacteria, virus or environmental samples can be the source of protein and thus Western blotting is not restricted to cellular studies only. Assorted detergents, salts, and buffers may be employed to encourage lysis of cells and to solubilize proteins. Protease and phosphatase inhibitors are often added to prevent the digestion of the sample by its own enzymes. Tissue preparation is often done at cold temperatures to avoid protein denaturing.
  • the proteins of the sample are separated using gel electrophoresis. Separation of proteins may be by isoelectric point (pi), molecular weight, electric charge, or a combination of these factors. The nature of the separation depends on the treatment of the sample and the nature of the gel. This is a very useful way to determine a protein. It is also possible to use a two-dimensional (2-D) gel which spreads the proteins from a single sample out in two dimensions. Proteins are separated according to isoelectric point (pH at which they have neutral net charge) in the first dimension, and according to their molecular weight in the second dimension.
  • isoelectric point pH at which they have neutral net charge
  • the proteins In order to make the proteins accessible to antibody detection, they are moved from within the gel onto a membrane made of nitrocellulose or polyvinylidene difluoride (PVDF).
  • PVDF polyvinylidene difluoride
  • the membrane is placed on top of the gel, and a stack of filter papers placed on top of that. The entire stack is placed in a buffer solution which moves up the paper by capillary action, bringing the proteins with it.
  • Another method for transferring the proteins is called electroblotting and uses an electric current to pull proteins from the gel into the PVDF or nitrocellulose membrane.
  • the proteins move from within the gel onto the membrane while maintaining the organization they had within the gel. As a result of this blotting process, the proteins are exposed on a thin surface layer for detection (see below).
  • Both varieties of membrane are chosen for their non specific protein binding properties (i.e., binds all proteins equally well). Protein binding is based upon hydrophobic interactions, as well as charged interactions between the membrane and protein. Nitrocellulose membranes are cheaper than PVDF but are far more fragile and do not stand up well to repeated probings. The uniformity and overall effectiveness of transfer of protein from the gel to the membrane can be checked by staining the membrane with Coomassie Brilliant Blue or Ponceau S dyes. Once transferred, proteins are detected using labeled primary antibodies, or unlabeled primary antibodies followed by indirect detection using labeled protein A or secondary labeled antibodies binding to the Fc region of the primary antibodies.
  • Lateral flow assays also known as lateral flow immunochromatographic assays, are simple devices intended to detect the presence (or absence) of a target analyte in sample (matrix) without the need for specialized and costly equipment, though many laboratory-based applications exist that are supported by reading equipment. Typically, these tests are used as low resources medical diagnostics, either for home testing, point of care testing, or laboratory use. A widely spread and well-known application is the home pregnancy test.
  • the technology is based on a series of capillary beds, such as pieces of porous paper or sintered polymer.
  • Each of these elements has the capacity to transport fluid (e.g., urine) spontaneously.
  • the first element acts as a sponge and holds an excess of sample fluid. Once soaked, the fluid migrates to the second element (conjugate pad) in which the manufacturer has stored the so-called conjugate, a dried format of bio-active particles (see below) in a salt-sugar matrix that contains everything to guarantee an optimized chemical reaction between the target molecule (e.g., an antigen) and its chemical partner (e.g., antibody) that has been immobilized on the particle's surface.
  • the target molecule e.g., an antigen
  • its chemical partner e.g., antibody
  • the sample fluid dissolves the salt- sugar matrix, it also dissolves the particles and in one combined transport action the sample and conjugate mix while flowing through the porous structure.
  • the analyte binds to the particles while migrating further through the third capillary bed.
  • This material has one or more areas (often called stripes) where a third molecule has been immobilized by the manufacturer. By the time the sample-conjugate mix reaches these strips, analyte has been bound on the particle and the third 'capture' molecule binds the complex. After a while, when more and more fluid has passed the stripes, particles accumulate and the stripe-area changes color.
  • the antibodies of the present disclosure may also be used in conjunction with both fresh-frozen and/or formalin-fixed, paraffin-embedded tissue blocks prepared for study by immunohistochemistry (IHC).
  • IHC immunohistochemistry
  • the method of preparing tissue blocks from these particulate specimens has been successfully used in previous IHC studies of various prognostic factors and is well known to those of skill in the art (Brown et al, 1990; Abbondanzo et al, 1990; Allred et al, 1990).
  • frozen-sections may be prepared by rehydrating 50 ng of frozen“pulverized” tissue at room temperature in phosphate buffered saline (PBS) in small plastic capsules; pelleting the particles by centrifugation; resuspending them in a viscous embedding medium (OCT); inverting the capsule and/or pelleting again by centrifugation; snap-freezing in -70°C isopentane; cutting the plastic capsule and/or removing the frozen cylinder of tissue; securing the tissue cylinder on a cryostat microtome chuck; and/or cutting 25-50 serial sections from the capsule.
  • whole frozen tissue samples may be used for serial section cuttings.
  • Permanent-sections may be prepared by a similar method involving rehydration of the 50 mg sample in a plastic microfuge tube; pelleting; resuspending in 10% formalin for 4 hours fixation; washing/pelleting; resuspending in warm 2.5% agar; pelleting; cooling in ice water to harden the agar; removing the tissue/agar block from the tube; infiltrating and/or embedding the block in paraffin; and/or cutting up to 50 serial permanent sections. Again, whole tissue samples may be substituted.
  • whole tissue samples may be substituted.
  • the present disclosure concerns immunodetection kits for use with the immunodetection methods described above.
  • the antibodies may be used to detect Zika virus or Zika virus antigens, the antibodies may be included in the kit.
  • the immunodetection kits will thus comprise, in suitable container means, a first antibody that binds to Zika virus or Zika virus antigen, and optionally an immunodetection reagent.
  • the Zika virus antibody may be pre-bound to a solid support, such as a column matrix and/or well of a microtiter plate.
  • the immunodetection reagents of the kit may take any one of a variety of forms, including those detectable labels that are associated with or linked to the given antibody. Detectable labels that are associated with or attached to a secondary binding ligand are also contemplated. Exemplary secondary ligands are those secondary antibodies that have binding affinity for the first antibody.
  • suitable immunodetection reagents for use in the present kits include the two- component reagent that comprises a secondary antibody that has binding affinity for the first antibody, along with a third antibody that has binding affinity for the second antibody, the third antibody being linked to a detectable label.
  • a number of exemplary labels are known in the art and all such labels may be employed in connection with the present disclosure.
  • kits may further comprise a suitably aliquoted composition of the Zika virus or Zika virus antigens, whether labeled or unlabeled, as may be used to prepare a standard curve for a detection assay.
  • the kits may contain antibody-label conjugates either in fully conjugated form, in the form of intermediates, or as separate moieties to be conjugated by the user of the kit.
  • the components of the kits may be packaged either in aqueous media or in lyophilized form.
  • the container means of the kits will generally include at least one vial, test tube, flask, bottle, syringe or other container means, into which the antibody may be placed, or preferably, suitably aliquoted.
  • the kits of the present disclosure will also typically include a means for containing the antibody, antigen, and any other reagent containers in close confinement for commercial sale.
  • Such containers may include injection or blow-molded plastic containers into which the desired vials are retained.
  • the present disclosure also contemplates the use of antibodies and antibody fragments as described herein for use in assessing the antigenic integrity of a viral antigen in a sample.
  • Biological medicinal products like vaccines differ from chemical drugs in that they cannot normally be characterized molecularly; antibodies are large molecules of significant complexity and have the capacity to vary widely from preparation to preparation. They are also administered to healthy individuals, including children at the start of their lives, and thus a strong emphasis must be placed on their quality to ensure, to the greatest extent possible, that they are efficacious in preventing or treating life-threatening disease, without themselves causing harm.
  • an antigen or vaccine from any source or at any point during a manufacturing process.
  • the quality control processes may therefore begin with preparing a sample for an immunoassay that identifies binding of an antibody or fragment disclosed herein to a viral antigen.
  • immunoassays are disclosed elsewhere in this document, and any of these may be used to assess the structural/antigenic integrity of the antigen. Standards for finding the sample to contain acceptable amounts of antigenically correct and intact antigen may be established by regulatory agencies.
  • antigen integrity is assessed is in determining shelf-life and storage stability. Most medicines, including vaccines, can deteriorate over time. Therefore, it is critical to determine whether, over time, the degree to which an antigen, such as in a vaccine, degrades or destabilizes such that is it no longer antigenic and/or capable of generating an immune response when administered to a subject. Again, standards for finding the sample to contain acceptable amounts of antigenically intact antigen may be established by regulatory agencies.
  • viral antigens may contain more than one protective epitope.
  • assays that look at the binding of more than one antibody, such as 2, 3, 4, 5 or even more antibodies.
  • These antibodies bind to closely related epitopes, such that they are adjacent or even overlap each other.
  • they may represent distinct epitopes from disparate parts of the antigen.
  • Antibodies and fragments thereof as described in the present disclosure may also be used in a kit for monitoring the efficacy of vaccination procedures by detecting the presence of protective Zika virus antibodies.
  • Antibodies, antibody fragment, or variants and derivatives thereof, as described in the present disclosure may also be used in a kit for monitoring vaccine manufacture with the desired immunogenicity.
  • PBMCs Peripheral blood mononuclear cells
  • PBMCs were cultured in 384-well plates (Nunc) using culture medium (ClonaCell-HY Medium A, StemCell Technologies) supplemented with 8 pg/ml of the TLR agonist CpG (phosphorothioate-modified oligodeoxynucleotide ZOEZOEZZZZZOEEZOEZZZT (SEQ ID NO: 21), Invitrogen), 3 pg/ml of Chk2 inhibitor (Sigma), 1 pg/ml of cyclosporine A (Sigma), and clarified supernatants from cultures of B95.8 cells (ATCC) containing Epstein-Barr virus (EBV).
  • culture medium ClonaCell-HY Medium A, StemCell Technologies
  • CpG phosphorothioate-modified oligodeoxynucleotide ZOEZOEZZZZZZOEEZOEZZZT
  • CpG phosphorothioate-modified oli
  • E-reactive B cell frequency (number of wells with E-reactive supernatants) divided by (number of LCL colonies in the plate) x 100]
  • ZIKV Dill (residues 299-407 of strain H/PF/2013), WNV-DIII (residues 296-405 of strain New York 1999) and DENV2-DIII (residues 299-410 of strain 16681) were expressed in BL21 (DE3) as inclusion bodies and refolded in vitro (Nelson et al, 2014). Briefly, inclusion bodies were denatured and refolded by gradual dilution into a refolding buffer (400 mM L-arginine, 100 mM Tris [pH 8.3], 2 mM EDTA, 5 and 0.5 mM reduced and oxidized glutathione) at 4°C. Refolded proteins were purified by size- exclusion chromatography using a Superdex 75, 16/60 (GE Healthcare).
  • a refolding buffer 400 mM L-arginine, 100 mM Tris [pH 8.3], 2 mM EDTA, 5 and
  • hybridomas were suspended in a selection medium containing 100 mM hypoxanthine, 0.4 pM aminopterin, 16 pM thymidine (HAT Media Supplement, Sigma), and 7 pg/ml ouabain (Sigma) and cultured in 384-well plates for 18 days before screening hybridomas for antibody production by ELISA.
  • hybridomas producing ZIKV E-specific antibodies were cloned biologically by single-cell fluorescence-activated cell sorting. Hybridomas were expanded in post-fusion medium (ClonaCell-HY Medium E, STEMCELL Technologies) until 50% confluent in 75-cm 2 flasks (Coming).
  • cells from one 75-cm 2 flask were collected with a cell scraper and expanded to four 225-cm 2 flasks (Coming) in serum-free medium (Hybridoma-SFM, Life Technologies). After 21 days, supernatants were clarified by centrifugation and filtered using 0.45-pm pore size filter devices. HiTrap Protein G or HiTrap MabSelectSure columns (GE Healthcare Life Sciences) were used to purify antibodies from filtered supernatants.
  • RNA sequence analysis of antibody variable region genes Total cellular RNA was extracted from pelleted cells from hybridoma clones, and an RT-PCR reaction was performed using mixtures of primers designed to amplify all heavy-chain or light-chain antibody variable regions (Nelson et al, 2014). The generated PCR products were purified using AMPure XP magnetic beads (Beckman Coulter) and sequenced directly using an ABI3700 automated DNA sequencer. The variable region sequences of the heavy and light chains were analyzed using the IMGT/V -Quest program (Brochet et al. , 2008; Gui dicell & Lefranc, 2011).
  • ELISA and half-maximal effective concentration (ECso) binding analysis Wells of microtiter plates were coated with purified, recombinant ectodomain of ZIKV E, Dill, Dill LRM (Dill containing A310E and T335K mutations in the lateral ridge of Dill) or Dill of related flaviviruses DENV2 or WNV and incubated at 4°C overnight.
  • the inventor used recombinant ZIKV E protein ectodomain with His6 tag produced in Sf9 insect cells (Meridian Life Sciences R01635). Plates were blocked with 5% skim milk in PBS-T for 1 hr.
  • B cell culture supernatants or purified antibodies were added to the wells and incubated for 1 hr at ambient temperature.
  • the bound antibodies were detected using goat anti-human IgG (g-specific) conjugated with alkaline phosphatase (Southern Biotech) and pNPP disodium salt hexahydrate substrate (Sigma).
  • g-specific conjugated with alkaline phosphatase
  • pNPP disodium salt hexahydrate substrate Sigma.
  • ELISAs that assessed binding of mAbs to Dill and Dill LRM, the inventor used previously described murine mAbs ZV-2 and ZV-54 (Zhao et al. , 2016) as controls.
  • a goat anti-mouse IgG conjugated with alkaline phosphatase was used for detection of these antibodies.
  • ELISA plates were coated with ZIKV E protein, and thawed, clarified tissue homogenates were applied undiluted in triplicate. Bound antibodies were detected using goat anti -human IgG (Fc-specific) antibody conjugated with alkaline phosphatase. The quantity of antibody was determined by comparison with a standard curve constructed using purified ZIKV-117 in a dilution series.
  • Biolayer interferometry competition binding assay His6-tagged ZIKV E protein was immobilized on anti-His coated biosensor tips (Pall) for 2 min on an Octet Red biosensor instrument. After measuring the baseline signal in kinetics buffer (PBS, 0.01% BSA, and 0.002% Tween 20) for 1 min, biosensor tips were immersed into the wells containing first antibody at a concentration of 10 pg/ml for 7 min. Biosensors then were immersed into wells containing a second mAh at a concentration of 10 pg/ml for 7 min. The signal obtained for binding of the second antibody in the presence of the first antibody was expressed as a percent of the uncompeted binding of the second antibody that was derived independently. The antibodies were considered competing if the presence of first antibody reduced the signal of the second antibody to less than 30% of its maximal binding and non-competing if the signal was greater than 70%. A level of 30 -70% was considered intermediate competition.
  • Shotgun mutagenesis epitope mapping was performed by shotgun mutagenesis essentially as described previously (Davidson & Doranz, 2014.
  • a ZIKV prM/E protein expression construct (strain ZikaSPH20l5) was subjected to high-throughput alanine scanning mutagenesis to generate a comprehensive mutation library. Each residue within prM/E was changed to alanine, with alanine codons mutated to serine. In total, 672 ZIKV prM/E mutants were generated (100% coverage), sequence confirmed, and arrayed into 384- well plates. Each ZIKV prM/E mutant was transfected into HEK-293T cells and allowed to express for 22 h.
  • Antibodies were detected using 3.75 pg/ml of AlexaFluor488-conjugated secondary antibody (Jackson ImmunoResearch Laboratories) in 10% NGS/0.l% saponin. Cells were washed three times with PBS++/0.l% saponin followed by two washes in PBS. Mean cellular fluorescence was detected using a high-throughput flow cytometer (HTFC, Intellicyt). Antibody reactivity against each mutant prM/E clone was calculated relative to WT prM/E protein reactivity by subtracting the signal from mock-transfected controls and normalizing to the signal from WT prM/E-transfected controls.
  • Vertebrate animal studies ethics statement This study was carried out in accordance with the recommendations in the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health. The protocols were approved by the Institutional Animal Care and Use Committee at the Washington University School of Medicine (Assurance number A3381-01). Inoculations were performed under anesthesia induced and maintained with ketamine hydrochloride and xylazine, and all efforts were made to minimize animal suffering.
  • ZIKV strain H/PF/2013 (French Polynesia, 2013) was obtained from X. de Lamballerie (Aix Marseille Universite). ZIKV Brazil Paraiba 2015 was provided by S. Whitehead (Bethesda) and originally obtained from P.F.C. Vasconcelos (Instituto Evandro Cargas). ZIKV MR 766 (Uganda, 1947), Malaysia P6740 (1966), and Dakar 41519 (Senegal, 1982) were provided by the World Reference Center or Emerging Viruses and Arboviruses (R. Tesh, University of Texas Medical Branch).
  • DENV-l 1254-4, DENV-2 172-08, DENV-3 N2845-09, and DENV-4 N703-99 were provided generously by E. Harris (University of California, Berkeley).
  • Virus stocks were propagated in C6/36 Aedes albopictus cells (DENV) or Vero cells (ZIKV).
  • ZIKV Dakar 41519 ZIKV-Dakar was passaged twice in vivo in Ragl 1 mice (M. Gorman and M. Diamond, unpublished data) to create a mouse-adapted strain.
  • Virus stocks were titrated by focus-forming assay (FFA) on Vero cells.
  • the plates were incubated sequentially with 500 ng/ml mouse anti-ZIKV (ZV-16, E. Fernandez and M. Diamond, unpublished) and HRP-conjugated goat anti-mouse IgG in PBS supplemented with 0.1% (w/v) saponin (Sigma) and 0.1% BSA.
  • ZIKV-infected cell foci were visualized using TrueBlue peroxidase substrate (KPL) and quantitated on an ImmunoSpot 5.0.37 macroanalyzer (Cellular Technologies).
  • C6/36 Aedes albopictus cells were inoculated with a MOI 0.01 of ZIKV (H/PF/2013) or different DENV serotypes (Nicaraguan strains DENV-l 1254-4, DENV-2 172-08, DENV-3 N2845-09, DENV-4 N703-99).
  • H/PF/2013 ZI 0.01 of ZIKV
  • DENV serotypes Naraguan strains DENV-l 1254-4, DENV-2 172-08, DENV-3 N2845-09, DENV-4 N703-99.
  • cells were fixed with 4% PFA diluted in PBS for 20 min at room temperature and permeabilized with HBSS supplemented with 10 mM HEPES, 0.1% saponin and 0.025% NaN 3 for 10 min at room temperature.
  • Fifty -thousand cells were transferred to U-bottom plates and incubated for 30 min at 4°C with 5 pg/ml of anti-ZIKV human mAbs or negative (hCHK- 152) 12 ; or positive (hE60) (Williams el al, 2013) isotype controls. After washing, cells were incubated with Alexa Fluor 647-conjugated goat anti-human IgG (Invitrogen) at 1:500, fixed in 1% PFA in PBS, processed on MACSQuant Analyzed (Miltenyi Biotec), and analyzed using FlowJo software (Tree Star).
  • the PCR products were directly cloned into antibody expression vectors containing the constant domains of WT gammal chain, LALA mutant (a leucine (L) to alanine (A) substitution at positions 234 and 235) gammal chain for the VH domains, and WT kappa chain for the VL domain in an isothermal amplification reaction (Gibson reaction) (Gibson et al. , 2009).
  • Plasmids encoding the heavy and light chain were transfected into 293F cells and full-length recombinant IgG was secreted into transfected cell supernatants. Supernatants were collected and IgG purified using Protein G chromatography and eluted into PBS. The functional abrogation of the binding of the LALA variant IgG was confirmed in an ELISA binding assay with recombinant human FcyRI. The binding of ZIKV- 117 WT or LALA antibody to FcyRI was evaluated, in comparison with the binding pattern of control antibodies (human mAh CKV063 (Fong et al, 2014); LALA-mutated IgG).
  • mice C57BL/6J male mice (4- to 5-week-old, Jackson Laboratories) were inoculated with 10 3 FFU of mouse-adapted ZIKV Dakar by subcutaneous route in the footpad.
  • mice One-day prior to infection, mice were treated with 2 mg anti-Ifnarl mAh (MAR1-5A3, Leinco Technologies) by intraperitoneal injection.
  • ZIKV- specific human mAb ZIKV- 117
  • hCHK-l52 was administered as a single dose at day +1 (100 pg) or day +5 (250 pg) after infection via an intraperitoneal route. Animals were monitored for 21 days. Pregnant mouse protection experiments.
  • WT C57BL/6J mice were bred in a specific pathogen-free facility at Washington University School of Medicine.
  • WT dams prophylaxis studies.
  • WT female and male mice were mated; at embryonic days E5.5, dams were treated with a single 250 pg dose of ZIKV mAh or isotype control by intraperitoneal injection as well as a 1 mg injection of anti-Ifnarl (MAR1-5A3).
  • mice were inoculated with 10 3 FFU of mouse-adapted ZIKV Dakar 41519 by subcutaneous injection in the footpad.
  • dams received a second 1 mg dose of anti-Ifnarl via an intraperitoneal route.
  • WT dams therapy.
  • ZIKV -infected tissues were weighed and homogenized with stainless steel beads in a Bullet Blender instrument (Next Advance) in 200 pL of PBS. Samples were clarified by centrifugation (2,000 x g for 10 min). All homogenized tissues from infected animals were stored at -20°C. Tissue samples and serum from ZIKV-infected mice were extracted with RNeasy 96 Kit (tissues) or Viral RNA Mini Kit (serum) (Qiagen). ZIKV RNA levels were determined by TaqMan one-step quantitative reverse transcriptase PCR (qRT-PCR) on an ABI7500 Fast Instrument using published primers and conditions (Lanciotti et ah, 2008). Viral burden was expressed on a logio scale as viral RNA equivalents per g or ml after comparison with a standard curve produced using serial 10-fold dilutions of ZIKV RNA.
  • RNA ISH was performed with RNAscope 2.5 (Advanced Cell Diagnostics) according to the manufacturer’s instructions. PFA-fixed paraffin embedded placental sections were deparaffmized by incubation for 60 min at 60°C. Endogenous peroxidases were quenched with H2O2 for 10 min at room temperature. Slides were boiled for 15 min in RNAscope Target Retrieval Reagents and incubated for 30 min in RNAscope Protease Plus before probe hybridization. The probe targeting ZIKV RNA was designed and synthesized by Advanced Cell Diagnostics (catalog no. 467771). Negative (targeting bacterial gene dapB) control probes were also obtained from Advanced Cell Diagnostics (catalog no.
  • Tissues were counterstained with Gill’s hematoxylin and visualized with standard bright- field microscopy. Histology and immunohistochemistry.
  • Harvested placentas were fixed in 10% neutral buffered formalin at room temperature and embedded in paraffin. At least three placentas from different litters with the indicated treatments were sectioned and stained with hematoxylin and eosin to assess morphology. Surface area and thickness of placenta and different layers were measured using Image J software.
  • SMRT Pacific Bioscience long-read single-molecule real-time sequencing
  • CCS circular consensus sequencing
  • grouping multiple sequencing reads from the same cDNA starting molecule results in a high-quality consensus read, which can be used to obtain high-quality sequence throughout the whole antibody heavy or light chain variable region. For example, if the Pacific Biosciences quality report states that there is a 1% chance that‘A’ at position X is erroneous, but there are four such reads covering the same original starting molecule, the resulting error probability is only 0.000001%.
  • the inventor sought to isolate neutralizing human mAbs with broad specificity against all ZIKV strains. To do this, they initially tested the serological response of human survivors who had been infected with African or Asian lineage strain ZIKV in diverse geographic locations. Serum from each subject contained antibodies that reacted by ELISA with ZIKV E protein and neutralized infection of a contemporary Asian isolate (H/PF/2013) from French Polynesia (FIGS. 1A-B). The inventor studied the B cells of Subject 1001 in detail. The frequency of B cells secreting antibodies to ZIKV E protein in the peripheral blood of Subject 1001 was 0.61% (FIG. 1C), when a threshold for detection of binding [absorbance at 405 nm (A405)] of 1.5 was used.
  • the inventor obtained 32 stable cloned hybridomas secreting antibodies that bound to ZIKV E protein from the cells of three donors (mAb ZIKV-195 from Subject 1011, mAbs ZIKV-204 and ZIKV-216 from Subject 973, and the remaining 29 mAbs from Subject 1001). All except one mAb belonged to IgGl isotype, with an equal distribution of light chain isotypes (FIG. 2A). Sanger sequencing of cDNA of the antibody variable gene regions revealed that each mAb represented an independently derived clone. The inventor determined the half maximal effective concentration for binding (EC50) to ZIKV E protein (FIGS. 2A and FIG.
  • This group of fusion loop-specific mAbs had a single neutralizing clone (ZIKV-88), with moderate potency.
  • Group B mAbs (ZIKV-l 16 and ZIKV- 161) neutralized ZIKV infection and bound to E, Dill, and E-FLM.
  • Group C mAbs (ZIKV- 19 and ZIKV- 190) bound to E and E-FLM weakly but did not potently neutralize infection.
  • Group D mAbs ZIKV- 195 and ZIKV-216 neutralized with moderate potency and were similar in binding to both E and E-FLM.
  • the most potently inhibitory Group D mAb, ZIKV-l 17, bound to both E and E-FLM weakly.
  • One antibody (ZIKV-216) competed with members of both Groups C and D and neutralized with moderate potency.
  • the inventor mapped the epitopes of representative mAbs from each competition group using a complete shotgun mutagenesis library (Davidson & Doranz, 2014) of ZIKV prM/E (Brazil Paraiba 2015 strain) protein variants in which each residue was changed individually to alanine (FIG. 2B and FIGS. 6A-C). Loss-of-binding analysis confirmed that Group A mAbs bound to the fusion loop in DII, whereas Group B mAbs bound Dill.
  • Group B mAb ZIKV-l 16 bound an epitope involving residue K394 in the lateral ridge of Dill, which was confirmed in an ELISA showing reduced binding to a Dill protein with mutations A310E and T335K in the Dill lateral ridge [DIII-LR] (Zhao etal, 2016).
  • the non-neutralizing clones comprising Group C mAbs bound DII, and the group D neutralizing mAbs bound to a unique epitope in DII not described previously for the closely related DENV (Screaton et al, 2015).
  • the FRNT50 values for the mAbs were as follows: Group A mAb ZIKV-88 (420 ng/ml), Group B mAbs ZIKV-l 16 (16 ng/ml) and ZIKV-161 (0.9 ng/ml), Group C/D mAb ZIKV-216 (16 ng/ml) and Group D mAbs ZIKV-195 (346 ng/ml) and ZIKV-l 17 (5 ng/ml). The inventor assessed whether Group B mAb ZIKV-l 16 and Group D mAb ZIKV-l 17 could inhibit diverse ZIKV strains encompassing the African, Asian, and American lineages.
  • ZIKV-l 17 neutralized potently all ZIKV strains tested including two African (MR 766 and Dakar 41519), two Asian (Malaysia P6740 and H/PF/2013), and an American (Brazil Paraiba 2015) strain with FRNT50 values of 5 to 25 ng/ml (FIGS. 2D-E).
  • ZIKV-l 16 inhibited four of the five strains efficiently, but lost activity against MR 766, the original African strain (FIGS 2D-E).
  • ZIKV- 117 showed a type-specific pattern of binding as it failed to stain permeabilized cells infected with DENV-l, DENV-2, DENV-3, or DENV-4 or bind to purified WNV E protein (FIG. 7 and data not shown).
  • ZIKV-l 16 bound to cells infected with DENV1, DENV2, or DENV4, but did not bind to DENV2 Dill or WNV Dill in ELISA.
  • mice were treated with a single dose of ZIKV-l 17 or isotype control (hCHK-l52) (Pal et al, 2013), on day +1 (100 pg; 6.7 mg/kg) or day +5 (250 pg; 16.7 mg/kg).
  • Animals treated with the non-binding isotype control (hCHK- 152) developed significant lethality compared to those receiving ZIKV-l 17 (FIG. 3A), which were protected even when administered only a single dose five days after virus inoculation.
  • the inventor and others have demonstrated intrauterine growth restriction, placental injury, and fetal demise following ZIKV infection of pregnant mice with deficiencies in type I IFN signaling (Mysorekar et al, 2016; Miner et al, 2016; Yockey et al, 2016).
  • WT pregnant dams were treated at day -1 (embryo day (E)5.5) with an anti-Ifnarl mAb.
  • these animals were administered vehicle control (PBS), 250 mg isotype control hCHK-l52, or 250 pg ZIKV-117 as prophylaxis.
  • dams were infected subcutaneously with 10 3 FFU of ZIKV- Dakar.
  • Fetuses at E13.5 from anti-Ifnarl mAh treated dams given PBS or hCHK-l52 showed high levels (e.g., -10 5 to 10 7 FFU equivalents/g) of viral RNA in the placenta and fetal brain (FIG. 3B).
  • mice treated with ZIKV-117 had markedly reduced levels of virus in the placenta and fetal brain (e.g., -10° to 10 3 FFU equivalents/g) (FIG. 3B).
  • This phenotype was associated with transport of antibody across the maternal-fetal placental barrier such that levels (816 + 53 ng/ml for the placenta and 1,675 + 203 ng/ml for the fetal head) of human ZIKV E-specific IgG were detected (FIG. 8). It should be noted that the levels of neonatal Fc receptor (FcRn) in the placenta of mice are lower than other mammalian species (Kim el al, 2009), thus reduced levels of transport of maternal or exogenous IgG into the fetus is expected (Pentsuk & van der Laan, 2009).
  • Antibody-dependent enhancement (ADE) of infection of the closely related DENV is due to cross-reactive antibodies that fail to neutralize heterologous serotype infection and instead facilitate uptake and infection of FcyR-expressing myeloid cells (Morens, 1994). Because flavivirus antibodies can promote ADE in cell culture (Dejnirattisai el al, 2016; Charles and Christofferson, 2016) with unknown consequences in vivo, the inventor evaluated the protective efficacy of a recombinant form of ZIKV-l 17 IgG containing a leucine (L) to alanine (A) substitution at positions 234 and 235 (LALA) (Hessell et al, 2007), which lacked efficient binding to FcyR, retained interactions with FcRn (Hessell et al.
  • L leucine
  • A alanine
  • LALA variant of ZIKV-l 17 showed similar protective activity against infection of the placenta and fetus relative to the parent mAh (FIG. 3D). As the majority of the protection conferred by ZIKV-l 17 in the pregnancy model likely is due to neutralization and not Fc effector functions, LALA variants could be used without a loss in potency or risk of ADE from a future infection with a heterologous flavivirus such as DENV.
  • administration of ZIKV-117 resulted in markedly reduced viral burden in the dams, the placenta, and fetus when measured at El 3.5 (FIGS. 3E-F).
  • the inventor also evaluated the consequences of ZIKV-117 administration on pathology in the placenta and fetus.
  • the reduction in viral load mediated by ZIKV-117 was associated with decreased destruction of the placenta (as judged by labyrinth layer and overall placenta area), less trophoblast cell death, and increased body size of the fetus (FIGS. 4A-C) compared to fetuses of PBS- or hCHK-l52-treated dams.
  • ZIKV-117 When administered as prophylaxis, ZIKV-117 fully protected against ZIKV -induced placental insufficiency and intrauterine growth restriction, as the placental area and fetal size from infected dams treated with anti- ZIKV mAb were similar to that of uninfected placentas.
  • In situ hybridization revealed an almost complete absence of viral RNA in the junctional zone and decidua of the placenta in animals treated with ZIKV-117 compared to staining observed in PBS or hCHK-l52-treated controls (FIG. 4D).
  • the inventor also observed vascular damage associated with ZIKV infection of the placenta (Miner et al, 2016), characterized as diminished vimentin staining of fetal endothelial cells, which was rescued by ZIKV-117 to levels similar to those in uninfected placentas (FIG. 4E).
  • the histopathological data suggests that ZIKV-117 treatment can reduce the ability of ZIKV to cross the fetal endothelial cell barrier, and thereby prevent vertical transmission and improve placental health and fetal outcome.
  • the inventor determined the protective and therapeutic efficacy of ZIKV-117 against ZIKV Brazil strain challenge in rhesus monkeys.
  • the antibody was 100% effective when used in protective or therapeutic experiments (FIG. 10).
  • ZIKV-117 or human antibodies with similar profiles could be developed as a preventive or treatment measure during pregnancy for at-risk humans.
  • these studies also inform vaccine efforts to design new epitope-based immunogens that elicit highly protective antibody responses against ZIKV.
  • GGC C GGAGT GGGT GGC ATTT GT AC GGT AT GAT GGA A AT A AC A A GTACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGA GACAATGCCAAGAACACGCTGTCTCTGCAAATGAACAGCCTGA GAGTTGAAGACACGGCTGTCTATTTCTGTGCGAGGGATCCTGA AACTTTCGGGGGGTTTGACTACTGGGGCCAGGGAACCCTGGTC ACCGTCCTCA
  • compositions and methods disclosed and claimed herein can be made and executed without undue experimentation in light of the present disclosure. While the compositions and methods of this disclosure have been described in terms of preferred embodiments, it will be apparent to those of skill in the art that variations may be applied to the compositions and methods and in the steps or in the sequence of steps of the method described herein without departing from the concept, spirit and scope of the disclosure. More specifically, it will be apparent that certain agents which are both chemically and physiologically related may be substituted for the agents described herein while the same or similar results would be achieved. All such similar substitutes and modifications apparent to those skilled in the art are deemed to be within the spirit, scope and concept of the disclosure as defined by the appended claims.

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Abstract

The present disclosure is directed to antibodies binding to and neutralizing Zika virus and methods for use thereof. In accordance with the present disclosure, provided are methods comprising: a method of detecting a Zika virus infection in a subject; a method of treating a subject infected with Zika virus or reducing the likelihood of infection of a subject at risk of contracting Zika virus; and a method of protecting the health of a placenta and/or fetus of a pregnant a subject infected with or at risk of infection with Zika virus. Also provided is a hybridoma or engineered cell encoding an antibody or antibody fragment; and a vaccine formulation comprising one or more antibodies or antibody fragments described herein.

Description

DESCRIPTION
HUMAN ANTIBODIES TO ZIKA VIRUS
PRIORITY CUAIM
The present application claims benefit of priority to U.S. Provisional Application Serial No. 62/734,200, filed September 20, 2018, the entire contents of which are hereby incorporated by reference.
BACKGROUND
This invention was made with government support under grant no. R01 AI127828 awarded by National Institutes of Health/National Institute of Allergy and Infection Disease. The government has certain rights in the invention.
1. Field of the Disclosure
The present disclosure relates generally to the fields of medicine, infectious disease, and immunology. More particular, the disclosure relates to human antibodies binding to Zika virus.
2. Background
ZIKV is an emerging mosquito-transmitted flavivirus that has become a global public health threat. Recent ZIKV epidemics in Micronesia, Brazil, other parts of South and Central America, and Mexico (Duffy et al. , 2009) are linked to Guillain-Barre syndrome in adults and microcephaly in newborn infants (Oehler et al, 2014; Musso et al, 2014) in the setting of infection during pregnancy (Araugo et al. , 2016; Gatherer & Kohl, 2016). As ZIKV is transmitted by Aedes species mosquitoes, which are global in distribution, countries in which these vectors are present could be sites for future epidemics. Despite the potential for causing disease in millions, specific treatments or vaccines for ZIKV are not available, leaving a considerable unmet need in the field. SUMMARY
Thus, in accordance with the present disclosure, there is provided a method of detecting a Zika virus infection in a subject comprising (a) contacting a sample from said subject with an antibody or antibody fragment having clone-paired heavy and light chain sequences from Table 2; and (b) detecting Zika virus in said sample by binding of said antibody or antibody fragment to a Zika virus antigen in said sample. The sample may be a body fluid, such as blood, sputum, tears, saliva, mucous or serum, semen, cervical or vaginal secretions, amniotic fluid, placental tissues, urine, exudate, transudate, tissue scrapings or feces. Detection may comprise ELISA, RIA, lateral flow assay or Western blot. The method may further comprise performing steps (a) and (b) a second time and determining a change in Zika virus antigen levels as compared to the first assay. The antibody or antibody fragment may be encoded by clone- paired variable sequences as set forth in Table 1. The antibody fragment may be a recombinant scFv (single chain fragment variable) antibody, Fab fragment, F(ab')2 fragment, or Fv fragment.
Also provided is a method of treating a subject infected with Zika virus, or reducing the likelihood of infection of a subject at risk of contracting Zika virus, comprising delivering to said subject an antibody or antibody fragment having clone-paired heavy and light chain sequences from Table 2. The antibody or antibody fragment may be encoded by clone-paired light and heavy chain variable sequences as set forth in Table 1. The antibody fragment may be a recombinant scFv (single chain fragment variable) antibody, Fab fragment, F(ab')2 fragment, or Fv fragment. The antibody may be an IgG, or a recombinant IgG antibody or antibody fragment comprising an Fc portion mutated to alter (eliminate or enhance) FcR interactions, to increase half-life and/or increase therapeutic efficacy, such as a LALA, N297, GASD/ALIE, YTE or LS mutation or glycan modified to alter (eliminate or enhance) FcR interactions such as enzymatic or chemical addition or removal of glycans or expression in a cell line engineered with a defined glycosylating pattern. In a particular embodiment, the antibody or antibody fragment comprises both LALA and YTE mutations. The antibody may be a chimeric antibody or a bispecific antibody.
The antibody or antibody fragment may be administered prior to infection or after infection. The subject may be a pregnant female, a sexually active female, or a female undergoing fertility treatments. Delivering comprises antibody or antibody fragment administration, or genetic delivery with an RNA or DNA sequence or vector encoding the antibody or antibody fragment. In another embodiment, there is provided a monoclonal antibody, wherein the antibody or antibody fragment is characterized by clone-paired heavy and light chain sequences from Table 2. The antibody or antibody fragment may be encoded by clone-paired light and heavy chain variable sequences as set forth in Table 1. The antibody fragment may be a recombinant scFv (single chain fragment variable) antibody, Fab fragment, F(ab')2 fragment, or Fv fragment. The antibody may be an IgG, or a recombinant IgG antibody or antibody fragment comprising an Fc portion mutated to alter (eliminate or enhance) FcR interactions, to increase half-life and/or increase therapeutic efficacy, such as a LALA, N297, GASD/ALIE, YTE or LS mutation or glycan modified to alter (eliminate or enhance) FcR interactions such as enzymatic or chemical addition or removal of glycans or expression in a cell line engineered with a defined glycosylating pattern. In a particular embodiment, the antibody or antibody fragment comprises both LALA and YTE mutations. The antibody may bea chimeric antibody or a bispecific antibody. The antibody or antibody fragment may further comprise a cell penetrating peptide and/or is an intrabody.
In still another embodiment, there is provided a hybridoma or engineered cell encoding an antibody or antibody fragment wherein the antibody or antibody fragment is characterized by clone-paired heavy and light chain sequences from Table 2. The antibody or antibody fragment may be encoded by clone-paired light and heavy chain variable sequences as set forth in Table 1. The antibody fragment may be a recombinant scFv (single chain fragment variable) antibody, Fab fragment, F(ab')2 fragment, or Fv fragment. The antibody may be an IgG, or a recombinant IgG antibody or antibody fragment comprising an Fc portion mutated to alter (eliminate or enhance) FcR interactions, to increase half-life and/or increase therapeutic efficacy, such as a LALA, N297, GASD/ALIE, YTE or LS mutation or glycan modified to alter (eliminate or enhance) FcR interactions such as enzymatic or chemical addition or removal of glycans or expression in a cell line engineered with a defined glycosylating pattern. The antibody may bea chimeric antibody or a bispecific antibody. In a particular embodiment, the antibody or antibody fragment comprises both LALA and YTE mutations. The antibody or antibody fragment may further comprise a cell penetrating peptide and/or is an intrabody.
In still yet another embodiment, there is provided a vaccine formulation comprising one or more antibodies or antibody fragments characterized by clone-paired heavy and light chain sequences from Table 2. The antibody or antibody fragment may be encoded by clone-paired light and heavy chain variable sequences as set forth in Table 1. The antibody fragment may be a recombinant scFv (single chain fragment variable) antibody, Fab fragment, F(ab')2 fragment, or Fv fragment. The antibody may be an IgG, or a recombinant IgG antibody or antibody fragment comprising an Fc portion mutated to alter (eliminate or enhance) FcR interactions, to increase half-life and/or increase therapeutic efficacy, such as a LALA, N297, GASD/ALIE, YTE or LS mutation or glycan modified to alter (eliminate or enhance) FcR interactions such as enzymatic or chemical addition or removal of glycans or expression in a cell line engineered with a defined glycosylating pattern. In a particular embodiment, the antibody or antibody fragment comprises both LALA and YTE mutations. The antibody may be a chimeric antibody or abispecific antibody. The antibody or antibody fragment may further comprise a cell penetrating peptide and/or is an intrabody.
Also provided is vaccine formulation comprising one or more expression vectors encoding a first antibody or antibody fragment as described above. The expression vector(s) may be Sindbis virus or VEE vector(s). The formulation may be formulated for delivery by needle injection, jet injection, or electroporation. The vaccine formulation may further comprise one or more expression vectors encoding for a second antibody or antibody fragment, such as a defined above.
An additional embodiment comprises a method of protecting the health of a placenta and/or fetus of a pregnant a subject infected with or at risk of infection with Zika virus comprising delivering to said subject an antibody or antibody fragment having clone-paired heavy and light chain sequences from Table 2. The antibody or antibody fragment may be encoded by clone-paired light and heavy chain variable sequences as set forth in Table 1. The antibody fragment may be a recombinant scFv (single chain fragment variable) antibody, Fab fragment, F(ab')2 fragment, or Fv fragment. The antibody may be an IgG, or a recombinant IgG antibody or antibody fragment comprising an Fc portion mutated to alter (eliminate or enhance) FcR interactions, to increase half-life and/or increase therapeutic efficacy, such as a LALA, N297, GASD/ALIE, YTE or LS mutation or glycan modified to alter (eliminate or enhance) FcR interactions such as enzymatic or chemical addition or removal of glycans or expression in a cell line engineered with a defined glycosylating pattern. In a particular embodiment, the antibody or antibody fragment comprises both LALA and YTE mutations. The antibody may bea chimeric antibody or a bispecific antibody. The antibody or antibody fragment may further comprise a cell penetrating peptide and/or is an intrabody. The method of claims 48-52, wherein said antibody or antibody fragment is administered prior to infection or after infection. The subject may be a pregnant female, a sexually active female, or a female undergoing fertility treatments. Delivering may comprise antibody or antibody fragment administration, or genetic delivery with an RNA or DNA sequence or vector encoding the antibody or antibody fragment. The antibody or antibody fragment may increase the size of the placenta as compared to an untreated control. The antibody or antibody fragment may reduce viral load and/or pathology of the fetus as compared to an untreated control.
A further embodiment comprises a method of determining the antigenic integrity, correct conformation and/or correct sequence of a Zika virus antigen comprising (a) contacting a sample comprising said antigen with a first antibody or antibody fragment having clone- paired heavy and light chain sequences from Table 2; and (b) determining antigenic integrity, correct conformation and/or correct sequence of said antigen by detectable binding of said first antibody or antibody fragment to said antigen. The sample may comprise recombinantly produced antigen, or the sample may comprise a vaccine formulation or vaccine production batch. Detection may comprise ELISA, RIA, western blot, a biosensor using surface plasmon resonance or biolayer interferometry, or flow cytometric staining.
The first antibody or antibody fragment may be encoded by clone-paired variable sequences as set forth in Table 1. The first antibody fragment may be a recombinant scFv (single chain fragment variable) antibody, Fab fragment, F(ab')2 fragment, or Fv fragment. The method may further comprise performing steps (a) and (b) a second time to determine the antigenic stability of the antigen over time. The method may further comprise (c) contacting a sample comprising said antigen with a second antibody or antibody fragment having clone- paired heavy and light chain sequences from Table 2; and (d) determining antigenic integrity of said antigen by detectable binding of said second antibody or antibody fragment to said antigen. The second antibody or antibody fragment may beencoded by clone-paired variable sequences as set forth in Table 1. The second antibody fragment may be a recombinant ScFv (single chain fragment variable) antibody, Fab fragment, F(ab')2 fragment, or Fv fragment. The method may further comprise performing steps (c) and (d) a second time to determine the antigenic stability of the antigen over time.
The use of the word“a” or“an” when used in conjunction with the term“comprising” in the claims and/or the specification may mean“one,” but it is also consistent with the meaning of“one or more,”“at least one,” and“one or more than one.” The word“about” means plus or minus 5% of the stated number. It is contemplated that any method or composition described herein can be implemented with respect to any other method or composition described herein. Other objects, features and advantages of the present disclosure will become apparent from the following detailed description. It should be understood, however, that the detailed description and the specific examples, while indicating specific embodiments of the disclosure, are given by way of illustration only, since various changes and modifications within the spirit and scope of the disclosure will become apparent to those skilled in the art from this detailed description.
BRIEF DESCRIPTION OF THE DRAWINGS
The following drawings form part of the present specification and are included to further demonstrate certain aspects of the present disclosure. The disclosure may be better understood by reference to one or more of these drawings in combination with the detailed description of specific embodiments presented herein.
FIGS. 1A-D. Human antibody and B cell response to ZIKV infection. Serum samples from humans with a previous diagnosis of ZIKV infection were tested for (FIG.
1 A) binding to ZIKV E protein in ELISA (with two technical replicates) and (FIG. 1B) neutralization of ZIKV in a FRNT assay (performed with at least two independent repeats in triplicate). Subjects 973 and 972 sera were tested from two separate time points with similar results - these data were combined). Subject 1001 had the highest endpoint titer in the binding assay and displayed potent neutralizing activity. Subject 657 was a control without history of exposure to ZIKV. (FIG. 1C) Supernatants of EBV -transformed B cell cultures from Subject 1001 were tested for binding to ZIKV E or Dill of ZIKV E or related flavivirus E proteins to assess the specificity of the immune response. The frequency of antigen-specific cells against each viral protein was determined with a threshold optical density (OD) of 1.5; with alternate lower OD thresholds of 1.0 or 0.5, the frequency was 0.69% or 0.97% for ZIKV E, respectively. (FIG. 1D) In four additional separate B cell transformation experiments, the frequency of B cells reactive with intact ZIKV E or E-FLM was determined.
FIG. 2A-E. Characterization of anti-ZIKV mAbs. (FIG. 2A) 29 mAbs were tested in binding, neutralization, and competition binding assays. The half-maximal binding concentration (EC50) against ZIKV E and the IC50 (by focus reduction neutralization test) against H/PF/2013 strain for neutralizing antibodies (highlighted in blue) are shown. The mAbs are displayed in four groups (A, B, C, or D) based on a competition binding assay. The values are the percent of binding that occurred during competition compared to uncompeted binding, which was normalized to 100% and the range of competition is indicated by the box colors. Black filled boxes indicate strongly competing pairs (residual binding <30%), grey filled boxes indicate intermediate competition (residual binding 30-69%), and white filled boxes indicate non-competing pairs (residual binding > 70%). The IC50 against H/PF/2013 strain for neutralizing antibodies is shown with active clones highlighted in blue. (FIG. 2B) A ribbon diagram of three protomers of ZIKV E (DI in red, DII in yellow and Dill in blue) is shown with critical residues highlighted as spheres from epitope mapping experiments for representative antibodies in each of the competition binding groups. The colors of the critical residues correspond to the competition group designation as in FIG. 2A. The mutations in the E-FLM and DIII-LR mutants are indicated by black and silver spheres, respectively. (FIG. 2C) Representative mAbs from each competition binding group are listed with the domains and residues critical for binding. (FIG. 2D) Two mAbs were tested for neutralization of five strains of ZIKV. The concentrations at which 50% or 90% neutralization occurred are listed in (FIG. 2E). The neutralization data are pooled from at least three independent experiments performed in triplicate.
FIGS. 3A-F. Protective activity of ZIKV-117 in adult male and pregnant female mice. (FIG. 3 A) Four to five week-old WT male mice were treated with 2 mg of anti-Ifharl mAh followed by subcutaneous inoculation with 103 FFU of mouse- adapted ZIKV -Dakar. Mice were treated with a single 100 pg or 250 pg dose of isotype control mAh (hCHK-l52) or ZIKV-117 on D+l or D+5 (n = 10 per group from two independent experiments), respectively. Significance was analyzed by the log-rank test (*, P < 0.05; **, P < 0.01). (FIGS. 3B-C) IftiarP female mice were mated with WT sires. At E5.5, dams were treated with 250 ug of either hCHK-l52 isotype control mAh or ZIKV-117. Bars indicate the median values and reflect data pooled from four independent experiments. Significance for fetal survival and viral RNA was analyzed by chi-square (FIG. 3B; ****, P < 0.0001) and Mann- Whitney (FIG. 3C; *, P < 0.05) tests, respectively. (FIGS. 3D-F) WT female mice were mated with WT sires. At E5.5, dams were treated with anti-Ifnarl mAh and one of the following: (FIGS. 3D-E) PBS, (FIGS. 3D-F) 250 pg of hCHK-l52 isotype control mAh, (FIGS. 3D-F) 250 pg of ZIKV- 117, or (FIG. 3F) 250 pg of ZIKV-117 LALA. At E6.5, dams were inoculated with 103 FFU of ZIKV-Dakar. (FIGS. 3D, 3F) Fetuses and placentas and (FIG. 3E) maternal brain and serum were harvested on E13.5 and viral RNA was measured by qRT-PCR. Bars indicate the median values of samples collected from three biological replicates (FIG. 3D): n = 20 to 36; (FIG. 3E): n = 5 to 9; f: n = 23 to 28). Significance was analyzed by ANOVA with a Dunn’s multiple comparison test (*, P < 0.05; **, P < 0.01, ***, P < 0.001; ****, P < 0.0001).
FIGS. 4A-E. Effect of ZIKV-117 treatment on the placenta and the fetus. (FIG. 4A) Cartoon depicting murine placental structures and zones. (FIG. 4B-E) Pregnant dams were treated with PBS, hCHK-l52, or ZIKV-117 as described in (FIG. 4D-F) prior to infection with ZIKV-Dakar or mock-infected. (FIG. 4B) Hematoxylin and eosin staining of placenta at El 3.5. Placental labyrinth zone is marked with a solid line. Low power (scale bar = 1 mm) and high power (scale bar = 50 pm) images are presented in sequence. Black arrows indicate apoptotic trophoblasts in areas corresponding to regions of ZIKV infectivity (see panel (FIG. 4D), below). (FIG. 4C) Measurements of thickness and indicated areas of placenta and fetus body size. Each symbol represents data from an individual placenta or fetus. Significance was analyzed by ANOVA with a Dunn’s multiple comparison test (*, P < 0.05; **, P < 0.01, ***, P < 0.001; ****, p < 0.0001, n.s.; not significant, P > 0.05). (FIG. 4D) In situ hybridization (ISH). Low power (scale bar = 500 pm) and high power (scale bar = 50 pm) images are presented in sequence. Black arrows indicate cells positive for ZIKV RNA in the junctional zone of the placenta. The images in panels are representative of several placentas from independent dams. (FIG. 4E). Low (scale bar = 50 pm) and high (scale bar = 10 pm) power magnified images of immunofluorescence staining of placentas for vimentin (in green, which marks fetal capillary endothelium) from ZIKV -infected dams treated with PBS orZIKV-H7 or from uninfected pregnant animals. Nuclei are counter-stained blue with DAPI.
FIG. 5. Binding of human mAbs to Zika E protein, E Dill, or E fusion loop mutant (FLM). MAbs are organized by competition binding groups A to D.
FIGS. 6A-C. High resolution epitope mapping of ZIKV mAbs. (FIG. 6A) An alanine scanning mutation library for ZIKV envelope protein was constructed where each amino acid of prM/E was mutated individually to alanine (and alanine to serine) and expression constructs arrayed into 384-well plates, one mutation per well. Each clone in the ZIKV prM/E mutation library, expressed in HEK-293T cells, was tested for immunoreactivity with five mAbs from competition groups A-D, measured using an Intellicyt high-throughput flow cytometer. Shown here for each of the five mAbs is the reactivity with the ZIKV E protein mutants that identified the epitope residues for these mAbs. MAb reactivity for each alanine mutant are expressed as percent of the reactivity of mAb with wild-type ZIKV prM/E. Clones with reactivity <30% relative to WT ZIKV prM/E were identified as critical for mAb binding. Bars represent the mean and range of at least two replicate data points. Binding of Group B mAbs, ZIKV- 116 and ZIKV- 161, to (FIG. 6B) ZIKV E Dill WT or (FIG. 6C) Dill LR mutant was compared with mouse mAbs ZV-2 and ZV-54. Binding of ZIKV-116 and ZIKV-161 was decreased by mutations in Dill LR (ZIK-l 17 is the lowest). The order (from left to right) for each mutation in FIG. 6A is ZIK-l 2, ZIK-l 5, ZIK-l 6, ZIK-l 9 and ZIK-l 17. FIG. 7. Binding of human mAbs to permeabilized DENV-infected C6/36 cells.
C6/36 cells were infected with DENV-l, DENV-2, DENV-3, DENV-4 or mock- infected. Cells were stained with the indicated anti-ZIKV mAbs, an isotype control (a humanized antibody to chikungunya virus; hCHK-l52), or a positive control (a cross reactive antibody to DENV; chimeric human E60 [chE60]) and processed by flow cytometry. The data are representative of two independent experiments. The numbers in the box indicate the fraction of cells that stained positively.
FIG. 8. Detection of human IgG in placenta or fetal head tissues after treatment of dams with ZIKV-117 or PBS treated pregnant mice. As described in FIGS. 3A-F, WT female mice were mated with WT sires and monitored for pregnancy. At E5.5, dams were treated with anti-Ifnarl mAh and PBS or 250 pg of ZIKV-l 17. One day later (E6.5), dams were infected with 103 FFU of ZIKV-Dakar. Fetuses and placentas (n = 4 each) were harvested on E13.5, homogenized, and tested for human IgG by ELISA. Human antibody in tissues was captured on ELISA plates coated with ZIKV E protein and detected using goat anti-human IgG (Fc-specific) antibody. The quantity of antibody was determined by comparison with a standard curve constructed using purified ZIKV-l 17 in a dilution series. Concentration of ZIKV-l 17 detected in treated or PBS mock-treated placenta or fetal head tissues, with standard curve. Four replicates were performed for each mouse tissue; results were averaged for each mouse. The graphs represent the mean + SEM from 3 mice per group.
FIGS. 9A-B. Comparison of WT and LALA mutated antibodies. (FIG. 9A) Binding to recombinant human FcvRl. The functional abrogation of the binding of the LALA variant IgG was confirmed in an ELISA binding assay with recombinant human FcyRI. ZIKV-l 17 WT bound to FcyRI, whereas the ZIKV-l 17 LALA antibody did not. WT and LALA versions of another human mAh, CKV063, were used as controls. (FIG. 9B) Neutralization. ZIKV-l 17 WT and LALA antibodies exhibited equivalent neutralizing activity in vitro to each other and to the hybridoma-derived antibody.
FIG. 10. Effect of ZIKV-117 in NHP challenge studies. Rhesus macaques were protected against viremia by ZIKV-l 17 at 10 mg/kg compared to the unrelated control mAh (10 mg/kg) after ZIKV challenge 1 day later (103 PFU ZIKV-Brazil) (left hand panels. Rhesus macaques were rescued from ZIKV viremia by administration of ZIKV - 117 (10 mg/kg) on day +2 after ZIKV challenge (103 PFU ZIKV-Brazil) (right hand panels). DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS
As discussed above, Zika virus (ZIKV) infection causes systemic and central nervous system pathology or disease, with congenital birth defects linked to infection during pregnancy (Coyne et ah, 2016). To develop candidate therapeutic agents against ZIKV, the inventor isolated a panel of human monoclonal antibodies (mAbs) from healthy subjects with prior ZIKV infection. A subset of mAbs recognized diverse epitopes on the envelope (E) protein and exhibited potent neutralizing activity. One of the most inhibitory mAbs, ZIKV- 117, broadly neutralized infection of ZIKV strains corresponding to African, Asian, and American lineages. Epitope mapping studies revealed that ZIKV-117 recognized a quaternary epitope on the E protein dimer-dimer interface. The inventor then evaluated the therapeutic efficacy of ZIKV- 117 in pregnant or non-pregnant mice. In these models, mAb treatment markedly reduced tissue pathology, placental and fetal infection, and mortality. Thus, neutralizing human mAbs can protect against matemal-fetal transmission, infection and disease, and reveal important determinants for structure-based rational vaccine design efforts. These and other aspects of the disclosure are described in detail below.
These and other aspects of the disclosure are described in detail below.
I. Zika Virus
Zika virus (ZIKV) is a member of the virus family Flaviviridae. It is spread by daytime- active Aedes mosquitoes, such as A. aegypti and A. albopictus. Its name comes from the Zika Forest of Uganda, where the virus was first isolated in 1947. Zika virus is related to the dengue, yellow fever, Japanese encephalitis, and West Nile viruses. Since the l950s, it has been known to occur within a narrow equatorial belt from Africa to Asia. From 2007 to 2016, the virus spread eastward, across the Pacific Ocean to the Americas, leading to the 2015-16 Zika virus epidemic.
The infection, known as Zika fever or Zika virus disease, often causes no or only mild symptoms, similar to a very mild form of dengue fever. While there is no specific treatment, paracetamol (acetaminophen) and rest may help with the symptoms. As of 2016, the illness cannot be prevented by medications or vaccines. Zika can also spread from a pregnant woman to her fetus. This can result in microcephaly, severe brain malformations, and other birth defects. Zika infections in adults may result rarely in Guillain-Barre syndrome. In January 2016, the United States Centers for Disease Control and Prevention (CDC) issued travel guidance on affected countries, including the use of enhanced precautions, and guidelines for pregnant women including considering postponing travel. Other governments or health agencies also issued similar travel warnings, while Colombia, the Dominican Republic, Puerto Rico, Ecuador, El Salvador, and Jamaica advised women to postpone getting pregnant until more is known about the risks.
The Zika virus belongs to the Flaviviridae family and the Flavivirus genus, and is thus related to the dengue, yellow fever, Japanese encephalitis, and West Nile viruses. Like other flaviviruses, Zika virus is enveloped and icosahedral and has a nonsegmented, single-stranded, 10 kb positive-sense RNA genome. It is most closely related to the Spondweni virus and is one of the two known viruses in the Spondweni virus clade.
A positive-sense RNA genome can be directly translated into viral proteins. As in other flaviviruses, such as the similarly sized West Nile virus, the RNA genome encodes seven nonstructural proteins and three structural proteins. One of the structural proteins encapsulates the virus. The RNA genome forms a nucleocapsid along with copies of the l2-kDa capsid protein. The nucleocapsid, in turn, is enveloped within a host-derived membrane modified with two viral glycoproteins. Viral genome replication depends on the synthesis of double sided RNA from the single stranded positive sense RNA (ssRNA(+)) genome followed by transcription and replication to provide viral mRNAs and new ssRNA(+) genomes.
There are two Zika lineages: the African lineage and the Asian lineage. Phylogenetic studies indicate that the virus spreading in the Americas is 89% identical to African genotypes but is most closely related to the Asian strain that circulated in French Polynesia during the 2013-2014 outbreak.
The vertebrate hosts of the virus were primarily monkeys in a so-called enzootic mosquito-monkey-mosquito cycle, with only occasional transmission to humans. Before the current pandemic began in 2007, Zika“rarely caused recognized 'spillover' infections in humans, even in highly enzootic areas.” Infrequently, however, other arboviruses have become established as a human disease and spread in a mosquito-human-mosquito cycle, like the yellow fever virus and the dengue fever virus (both flaviviruses), and the chikungunya virus (a togavirus). Though the reason for the pandemic is unknown, dengue, a related arbovirus that infects the same species of mosquito vectors, is known in particular to be intensified by urbanization and globalization. Zika is primarily spread by Aedes aegypti mosquitoes and can also be transmitted through sexual contact or blood transfusions. The basic reproduction number Ro, a measure of transmissibility) of Zika virus has been estimated to be between 1.4 and 6.6.
In 2015, news reports drew attention to the rapid spread of Zika in Latin America and the Caribbean. At that time, the Pan American Health Organization published a list of countries and territories that experienced "local Zika virus transmission" comprising Barbados, Bolivia, Brazil, Colombia, the Dominican Republic, Ecuador, El Salvador, French Guiana, Guadeloupe, Guatemala, Guyana, Haiti, Honduras, Martinique, Mexico, Panama, Paraguay, Puerto Rico, Saint Martin, Suriname, and Venezuela. By August 2016, more than 50 countries had experienced active (local) transmission of Zika virus.
Zika is primarily spread by the femal Q Aedes aegypti mosquito, which is active mostly in the daytime, although researchers have found the virus in common Culex house mosquitoes as well. The mosquitos must feed on blood in order to lay eggs. The virus has also been isolated from a number of arboreal mosquito species in the Aedes genus, such as A. africanus, A. apicoargenteus , A. furcifer, A. hensilli, A. luteocephalus and A. vittatus, with an extrinsic incubation period in mosquitoes of about 10 days.
The true extent of the vectors is still unknown. Zika has been detected in many more species of Aedes, along with Anopheles coustani, Mansonia uniformis, and Culex perfuscus, although this alone does not incriminate them as a vector.
Transmission by A. albopictus, the tiger mosquito, was reported from a 2007 urban outbreak in Gabon where it had newly invaded the country and become the primary vector for the concomitant chikungunya and dengue virus outbreaks. There is concern for autochthonous infections in urban areas of European countries infested by A. albopictus because the first two cases of laboratory-confirmed Zika infections imported into Italy were reported from viremic travelers returning from French Polynesia.
The potential societal risk of Zika can be delimited by the distribution of the mosquito species that transmit it. The global distribution of the most cited carrier of Zika, A. aegypti, is expanding due to global trade and travel. A. aegypti distribution is now the most extensive ever recorded - across all continents including North America and even the European periphery (Madeira, the Netherlands, and the northeastern Black Sea coast). A mosquito population capable of carrying Zika has been found in a Capitol Hill neighborhood of Washington, D.C., and genetic evidence suggests they survived at least four consecutive winters in the region. The study authors conclude that mosquitos are adapting for persistence in a northern climate. The Zika virus appears to be contagious via mosquitoes for around a week after infection. The virus is thought to be infectious for a longer period of time after infection (at least 2 weeks) when transmitted via semen.
Research into its ecological niche suggests that Zika may be influenced to a greater degree by changes in precipitation and temperature than Dengue, making it more likely to be confined to tropical areas. However, rising global temperatures would allow for the disease vector to expand their range further north, allowing Zika to follow.
Zika can be transmitted from men and women to their sexual partners. As of April 2016, sexual transmission of Zika has been documented in six countries - Argentina, Chile, France, Italy, New Zealand and the United States - during the 2015 outbreak.
In 2014, Zika capable of growth in lab culture was found in the semen of a man at least two weeks (and possibly up to 10 weeks) after he fell ill with Zika fever. In 2011 a study found that a U.S. biologist who had been bitten many times while studying mosquitoes in Senegal developed symptoms six days after returning home in August 2008, but not before having unprotected intercourse with his wife, who had not been outside the U.S. since 2008. Both husband and wife were confirmed to have Zika antibodies, raising awareness of the possibility of sexual transmission. In early February 2016, the Dallas County Health and Human Services department reported that a man from Texas who had not travelled abroad had been infected after his male monogamous sexual partner had anal penetrative sex with him one day before and one day after onset of symptoms. As of February 2016, fourteen additional cases of possible sexual transmission have been under investigation, but it remained unknown whether women can transmit Zika to their sexual partners. At that time, the understanding of the "incidence and duration of shedding in the male genitourinary tract [was] limited to one case report." Therefore, the CDC interim guideline recommended against testing men for purposes of assessing the risk of sexual transmission.
In March 2016, the CDC updated its recommendations about length of precautions for couples and advised that heterosexual couples with men who have confirmed Zika fever or symptoms of Zika should consider using condoms or not having penetrative sex (i.e., vaginal intercourse, anal intercourse, or fellatio) for at least 6 months after symptoms begin. This includes men who live in— and men who traveled to— areas with Zika. Couples with men who traveled to an area with Zika, but did not develop symptoms of Zika, should consider using condoms or not having sex for at least 8 weeks after their return in order to minimize risk. Couples with men who live in an area with Zika, but have not developed symptoms, might consider using condoms or not having sex while there is active Zika transmission in the area. The Zika virus can spread from an infected mother to her fetus during pregnancy or at delivery. As of April 2016, two cases of Zika transmission through blood transfusions have been reported globally, both from Brazil, after which the US Food and Drug Administration (FDA) recommended screening blood donors and deferring high-risk donors for 4 weeks. A potential risk had been suspected based on a blood-donor screening study during the French Polynesian Zika outbreak, in which 2.8% (42) of donors from November 2013 and February 2014 tested positive for Zika RNA and were all asymptomatic at the time of blood donation. Eleven of the positive donors reported symptoms of Zika fever after their donation, but only three of 34 samples grew in culture.
Zika virus replicates in the mosquito's midgut epithelial cells and then its salivary gland cells. After 5-10 days, the virus can be found in the mosquito’s saliva. If the mosquito’s saliva is inoculated into human skin, the virus can infect epidermal keratinocytes, skin fibroblasts in the skin and the Langerhans cells. The pathogenesis of the virus is hypothesized to continue with a spread to lymph nodes and the bloodstream. Flaviviruses generally replicate in the cytoplasm, but Zika antigens have been found in infected cell nuclei.
Zika fever (also known as Zika virus disease) is an illness caused by the Zika virus. Most cases have no symptoms, but when present they are usually mild and can resemble dengue fever. Symptoms may include fever, red eyes, joint pain, headache, and a maculopapular rash. Symptoms generally last less than seven days. It has not caused any reported deaths during the initial infection. Infection during pregnancy causes microcephaly and other brain malformations in some babies. Infection in adults has been linked to Guillain-Barre syndrome (GBS). Diagnosis is by testing the blood, urine, or saliva for the presence of Zika virus RNA when the person is sick.
Prevention involves decreasing mosquito bites in areas where the disease occurs, and proper use of condoms. Efforts to prevent bites include the use of insect repellent, covering much of the body with clothing, mosquito nets, and getting rid of standing water where mosquitoes reproduce. There is no effective vaccine. Health officials recommended that women in areas affected by the 2015-16 Zika outbreak consider putting off pregnancy and that pregnant women not travel to these areas. While there is no specific treatment, paracetamol (acetaminophen) and rest may help with the symptoms. Admission to hospital is rarely necessary.
Effective vaccines have existed for several viruses of the flaviviridae family, namely yellow fever vaccine, Japanese encephalitis vaccine, and tick-borne encephalitis vaccine, since the l930s, and dengue fever vaccine since the mid-20l0s. World Health Organization (WHO) experts have suggested that the priority should be to develop inactivated vaccines and other non-live vaccines, which are safe to use in pregnant women and those of childbearing age.
As of March 2016, eighteen companies and institutions internationally were developing vaccines against Zika but a vaccine was unlikely to be widely available for about ten years. In June 2016 the FDA granted the first approval for a human clinical trial for a Zika vaccine.
The virus was first isolated in April 1947 from a rhesus macaque monkey that had been placed in a cage in the Zika Forest of Uganda, near Lake Victoria, by the scientists of the Yellow Fever Research Institute. A second isolation from the mosquito A. africanus followed at the same site in January 1948. When the monkey developed a fever, researchers isolated from its serum a "filterable transmissible agent" that was named Zika in 1948.
Zika had been known to infect humans from the results of serological surveys in Uganda and Nigeria, published in 1952: Among 84 people of all ages, 50 individuals had antibodies to Zika, and all above 40 years of age were immune. A 1952 research study conducted in India had shown a "significant number" of Indians tested for Zika had exhibited an immune response to the virus, suggesting it had long been widespread within human populations.
It was not until 1954 that the isolation of Zika from a human was published. This came as part of a 1952 outbreak investigation of jaundice suspected to be yellow fever. It was found in the blood of a 10-year-old Nigerian female with low-grade fever, headache, and evidence of malaria, but no jaundice, who recovered within three days. Blood was injected into the brain of laboratory mice, followed by up to 15 mice passages. The virus from mouse brains was then tested in neutralization tests using rhesus monkey sera specifically immune to Zika. In contrast, no virus was isolated from the blood of two infected adults with fever, jaundice, cough, diffuse joint pains in one and fever, headache, pain behind the eyes and in the joints. Infection was proven by a rise in Zika-specific serum antibodies.
From 1951 through 1983, evidence of human infection with Zika was reported from other African countries, such as the Central African Republic, Egypt, Gabon, Sierra Leone, Tanzania, and Uganda, as well as in parts of Asia including India, Indonesia, Malaysia, the Philippines, Thailand, Vietnam and Pakistan. From its discovery until 2007, there were only 14 confirmed human cases of Zika infection from Africa and Southeast Asia.
In April 2007, the first outbreak outside of Africa and Asia occurred on the island of Yap in the Federated States of Micronesia, characterized by rash, conjunctivitis, and arthralgia, which was initially thought to be dengue, chikungunya, or Ross River disease. Serum samples from patients in the acute phase of illness contained RNA of Zika. There were 49 confirmed cases, 59 unconfirmed cases, no hospitalizations, and no deaths. Between 2013 and 2014, further epidemics occurred in French Polynesia, Easter Island, the Cook Islands, and New Caledonia. On 22 March 2016 Reuters reported that Zika was isolated from a 2014 blood sample of an elderly man in Chittagong in Bangladesh as part of a retrospective study.
As of early 2016, a widespread outbreak of Zika was ongoing, primarily in the Americas. The outbreak began in April 2015 in Brazil, and has spread to other countries in South America, Central America, North America, and the Caribbean. The Zika virus reached Singapore and Malaysia in Aug 2016. In January 2016, the WHO said the virus was likely to spread throughout most of the Americas by the end of the year; and in February 2016, the WHO declared the cluster of microcephaly and Guillain-Barre syndrome cases reported in Brazil - strongly suspected to be associated with the Zika outbreak - a Public Health Emergency of International Concern. It is estimated that 1.5 million people have been infected by Zika in Brazil, with over 3,500 cases of microcephaly reported between October 2015 and January 2016.
A number of countries have issued travel warnings, and the outbreak is expected to significantly impact the tourism industry. Several countries have taken the unusual step of advising their citizens to delay pregnancy until more is known about the virus and its impact on fetal development. With the 2016 Summer Olympic Games hosted in Rio de Janeiro, health officials worldwide have voiced concerns over a potential crisis, both in Brazil and when international athletes and tourists, who may be unknowingly infected, return home and possibly spread the virus. Some researchers speculate that only one or two tourists may be infected during the three- week period, or approximately 3.2 infections per 100,000 tourists.
II. Monoclonal Antibodies and Production Thereof
An "isolated antibody" is one that has been separated and/or recovered from a component of its natural environment. Contaminant components of its natural environment are materials that would interfere with diagnostic or therapeutic uses for the antibody, and may include enzymes, hormones, and other proteinaceous or non-proteinaceous solutes. In particular embodiments, the antibody is purified: (1) to greater than 95% by weight of antibody as determined by the Lowry method, and most particularly more than 99% by weight; (2) to a degree sufficient to obtain at least 15 residues of N-terminal or internal amino acid sequence by use of a spinning cup sequenator; or (3) to homogeneity by SDS-PAGE under reducing or non-reducing conditions using Coomassie blue or silver stain. Isolated antibody includes the antibody in situ within recombinant cells since at least one component of the antibody's natural environment will not be present. Ordinarily, however, isolated antibody will be prepared by at least one purification step.
The basic four-chain antibody unit is a heterotetrameric glycoprotein composed of two identical light (L) chains and two identical heavy (H) chains. An IgM antibody consists of 5 basic heterotetramer units along with an additional polypeptide called J chain, and therefore contain 10 antigen binding sites, while secreted IgA antibodies can polymerize to form polyvalent assemblages comprising 2-5 of the basic 4-chain units along with J chain. In the case of IgGs, the 4-chain unit is generally about 150,000 daltons. Each L chain is linked to an H chain by one covalent disulfide bond, while the two H chains are linked to each other by one or more disulfide bonds depending on the H chain isotype. Each H and L chain also has regularly spaced intrachain disulfide bridges. Each H chain has at the N-terminus, a variable region (VH) followed by three constant domains (CH) for each of the alpha and gamma chains and four CH domains for mu and isotypes. Each L chain has at the N-terminus, a variable region (VL) followed by a constant domain (CL) at its other end. The VL is aligned with the VH and the CL is aligned with the first constant domain of the heavy chain (CHI). Particular amino acid residues are believed to form an interface between the light chain and heavy chain variable regions. The pairing of a VH and VL together forms a single antigen-binding site. For the structure and properties of the different classes of antibodies, see, e.g., Basic and Clinical Immunology, 8th edition, Daniel P. Stites, Abba I. Terr and Tristram G. Parslow (eds.), Appleton & Lange, Norwalk, Conn., 1994, page 71, and Chapter 6.
The L chain from any vertebrate species can be assigned to one of two clearly distinct types, called kappa and lambda based on the amino acid sequences of their constant domains (CL). Depending on the amino acid sequence of the constant domain of their heavy chains (CH), immunoglobulins can be assigned to different classes or isotypes. There are five classes of immunoglobulins: IgA, IgD, IgE, IgG, and IgM, having heavy chains designated alpha, delta, epsilon, gamma and mu, respectively. They gamma and alpha classes are further divided into subclasses on the basis of relatively minor differences in CH sequence and function, humans express the following subclasses: IgGl, IgG2, IgG3, IgG4, IgAl, and IgA2.
The term "variable" refers to the fact that certain segments of the V domains differ extensively in sequence among antibodies. The V domain mediates antigen binding and defines specificity of a particular antibody for its particular antigen. However, the variability is not evenly distributed across the 110-amino acid span of the variable regions. Instead, the V regions consist of relatively invariant stretches called framework regions (FRs) of 15-30 amino acids separated by shorter regions of extreme variability called "hypervariable regions" that are each 9-12 amino acids long. The variable regions of native heavy and light chains each comprise four FRs, largely adopting a beta-sheet configuration, connected by three hypervariable regions, which form loops connecting, and in some cases forming part of, the beta-sheet structure. The hypervariable regions in each chain are held together in close proximity by the FRs and, with the hypervariable regions from the other chain, contribute to the formation of the antigen-binding site of antibodies (see Rabat et al., Sequences of Proteins of Immunological Interest, 5th Ed. Public Health Service, National Institutes of Health, Bethesda, Md. (1991)). The constant domains are not involved directly in binding an antibody to an antigen, but exhibit various effector functions, such as participation of the antibody in antibody dependent cellular cytotoxicity (ADCC), antibody-dependent cellular phagocytosis (ADCP), antibody-dependent neutrophil phagocytosis (ADNP), and antibody-dependent complement deposition (ADCD).
The term "hypervariable region" when used herein refers to the amino acid residues of an antibody that are responsible for antigen binding. The hypervariable region generally comprises amino acid residues from a "complementarity determining region" or "CDR" (e.g., around about residues 24-34 (Ll), 50-56 (L2) and 89-97 (L3) in the VL, and around about 31- 35 (Hl), 50-65 (H2) and 95-102 (H3) in the VH when numbered in accordance with the Rabat numbering system; Rabat et al, Sequences of Proteins of Immunological Interest, 5th Ed. Public Health Service, National Institutes of Health, Bethesda, Md. (1991)); and/or those residues from a "hypervariable loop" (e.g., residues 24-34 (Ll), 50-56 (L2) and 89-97 (L3) in the VL, and 26-32 (Hl), 52-56 (H2) and 95-101 (H3) in the VH when numbered in accordance with the Chothia numbering system; Chothia and Lesk, J. Mol. Biol. 196:901-917 (1987)); and/or those residues from a "hypervariable loop'VCDR (e.g., residues 27-38 (Ll), 56-65 (L2) and 105-120 (L3) in the VL, and 27-38 (Hl), 56-65 (H2) and 105-120 (H3) in the VH when numbered in accordance with the IMGT numbering system; Lefranc, M. P. et al. Nucl. Acids Res. 27:209-212 (1999), Ruiz, M. et al. Nucl. Acids Res. 28:219-221 (2000)). Optionally the antibody has symmetrical insertions at one or more of the following points 28, 36 (Ll), 63, 74- 75 (L2) and 123 (L3) in the VL, and 28, 36 (Hl), 63, 74-75 (H2) and 123 (H3) in the VsubH when numbered in accordance with AHo; Honneger, A. and Plunkthun, A. J. Mol. Biol. 309:657-670 (2001)).
By "germline nucleic acid residue" is meant the nucleic acid residue that naturally occurs in a germline gene encoding a constant or variable region. "Germline gene" is the DNA found in a germ cell (i.e., a cell destined to become an egg or in the sperm). A "germline mutation" refers to a heritable change in a particular DNA that has occurred in a germ cell or the zygote at the single-cell stage, and when transmitted to offspring, such a mutation is incorporated in every cell of the body. A germline mutation is in contrast to a somatic mutation which is acquired in a single body cell. In some cases, nucleotides in a germline DNA sequence encoding for a variable region are mutated (i.e.. a somatic mutation) and replaced with a different nucleotide.
The term "monoclonal antibody" as used herein refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e., the individual antibodies comprising the population are identical except for possible naturally occurring mutations that may be present in minor amounts. Monoclonal antibodies are highly specific, being directed against a single antigenic site. Furthermore, in contrast to polyclonal antibody preparations that include different antibodies directed against different determinants (epitopes), each monoclonal antibody is directed against a single determinant on the antigen. In addition to their specificity, the monoclonal antibodies are advantageous in that they may be synthesized uncontaminated by other antibodies. The modifier "monoclonal" is not to be construed as requiring production of the antibody by any particular method. For example, the monoclonal antibodies useful in the present disclosure may be prepared by the hybridoma methodology first described by Kohler et al, Nature, 256:495 (1975), or may be made using recombinant DNA methods in bacterial, eukaryotic animal or plant cells (see, e.g., U.S. Pat. No. 4,816,567) after single cell sorting of an antigen specific B cell, an antigen specific plasmablast responding to an infection or immunization, or capture of linked heavy and light chains from single cells in a bulk sorted antigen specific collection. The "monoclonal antibodies" may also be isolated from phage antibody libraries using the techniques described in Clackson et al, Nature, 352:624-628 (1991) and Marks et al, J. Mol. Biol., 222:581-597 (1991), for example.
A. General Methods
It will be understood that monoclonal antibodies binding to Zika virus will have several applications. These include the production of diagnostic kits for use in detecting and diagnosing Zika virus infection, as well as for treating the same. In these contexts, one may link such antibodies to diagnostic or therapeutic agents, use them as capture agents or competitors in competitive assays, or use them individually without additional agents being attached thereto. The antibodies may be mutated or modified, as discussed further below. Methods for preparing and characterizing antibodies are well known in the art (see, e.g., Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, 1988; U.S. Patent 4,196,265). The methods for generating monoclonal antibodies (MAbs) generally begin along the same lines as those for preparing polyclonal antibodies. The first step for both these methods is immunization of an appropriate host or identification of subjects who are immune due to prior natural infection or vaccination with a licensed or experimental vaccine. As is well known in the art, a given composition for immunization may vary in its immunogenicity. It is often necessary therefore to boost the host immune system, as may be achieved by coupling a peptide or polypeptide immunogen to a carrier. Exemplary and preferred carriers are keyhole limpet hemocyanin (KLH) and bovine serum albumin (BSA). Other albumins such as ovalbumin, mouse serum albumin or rabbit serum albumin can also be used as carriers. Means for conjugating a polypeptide to a carrier protein are well known in the art and include glutaraldehyde, m-maleimidobencoyl-N-hydroxysuccinimide ester, carbodiimyde and bis- biazotized benzidine. As also is well known in the art, the immunogenicity of a particular immunogen composition can be enhanced by the use of non-specific stimulators of the immune response, known as adjuvants. Exemplary and preferred adjuvants in animals include complete Freund’s adjuvant (a non-specific stimulator of the immune response containing killed Mycobacterium tuberculosis), incomplete Freund’s adjuvants and aluminum hydroxide adjuvant and in humans include alum, CpG, MFP59 and combinations of immunostimulatory molecules (“Adjuvant Systems”, such as AS01 or AS03). Additional experimental forms of inoculation to induce Zika virus-specific B cells is possible, including nanoparticle vaccines, or gene-encoded antigens delivered as DNA or RNA genes in a physical delivery system (such as lipid nanoparticle or on a gold biolistic bead), and delivered with needle, gene gun, transcutaneous electroporation device. The antigen gene also can be carried as encoded by a replication competent or defective viral vector such as adenovirus, adeno-associated virus, poxvirus, herpesvirus, or alphavirus replicon, or alternatively a virus like particle.
In the case of human antibodies against natural pathogens, a suitable approach is to identify subjects that have been exposed to the pathogens, such as those who have been diagnosed as having contracted the disease, or those who have been vaccinated to generate protective immunity against the pathogen or to test the safety or efficacy of an experimental vaccine. Circulating anti-pathogen antibodies can be detected, and antibody encoding or producing B cells from the antibody-positive subject may then be obtained.
The amount of immunogen composition used in the production of polyclonal antibodies varies upon the nature of the immunogen as well as the animal used for immunization. A variety of routes can be used to administer the immunogen (subcutaneous, intramuscular, intradermal, intravenous and intraperitoneal). The production of polyclonal antibodies may be monitored by sampling blood of the immunized animal at various points following immunization. A second, booster injection, also may be given. The process of boosting and titering is repeated until a suitable titer is achieved. When a desired level of immunogenicity is obtained, the immunized animal can be bled and the serum isolated and stored, and/or the animal can be used to generate MAbs.
Following immunization, somatic cells with the potential for producing antibodies, specifically B lymphocytes (B cells), are selected for use in the MAb generating protocol. These cells may be obtained from biopsied spleens, lymph nodes, tonsils or adenoids, bone marrow aspirates or biopsies, tissue biopsies from mucosal organs like lung or GI tract, or from circulating blood. The antibody-producing B lymphocytes from the immunized animal or immune human are then fused with cells of an immortal myeloma cell, generally one of the same species as the animal that was immunized or human or human/mouse chimeric cells. Myeloma cell lines suited for use in hybridoma-producing fusion procedures preferably are non-antibody-producing, have high fusion efficiency, and enzyme deficiencies that render then incapable of growing in certain selective media which support the growth of only the desired fused cells (hybridomas). Any one of a number of myeloma cells may be used, as are known to those of skill in the art (Goding, pp. 65-66, 1986; Campbell, pp. 75-83, 1984). HMMA2.5 cells or MFP-2 cells are particularly useful examples of such cells.
Methods for generating hybrids of antibody -producing spleen or lymph node cells and myeloma cells usually comprise mixing somatic cells with myeloma cells in a 2: 1 proportion, though the proportion may vary from about 20: 1 to about 1 : 1, respectively, in the presence of an agent or agents (chemical or electrical) that promote the fusion of cell membranes. In some cases, transformation of human B cells with Epstein Barr virus (EBV) as an initial step increases the size of the B cells, enhancing fusion with the relatively large-sized myeloma cells. Transformation efficiency by EBV is enhanced by using CpG and a Chk2 inhibitor drug in the transforming medium. Alternatively, human B cells can be activated by co-culture with transfected cell lines expressing CD40 Ligand (CD 154) in medium containing additional soluble factors, such as IL-21 and human B cell Activating Factor (BAFF), a Type II member of the TNF superfamily. Fusion methods using Sendai virus have been described by Kohler and Milstein (1975; 1976), and those using polyethylene glycol (PEG), such as 37% (v/v) PEG, by Gefter el al. (1977). The use of electrically induced fusion methods also is appropriate (Goding, pp. 71-74, 1986) and there are processes for better efficiency (Yu et al, 2008). Fusion procedures usually produce viable hybrids at low frequencies, about 1 x 10 6 to 1 x 10 8, but with optimized procedures one can achieve fusion efficiencies close to 1 in 200 (Yu et al. , 2008). However, relatively low efficiency of fusion does not pose a problem, as the viable, fused hybrids are differentiated from the parental, infused cells (particularly the infused myeloma cells that would normally continue to divide indefinitely) by culturing in a selective medium. The selective medium is generally one that contains an agent that blocks the de novo synthesis of nucleotides in the tissue culture medium. Exemplary and preferred agents are aminopterin, methotrexate, and azaserine. Aminopterin and methotrexate block de novo synthesis of both purines and pyrimidines, whereas azaserine blocks only purine synthesis. Where aminopterin or methotrexate is used, the medium is supplemented with hypoxanthine and thymidine as a source of nucleotides (HAT medium). Where azaserine is used, the medium is supplemented with hypoxanthine. Ouabain is added if the B cell source is an EBV- transformed human B cell line, in order to eliminate EBV -transformed lines that have not fused to the myeloma.
The preferred selection medium is HAT or HAT with ouabain. Only cells capable of operating nucleotide salvage pathways are able to survive in HAT medium. The myeloma cells are defective in key enzymes of the salvage pathway, e.g., hypoxanthine phosphoribosyl transferase (HPRT), and they cannot survive. The B cells can operate this pathway, but they have a limited life span in culture and generally die within about two weeks. Therefore, the only cells that can survive in the selective media are those hybrids formed from myeloma and B cells. When the source of B cells used for fusion is a line of EBV-transformed B cells, as here, ouabain may also be used for drug selection of hybrids as EBV-transformed B cells are susceptible to drug killing, whereas the myeloma partner used is chosen to be ouabain resistant.
Culturing provides a population of hybridomas from which specific hybridomas are selected. Typically, selection of hybridomas is performed by culturing the cells by single-clone dilution in microtiter plates, followed by testing the individual clonal supernatants (after about two to three weeks) for the desired reactivity. The assay should be sensitive, simple and rapid, such as radioimmunoassays, enzyme immunoassays, cytotoxicity assays, plaque assays dot immunobinding assays, and the like. The selected hybridomas are then serially diluted or single-cell sorted by flow cytometric sorting and cloned into individual antibody-producing cell lines, which clones can then be propagated indefinitely to provide mAbs. The cell lines may be exploited for MAb production in two basic ways. A sample of the hybridoma can be injected (often into the peritoneal cavity) into an animal (e.g. , a mouse). Optionally, the animals are primed with a hydrocarbon, especially oils such as pristane (tetramethylpentadecane) prior to injection. When human hybridomas are used in this way, it is optimal to inject immunocompromised mice, such as SCID mice, to prevent tumor rejection. The injected animal develops tumors secreting the specific monoclonal antibody produced by the fused cell hybrid. The body fluids of the animal, such as serum or ascites fluid, can then be tapped to provide MAbs in high concentration. The individual cell lines could also be cultured in vitro, where the MAbs are naturally secreted into the culture medium from which they can be readily obtained in high concentrations. Alternatively, human hybridoma cells lines can be used in vitro to produce immunoglobulins in cell supernatant. The cell lines can be adapted for growth in serum-free medium to optimize the ability to recover human monoclonal immunoglobulins of high purity.
MAbs produced by either means may be further purified, if desired, using filtration, centrifugation and various chromatographic methods such as FPLC or affinity chromatography. Fragments of the monoclonal antibodies of the disclosure can be obtained from the purified monoclonal antibodies by methods which include digestion with enzymes, such as pepsin or papain, and/or by cleavage of disulfide bonds by chemical reduction. Alternatively, monoclonal antibody fragments encompassed by the present disclosure can be synthesized using an automated peptide synthesizer.
It also is contemplated that a molecular cloning approach may be used to generate monoclonal antibodies. Single B cells labelled with the antigen of interest can be sorted physically using paramagnetic bead selection or flow cytometric sorting, then RNA can be isolated from the single cells and antibody genes amplified by RT-PCR. Alternatively, antigen- specific bulk sorted populations of cells can be segregated into microvesicles and the matched heavy and light chain variable genes recovered from single cells using physical linkage of heavy and light chain amplicons, or common barcoding of heavy and light chain genes from a vesicle. Matched heavy and light chain genes form single cells also can be obtained from populations of antigen specific B cells by treating cells with cell-penetrating nanoparticles bearing RT-PCR primers and barcodes for marking transcripts with one barcode per cell. The antibody variable genes also can be isolated by RNA extraction of a hybridoma line and the antibody genes obtained by RT-PCR and cloned into an immunoglobulin expression vector. Alternatively, combinatorial immunoglobulin phagemid libraries are prepared from RNA isolated from the cell lines and phagemids expressing appropriate antibodies are selected by panning using viral antigens. The advantages of this approach over conventional hybridoma techniques are that approximately 104 times as many antibodies can be produced and screened in a single round, and that new specificities are generated by H and L chain combination which further increases the chance of finding appropriate antibodies. Other U.S. patents, each incorporated herein by reference, that teach the production of antibodies useful in the present disclosure include U.S. Patent 5,565,332, which describes the production of chimeric antibodies using a combinatorial approach; U.S. Patent 4,816,567 which describes recombinant immunoglobulin preparations; and U.S. Patent 4,867,973 which describes antibody-therapeutic agent conjugates.
B. Antibodies of the Present Disclosure
Antibodies according to the present disclosure may be defined, in the first instance, by their binding specificity. Those of skill in the art, by assessing the binding specificity/affmity of a given antibody using techniques well known to those of skill in the art, can determine whether such antibodies fall within the scope of the instant claims. For example, the epitope to which a given antibody bind may consist of a single contiguous sequence of 3 or more (e.g., 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20) amino acids located within the antigen molecule (e.g., a linear epitope in a domain). Alternatively, the epitope may consist of a plurality of non-contiguous amino acids (or amino acid sequences) located within the antigen molecule (e.g., a conformational epitope).
Various techniques known to persons of ordinary skill in the art can be used to determine whether an antibody“interacts with one or more amino acids” within a polypeptide or protein. Exemplary techniques include, for example, routine cross-blocking assays, such as that described in Antibodies, Harlow and Lane (Cold Spring Harbor Press, Cold Spring Harbor, N.Y.). Cross-blocking can be measured in various binding assays such as ELISA, biolayer interferometry, or surface plasmon resonance. Other methods include alanine scanning mutational analysis, peptide blot analysis (Reineke (2004) Methods Mol. Biol. 248: 443-63), peptide cleavage analysis, high-resolution electron microscopy techniques using single particle reconstruction, cryoEM, or tomography, crystallographic studies and NMR analysis. In addition, methods such as epitope excision, epitope extraction and chemical modification of antigens can be employed (Tomer (2000) Prot. Sci. 9: 487-496). Another method that can be used to identify the amino acids within a polypeptide with which an antibody interacts is hydrogen/deuterium exchange detected by mass spectrometry. In general terms, the hydrogen/deuterium exchange method involves deuterium-labeling the protein of interest, followed by binding the antibody to the deuterium-labeled protein. Next, the protein/antibody complex is transferred to water and exchangeable protons within amino acids that are protected by the antibody complex undergo deuterium-to-hydrogen back-exchange at a slower rate than exchangeable protons within amino acids that are not part of the interface. As a result, amino acids that form part of the protein/antibody interface may retain deuterium and therefore exhibit relatively higher mass compared to amino acids not included in the interface. After dissociation of the antibody, the target protein is subjected to protease cleavage and mass spectrometry analysis, thereby revealing the deuterium-labeled residues which correspond to the specific amino acids with which the antibody interacts. See, e.g., Ehring (1999) Analytical Biochemistry 267: 252-259; Engen and Smith (2001) Anal. Chem. 73: 256A-265A. When the antibody neutralizes Zika virus, antibody escape mutant variant organisms can be isolated by propagating Zika virus in vitro or in animal models in the presence of high concentrations of the antibody. Sequence analysis of the Zika virus gene encoding the antigen targeted by the antibody reveals the mutation(s) conferring antibody escape, indicating residues in the epitope or that affect the structure of the epitope allosterically.
The term“epitope” refers to a site on an antigen to which B and/or T cells respond. B- cell epitopes can be formed both from contiguous amino acids or noncontiguous amino acids juxtaposed by tertiary folding of a protein. Epitopes formed from contiguous amino acids are typically retained on exposure to denaturing solvents, whereas epitopes formed by tertiary folding are typically lost on treatment with denaturing solvents. An epitope typically includes at least 3, and more usually, at least 5 or 8-10 amino acids in a unique spatial conformation.
Modification-Assisted Profiling (MAP), also known as Antigen Structure-based Antibody Profiling (ASAP) is a method that categorizes large numbers of monoclonal antibodies (mAbs) directed against the same antigen according to the similarities of the binding profile of each antibody to chemically or enzymatically modified antigen surfaces (see US 2004/0101920, herein specifically incorporated by reference in its entirety). Each category may reflect a unique epitope either distinctly different from or partially overlapping with epitope represented by another category. This technology allows rapid filtering of genetically identical antibodies, such that characterization can be focused on genetically distinct antibodies. When applied to hybridoma screening, MAP may facilitate identification of rare hybridoma clones that produce mAbs having the desired characteristics. MAP may be used to sort the antibodies of the disclosure into groups of antibodies binding different epitopes.
The present disclosure includes antibodies that may bind to the same epitope, or a portion of the epitope. Likewise, the present disclosure also includes antibodies that compete for binding to a target or a fragment thereof with any of the specific exemplary antibodies described herein. One can easily determine whether an antibody binds to the same epitope as, or competes for binding with, a reference antibody by using routine methods known in the art. For example, to determine if a test antibody binds to the same epitope as a reference, the reference antibody is allowed to bind to target under saturating conditions. Next, the ability of a test antibody to bind to the target molecule is assessed. If the test antibody is able to bind to the target molecule following saturation binding with the reference antibody, it can be concluded that the test antibody binds to a different epitope than the reference antibody. On the other hand, if the test antibody is not able to bind to the target molecule following saturation binding with the reference antibody, then the test antibody may bind to the same epitope as the epitope bound by the reference antibody.
To determine if an antibody competes for binding with a reference anti-Zika antibody, the above-described binding methodology is performed in two orientations: In a first orientation, the reference antibody is allowed to bind to the Zika virus antigen under saturating conditions followed by assessment of binding of the test antibody to the Zika virus antigen. In a second orientation, the test antibody is allowed to bind to the Zika virus antigen molecule under saturating conditions followed by assessment of binding of the reference antibody to the Zika virus antigen. If, in both orientations, only the first (saturating) antibody is capable of binding to the Zika virus antigen, then it is concluded that the test antibody and the reference antibody compete for binding to the Zika virus antigen. As will be appreciated by a person of ordinary skill in the art, an antibody that competes for binding with a reference antibody may not necessarily bind to the identical epitope as the reference antibody but may sterically block binding of the reference antibody by binding an overlapping or adjacent epitope.
Two antibodies bind to the same or overlapping epitope if each competitively inhibits (blocks) binding of the other to the antigen. That is, a 1-, 5-, 10-, 20- or lOO-fold excess of one antibody inhibits binding of the other by at least 50% but preferably 75%, 90% or even 99% as measured in a competitive binding assay (see, e.g., Junghans el al, Cancer Res. 1990 50: 1495-1502). Alternatively, two antibodies have the same epitope if essentially all amino acid mutations in the antigen that reduce or eliminate binding of one antibody reduce or eliminate binding of the other. Two antibodies have overlapping epitopes if some amino acid mutations that reduce or eliminate binding of one antibody reduce or eliminate binding of the other.
Additional routine experimentation (e.g., peptide mutation and binding analyses) can then be carried out to confirm whether the observed lack of binding of the test antibody is in fact due to binding to the same epitope as the reference antibody or if steric blocking (or another phenomenon) is responsible for the lack of observed binding. Experiments of this sort can be performed using ELISA, RIA, surface plasmon resonance, flow cytometry or any other quantitative or qualitative antibody-binding assay available in the art. Structural studies with EM or crystallography also can demonstrate whether or not two antibodies that compete for binding recognize the same epitope.
In another aspect, there are provided monoclonal antibodies having clone-paired CDRs from the heavy and light chains as illustrated in Tables 3 and 4, respectively. Such antibodies may be produced by the clones discussed below in the Examples section using methods described herein.
In another aspect, the antibodies may be defined by their variable sequence, which include additional“framework” regions. These are provided in Tables 1 and 2 that encode or represent full variable regions. Furthermore, the antibodies sequences may vary from these sequences, optionally using methods discussed in greater detail below. For example, nucleic acid sequences may vary from those set out above in that (a) the variable regions may be segregated away from the constant domains of the light and heavy chains, (b) the nucleic acids may vary from those set out above while not affecting the residues encoded thereby, (c) the nucleic acids may vary from those set out above by a given percentage, e.g., 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% homology, (d) the nucleic acids may vary from those set out above by virtue of the ability to hybridize under high stringency conditions, as exemplified by low salt and/or high temperature conditions, such as provided by about 0.02 M to about 0.15 M NaCl at temperatures of about 50°C to about 70°C, (e) the amino acids may vary from those set out above by a given percentage, e.g., 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% homology, or (f) the amino acids may vary from those set out above by permitting conservative substitutions (discussed below). Each of the foregoing applies to the nucleic acid sequences set forth as Table 1 and the amino acid sequences of Table 2.
When comparing polynucleotide and polypeptide sequences, two sequences are said to be "identical" if the sequence of nucleotides or amino acids in the two sequences is the same when aligned for maximum correspondence, as described below. Comparisons between two sequences are typically performed by comparing the sequences over a comparison window to identify and compare local regions of sequence similarity. A "comparison window" as used herein, refers to a segment of at least about 20 contiguous positions, usually 30 to about 75, 40 to about 50, in which a sequence may be compared to a reference sequence of the same number of contiguous positions after the two sequences are optimally aligned.
Optimal alignment of sequences for comparison may be conducted using the Megalign program in the Lasergene suite of bioinformatics software (DNASTAR, Inc., Madison, Wis.), using default parameters. This program embodies several alignment schemes described in the following references: Dayhoff, M. O. (1978) A model of evolutionary change in proteins- Matrices for detecting distant relationships. In Dayhoff, M. O. (ed.) Atlas of Protein Sequence and Structure, National Biomedical Research Foundation, Washington D.C. Vol. 5, Suppl. 3, pp. 345-358; Hein J. (1990) Unified Approach to Alignment and Phylogeny pp. 626-645 Methods in Enzymology vol. 183, Academic Press, Inc., San Diego, Calif.; Higgins, D. G. and Sharp, P. M. (1989) CABIOS 5: 151-153; Myers, E. W. and Muller W. (1988) CABIOS 4: 11- 17; Robinson, E. D. (1971) Comb. Theor 11 : 105; Santou, N. Nes, M. (1987) Mol. Biol. Evol. 4:406-425; Sneath, P. H. A. and Sokal, R. R. (1973) Numerical Taxonomy— the Principles and Practice of Numerical Taxonomy, Freeman Press, San Francisco, Calif.; Wilbur, W. J. and Lipman, D. J. (1983) Proc. Natl. Acad., Sci. USA 80:726-730.
Alternatively, optimal alignment of sequences for comparison may be conducted by the local identity algorithm of Smith and Waterman (1981) Add. APL. Math 2:482, by the identity alignment algorithm of Needleman and Wunsch (1970) J. Mol. Biol. 48:443, by the search for similarity methods of Pearson and Lipman (1988) Proc. Natl. Acad. Sci. USA 85: 2444, by computerized implementations of these algorithms (GAP, BESTFIT, BLAST, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group (GCG), 575 Science Dr., Madison, Wis.), or by inspection.
One particular example of algorithms that are suitable for determining percent sequence identity and sequence similarity are the BLAST and BLAST 2.0 algorithms, which are described in Altschul et al. (1977) Nucl. Acids Res. 25:3389-3402 and Altschul et al. (1990) J. Mol. Biol. 215:403-410, respectively. BLAST and BLAST 2.0 can be used, for example with the parameters described herein, to determine percent sequence identity for the polynucleotides and polypeptides of the disclosure. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information. The rearranged nature of an antibody sequence and the variable length of each gene requires multiple rounds of BLAST searches for a single antibody sequence. Also, manual assembly of different genes is difficult and error-prone. The sequence analysis tool IgBLAST (world-wide-web at ncbi.nlm.nih.gov/igblast/) identifies matches to the germline V, D and J genes, details at rearrangement junctions, the delineation of Ig V domain framework regions and complementarity determining regions. IgBLAST can analyze nucleotide or protein sequences and can process sequences in batches and allows searches against the germline gene databases and other sequence databases simultaneously to minimize the chance of missing possibly the best matching germline V gene. In one illustrative example, cumulative scores can be calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always >0) and N (penalty score for mismatching residues; always <0). Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T and X determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a wordlength (W) of 11, and expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff and Henikoff (1989) Proc. Natl. Acad. Sci. USA 89: 10915) alignments, (B) of 50, expectation (E) of 10, M=5, N=-4 and a comparison of both strands.
For amino acid sequences, a scoring matrix can be used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T and X determine the sensitivity and speed of the alignment.
In one approach, the "percentage of sequence identity" is determined by comparing two optimally aligned sequences over a window of comparison of at least 20 positions, wherein the portion of the polynucleotide or polypeptide sequence in the comparison window may comprise additions or deletions (i.e., gaps) of 20 percent or less, usually 5 to 15 percent, or 10 to 12 percent, as compared to the reference sequences (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical nucleic acid bases or amino acid residues occur in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the reference sequence (i.e., the window size) and multiplying the results by 100 to yield the percentage of sequence identity.
Yet another way of defining an antibody is as a“derivative” of any of the below- described antibodies and their antigen-binding fragments. The term“derivative” refers to an antibody or antigen-binding fragment thereof that immunospecifically binds to an antigen but which comprises, one, two, three, four, five or more amino acid substitutions, additions, deletions or modifications relative to a“parental” (or wild-type) molecule. Such amino acid substitutions or additions may introduce naturally occurring (i.e., DNA-encoded) or non- naturally occurring amino acid residues. The term“derivative” encompasses, for example, as variants having altered CH1, hinge, CH2, CH3 or CH4 regions, so as to form, for example antibodies, etc. , having variant Fc regions that exhibit enhanced or impaired effector or binding characteristics. The term“derivative” additionally encompasses non-amino acid modifications, for example, amino acids that may be glycosylated (e.g., have altered mannose, 2-N- acetylglucosamine, galactose, fucose, glucose, sialic acid, 5-N-acetylneuraminic acid, 5- glycolneuraminic acid, etc. content), acetylated, pegylated, phosphorylated, amidated, derivatized by known protecting/blocking groups, proteolytic cleavage, linked to a cellular ligand or other protein, etc. In some embodiments, the altered carbohydrate modifications modulate one or more of the following: solubilization of the antibody, facilitation of subcellular transport and secretion of the antibody, promotion of antibody assembly, conformational integrity, and antibody-mediated effector function. In a specific embodiment, the altered carbohydrate modifications enhance antibody mediated effector function relative to the antibody lacking the carbohydrate modification. Carbohydrate modifications that lead to altered antibody mediated effector function are well known in the art (for example, see Shields, R. L. et al. (2002)“ Lack Of Fucose On Human IgG N-Linked Oligosaccharide Improves Binding To Human Fcgamma RIII And Antibody-Dependent Cellular Toxicity ,” J. Biol. Chem. 277(30): 26733-26740; Davies J. et al. (2001)“ Expression Of GnTIII In A Recombinant Anti- CD20 CHO Production Cell Line: Expression Of Antibodies With Altered Glycoforms Leads To An Increase In ADCC Through Higher Affinity For FC Gamma RIII. Biotechnology & Bioengineering 74(4): 288-294). Methods of altering carbohydrate contents are known to those skilled in the art, see, e.g., Wallick, S. C. et al. (1988)“ Glycosylation Of A VH Residue Of A Monoclonal Antibody Against Alpha (1— 6) Dextran Increases Its Affinity For Antigen ,” J. Exp. Med. 168(3): 1099-1109; Tao, M. H. et al. (1989)“ Studies Of Aglycosylated Chimeric Mouse-Human IgG. Role Of Carbohydrate In The Structure And Effector Functions Mediated By The Human IgG Constant Region ,” J. Immunol. 143(8): 2595-2601; Routledge, E. G. et al. (1995)“The Effect Of Aglycosylation On The Immunogenicity Of A Humanized Therapeutic CD3 Monoclonal Antibody ,” Transplantation 60(8):847-53; Elliott, S. et al. (2003) “ Enhancement Of Therapeutic Protein In Vivo Activities Through Glycoengineeringf Nature Biotechnol. 21:414-21; Shields, R. L. et al. (2002)“Lack Of Fucose On Human IgG N-Linked Oligosaccharide Improves Binding To Human Fcgamma RIII And Antibody-Dependent Cellular Toxicity ,” J. Biol. Chem. 277(30): 26733-26740).
A derivative antibody or antibody fragment can be generated with an engineered sequence or glycosylation state to confer preferred levels of activity in antibody dependent cellular cytotoxicity (ADCC), antibody-dependent cellular phagocytosis (ADCP), antibody- dependent neutrophil phagocytosis (ADNP), or antibody-dependent complement deposition (ADCD) functions as measured by bead-based or cell-based assays or in vivo studies in animal models.
A derivative antibody or antibody fragment may be modified by chemical modifications using techniques known to those of skill in the art, including, but not limited to, specific chemical cleavage, acetylation, formulation, metabolic synthesis of tunicamycin, etc. In one embodiment, an antibody derivative will possess a similar or identical function as the parental antibody. In another embodiment, an antibody derivative will exhibit an altered activity relative to the parental antibody. For example, a derivative antibody (or fragment thereof) can bind to its epitope more tightly or be more resistant to proteolysis than the parental antibody.
C. Engineering of Antibody Sequences
In various embodiments, one may choose to engineer sequences of the identified antibodies for a variety of reasons, such as improved expression, improved cross-reactivity or diminished off-target binding. Modified antibodies may be made by any technique known to those of skill in the art, including expression through standard molecular biological techniques, or the chemical synthesis of polypeptides. Methods for recombinant expression are addressed elsewhere in this document. The following is a general discussion of relevant goals techniques for antibody engineering.
Hybridomas may be cultured, then cells lysed, and total RNA extracted. Random hexamers may be used with RT to generate cDNA copies of RNA, and then PCR performed using a multiplex mixture of PCR primers expected to amplify all human variable gene sequences. PCR product can be cloned into pGEM-T Easy vector, then sequenced by automated DNA sequencing using standard vector primers. Assay of binding and neutralization may be performed using antibodies collected from hybridoma supernatants and purified by FPLC, using Protein G columns.
Recombinant full-length IgG antibodies can be generated by subcloning heavy and light chain Fv DNAs from the cloning vector into an IgG plasmid vector, transfected into 293 (e.g., Freestyle) cells or CHO cells, and antibodies can be collected and purified from the 293 or CHO cell supernatant. Other appropriate host cells systems include bacteria, such as E. coli, insect cells (S2, Sf9, Sf29, High Five), plant cells (e.g., tobacco, with or without engineering for human-like glycans), algae, or in a variety of non-human transgenic contexts, such as mice, rats, goats or cows. Expression of nucleic acids encoding antibodies, both for the purpose of subsequent antibody purification, and for immunization of a host, is also contemplated. Antibody coding sequences can be RNA, such as native RNA or modified RNA. Modified RNA contemplates certain chemical modifications that confer increased stability and low immunogenicity to mRNAs, thereby facilitating expression of therapeutically important proteins. For instance, Nl -methyl-pseudouridine (N 1 hiY) outperforms several other nucleoside modifications and their combinations in terms of translation capacity. In addition to turning off the immune/eIF2a phosphorylation-dependent inhibition of translation, incorporated N 1 hiY nucleotides dramatically alter the dynamics of the translation process by increasing ribosome pausing and density on the mRNA. Increased ribosome loading of modified mRNAs renders them more permissive for initiation by favoring either ribosome recycling on the same mRNA or de novo ribosome recruitment. Such modifications could be used to enhance antibody expression in vivo following inoculation with RNA. The RNA, whether native or modified, may be delivered as naked RNA or in a delivery vehicle, such as a lipid nanoparticle.
Alternatively, DNA encoding the antibody may be employed for the same purposes. The DNA is included in an expression cassette comprising a promoter active in the host cell for which it is designed. The expression cassette is advantageously included in a replicable vector, such as a conventional plasmid or minivector. Vectors include viral vectors, such as poxviruses, adenoviruses, herpesviruses, adeno-associated viruses, and lentiviruses are contemplated. Replicons encoding antibody genes such as alphavirus replicons based on VEE virus or Sindbis virus are also contemplated. Delivery of such vectors can be performed by needle through intramuscular, subcutaneous, or intradermal routes, or by transcutaneous electroporation when in vivo expression is desired.
The rapid availability of antibody produced in the same host cell and cell culture process as the final cGMP manufacturing process has the potential to reduce the duration of process development programs. Lonza has developed a generic method using pooled transfectants grown in CDACF medium, for the rapid production of small quantities (up to 50 g) of antibodies in CHO cells. Although slightly slower than a true transient system, the advantages include a higher product concentration and use of the same host and process as the production cell line. Example of growth and productivity of GS-CHO pools, expressing a model antibody, in a disposable bioreactor: in a disposable bag bioreactor culture (5 L working volume) operated in fed-batch mode, a harvest antibody concentration of 2 g/L was achieved within 9 weeks of transfection. Antibody molecules will comprise fragments (such as F(ab'), F(ab')2) that are produced, for example, by the proteolytic cleavage of the mAbs, or single-chain immunoglobulins producible, for example, via recombinant means. F(ab') antibody derivatives are monovalent, while F(ab')2 antibody derivatives are bivalent. In one embodiment, such fragments can be combined with one another, or with other antibody fragments or receptor ligands to form “chimeric” binding molecules. Significantly, such chimeric molecules may contain substituents capable of binding to different epitopes of the same molecule.
In related embodiments, the antibody is a derivative of the disclosed antibodies, e.g., an antibody comprising the CDR sequences identical to those in the disclosed antibodies (e.g., a chimeric, or CDR-grafted antibody). Alternatively, one may wish to make modifications, such as introducing conservative changes into an antibody molecule. In making such changes, the hydropathic index of amino acids may be considered. The importance of the hydropathic amino acid index in conferring interactive biologic function on a protein is generally understood in the art (Kyte and Doolittle, 1982). It is accepted that the relative hydropathic character of the amino acid contributes to the secondary structure of the resultant protein, which in turn defines the interaction of the protein with other molecules, for example, enzymes, substrates, receptors, DNA, antibodies, antigens, and the like.
It also is understood in the art that the substitution of like amino acids can be made effectively on the basis of hydrophilicity. U.S. Patent 4,554,101, incorporated herein by reference, states that the greatest local average hydrophilicity of a protein, as governed by the hydrophilicity of its adjacent amino acids, correlates with a biological property of the protein. As detailed in U.S. Patent 4,554,101, the following hydrophilicity values have been assigned to amino acid residues: basic amino acids: arginine (+3.0), lysine (+3.0), and histidine (-0.5); acidic amino acids: aspartate (+3.0 ± 1), glutamate (+3.0 ± 1), asparagine (+0.2), and glutamine (+0.2); hydrophilic, nonionic amino acids: serine (+0.3), asparagine (+0.2), glutamine (+0.2), and threonine (-0.4), sulfur containing amino acids: cysteine (-1.0) and methionine (-1.3); hydrophobic, nonaromatic amino acids: valine (-1.5), leucine (-1.8), isoleucine (-1.8), proline (-0.5 ± 1), alanine (-0.5), and glycine (0); hydrophobic, aromatic amino acids: tryptophan (- 3.4), phenylalanine (-2.5), and tyrosine (-2.3).
It is understood that an amino acid can be substituted for another having a similar hydrophilicity and produce a biologically or immunologically modified protein. In such changes, the substitution of amino acids whose hydrophilicity values are within ± 2 is preferred, those that are within ± 1 are particularly preferred, and those within ± 0.5 are even more particularly preferred.
As outlined above, amino acid substitutions generally are based on the relative similarity of the amino acid side-chain substituents, for example, their hydrophobicity, hydrophilicity, charge, size, and the like. Exemplary substitutions that take into consideration the various foregoing characteristics are well known to those of skill in the art and include: arginine and lysine; glutamate and aspartate; serine and threonine; glutamine and asparagine; and valine, leucine and isoleucine.
The present disclosure also contemplates isotype modification. By modifying the Fc region to have a different isotype, different functionalities can be achieved. For example, changing to IgGi can increase antibody dependent cell cytotoxicity, switching to class A can improve tissue distribution, and switching to class M can improve valency.
Alternatively or additionally, it may be useful to combine amino acid modifications with one or more further amino acid modifications that alter Clq binding and/or the complement dependent cytotoxicity (CDC) function of the Fc region of an IL-23pl9 binding molecule. The binding polypeptide of particular interest may be one that binds to Clq and displays complement dependent cytotoxicity. Polypeptides with pre-existing Clq binding activity, optionally further having the ability to mediate CDC may be modified such that one or both of these activities are enhanced. Amino acid modifications that alter Clq and/or modify its complement dependent cytotoxicity function are described, for example, in WO/0042072, which is hereby incorporated by reference.
One can design an Fc region of an antibody with altered effector function, e.g., by modifying Clq binding and/or FcyR binding and thereby changing CDC activity and/or ADCC activity.“Effector functions” are responsible for activating or diminishing a biological activity (e.g., in a subject). Examples of effector functions include, but are not limited to: Clq binding; complement dependent cytotoxicity (CDC); Fc receptor binding; antibody-dependent cell- mediated cytotoxicity (ADCC); phagocytosis; down regulation of cell surface receptors (e.g., B cell receptor; BCR), etc. Such effector functions may require the Fc region to be combined with a binding domain (e.g., an antibody variable domain) and can be assessed using various assays (e.g., Fc binding assays, ADCC assays, CDC assays, etc.).
For example, one can generate a variant Fc region of an antibody with improved Clq binding and improved FcyRIII binding (e.g., having both improved ADCC activity and improved CDC activity). Alternatively, if it is desired that effector function be reduced or ablated, a variant Fc region can be engineered with reduced CDC activity and/or reduced ADCC activity. In other embodiments, only one of these activities may be increased, and, optionally, also the other activity reduced (e.g., to generate an Fc region variant with improved ADCC activity, but reduced CDC activity and vice versa).
FcRn binding. Fc mutations can also be introduced and engineered to alter their interaction with the neonatal Fc receptor (FcRn) and improve their pharmacokinetic properties. A collection of human Fc variants with improved binding to the FcRn have been described (Shields et al., (2001). High resolution mapping of the binding site on human IgGl for FcyRI, FcyRII, FcyRIII, and FcRn and design of IgGl variants with improved binding to the FcyR, (J. Biol. Chem. 276:6591-6604). A number of methods are known that can result in increased half- life (Kuo and Aveson, (2011)), including amino acid modifications may be generated through techniques including alanine scanning mutagenesis, random mutagenesis and screening to assess the binding to the neonatal Fc receptor (FcRn) and/or the in vivo behavior. Computational strategies followed by mutagenesis may also be used to select one of amino acid mutations to mutate.
The present disclosure therefore provides a variant of an antigen binding protein with optimized binding to FcRn. In a particular embodiment, the said variant of an antigen binding protein comprises at least one amino acid modification in the Fc region of said antigen binding protein, wherein said modification is selected from the group consisting of 226, 227, 228, 230, 231, 233, 234, 239, 241, 243, 246, 250, 252, 256, 259, 264, 265, 267, 269, 270, 276, 284, 285,
288, 289, 290, 291, 292, 294, 297, 298, 299, 301, 302, 303, 305, 307, 308, 309, 311, 315, 317,
320, 322, 325, 327, 330, 332, 334, 335, 338, 340, 342, 343, 345, 347, 350, 352, 354, 355, 356,
359, 360, 361, 362, 369, 370, 371, 375, 378, 380, 382, 384, 385, 386, 387, 389, 390, 392, 393,
394, 395, 396, 397, 398, 399, 400, 401 403, 404, 408, 411, 412, 414, 415, 416, 418, 419, 420,
421, 422, 424, 426, 428, 433, 434, 438, 439, 440, 443, 444, 445, 446 and 447 of the Fc region as compared to said parent polypeptide, wherein the numbering of the amino acids in the Fc region is that of the EU index in Kabat. In a further aspect of the disclosure the modifications are M252Y/S254T/T256E.
Additionally, various publications describe methods for obtaining physiologically active molecules whose half-lives are modified, see for example Kontermann (2009) either by introducing an FcRn-binding polypeptide into the molecules or by fusing the molecules with antibodies whose FcRn-binding affinities are preserved but affinities for other Fc receptors have been greatly reduced or fusing with FcRn binding domains of antibodies.
Derivatized antibodies may be used to alter the half-lives (e.g., serum half-lives) of parental antibodies in a mammal, particularly a human. Such alterations may result in a half- life of greater than 15 days, preferably greater than 20 days, greater than 25 days, greater than 30 days, greater than 35 days, greater than 40 days, greater than 45 days, greater than 2 months, greater than 3 months, greater than 4 months, or greater than 5 months. The increased half- lives of the antibodies of the present disclosure or fragments thereof in a mammal, preferably a human, results in a higher serum titer of said antibodies or antibody fragments in the mammal, and thus reduces the frequency of the administration of said antibodies or antibody fragments and/or reduces the concentration of said antibodies or antibody fragments to be administered. Antibodies or fragments thereof having increased in vivo half-lives can be generated by techniques known to those of skill in the art. For example, antibodies or fragments thereof with increased in vivo half-lives can be generated by modifying (e.g., substituting, deleting or adding) amino acid residues identified as involved in the interaction between the Fc domain and the FcRn receptor.
Beltramello et al. (2010) previously reported the modification of neutralizing mAbs, due to their tendency to enhance dengue virus infection, by generating in which leucine residues at positions 1.3 and 1.2 of CH2 domain (according to the IMGT unique numbering for C-domain) were substituted with alanine residues. This modification, also known as“LALA” mutation, abolishes antibody binding to FcyRI, FcyRII and FcyRIIIa, as described by Hessell et al. (2007). The variant and unmodified recombinant mAbs were compared for their capacity to neutralize and enhance infection by the four dengue virus serotypes. LALA variants retained the same neutralizing activity as unmodified mAh but were completely devoid of enhancing activity. LALA mutations of this nature are therefore contemplated in the context of the presently disclosed antibodies.
Altered Glycosylation. A particular embodiment of the present disclosure is an isolated monoclonal antibody, or antigen binding fragment thereof, containing a substantially homogeneous glycan without sialic acid, galactose, or fucose. The monoclonal antibody comprises a heavy chain variable region and a light chain variable region, both of which may be attached to heavy chain or light chain constant regions respectively. The aforementioned substantially homogeneous glycan may be covalently attached to the heavy chain constant region.
Another embodiment of the present disclosure comprises a mAh with a novel Fc glycosylation pattern. The isolated monoclonal antibody, or antigen binding fragment thereof, is present in a substantially homogenous composition represented by the GNGN or G1/G2 gly coform. Fc glycosylation plays a significant role in anti-viral and anti-cancer properties of therapeutic mAbs. The disclosure is in line with a recent study that shows increased anti- lentivirus cell-mediated viral inhibition of a fucose free anti-HIV mAh in vitro. This embodiment of the present disclosure with homogenous glycans lacking a core fucose, showed increased protection against specific viruses by a factor greater than two-fold. Elimination of core fucose dramatically improves the ADCC activity of mAbs mediated by natural killer (NK) cells but appears to have the opposite effect on the ADCC activity of polymorphonuclear cells (PMNs).
The isolated monoclonal antibody, or antigen binding fragment thereof, comprising a substantially homogenous composition represented by the GNGN or G1/G2 gly coform exhibits increased binding affinity for Fc gamma RI and Fc gamma RIII compared to the same antibody without the substantially homogeneous GNGN glycoform and with GO, G1F, G2F, GNF, GNGNF or GNGNFX containing glycoforms. In one embodiment of the present disclosure, the antibody dissociates from Fc gamma RI with a Kd of 1 x 10 8 M or less and from Fc gamma RIII with a Kd of 1 x 10 7 M or less.
Glycosylation of an Fc region is typically either N-linked or O-linked. N-linked refers to the attachment of the carbohydrate moiety to the side chain of an asparagine residue. O- linked glycosylation refers to the attachment of one of the sugars N-acetylgalactosamine, galactose, or xylose to a hydroxyamino acid, most commonly serine or threonine, although 5- hydroxyproline or 5-hydroxylysine may also be used. The recognition sequences for enzymatic attachment of the carbohydrate moiety to the asparagine side chain peptide sequences are asparagine-X-serine and asparagine-X-threonine, where X is any amino acid except proline. Thus, the presence of either of these peptide sequences in a polypeptide creates a potential glycosylation site.
The glycosylation pattern may be altered, for example, by deleting one or more glycosylation site(s) found in the polypeptide, and/or adding one or more glycosylation site(s) that are not present in the polypeptide. Addition of glycosylation sites to the Fc region of an antibody is conveniently accomplished by altering the amino acid sequence such that it contains one or more of the above-described tripeptide sequences (for N-linked glycosylation sites). An exemplary glycosylation variant has an amino acid substitution of residue Asn 297 of the heavy chain. The alteration may also be made by the addition of, or substitution by, one or more serine or threonine residues to the sequence of the original polypeptide (for O-linked glycosylation sites). Additionally, a change of Asn 297 to Ala can remove one of the glycosylation sites.
In certain embodiments, the antibody is expressed in cells that express beta (l,4)-N- acetylglucosaminyltransferase III (GnT III), such that GnT III adds GlcNAc to the IL-23pl9 antibody. Methods for producing antibodies in such a fashion are provided in WO/9954342, WO/03011878, patent publication 20030003097A1, and Umana et al., Nature Biotechnology, 17: 176-180, February 1999. Cell lines can be altered to enhance or reduce or eliminate certain post-translational modifications, such as glycosylation, using genome editing technology such as Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR). For example, CRISPR technology can be used to eliminate genes encoding glycosylating enzymes in 293 or CHO cells used to express recombinant monoclonal antibodies.
Elimination of monoclonal antibody protein sequence liabilities. It is possible to engineer the antibody variable gene sequences obtained from human B cells to enhance their manufacturability and safety. Potential protein sequence liabilities can be identified by searching for sequence motifs associated with sites containing:
1) Unpaired Cys residues,
2) N-linked glycosylation,
3) Asn deamidation,
4) Asp isomerization,
5) SYE truncation,
6) Met oxidation,
7) Trp oxidation,
8) N-terminal glutamate,
9) Integrin binding,
10) CDl lc/CDl8 binding, or
11) Fragmentation
Such motifs can be eliminated by altering the synthetic gene for the cDNA encoding recombinant antibodies.
Protein engineering efforts in the field of development of therapeutic antibodies clearly reveal that certain sequences or residues are associated with solubility differences (Femandez- Escamilla et al, Nature Biotech, 22 (10), 1302-1306, 2004; Chennamsetty et al, PNAS, 106 (29), 11937-11942, 2009; Voynov et al, Biocon. Chem., 21 (2), 385-392, 2010) Evidence from solubility-altering mutations in the literature indicate that some hydrophilic residues such as aspartic acid, glutamic acid, and serine contribute significantly more favorably to protein solubility than other hydrophilic residues, such as asparagine, glutamine, threonine, lysine, and arginine.
Stability. Antibodies can be engineered for enhanced biophysical properties. One can use elevated temperature to unfold antibodies to determine relative stability, using average apparent melting temperatures. Differential Scanning Calorimetry (DSC) measures the heat capacity, CP, of a molecule (the heat required to warm it, per degree) as a function of temperature. One can use DSC to study the thermal stability of antibodies. DSC data for mAbs is particularly interesting because it sometimes resolves the unfolding of individual domains within the mAh structure, producing up to three peaks in the thermogram (from unfolding of the Fab, CH2, and CH3 domains). Typically unfolding of the Fab domain produces the strongest peak. The DSC profiles and relative stability of the Fc portion show characteristic differences for the human IgGi, IgG2, IgGv and IgGr subclasses (Garber and Demarest, Biochem. Biophys. Res. Commun. 355, 751-757, 2007). One also can determine average apparent melting temperature using circular dichroism (CD), performed with a CD spectrometer. Far-UV CD spectra will be measured for antibodies in the range of 200 to 260 nm at increments of 0.5 nm. The final spectra can be determined as averages of 20 accumulations. Residue ellipticity values can be calculated after background subtraction. Thermal unfolding of antibodies (0.1 mg/mL) can be monitored at 235 nm from 25-95 °C and a heating rate of 1 °C/min. One can use dynamic light scattering (DLS) to assess for propensity for aggregation. DLS is used to characterize size of various particles including proteins. If the system is not disperse in size, the mean effective diameter of the particles can be determined. This measurement depends on the size of the particle core, the size of surface structures, and particle concentration. Since DLS essentially measures fluctuations in scattered light intensity due to particles, the diffusion coefficient of the particles can be determined. DLS software in commercial DLA instruments displays the particle population at different diameters. Stability studies can be done conveniently using DLS. DLS measurements of a sample can show whether the particles aggregate over time or with temperature variation by determining whether the hydrodynamic radius of the particle increases. If particles aggregate, one can see a larger population of particles with a larger radius. Stability depending on temperature can be analyzed by controlling the temperature in situ. Capillary electrophoresis (CE) techniques include proven methodologies for determining features of antibody stability. One can use an iCE approach to resolve antibody protein charge variants due to deamidation, C-terminal lysines, sialylation, oxidation, glycosylation, and any other change to the protein that can result in a change in pi of the protein. Each of the expressed antibody proteins can be evaluated by high throughput, free solution isoelectric focusing (IEF) in a capillary column (cIEF), using a Protein Simple Maurice instrument. Whole-column UV absorption detection can be performed every 30 seconds for real time monitoring of molecules focusing at the isoelectric points (pis). This approach combines the high resolution of traditional gel IEF with the advantages of quantitation and automation found in column-based separations while eliminating the need for a mobilization step. The technique yields reproducible, quantitative analysis of identity, purity, and heterogeneity profiles for the expressed antibodies. The results identify charge heterogeneity and molecular sizing on the antibodies, with both absorbance and native fluorescence detection modes and with sensitivity of detection down to 0.7 pg/mL.
Solubility. One can determine the intrinsic solubility score of antibody sequences. The intrinsic solubility scores can be calculated using CamSol Intrinsic (Sormanni el al. , JMol Biol 427, 478-490, 2015). The amino acid sequences for residues 95-102 (Kabat numbering) in HCDR3 of each antibody fragment such as a scFv can be evaluated via the online program to calculate the solubility scores. One also can determine solubility using laboratory techniques. Various techniques exist, including addition of lyophilized protein to a solution until the solution becomes saturated and the solubility limit is reached, or concentration by ultrafiltration in a microconcentrator with a suitable molecular weight cut-off. The most straightforward method is induction of amorphous precipitation, which measures protein solubility using a method involving protein precipitation using ammonium sulfate (Trevino et al. , J Mol Biol, 366: 449-460, 2007). Ammonium sulfate precipitation gives quick and accurate information on relative solubility values. Ammonium sulfate precipitation produces precipitated solutions with well-defined aqueous and solid phases and requires relatively small amounts of protein. Solubility measurements performed using induction of amorphous precipitation by ammonium sulfate also can be done easily at different pH values. Protein solubility is highly pH dependent, and pH is considered the most important extrinsic factor that affects solubility.
Autoreactivity. Generally, it is thought that autoreactive clones should be eliminated during ontogeny by negative selection, however it has become clear that many human naturally occurring antibodies with autoreactive properties persist in adult mature repertoires, and the autoreactivity may enhance the antiviral function of many antibodies to pathogens. It has been noted that HCDR3 loops in antibodies during early B cell development are often rich in positive charge and exhibit autoreactive patterns (Wardemann et al, Science 301, 1374-1377, 2003). One can test a given antibody for autoreactivity by assessing the level of binding to human origin cells in microscopy (using adherent HeLa or HEp-2 epithelial cells) and flow cytometric cell surface staining (using suspension Jurkat T cells and 293 S human embryonic kidney cells). Autoreactivity also can be surveyed using assessment of binding to tissues in tissue arrays.
Preferred residues (“Human Likeness”). B cell repertoire deep sequencing of human B cells from blood donors is being performed on a wide scale in many recent studies. Sequence information about a significant portion of the human antibody repertoire facilitates statistical assessment of antibody sequence features common in healthy humans. With knowledge about the antibody sequence features in a human recombined antibody variable gene reference database, the position specific degree of“Human Likeness” (HL) of an antibody sequence can be estimated. HL has been shown to be useful for the development of antibodies in clinical use, like therapeutic antibodies or antibodies as vaccines. The goal is to increase the human likeness of antibodies to reduce potential adverse effects and anti-antibody immune responses that will lead to significantly decreased efficacy of the antibody drug or can induce serious health implications. One can assess antibody characteristics of the combined antibody repertoire of three healthy human blood donors of about 400 million sequences in total and created a novel “relative Human Likeness” (rHL) score that focuses on the hypervariable region of the antibody. The rHL score allows one to easily distinguish between human (positive score) and non-human sequences (negative score). Antibodies can be engineered to eliminate residues that are not common in human repertoires.
D. Single Chain Antibodies
A single chain variable fragment (scFv) is a fusion of the variable regions of the heavy and light chains of immunoglobulins, linked together with a short (usually serine, glycine) linker. This chimeric molecule retains the specificity of the original immunoglobulin, despite removal of the constant regions and the introduction of a linker peptide. This modification usually leaves the specificity unaltered. These molecules were created historically to facilitate phage display where it is highly convenient to express the antigen binding domain as a single peptide. Alternatively, scFv can be created directly from subcloned heavy and light chains derived from a hybridoma or B cell. Single chain variable fragments lack the constant F c region found in complete antibody molecules, and thus, the common binding sites (e.g., protein A/G) used to purify antibodies. These fragments can often be purified/immobilized using Protein L since Protein L interacts with the variable region of kappa light chains.
Flexible linkers generally are comprised of helix- and turn-promoting amino acid residues such as alanine, serine and glycine. However, other residues can function as well. Tang et al. (1996) used phage display as a means of rapidly selecting tailored linkers for single chain antibodies (scFvs) from protein linker libraries. A random linker library was constructed in which the genes for the heavy and light chain variable domains were linked by a segment encoding an 18-amino acid polypeptide of variable composition. The scFv repertoire (approx. 5 x 106 different members) was displayed on filamentous phage and subjected to affinity selection with hapten. The population of selected variants exhibited significant increases in binding activity but retained considerable sequence diversity. Screening 1054 individual variants subsequently yielded a catalytically active scFv that was produced efficiently in soluble form. Sequence analysis revealed a conserved proline in the linker two residues after the VH C terminus and an abundance of arginines and prolines at other positions as the only common features of the selected tethers.
The recombinant antibodies of the present disclosure may also involve sequences or moieties that permit dimerization or multimerization of the receptors. Such sequences include those derived from IgA, which permit formation of multimers in conjunction with the J-chain. Another multimerization domain is the Gal4 dimerization domain. In other embodiments, the chains may be modified with agents such as biotin/avidin, which permit the combination of two antibodies.
In a separate embodiment, a single-chain antibody can be created by joining receptor light and heavy chains using a non-peptide linker or chemical unit. Generally, the light and heavy chains will be produced in distinct cells, purified, and subsequently linked together in an appropriate fashion (/. e. , the N-terminus of the heavy chain being attached to the C-terminus of the light chain via an appropriate chemical bridge).
Cross-linking reagents are used to form molecular bridges that tie functional groups of two different molecules, e.g., a stabilizing and coagulating agent. However, it is contemplated that dimers or multimers of the same analog or heteromeric complexes comprised of different analogs can be created. To link two different compounds in a step-wise manner, hetero- bifunctional cross-linkers can be used that eliminate unwanted homopolymer formation.
An exemplary hetero-bifunctional cross-linker contains two reactive groups: one reacting with primary amine group (e.g., N-hydroxy succinimide) and the other reacting with a thiol group (e.g., pyridyl disulfide, maleimides, halogens, etc.). Through the primary amine reactive group, the cross-linker may react with the lysine residue(s) of one protein (e.g., the selected antibody or fragment) and through the thiol reactive group, the cross-linker, already tied up to the first protein, reacts with the cysteine residue (free sulfhydryl group) of the other protein (e.g., the selective agent).
It is preferred that a cross-linker having reasonable stability in blood will be employed. Numerous types of disulfide-bond containing linkers are known that can be successfully employed to conjugate targeting and therapeutic/preventative agents. Linkers that contain a disulfide bond that is sterically hindered may prove to give greater stability in vivo, preventing release of the targeting peptide prior to reaching the site of action. These linkers are thus one group of linking agents. Another cross-linking reagent is SMPT, which is a bifunctional cross-linker containing a disulfide bond that is“sterically hindered” by an adjacent benzene ring and methyl groups. It is believed that steric hindrance of the disulfide bond serves a function of protecting the bond from attack by thiolate anions such as glutathione which can be present in tissues and blood, and thereby help in preventing decoupling of the conjugate prior to the delivery of the attached agent to the target site.
The SMPT cross-linking reagent, as with many other known cross-linking reagents, lends the ability to cross-link functional groups such as the SH of cysteine or primary amines (e.g., the epsilon amino group of lysine). Another possible type of cross-linker includes the hetero-bifunctional photoreactive phenylazides containing a cleavable disulfide bond such as sulfosuccinimidyl-2-(p-azido salicylamido) ethyl-l,3'-dithiopropionate. The N-hydroxy- succinimidyl group reacts with primary amino groups and the phenylazide (upon photolysis) reacts non-selectively with any amino acid residue.
In addition to hindered cross-linkers, non-hindered linkers also can be employed in accordance herewith. Other useful cross-linkers, not considered to contain or generate a protected disulfide, include SATA, SPDP and 2-iminothiolane (Wawrzynczak & Thorpe, 1987). The use of such cross-linkers is well understood in the art. Another embodiment involves the use of flexible linkers.
U.S. Patent 4,680,338 describes bifunctional linkers useful for producing conjugates of ligands with amine-containing polymers and/or proteins, especially for forming antibody conjugates with chelators, drugs, enzymes, detectable labels and the like. U.S. Patents 5,141,648 and 5,563,250 disclose cleavable conjugates containing a labile bond that is cleavable under a variety of mild conditions. This linker is particularly useful in that the agent of interest may be bonded directly to the linker, with cleavage resulting in release of the active agent. Particular uses include adding a free amino or free sulfhydryl group to a protein, such as an antibody, or a drug.
U.S. Patent 5,856,456 provides peptide linkers for use in connecting polypeptide constituents to make fusion proteins, e.g., single chain antibodies. The linker is up to about 50 amino acids in length, contains at least one occurrence of a charged amino acid (preferably arginine or lysine) followed by a proline, and is characterized by greater stability and reduced aggregation. U.S. Patent 5,880,270 discloses aminooxy-containing linkers useful in a variety of immunodiagnostic and separative techniques. E. Multispecific Antibodies
In certain embodiments, antibodies of the present disclosure are bispecific or multispecific. Bispecific antibodies are antibodies that have binding specificities for at least two different epitopes. Exemplary bispecific antibodies may bind to two different epitopes of a single antigen. Other such antibodies may combine a first antigen binding site with a binding site for a second antigen. Alternatively, an anti-pathogen arm may be combined with an arm that binds to a triggering molecule on a leukocyte, such as a T-cell receptor molecule (e.g., CD3), or Fc receptors for IgG (FcyR), such as FcyRI (CD64), FcyRII (CD32) and Fc gamma RIII (CD 16), so as to focus and localize cellular defense mechanisms to the infected cell. Bispecific antibodies may also be used to localize cytotoxic agents to infected cells. These antibodies possess a pathogen-binding arm and an arm that binds the cytotoxic agent (e.g., saporin, anti-interferon-a, vinca alkaloid, ricin A chain, methotrexate or radioactive isotope hapten). Bispecific antibodies can be prepared as full-length antibodies or antibody fragments (e.g., F(ab')2 bispecific antibodies). WO 96/16673 describes a bispecific anti-ErbB2/anti-Fc gamma RIII antibody and U.S. Pat. No. 5,837,234 discloses a bispecific anti-ErbB2/anti-Fc gamma RI antibody. A bispecific anti-ErbB2/Fc alpha antibody is shown in WO98/02463. U.S. Pat. No. 5,821,337 teaches a bispecific anti-ErbB2/anti-CD3 antibody.
Methods for making bispecific antibodies are known in the art. Traditional production of full-length bispecific antibodies is based on the co-expression of two immunoglobulin heavy chain-light chain pairs, where the two chains have different specificities (Millstein et al, Nature, 305:537-539 (1983)). Because of the random assortment of immunoglobulin heavy and light chains, these hybridomas (quadromas) produce a potential mixture of ten different antibody molecules, of which only one has the correct bispecific structure. Purification of the correct molecule, which is usually done by affinity chromatography steps, is rather cumbersome, and the product yields are low. Similar procedures are disclosed in WO 93/08829, and in Traunecker et al, EMBO J., 10:3655-3659 (1991).
According to a different approach, antibody variable regions with the desired binding specificities (antibody-antigen combining sites) are fused to immunoglobulin constant domain sequences. Preferably, the fusion is with an Ig heavy chain constant domain, comprising at least part of the hinge, Cm, and Cm regions. It is preferred to have the first heavy-chain constant region (Cm) containing the site necessary for light chain bonding, present in at least one of the fusions. DNAs encoding the immunoglobulin heavy chain fusions and, if desired, the immunoglobulin light chain, are inserted into separate expression vectors, and are co- transfected into a suitable host cell. This provides for greater flexibility in adjusting the mutual proportions of the three polypeptide fragments in embodiments when unequal ratios of the three polypeptide chains used in the construction provide the optimum yield of the desired bispecific antibody. It is, however, possible to insert the coding sequences for two or all three polypeptide chains into a single expression vector when the expression of at least two polypeptide chains in equal ratios results in high yields or when the ratios have no significant effect on the yield of the desired chain combination.
In a particular embodiment of this approach, the bispecific antibodies are composed of a hybrid immunoglobulin heavy chain with a first binding specificity in one arm, and a hybrid immunoglobulin heavy chain-light chain pair (providing a second binding specificity) in the other arm. It was found that this asymmetric structure facilitates the separation of the desired bispecific compound from unwanted immunoglobulin chain combinations, as the presence of an immunoglobulin light chain in only one half of the bispecific molecule provides for a facile way of separation. This approach is disclosed in WO 94/04690. For further details of generating bispecific antibodies see, for example, Suresh etal., Methods in Enzymology, 121 :210 (1986).
According to another approach described in U.S. Pat. No. 5,731,168, the interface between a pair of antibody molecules can be engineered to maximize the percentage of heterodimers that are recovered from recombinant cell culture. The preferred interface comprises at least a part of the Cro domain. In this method, one or more small amino acid side chains from the interface of the first antibody molecule are replaced with larger side chains (e.g., tyrosine or tryptophan). Compensatory "cavities" of identical or similar size to the large side chain(s) are created on the interface of the second antibody molecule by replacing large amino acid side chains with smaller ones (e.g., alanine or threonine). This provides a mechanism for increasing the yield of the heterodimer over other unwanted end-products such as homodimers.
Bispecific antibodies include cross-linked or "heteroconjugate" antibodies. For example, one of the antibodies in the heteroconjugate can be coupled to avidin, the other to biotin. Such antibodies have, for example, been proposed to target immune system cells to unwanted cells (U.S. Pat. No. 4,676,980), and for treatment of HIV infection (WO 91/00360, WO 92/200373, and EP 03089). Heteroconjugate antibodies may be made using any convenient cross-linking methods. Suitable cross-linking agents are well known in the art, and are disclosed in U.S. Pat. No. 4,676,980, along with a number of cross-linking techniques.
Techniques for generating bispecific antibodies from antibody fragments have also been described in the literature. For example, bispecific antibodies can be prepared using chemical linkage. Brennan et al., Science, 229: 81 (1985) describe a procedure wherein intact antibodies are proteolytically cleaved to generate F(ab')2 fragments. These fragments are reduced in the presence of the dithiol complexing agent, sodium arsenite, to stabilize vicinal dithiols and prevent intermolecular disulfide formation. The Fab' fragments generated are then converted to thionitrobenzoate (TNB) derivatives. One of the Fab'-TNB derivatives is then reconverted to the Fab'-thiol by reduction with mercaptoethylamine and is mixed with an equimolar amount of the other Fab'-TNB derivative to form the bispecific antibody. The bispecific antibodies produced can be used as agents for the selective immobilization of enzymes.
Techniques exist that facilitate the direct recovery of Fab'-SH fragments from E. coli, which can be chemically coupled to form bispecific antibodies. Shalaby et al, J. Exp. Med., 175: 217-225 (1992) describe the production of a humanized bispecific antibody F(ab')2 molecule. Each Fab' fragment was separately secreted from E. coli and subjected to directed chemical coupling in vitro to form the bispecific antibody. The bispecific antibody thus formed was able to bind to cells overexpressing the ErbB2 receptor and normal human T cells, as well as trigger the lytic activity of human cytotoxic lymphocytes against human breast tumor targets.
Various techniques for making and isolating bispecific antibody fragments directly from recombinant cell culture have also been described (Merchant et al, Nat. Biotechnol. 16, 677-681 (1998). doi: l0. l038/nbt0798-677pmid:966l204). For example, bispecific antibodies have been produced using leucine zippers (Kostelny et al. , J. Immunol., 148(5): 1547-1553, 1992). The leucine zipper peptides from the Fos and Jun proteins were linked to the Fab' portions of two different antibodies by gene fusion. The antibody homodimers were reduced at the hinge region to form monomers and then re-oxidized to form the antibody heterodimers. This method can also be utilized for the production of antibody homodimers. The "diabody" technology described by Hollinger et al. , Proc. Natl. Acad. Sci. USA, 90:6444-6448 (1993) has provided an alternative mechanism for making bispecific antibody fragments. The fragments comprise a VH connected to a VL by a linker that is too short to allow pairing between the two domains on the same chain. Accordingly, the VH and VL domains of one fragment are forced to pair with the complementary VL and VH domains of another fragment, thereby forming two antigen-binding sites. Another strategy for making bispecific antibody fragments by the use of single-chain Fv (sFv) dimers has also been reported. See Gruber et al, J. Immunol., 152:5368 (1994).
In a particular embodiment, a bispecific or multispecific antibody may be formed as a DOCK-AND-LOCK™ (DNL™) complex (see, e.g., U.S. Pat. Nos. 7,521,056; 7,527,787; 7,534,866; 7,550,143 and 7,666,400, the Examples section of each of which is incorporated herein by reference.) Generally, the technique takes advantage of the specific and high-affinity binding interactions that occur between a dimerization and docking domain (DDD) sequence of the regulatory (R) subunits of cAMP-dependent protein kinase (PKA) and an anchor domain (AD) sequence derived from any of a variety of AKAP proteins (Baillie et al., FEES Letters. 2005; 579: 3264; Wong and Scott, Nat. Rev. Mol. Cell Biol. 2004; 5: 959). The DDD and AD peptides may be attached to any protein, peptide or other molecule. Because the DDD sequences spontaneously dimerize and bind to the AD sequence, the technique allows the formation of complexes between any selected molecules that may be attached to DDD or AD sequences.
Antibodies with more than two valencies are contemplated. For example, trispecific antibodies can be prepared (Tutt et al, J. Immunol. 147: 60, 1991; Xu et al, Science, 358(6359):85-90, 2017). A multivalent antibody may be internalized (and/or catabolized) faster than a bivalent antibody by a cell expressing an antigen to which the antibodies bind. The antibodies of the present disclosure can be multivalent antibodies with three or more antigen binding sites (e.g., tetravalent antibodies), which can be readily produced by recombinant expression of nucleic acid encoding the polypeptide chains of the antibody. The multivalent antibody can comprise a dimerization domain and three or more antigen binding sites. The preferred dimerization domain comprises (or consists of) an Fc region or a hinge region. In this scenario, the antibody will comprise an Fc region and three or more antigen binding sites amino-terminal to the Fc region. The preferred multivalent antibody herein comprises (or consists of) three to about eight, but preferably four, antigen binding sites. The multivalent antibody comprises at least one polypeptide chain (and preferably two polypeptide chains), wherein the polypeptide chain(s) comprise two or more variable regions. For instance, the polypeptide chain(s) may comprise VDl-(Xl).sub.n-VD2-(X2)n-Fc, wherein VD1 is a first variable region, VD2 is a second variable region, Fc is one polypeptide chain of an Fc region, XI and X2 represent an amino acid or polypeptide, and n is 0 or 1. For instance, the polypeptide chain(s) may comprise: VH-CH1 -flexible linker-VH-CHl-Fc region chain; or VH-CH1-VH- CHl-Fc region chain. The multivalent antibody herein preferably further comprises at least two (and preferably four) light chain variable region polypeptides. The multivalent antibody herein may, for instance, comprise from about two to about eight light chain variable region polypeptides. The light chain variable region polypeptides contemplated here comprise a light chain variable region and, optionally, further comprise a CL domain.
Charge modifications are particularly useful in the context of a multispecific antibody, where amino acid substitutions in Fab molecules result in reducing the mispairing of light chains with non-matching heavy chains (Bence-Jones-type side products), which can occur in the production of Fab-based bi-/multispecific antigen binding molecules with a VH/VL exchange in one (or more, in case of molecules comprising more than two antigen-binding Fab molecules) of their binding arms (see also PCT publication no. WO 2015/150447, particularly the examples therein, incorporated herein by reference in its entirety).
Accordingly, in particular embodiments, an antibody comprised in the therapeutic agent comprises
(a) a first Fab molecule which specifically binds to a first antigen
(b) a second Fab molecule which specifically binds to a second antigen, and wherein the variable domains VL and VH of the Fab light chain and the Fab heavy chain are replaced by each other,
wherein the first antigen is an activating T cell antigen and the second antigen is a target cell antigen, or the first antigen is a target cell antigen and the second antigen is an activating T cell antigen; and
wherein
i) in the constant domain CL of the first Fab molecule under a) the amino acid at position 124 is substituted by a positively charged amino acid (numbering according to Kabat), and wherein in the constant domain CH1 of the first Fab molecule under a) the amino acid at position 147 or the amino acid at position 213 is substituted by a negatively charged amino acid (numbering according to Kabat EU index); or ii) in the constant domain CL of the second Fab molecule under b) the amino acid at position 124 is substituted by a positively charged amino acid (numbering according to Kabat), and wherein in the constant domain CH1 of the second Fab molecule under b) the amino acid at position 147 or the amino acid at position 213 is substituted by a negatively charged amino acid (numbering according to Kabat EU index).
The antibody may not comprise both modifications mentioned under i) and ii). The constant domains CL and CH1 of the second Fab molecule are not replaced by each other (i.e., remain unexchanged).
In another embodiment of the antibody, in the constant domain CL of the first Fab molecule under a) the amino acid at position 124 is substituted independently by lysine (K), arginine (R) or histidine (H) (numbering according to Rabat) (in one preferred embodiment independently by lysine (K) or arginine (R)), and in the constant domain CH1 of the first Fab molecule under a) the amino acid at position 147 or the amino acid at position 213 is substituted independently by glutamic acid (E), or aspartic acid (D) (numbering according to Rabat EU index).
In a further embodiment, in the constant domain CL of the first Fab molecule under a) the amino acid at position 124 is substituted independently by lysine (R), arginine (R) or histidine (H) (numbering according to Rabat), and in the constant domain CH1 of the first Fab molecule under a) the amino acid at position 147 is substituted independently by glutamic acid (E), or aspartic acid (D) (numbering according to Rabat EU index).
In a particular embodiment, in the constant domain CL of the first Fab molecule under a) the amino acid at position 124 is substituted independently by lysine (R), arginine (R) or histidine (H) (numbering according to Rabat) (in one preferred embodiment independently by lysine (R) or arginine (R)) and the amino acid at position 123 is substituted independently by lysine (R), arginine (R) or histidine (H) (numbering according to Rabat) (in one preferred embodiment independently by lysine (R) or arginine (R)), and in the constant domain CH1 of the first Fab molecule under a) the amino acid at position 147 is substituted independently by glutamic acid (E), or aspartic acid (D) (numbering according to Rabat EU index) and the amino acid at position 213 is substituted independently by glutamic acid (E), or aspartic acid (D) (numbering according to Rabat EU index).
In a more particular embodiment, in the constant domain CL of the first Fab molecule under a) the amino acid at position 124 is substituted by lysine (R) (numbering according to Rabat) and the amino acid at position 123 is substituted by lysine (R) or arginine (R) (numbering according to Rabat), and in the constant domain CH1 of the first Fab molecule under a) the amino acid at position 147 is substituted by glutamic acid (E) (numbering according to Rabat EU index) and the amino acid at position 213 is substituted by glutamic acid (E) (numbering according to Rabat EU index).
In an even more particular embodiment, in the constant domain CL of the first Fab molecule under a) the amino acid at position 124 is substituted by lysine (R) (numbering according to Rabat) and the amino acid at position 123 is substituted by arginine (R) (numbering according to Rabat), and in the constant domain CH1 of the first Fab molecule under a) the amino acid at position 147 is substituted by glutamic acid (E) (numbering according to Rabat EU index) and the amino acid at position 213 is substituted by glutamic acid (E) (numbering according to Rabat EU index). F. Chimeric Antigen Receptors
Artificial T cell receptors (also known as chimeric T cell receptors, chimeric immunoreceptors, chimeric antigen receptors (CARs)) are engineered receptors, which graft an arbitrary specificity onto an immune effector cell. Typically, these receptors are used to graft the specificity of a monoclonal antibody onto a T cell, with transfer of their coding sequence facilitated by retroviral vectors. In this way, a large number of target-specific T cells can be generated for adoptive cell transfer. Phase I clinical studies of this approach show efficacy.
The most common form of these molecules are fusions of single-chain variable fragments (scFv) derived from monoclonal antibodies, fused to CD3-zeta transmembrane and endodomain. Such molecules result in the transmission of a zeta signal in response to recognition by the scFv of its target. An example of such a construct is l4g2a-Zeta, which is a fusion of a scFv derived from hybridoma l4g2a (which recognizes disialoganglioside GD2). When T cells express this molecule (usually achieved by oncoretroviral vector transduction), they recognize and kill target cells that express GD2 (e.g., neuroblastoma cells). To target malignant B cells, investigators have redirected the specificity of T cells using a chimeric immunoreceptor specific for the B-lineage molecule, CD 19.
The variable portions of an immunoglobulin heavy and light chain are fused by a flexible linker to form a scFv. This scFv is preceded by a signal peptide to direct the nascent protein to the endoplasmic reticulum and subsequent surface expression (this is cleaved). A flexible spacer allows to the scFv to orient in different directions to enable antigen binding. The transmembrane domain is a typical hydrophobic alpha helix usually derived from the original molecule of the signaling endodomain which protrudes into the cell and transmits the desired signal.
Type I proteins are in fact two protein domains linked by a transmembrane alpha helix in between. The cell membrane lipid bilayer, through which the transmembrane domain passes, acts to isolate the inside portion (endodomain) from the external portion (ectodomain). It is not so surprising that attaching an ectodomain from one protein to an endodomain of another protein results in a molecule that combines the recognition of the former to the signal of the latter.
Ectodomain. A signal peptide directs the nascent protein into the endoplasmic reticulum. This is essential if the receptor is to be glycosylated and anchored in the cell membrane. Any eukaryotic signal peptide sequence usually works fine. Generally, the signal peptide natively attached to the amino-terminal most component is used (e.g., in a scFv with orientation light chain - linker - heavy chain, the native signal of the light-chain is used
The antigen recognition domain is usually an scFv. There are however many alternatives. An antigen recognition domain from native T-cell receptor (TCR) alpha and beta single chains have been described, as have simple ectodomains (e.g., CD4 ectodomain to recognize HIV infected cells) and more exotic recognition components such as a linked cytokine (which leads to recognition of cells bearing the cytokine receptor). In fact, almost anything that binds a given target with high affinity can be used as an antigen recognition region.
A spacer region links the antigen binding domain to the transmembrane domain. It should be flexible enough to allow the antigen binding domain to orient in different directions to facilitate antigen recognition. The simplest form is the hinge region from IgGl . Alternatives include the CH2CH3 region of immunoglobulin and portions of CD3. For most scFv based constructs, the IgGl hinge suffices. However, the best spacer often has to be determined empirically.
Transmembrane domain. The transmembrane domain is a hydrophobic alpha helix that spans the membrane. Generally, the transmembrane domain from the most membrane proximal component of the endodomain is used. Interestingly, using the CD3-zeta transmembrane domain may result in incorporation of the artificial TCR into the native TCR a factor that is dependent on the presence of the native CD3-zeta transmembrane charged aspartic acid residue. Different transmembrane domains result in different receptor stability. The CD28 transmembrane domain results in a brightly expressed, stable receptor.
Endodomain. This is the "business-end" of the receptor. After antigen recognition, receptors cluster and a signal is transmitted to the cell. The most commonly used endodomain component is CD3-zeta which contains 3 ITAMs. This transmits an activation signal to the T cell after antigen is bound. CD3-zeta may not provide a fully competent activation signal and additional co-stimulatory signaling is needed.
"First-generation" CARs typically had the intracellular domain from the CD3 x- chain, which is the primary transmitter of signals from endogenous TCRs. "Second-generation" CARs add intracellular signaling domains from various costimulatory protein receptors (e.g., CD28, 41BB, ICOS) to the cytoplasmic tail of the CAR to provide additional signals to the T cell. Preclinical studies have indicated that the second generation of CAR designs improves the antitumor activity of T cells. More recent, "third-generation" CARs combine multiple signaling domains, such as CD3z-CD28-4lBB or CD3z-CD28-OX40, to further augment potency. G. ADCs
Antibody Drug Conjugates or ADCs are a new class of highly potent biopharmaceutical drugs designed as a targeted therapy for the treatment of people with infectious disease. ADCs are complex molecules composed of an antibody (a whole mAh or an antibody fragment such as a single-chain variable fragment, or scFv) linked, via a stable chemical linker with labile bonds, to a biological active cytotoxic/anti-viral payload or drug. Antibody Drug Conjugates are examples of bioconjugates and immunoconjugates.
By combining the unique targeting capabilities of monoclonal antibodies with the cancer-killing ability of cytotoxic drugs, antibody-drug conjugates allow sensitive discrimination between healthy and diseased tissue. This means that, in contrast to traditional systemic approaches, antibody-drug conjugates target and attack the infected cell so that healthy cells are less severely affected.
In the development ADC-based anti-tumor therapies, an anti cancer drug (e.g., a cell toxin or cytotoxin) is coupled to an antibody that specifically targets a certain cell marker (e.g., a protein that, ideally, is only to be found in or on infected cells). Antibodies track these proteins down in the body and attach themselves to the surface of cancer cells. The biochemical reaction between the antibody and the target protein (antigen) triggers a signal in the tumor cell, which then absorbs or internalizes the antibody together with the cytotoxin. After the ADC is internalized, the cytotoxic drug is released and kills the cell or impairs viral replication. Due to this targeting, ideally the drug has lower side effects and gives a wider therapeutic window than other agents.
A stable link between the antibody and cytotoxic/anti-viral agent is a crucial aspect of an ADC. Linkers are based on chemical motifs including disulfides, hydrazones or peptides (cleavable), or thioethers (noncleavable) and control the distribution and delivery of the cytotoxic agent to the target cell. Cleavable and noncleavable types of linkers have been proven to be safe in preclinical and clinical trials. Brentuximab vedotin includes an enzyme-sensitive cleavable linker that delivers the potent and highly toxic antimicrotubule agent Monomethyl auristatin E or MMAE, a synthetic antineoplastic agent, to human specific CD30-positive malignant cells. Because of its high toxicity MMAE, which inhibits cell division by blocking the polymerization of tubulin, cannot be used as a single-agent chemotherapeutic drug. However, the combination of MMAE linked to an anti-CD30 monoclonal antibody (cAClO, a cell membrane protein of the tumor necrosis factor or TNF receptor) proved to be stable in extracellular fluid, cleavable by cathepsin and safe for therapy. Trastuzumab emtansine, the other approved ADC, is a combination of the microtubule-formation inhibitor mertansine (DM- 1), a derivative of the Maytansine, and antibody trastuzumab (Herceptin®/Genentech/Roche) atached by a stable, non-cleavable linker. The availability of better and more stable linkers has changed the function of the chemical bond. The type of linker, cleavable or noncleavable, lends specific properties to the cytotoxic (anti-cancer) drug. For example, a non-cleavable linker keeps the drug within the cell. As a result, the entire antibody, linker and cytotoxic agent enter the targeted cancer cell where the antibody is degraded to the level of an amino acid. The resulting complex - amino acid, linker and cytotoxic agent - now becomes the active drug. In contrast, cleavable linkers are catalyzed by enzymes in the host cell where it releases the cytotoxic agent.
Another type of cleavable linker, currently in development, adds an extra molecule between the cytotoxic/anti-viral drug and the cleavage site. This linker technology allows researchers to create ADCs with more flexibility without worrying about changing cleavage kinetics. Researchers are also developing a new method of peptide cleavage based on Edman degradation, a method of sequencing amino acids in a peptide. Future direction in the development of ADCs also include the development of site-specific conjugation (TDCs) to further improve stability and therapeutic index and a emiting immunoconjugates and antibody-conjugated nanoparticles.
H. BiTES
Bi-specific T-cell engagers (BiTEs) are a class of artificial bispecific monoclonal antibodies that are investigated for the use as anti-cancer drugs. They direct a host's immune system, more specifically the T cells' cytotoxic activity, against infected cells. BiTE is a registered trademark of Micromet AG.
BiTEs are fusion proteins consisting of two single-chain variable fragments (scFvs) of different antibodies, or amino acid sequences from four different genes, on a single peptide chain of about 55 kilodaltons. One of the scFvs binds to T cells via the CD3 receptor, and the other to an infected cell via a specific molecule.
Like other bispecific antibodies, and unlike ordinary monoclonal antibodies, BiTEs form a link between T cells and target cells. This causes T cells to exert cytotoxic/anti-viral activity on infected cells by producing proteins like perforin and granzymes, independently of the presence of MHC I or co-stimulatory molecules. These proteins enter infected cells and initiate the cell's apoptosis. This action mimics physiological processes observed during T cell attacks against infected cells. I. Intrabodies
In a particular embodiment, the antibody is a recombinant antibody that is suitable for action inside of a cell - such antibodies are known as“intrabodies.” These antibodies may interfere with target function by a variety of mechanism, such as by altering intracellular protein trafficking, interfering with enzymatic function, and blocking protein-protein or protein-DNA interactions. In many ways, their structures mimic or parallel those of single chain and single domain antibodies, discussed above. Indeed, single-transcript/single-chain is an important feature that permits intracellular expression in a target cell, and also makes protein transit across cell membranes more feasible. However, additional features are required.
The two major issues impacting the implementation of intrabody therapeutic are delivery, including cell/tissue targeting, and stability. With respect to delivery, a variety of approaches have been employed, such as tissue-directed delivery, use of cell-type specific promoters, viral-based delivery and use of cell-permeability/membrane translocating peptides. With respect to the stability, the approach is generally to either screen by brute force, including methods that involve phage display and may include sequence maturation or development of consensus sequences, or more directed modifications such as insertion stabilizing sequences (e.g., Fc regions, chaperone protein sequences, leucine zippers) and disulfide replacement/modification.
An additional feature that intrabodies may require is a signal for intracellular targeting. Vectors that can target intrabodies (or other proteins) to subcellular regions such as the cytoplasm, nucleus, mitochondria and ER have been designed and are commercially available (Invitrogen Corp.; Persic et al, 1997).
By virtue of their ability to enter cells, intrabodies have additional uses that other types of antibodies may not achieve. In the case of the present antibodies, the ability to interact with the MUC1 cytoplasmic domain in a living cell may interfere with functions associated with the MUC1 CD, such as signaling functions (binding to other molecules) or oligomer formation. In particular, it is contemplated that such antibodies can be used to inhibit MUC1 dimer formation.
J. Purification
In certain embodiments, the antibodies of the present disclosure may be purified. The term“purified,” as used herein, is intended to refer to a composition, isolatable from other components, wherein the protein is purified to any degree relative to its naturally-obtainable state. A purified protein therefore also refers to a protein, free from the environment in which it may naturally occur. Where the term“substantially purified” is used, this designation will refer to a composition in which the protein or peptide forms the major component of the composition, such as constituting about 50%, about 60%, about 70%, about 80%, about 90%, about 95% or more of the proteins in the composition.
Protein purification techniques are well known to those of skill in the art. These techniques involve, at one level, the crude fractionation of the cellular milieu to polypeptide and non-polypeptide fractions. Having separated the polypeptide from other proteins, the polypeptide of interest may be further purified using chromatographic and electrophoretic techniques to achieve partial or complete purification (or purification to homogeneity). Analytical methods particularly suited to the preparation of a pure peptide are ion-exchange chromatography, exclusion chromatography; polyacrylamide gel electrophoresis; isoelectric focusing. Other methods for protein purification include, precipitation with ammonium sulfate, PEG, antibodies and the like or by heat denaturation, followed by centrifugation; gel filtration, reverse phase, hydroxylapatite and affinity chromatography; and combinations of such and other techniques.
In purifying an antibody of the present disclosure, it may be desirable to express the polypeptide in a prokaryotic or eukaryotic expression system and extract the protein using denaturing conditions. The polypeptide may be purified from other cellular components using an affinity column, which binds to a tagged portion of the polypeptide. As is generally known in the art, it is believed that the order of conducting the various purification steps may be changed, or that certain steps may be omitted, and still result in a suitable method for the preparation of a substantially purified protein or peptide.
Commonly, complete antibodies are fractionated utilizing agents (i.e.. protein A) that bind the Fc portion of the antibody. Alternatively, antigens may be used to simultaneously purify and select appropriate antibodies. Such methods often utilize the selection agent bound to a support, such as a column, filter or bead. The antibodies are bound to a support, contaminants removed (e.g., washed away), and the antibodies released by applying conditions (salt, heat, etc.).
Various methods for quantifying the degree of purification of the protein or peptide will be known to those of skill in the art in light of the present disclosure. These include, for example, determining the specific activity of an active fraction, or assessing the amount of polypeptides within a fraction by SDS/PAGE analysis. Another method for assessing the purity of a fraction is to calculate the specific activity of the fraction, to compare it to the specific activity of the initial extract, and to thus calculate the degree of purity. The actual units used to represent the amount of activity will, of course, be dependent upon the particular assay technique chosen to follow the purification and whether or not the expressed protein or peptide exhibits a detectable activity.
It is known that the migration of a polypeptide can vary, sometimes significantly, with different conditions of SDS/PAGE (Capaldi el al, 1977). It will therefore be appreciated that under differing electrophoresis conditions, the apparent molecular weights of purified or partially purified expression products may vary.
III. Active/Passive Immunization and Treatment/Prevention of Zika Vims Infection
A. Formulation and Administration
The present disclosure provides pharmaceutical compositions comprising anti-Zika virus antibodies and antigens for generating the same. Such compositions comprise a prophylactically or therapeutically effective amount of an antibody or a fragment thereof, or a peptide immunogen, and a pharmaceutically acceptable carrier. In a specific embodiment, the term“pharmaceutically acceptable” means approved by a regulatory agency of the Federal or a state government or listed in the U.S. Pharmacopeia or other generally recognized pharmacopeia for use in animals, and more particularly in humans. The term“carrier” refers to a diluent, excipient, or vehicle with which the therapeutic is administered. Such pharmaceutical carriers can be sterile liquids, such as water and oils, including those of petroleum, animal, vegetable or synthetic origin, such as peanut oil, soybean oil, mineral oil, sesame oil and the like. Water is a particular carrier when the pharmaceutical composition is administered intravenously. Saline solutions and aqueous dextrose and glycerol solutions can also be employed as liquid carriers, particularly for injectable solutions. Other suitable pharmaceutical excipients include starch, glucose, lactose, sucrose, gelatin, malt, rice, flour, chalk, silica gel, sodium stearate, glycerol monostearate, talc, sodium chloride, dried skim milk, glycerol, propylene, glycol, water, ethanol and the like.
The composition, if desired, can also contain minor amounts of wetting or emulsifying agents, or pH buffering agents. These compositions can take the form of solutions, suspensions, emulsion, tablets, pills, capsules, powders, sustained-release formulations and the like. Oral formulations can include standard carriers such as pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharine, cellulose, magnesium carbonate, etc. Examples of suitable pharmaceutical agents are described in“Remington's Pharmaceutical Sciences.” Such compositions will contain a prophylactically or therapeutically effective amount of the antibody or fragment thereof, preferably in purified form, together with a suitable amount of carrier so as to provide the form for proper administration to the patient. The formulation should suit the mode of administration, which can be oral, intravenous, intraarterial, intrabuccal, intranasal, nebulized, bronchial inhalation, intra-rectal, vaginal, topical or delivered by mechanical ventilation.
Active vaccines are also envisioned where antibodies like those disclosed are produced in vivo in a subject at risk of Zika virus infection. Such vaccines can be formulated for parenteral administration, e.g., formulated for injection via the intradermal, intravenous, intramuscular, subcutaneous, or even intraperitoneal routes. Administration by intradermal and intramuscular routes are contemplated. The vaccine could alternatively be administered by a topical route directly to the mucosa, for example by nasal drops, inhalation, by nebulizer, or via intrarectal or vaginal delivery. Pharmaceutically-acceptable salts, include the acid salts and those which are formed with inorganic acids such as, for example, hydrochloric or phosphoric acids, or such organic acids as acetic, oxalic, tartaric, mandelic, and the like. Salts formed with the free carboxyl groups may also be derived from inorganic bases such as, for example, sodium, potassium, ammonium, calcium, or ferric hydroxides, and such organic bases as isopropylamine, trimethylamine, 2-ethylamino ethanol, histidine, procaine, and the like.
Passive transfer of antibodies, known as artificially acquired passive immunity, generally will involve the use of intravenous or intramuscular injections. The forms of antibody can be human or animal blood plasma or serum, as pooled human immunoglobulin for intravenous (IVIG) or intramuscular (IG) use, as high-titer human IVIG or IG from immunized or from donors recovering from disease, and as monoclonal antibodies (MAb). Such immunity generally lasts for only a short period of time, and there is also a potential risk for hypersensitivity reactions, and serum sickness, especially from gamma globulin of non-human origin. However, passive immunity provides immediate protection. The antibodies will be formulated in a carrier suitable for injection, /. e.. sterile and syringeable.
Generally, the ingredients of compositions of the disclosure are supplied either separately or mixed together in unit dosage form, for example, as a dry lyophilized powder or water-free concentrate in a hermetically sealed container such as an ampoule or sachette indicating the quantity of active agent. Where the composition is to be administered by infusion, it can be dispensed with an infusion bottle containing sterile pharmaceutical grade water or saline. Where the composition is administered by injection, an ampoule of sterile water for injection or saline can be provided so that the ingredients may be mixed prior to administration.
The compositions of the disclosure can be formulated as neutral or salt forms. Pharmaceutically acceptable salts include those formed with anions such as those derived from hydrochloric, phosphoric, acetic, oxalic, tartaric acids, etc., and those formed with cations such as those derived from sodium, potassium, ammonium, calcium, ferric hydroxides, isopropylamine, triethylamine, 2-ethylamino ethanol, histidine, procaine, etc.
2. ADCC
Antibody-dependent cell-mediated cytotoxicity (ADCC) is an immune mechanism leading to the lysis of antibody-coated target cells by immune effector cells. The target cells are cells to which antibodies or fragments thereof comprising an Fc region specifically bind, generally via the protein part that is N-terminal to the Fc region. By“antibody having increased/reduced antibody dependent cell-mediated cytotoxicity (ADCC)” is meant an antibody having increased/reduced ADCC as determined by any suitable method known to those of ordinary skill in the art.
As used herein, the term “increased/reduced ADCC” is defined as either an increase/reduction in the number of target cells that are lysed in a given time, at a given concentration of antibody in the medium surrounding the target cells, by the mechanism of ADCC defined above, and/or a reduction/increase in the concentration of antibody, in the medium surrounding the target cells, required to achieve the lysis of a given number of target cells in a given time, by the mechanism of ADCC. The increase/reduction in ADCC is relative to the ADCC mediated by the same antibody produced by the same type of host cells, using the same standard production, purification, formulation and storage methods (which are known to those skilled in the art), but that has not been engineered. For example, the increase in ADCC mediated by an antibody produced by host cells engineered to have an altered pattern of glycosylation (e.g., to express the glycosyltransferase, GnTIII, or other glycosyltransferases) by the methods described herein, is relative to the ADCC mediated by the same antibody produced by the same type of non-engineered host cells.
3. CDC
Complement-dependent cytotoxicity (CDC) is a function of the complement system. It is the processes in the immune system that kill pathogens by damaging their membranes without the involvement of antibodies or cells of the immune system. There are three main processes. All three insert one or more membrane attack complexes (MAC) into the pathogen which cause lethal colloid-osmotic swelling, i.e., CDC. It is one of the mechanisms by which antibodies or antibody fragments have an anti-viral effect. IV. Antibody Conjugates
Antibodies of the present disclosure may be linked to at least one agent to form an antibody conjugate. In order to increase the efficacy of antibody molecules as diagnostic or therapeutic agents, it is conventional to link or covalently bind or complex at least one desired molecule or moiety. Such a molecule or moiety may be, but is not limited to, at least one effector or reporter molecule. Effector molecules comprise molecules having a desired activity, e.g. , cytotoxic activity. Non-limiting examples of effector molecules which have been attached to antibodies include toxins, anti-tumor agents, therapeutic enzymes, radionuclides, antiviral agents, chelating agents, cytokines, growth factors, and oligo- or polynucleotides. By contrast, a reporter molecule is defined as any moiety which may be detected using an assay. Non limiting examples of reporter molecules which have been conjugated to antibodies include enzymes, radiolabels, haptens, fluorescent labels, phosphorescent molecules, chemiluminescent molecules, chromophores, photoaffmity molecules, colored particles or ligands, such as biotin.
Antibody conjugates are generally preferred for use as diagnostic agents. Antibody diagnostics generally fall within two classes, those for use in in vitro diagnostics, such as in a variety of immunoassays, and those for use in vivo diagnostic protocols, generally known as "antibody-directed imaging." Many appropriate imaging agents are known in the art, as are methods for their attachment to antibodies (see, for e.g. , U.S. Patents 5,021,236, 4,938,948, and 4,472,509). The imaging moieties used can be paramagnetic ions, radioactive isotopes, fluorochromes, NMR-detectable substances, and X-ray imaging agents.
In the case of paramagnetic ions, one might mention by way of example ions such as chromium (III), manganese (II), iron (III), iron (II), cobalt (II), nickel (II), copper (II), neodymium (III), samarium (III), ytterbium (III), gadolinium (III), vanadium (II), terbium (III), dysprosium (III), holmium (III) and/or erbium (III), with gadolinium being particularly preferred. Ions useful in other contexts, such as X-ray imaging, include but are not limited to lanthanum (III), gold (III), lead (II), and especially bismuth (III).
In the case of radioactive isotopes for therapeutic and/or diagnostic application, one might mention astatine211, 14carbon, 51chromium, 36chlorine, 57cobalt, 58cobalt, copper67, 152Eu, gallium67, 3hydrogen, iodine123, iodine125, iodine131, indium111, 59iron, 32phosphorus, rhenium186, rhenium188, 75selenium, 35sulphur, technicium99"1 and/or yttrium90. 125I is often being preferred for use in certain embodiments, and technicium99"1 and/or indium111 are also often preferred due to their low energy and suitability for long range detection. Radioactively labeled monoclonal antibodies of the present disclosure may be produced according to well-known methods in the art. For instance, monoclonal antibodies can be iodinated by contact with sodium and/or potassium iodide and a chemical oxidizing agent such as sodium hypochlorite, or an enzymatic oxidizing agent, such as lactoperoxidase. Monoclonal antibodies according to the disclosure may be labeled with technetium99"1 by ligand exchange process, for example, by reducing pertechnate with stannous solution, chelating the reduced technetium onto a Sephadex column and applying the antibody to this column. Alternatively, direct labeling techniques may be used, e.g. , by incubating pertechnate, a reducing agent such as SNCh. a buffer solution such as sodium-potassium phthalate solution, and the antibody. Intermediary functional groups which are often used to bind radioisotopes which exist as metallic ions to antibody are diethylenetriaminepentaacetic acid (DTP A) or ethylene diaminetetracetic acid (EDTA).
Among the fluorescent labels contemplated for use as conjugates include Alexa 350, Alexa 430, AMCA, BODIPY 630/650, BODIPY 650/665, BODIPY-FL, BODIPY-R6G, BODIPY-TMR, BODIPY-TRX, Cascade Blue, Cy3, Cy5,6-FAM, Fluorescein Isothiocyanate, HEX, 6-JOE, Oregon Green 488, Oregon Green 500, Oregon Green 514, Pacific Blue, REG, Rhodamine Green, Rhodamine Red, Renographin, ROX, TAMRA, TET, Tetramethylrhodamine, and/or Texas Red.
Additional types of antibodies contemplated in the present disclosure are those intended primarily for use in vitro, where the antibody is linked to a secondary binding ligand and/or to an enzyme (an enzyme tag) that will generate a colored product upon contact with a chromogenic substrate. Examples of suitable enzymes include urease, alkaline phosphatase, (horseradish) hydrogen peroxidase or glucose oxidase. Preferred secondary binding ligands are biotin and avidin and streptavidin compounds. The use of such labels is well known to those of skill in the art and are described, for example, in U.S. Patents 3,817,837, 3,850,752, 3,939,350, 3,996,345, 4,277,437, 4,275,149 and 4,366,241.
Yet another known method of site-specific attachment of molecules to antibodies comprises the reaction of antibodies with hapten-based affinity labels. Essentially, hapten- based affinity labels react with amino acids in the antigen binding site, thereby destroying this site and blocking specific antigen reaction. However, this may not be advantageous since it results in loss of antigen binding by the antibody conjugate.
Molecules containing azido groups may also be used to form covalent bonds to proteins through reactive nitrene intermediates that are generated by low intensity ultraviolet light (Potter and Haley, 1983). In particular, 2- and 8-azido analogues of purine nucleotides have been used as site-directed photoprobes to identify nucleotide binding proteins in crude cell extracts (Owens & Haley, 1987; Atherton et al, 1985). The 2- and 8-azido nucleotides have also been used to map nucleotide binding domains of purified proteins (Khatoon et al, 1989; King et al, 1989; Dholakia et al, 1989) and may be used as antibody binding agents.
Several methods are known in the art for the attachment or conjugation of an antibody to its conjugate moiety. Some attachment methods involve the use of a metal chelate complex employing, for example, an organic chelating agent such a diethylenetriaminepentaacetic acid anhydride (DTP A); ethylenetriaminetetraacetic acid; N-chloro-p-toluenesulfonamide; and/or tetrachloro-3a-6a-diphenylglycouril-3 attached to the antibody (U.S. Patents 4,472,509 and 4,938,948). Monoclonal antibodies may also be reacted with an enzyme in the presence of a coupling agent such as glutaraldehyde or periodate. Conjugates with fluorescein markers are prepared in the presence of these coupling agents or by reaction with an isothiocyanate. In U.S. Patent 4,938,948, imaging of breast tumors is achieved using monoclonal antibodies and the detectable imaging moieties are bound to the antibody using linkers such as methyl-p- hydroxybenzimidate or N-succinimidyl-3-(4-hydroxyphenyl)propionate.
In other embodiments, derivatization of immunoglobulins by selectively introducing sulfhydryl groups in the Fc region of an immunoglobulin, using reaction conditions that do not alter the antibody combining site are contemplated. Antibody conjugates produced according to this methodology are disclosed to exhibit improved longevity, specificity and sensitivity (U.S. Patent 5,196,066, incorporated herein by reference). Site-specific attachment of effector or reporter molecules, wherein the reporter or effector molecule is conjugated to a carbohydrate residue in the Fc region have also been disclosed in the literature (O’Shannessy et al, 1987). This approach has been reported to produce diagnostically and therapeutically promising antibodies which are currently in clinical evaluation.
V. Immunodetection Methods
In still further embodiments, the present disclosure concerns immunodetection methods for binding, purifying, removing, quantifying and otherwise generally detecting Zika virus and its associated antigens. While such methods can be applied in a traditional sense, another use will be in quality control and monitoring of vaccine and other virus stocks, where antibodies according to the present disclosure can be used to assess the amount or integrity (/. e. , long term stability) of antigens in viruses. Alternatively, the methods may be used to screen various antibodies for appropriate/desired reactivity profiles.
Other immunodetection methods include specific assays for determining the presence of Zika virus in a subject. A wide variety of assay formats are contemplated, but specifically those that would be used to detect Zika virus in a fluid obtained from a subject, such as saliva, blood, plasma, sputum, semen or urine. In particular, semen has been demonstrated as a viable sample for detecting Zika virus (Purpura et al. , 2016; Mansuy et al., 2016; Barzon et al., 2016; Gomet etal., 2016; Duffy etal. , 2009; CDC, 2016; Halfon etal., 2010; Elder etal. 2005). The assays may be advantageously formatted for non-healthcare (home) use, including lateral flow assays (see below) analogous to home pregnancy tests. These assays may be packaged in the form of a kit with appropriate reagents and instructions to permit use by the subject of a family member.
Some immunodetection methods include enzyme linked immunosorbent assay (ELISA), radioimmunoassay (RIA), immunoradiometric assay, fluoroimmunoassay, chemiluminescent assay, bioluminescent assay, and Western blot to mention a few. In particular, a competitive assay for the detection and quantitation of Zika virus antibodies directed to specific parasite epitopes in samples also is provided. The steps of various useful immunodetection methods have been described in the scientific literature, such as, e.g., Doolittle and Ben-Zeev (1999), Gulbis and Galand (1993), De Jager et al. (1993), and Nakamura et al. (1987). In general, the immunobinding methods include obtaining a sample suspected of containing Zika virus, and contacting the sample with a first antibody in accordance with the present disclosure, as the case may be, under conditions effective to allow the formation of immunocomplexes.
These methods include methods for purifying Zika virus or related antigens from a sample. The antibody will preferably be linked to a solid support, such as in the form of a column matrix, and the sample suspected of containing the Zika virus or antigenic component will be applied to the immobilized antibody. The unwanted components will be washed from the column, leaving the Zika virus antigen immunocomplexed to the immobilized antibody, which is then collected by removing the organism or antigen from the column.
The immunobinding methods also include methods for detecting and quantifying the amount of Zika virus or related components in a sample and the detection and quantification of any immune complexes formed during the binding process. Here, one would obtain a sample suspected of containing Zika virus or its antigens and contact the sample with an antibody that binds Zika virus or components thereof, followed by detecting and quantifying the amount of immune complexes formed under the specific conditions. In terms of antigen detection, the biological sample analyzed may be any sample that is suspected of containing Zika virus or Zika virus antigen, such as a tissue section or specimen, a homogenized tissue extract, a biological fluid, including blood and serum, or a secretion, such as feces or urine. Contacting the chosen biological sample with the antibody under effective conditions and for a period of time sufficient to allow the formation of immune complexes (primary immune complexes) is generally a matter of simply adding the antibody composition to the sample and incubating the mixture for a period of time long enough for the antibodies to form immune complexes with, i.e., to bind to Zika virus or antigens present. After this time, the sample-antibody composition, such as a tissue section, ELISA plate, dot blot or Western blot, will generally be washed to remove any non-specifically bound antibody species, allowing only those antibodies specifically bound within the primary immune complexes to be detected.
In general, the detection of immunocomplex formation is well known in the art and may be achieved through the application of numerous approaches. These methods are generally based upon the detection of a label or marker, such as any of those radioactive, fluorescent, biological and enzymatic tags. Patents concerning the use of such labels include U.S. Patents 3,817,837, 3,850,752, 3,939,350, 3,996,345, 4,277,437, 4,275,149 and 4,366,241. Of course, one may find additional advantages through the use of a secondary binding ligand such as a second antibody and/or a biotin/avidin ligand binding arrangement, as is known in the art.
The antibody employed in the detection may itself be linked to a detectable label, wherein one would then simply detect this label, thereby allowing the amount of the primary immune complexes in the composition to be determined. Alternatively, the first antibody that becomes bound within the primary immune complexes may be detected by means of a second binding ligand that has binding affinity for the antibody. In these cases, the second binding ligand may be linked to a detectable label. The second binding ligand is itself often an antibody, which may thus be termed a“secondary” antibody. The primary immune complexes are contacted with the labeled, secondary binding ligand, or antibody, under effective conditions and for a period of time sufficient to allow the formation of secondary immune complexes. The secondary immune complexes are then generally washed to remove any non-specifically bound labeled secondary antibodies or ligands, and the remaining label in the secondary immune complexes is then detected.
Further methods include the detection of primary immune complexes by a two-step approach. A second binding ligand, such as an antibody that has binding affinity for the antibody, is used to form secondary immune complexes, as described above. After washing, the secondary immune complexes are contacted with a third binding ligand or antibody that has binding affinity for the second antibody, again under effective conditions and for a period of time sufficient to allow the formation of immune complexes (tertiary immune complexes). The third ligand or antibody is linked to a detectable label, allowing detection of the tertiary immune complexes thus formed. This system may provide for signal amplification if this is desired.
One method of immunodetection uses two different antibodies. A first biotinylated antibody is used to detect the target antigen, and a second antibody is then used to detect the biotin attached to the complexed biotin. In that method, the sample to be tested is first incubated in a solution containing the first step antibody. If the target antigen is present, some of the antibody binds to the antigen to form a biotinylated antibody/antigen complex. The antibody/antigen complex is then amplified by incubation in successive solutions of streptavidin (or avidin), biotinylated DNA, and/or complementary biotinylated DNA, with each step adding additional biotin sites to the antibody/antigen complex. The amplification steps are repeated until a suitable level of amplification is achieved, at which point the sample is incubated in a solution containing the second step antibody against biotin. This second step antibody is labeled, as for example with an enzyme that can be used to detect the presence of the antibody/antigen complex by histoenzymology using a chromogen substrate. With suitable amplification, a conjugate can be produced which is macroscopically visible.
Another known method of immunodetection takes advantage of the immuno-PCR (Polymerase Chain Reaction) methodology. The PCR method is similar to the Cantor method up to the incubation with biotinylated DNA, however, instead of using multiple rounds of streptavidin and biotinylated DNA incubation, the DNA/biotin/streptavidin/antibody complex is washed out with a low pH or high salt buffer that releases the antibody. The resulting wash solution is then used to carry out a PCR reaction with suitable primers with appropriate controls. At least in theory, the enormous amplification capability and specificity of PCR can be utilized to detect a single antigen molecule.
A. ELISAs
Immunoassays, in their most simple and direct sense, are binding assays. Certain preferred immunoassays are the various types of enzyme linked immunosorbent assays (ELISAs) and radioimmunoassays (RIA) known in the art. Immunohistochemical detection using tissue sections is also particularly useful. However, it will be readily appreciated that detection is not limited to such techniques, and western blotting, dot blotting, FACS analyses, and the like may also be used.
In one exemplary ELISA, the antibodies of the disclosure are immobilized onto a selected surface exhibiting protein affinity, such as a well in a polystyrene microtiter plate. Then, a test composition suspected of containing the Zika virus or Zika virus antigen is added to the wells. After binding and washing to remove non-specifically bound immune complexes, the bound antigen may be detected. Detection may be achieved by the addition of another anti-Zika virus antibody that is linked to a detectable label. This type of ELISA is a simple “sandwich ELISA.” Detection may also be achieved by the addition of a second anti-Zika virus antibody, followed by the addition of a third antibody that has binding affinity for the second antibody, with the third antibody being linked to a detectable label.
In another exemplary ELISA, the samples suspected of containing the Zika virus or Zika virus antigen are immobilized onto the well surface and then contacted with the anti-Zika virus antibodies of the disclosure. After binding and washing to remove non-specifically bound immune complexes, the bound anti-Zika virus antibodies are detected. Where the initial anti- Zika virus antibodies are linked to a detectable label, the immune complexes may be detected directly. Again, the immune complexes may be detected using a second antibody that has binding affinity for the first anti-Zika virus antibody, with the second antibody being linked to a detectable label.
Irrespective of the format employed, ELIS As have certain features in common, such as coating, incubating and binding, washing to remove non-specifically bound species, and detecting the bound immune complexes. These are described below.
In coating a plate with either antigen or antibody, one will generally incubate the wells of the plate with a solution of the antigen or antibody, either overnight or for a specified period of hours. The wells of the plate will then be washed to remove incompletely adsorbed material. Any remaining available surfaces of the wells are then“coated” with a nonspecific protein that is antigenically neutral with regard to the test antisera. These include bovine serum albumin (BSA), casein or solutions of milk powder. The coating allows for blocking of nonspecific adsorption sites on the immobilizing surface and thus reduces the background caused by nonspecific binding of antisera onto the surface.
In ELISAs, it is probably more customary to use a secondary or tertiary detection means rather than a direct procedure. Thus, after binding of a protein or antibody to the well, coating with a non-reactive material to reduce background, and washing to remove unbound material, the immobilizing surface is contacted with the biological sample to be tested under conditions effective to allow immune complex (antigen/antibody) formation. Detection of the immune complex then requires a labeled secondary binding ligand or antibody, and a secondary binding ligand or antibody in conjunction with a labeled tertiary antibody or a third binding ligand.
“Under conditions effective to allow immune complex (antigen/antibody) formation” means that the conditions preferably include diluting the antigens and/or antibodies with solutions such as BSA, bovine gamma globulin (BGG) or phosphate buffered saline (PBS)/Tween. These added agents also tend to assist in the reduction of nonspecific background.
The“suitable” conditions also mean that the incubation is at a temperature or for a period of time sufficient to allow effective binding. Incubation steps are typically from about 1 to 2 to 4 hours or so, at temperatures preferably on the order of 25°C to 27°C, or may be overnight at about 4°C or so.
Following all incubation steps in an ELISA, the contacted surface is washed so as to remove non-complexed material. A preferred washing procedure includes washing with a solution such as PBS/Tween, or borate buffer. Following the formation of specific immune complexes between the test sample and the originally bound material, and subsequent washing, the occurrence of even minute amounts of immune complexes may be determined.
To provide a detecting means, the second or third antibody will have an associated label to allow detection. Preferably, this will be an enzyme that will generate color development upon incubating with an appropriate chromogenic substrate. Thus, for example, one will desire to contact or incubate the first and second immune complex with a urease, glucose oxidase, alkaline phosphatase or hydrogen peroxidase-conjugated antibody for a period of time and under conditions that favor the development of further immune complex formation (e.g., incubation for 2 hours at room temperature in a PBS-containing solution such as PBS-Tween).
After incubation with the labeled antibody, and subsequent to washing to remove unbound material, the amount of label is quantified, e.g., by incubation with a chromogenic substrate such as urea, or bromocresol purple, or 2,2'-azino-di-(3-ethyl-benzthiazoline-6- sulfonic acid (ABTS), or H2O2, in the case of peroxidase as the enzyme label. Quantification is then achieved by measuring the degree of color generated, e.g., using a visible spectra spectrophotometer.
In another embodiment, the present disclosure contemplates the use of competitive formats. This is particularly useful in the detection of Zika virus antibodies in sample. In competition-based assays, an unknown amount of analyte or antibody is determined by its ability to displace a known amount of labeled antibody or analyte. Thus, the quantifiable loss of a signal is an indication of the amount of unknown antibody or analyte in a sample.
Here, the inventor proposes the use of labeled Zika virus monoclonal antibodies to determine the amount of Zika virus antibodies in a sample. The basic format would include contacting a known amount of Zika virus monoclonal antibody (linked to a detectable label) with Zika virus antigen or particle. The Zika virus antigen or organism is preferably attached to a support. After binding of the labeled monoclonal antibody to the support, the sample is added and incubated under conditions permitting any unlabeled antibody in the sample to compete with, and hence displace, the labeled monoclonal antibody. By measuring either the lost label or the label remaining (and subtracting that from the original amount of bound label), one can determine how much non-label ed antibody is bound to the support, and thus how much antibody was present in the sample.
B. Western Blot
The Western blot (alternatively, protein immunoblot) is an analytical technique used to detect specific proteins in a given sample of tissue homogenate or extract. It uses gel electrophoresis to separate native or denatured proteins by the length of the polypeptide (denaturing conditions) or by the 3-D structure of the protein (native/ non-denaturing conditions). The proteins are then transferred to a membrane (typically nitrocellulose or PVDF), where they are probed (detected) using antibodies specific to the target protein.
Samples may be taken from whole tissue or from cell culture. In most cases, solid tissues are first broken down mechanically using a blender (for larger sample volumes), using a homogenizer (smaller volumes), or by sonication. Cells may also be broken open by one of the above mechanical methods. However, it should be noted that bacteria, virus or environmental samples can be the source of protein and thus Western blotting is not restricted to cellular studies only. Assorted detergents, salts, and buffers may be employed to encourage lysis of cells and to solubilize proteins. Protease and phosphatase inhibitors are often added to prevent the digestion of the sample by its own enzymes. Tissue preparation is often done at cold temperatures to avoid protein denaturing.
The proteins of the sample are separated using gel electrophoresis. Separation of proteins may be by isoelectric point (pi), molecular weight, electric charge, or a combination of these factors. The nature of the separation depends on the treatment of the sample and the nature of the gel. This is a very useful way to determine a protein. It is also possible to use a two-dimensional (2-D) gel which spreads the proteins from a single sample out in two dimensions. Proteins are separated according to isoelectric point (pH at which they have neutral net charge) in the first dimension, and according to their molecular weight in the second dimension.
In order to make the proteins accessible to antibody detection, they are moved from within the gel onto a membrane made of nitrocellulose or polyvinylidene difluoride (PVDF). The membrane is placed on top of the gel, and a stack of filter papers placed on top of that. The entire stack is placed in a buffer solution which moves up the paper by capillary action, bringing the proteins with it. Another method for transferring the proteins is called electroblotting and uses an electric current to pull proteins from the gel into the PVDF or nitrocellulose membrane. The proteins move from within the gel onto the membrane while maintaining the organization they had within the gel. As a result of this blotting process, the proteins are exposed on a thin surface layer for detection (see below). Both varieties of membrane are chosen for their non specific protein binding properties (i.e., binds all proteins equally well). Protein binding is based upon hydrophobic interactions, as well as charged interactions between the membrane and protein. Nitrocellulose membranes are cheaper than PVDF but are far more fragile and do not stand up well to repeated probings. The uniformity and overall effectiveness of transfer of protein from the gel to the membrane can be checked by staining the membrane with Coomassie Brilliant Blue or Ponceau S dyes. Once transferred, proteins are detected using labeled primary antibodies, or unlabeled primary antibodies followed by indirect detection using labeled protein A or secondary labeled antibodies binding to the Fc region of the primary antibodies.
C. Lateral Flow Assays
Lateral flow assays, also known as lateral flow immunochromatographic assays, are simple devices intended to detect the presence (or absence) of a target analyte in sample (matrix) without the need for specialized and costly equipment, though many laboratory-based applications exist that are supported by reading equipment. Typically, these tests are used as low resources medical diagnostics, either for home testing, point of care testing, or laboratory use. A widely spread and well-known application is the home pregnancy test.
The technology is based on a series of capillary beds, such as pieces of porous paper or sintered polymer. Each of these elements has the capacity to transport fluid (e.g., urine) spontaneously. The first element (the sample pad) acts as a sponge and holds an excess of sample fluid. Once soaked, the fluid migrates to the second element (conjugate pad) in which the manufacturer has stored the so-called conjugate, a dried format of bio-active particles (see below) in a salt-sugar matrix that contains everything to guarantee an optimized chemical reaction between the target molecule (e.g., an antigen) and its chemical partner (e.g., antibody) that has been immobilized on the particle's surface. While the sample fluid dissolves the salt- sugar matrix, it also dissolves the particles and in one combined transport action the sample and conjugate mix while flowing through the porous structure. In this way, the analyte binds to the particles while migrating further through the third capillary bed. This material has one or more areas (often called stripes) where a third molecule has been immobilized by the manufacturer. By the time the sample-conjugate mix reaches these strips, analyte has been bound on the particle and the third 'capture' molecule binds the complex. After a while, when more and more fluid has passed the stripes, particles accumulate and the stripe-area changes color. Typically there are at least two stripes: one (the control) that captures any particle and thereby shows that reaction conditions and technology worked fine, the second contains a specific capture molecule and only captures those particles onto which an analyte molecule has been immobilized. After passing these reaction zones, the fluid enters the final porous material - the wick - that simply acts as a waste container. Lateral Flow Tests can operate as either competitive or sandwich assays. Lateral flow assays are disclosed in U.S. Patent 6,485,982.
D. Immunohistochemistry
The antibodies of the present disclosure may also be used in conjunction with both fresh-frozen and/or formalin-fixed, paraffin-embedded tissue blocks prepared for study by immunohistochemistry (IHC). The method of preparing tissue blocks from these particulate specimens has been successfully used in previous IHC studies of various prognostic factors and is well known to those of skill in the art (Brown et al, 1990; Abbondanzo et al, 1990; Allred et al, 1990).
Briefly, frozen-sections may be prepared by rehydrating 50 ng of frozen“pulverized” tissue at room temperature in phosphate buffered saline (PBS) in small plastic capsules; pelleting the particles by centrifugation; resuspending them in a viscous embedding medium (OCT); inverting the capsule and/or pelleting again by centrifugation; snap-freezing in -70°C isopentane; cutting the plastic capsule and/or removing the frozen cylinder of tissue; securing the tissue cylinder on a cryostat microtome chuck; and/or cutting 25-50 serial sections from the capsule. Alternatively, whole frozen tissue samples may be used for serial section cuttings.
Permanent-sections may be prepared by a similar method involving rehydration of the 50 mg sample in a plastic microfuge tube; pelleting; resuspending in 10% formalin for 4 hours fixation; washing/pelleting; resuspending in warm 2.5% agar; pelleting; cooling in ice water to harden the agar; removing the tissue/agar block from the tube; infiltrating and/or embedding the block in paraffin; and/or cutting up to 50 serial permanent sections. Again, whole tissue samples may be substituted. E. Immunodetection Kits
In still further embodiments, the present disclosure concerns immunodetection kits for use with the immunodetection methods described above. As the antibodies may be used to detect Zika virus or Zika virus antigens, the antibodies may be included in the kit. The immunodetection kits will thus comprise, in suitable container means, a first antibody that binds to Zika virus or Zika virus antigen, and optionally an immunodetection reagent.
In certain embodiments, the Zika virus antibody may be pre-bound to a solid support, such as a column matrix and/or well of a microtiter plate. The immunodetection reagents of the kit may take any one of a variety of forms, including those detectable labels that are associated with or linked to the given antibody. Detectable labels that are associated with or attached to a secondary binding ligand are also contemplated. Exemplary secondary ligands are those secondary antibodies that have binding affinity for the first antibody.
Further suitable immunodetection reagents for use in the present kits include the two- component reagent that comprises a secondary antibody that has binding affinity for the first antibody, along with a third antibody that has binding affinity for the second antibody, the third antibody being linked to a detectable label. As noted above, a number of exemplary labels are known in the art and all such labels may be employed in connection with the present disclosure.
The kits may further comprise a suitably aliquoted composition of the Zika virus or Zika virus antigens, whether labeled or unlabeled, as may be used to prepare a standard curve for a detection assay. The kits may contain antibody-label conjugates either in fully conjugated form, in the form of intermediates, or as separate moieties to be conjugated by the user of the kit. The components of the kits may be packaged either in aqueous media or in lyophilized form.
The container means of the kits will generally include at least one vial, test tube, flask, bottle, syringe or other container means, into which the antibody may be placed, or preferably, suitably aliquoted. The kits of the present disclosure will also typically include a means for containing the antibody, antigen, and any other reagent containers in close confinement for commercial sale. Such containers may include injection or blow-molded plastic containers into which the desired vials are retained.
F. Vaccine and Antigen Quality Control Assays
The present disclosure also contemplates the use of antibodies and antibody fragments as described herein for use in assessing the antigenic integrity of a viral antigen in a sample. Biological medicinal products like vaccines differ from chemical drugs in that they cannot normally be characterized molecularly; antibodies are large molecules of significant complexity and have the capacity to vary widely from preparation to preparation. They are also administered to healthy individuals, including children at the start of their lives, and thus a strong emphasis must be placed on their quality to ensure, to the greatest extent possible, that they are efficacious in preventing or treating life-threatening disease, without themselves causing harm.
The increasing globalization in the production and distribution of vaccines has opened new possibilities to beher manage public health concerns but has also raised questions about the equivalence and interchangeability of vaccines procured across a variety of sources. International standardization of starting materials, of production and quality control testing, and the sehing of high expectations for regulatory oversight on the way these products are manufactured and used, have thus been the cornerstone for continued success. But it remains a field in constant change, and continuous technical advances in the field offer a promise of developing potent new weapons against the oldest public health threats, as well as new ones - malaria, pandemic influenza, and HIV, to name a few - but also put a great pressure on manufacturers, regulatory authorities, and the wider medical community to ensure that products continue to meet the highest standards of quality attainable.
Thus, one may obtain an antigen or vaccine from any source or at any point during a manufacturing process. The quality control processes may therefore begin with preparing a sample for an immunoassay that identifies binding of an antibody or fragment disclosed herein to a viral antigen. Such immunoassays are disclosed elsewhere in this document, and any of these may be used to assess the structural/antigenic integrity of the antigen. Standards for finding the sample to contain acceptable amounts of antigenically correct and intact antigen may be established by regulatory agencies.
Another important embodiment where antigen integrity is assessed is in determining shelf-life and storage stability. Most medicines, including vaccines, can deteriorate over time. Therefore, it is critical to determine whether, over time, the degree to which an antigen, such as in a vaccine, degrades or destabilizes such that is it no longer antigenic and/or capable of generating an immune response when administered to a subject. Again, standards for finding the sample to contain acceptable amounts of antigenically intact antigen may be established by regulatory agencies.
In certain embodiments, viral antigens may contain more than one protective epitope. In these cases, it may prove useful to employ assays that look at the binding of more than one antibody, such as 2, 3, 4, 5 or even more antibodies. These antibodies bind to closely related epitopes, such that they are adjacent or even overlap each other. On the other hand, they may represent distinct epitopes from disparate parts of the antigen. By examining the integrity of multiple epitopes, a more complete picture of the antigen’s overall integrity, and hence ability to generate a protective immune response, may be determined.
Antibodies and fragments thereof as described in the present disclosure may also be used in a kit for monitoring the efficacy of vaccination procedures by detecting the presence of protective Zika virus antibodies. Antibodies, antibody fragment, or variants and derivatives thereof, as described in the present disclosure may also be used in a kit for monitoring vaccine manufacture with the desired immunogenicity.
VI. Examples
The following examples are included to demonstrate preferred embodiments. It should be appreciated by those of skill in the art that the techniques disclosed in the examples that follow represent techniques discovered by the inventor to function well in the practice of embodiments, and thus can be considered to constitute preferred modes for its practice. However, those of skill in the art should, in light of the present disclosure, appreciate that many changes can be made in the specific embodiments which are disclosed and still obtain a like or similar result without departing from the spirit and scope of the disclosure.
Example 1 - Materials and Methods
Research subjects. The inventor studied eight subjects in the U.S. with prior or recent ZIKV infection (Table 5). The studies were approved by the Institutional Review Board of Vanderbilt University Medical Center; samples were obtained after informed consent was obtained by the Vanderbilt Clinical Trials Center. Two subjects (972 and 973) were infected with an African lineage strain in 2008 (one subject while working in Senegal, the second acquired the infection by sexual transmission from the first, as previously reported (Foy et al, 2011). The other six subjects were infected during the current outbreak of an Asian lineage strain, following exposure in Brazil, Mexico, or Haiti.
Generation and quantification of human B cell lines secreting ZIKV E protein specific antibodies. Peripheral blood mononuclear cells (PBMCs) from heparinized blood were isolated with Ficoll-Histopaque by density gradient centrifugation. The cells either were used immediately or cryopreserved in the vapor phase of liquid nitrogen until use. Ten million PBMCs were cultured in 384-well plates (Nunc) using culture medium (ClonaCell-HY Medium A, StemCell Technologies) supplemented with 8 pg/ml of the TLR agonist CpG (phosphorothioate-modified oligodeoxynucleotide ZOEZOEZZZZZOEEZOEZZZT (SEQ ID NO: 21), Invitrogen), 3 pg/ml of Chk2 inhibitor (Sigma), 1 pg/ml of cyclosporine A (Sigma), and clarified supernatants from cultures of B95.8 cells (ATCC) containing Epstein-Barr virus (EBV). After 7 days, cells from each 384-well culture plate were expanded into four 96-well culture plates (Falcon) using ClonaCell-HY Medium A containing 8 pg/ml of CpG, 3 pg/ml of Chk2 inhibitor, and 107 irradiated heterologous human PBMCs (Nashville Red Cross) and cultured for an additional 4 days. Supernatants were screened in ELISA (described below) for reactivity with various ZIKV E proteins, which are described below.
The minimal frequency of ZIKV E-reactive B cells was estimated based on the number of wells with E protein-reactive supernatants compared with the total number of lymphoblastoid cell line colonies in the transformation plates [calculation: E-reactive B cell frequency = (number of wells with E-reactive supernatants) divided by (number of LCL colonies in the plate) x 100]
Protein expression and purification. The ectodomains of ZIKV E (H/PF/2013; GenBank Accession KJ776791) and the fusion-loop mutant E-FLM (containing four mutations: T76A, Q77G, W101R, L107R) were expressed transiently in Expi293F cells and purified as described previously (Zhao et al, 2016). ZIKV Dill (residues 299-407 of strain H/PF/2013), WNV-DIII (residues 296-405 of strain New York 1999) and DENV2-DIII (residues 299-410 of strain 16681) were expressed in BL21 (DE3) as inclusion bodies and refolded in vitro (Nelson et al, 2014). Briefly, inclusion bodies were denatured and refolded by gradual dilution into a refolding buffer (400 mM L-arginine, 100 mM Tris [pH 8.3], 2 mM EDTA, 5 and 0.5 mM reduced and oxidized glutathione) at 4°C. Refolded proteins were purified by size- exclusion chromatography using a Superdex 75, 16/60 (GE Healthcare).
Generation of human hybridomas. Cells from wells with transformed B cells containing supernatants that exhibited reactivity to ZIKV E protein were fused with HMMA2.5 myeloma cells (kind gift from L. Cavacini) using an established electrofusion technique (Yu et al. , 2008). After fusion, hybridomas were suspended in a selection medium containing 100 mM hypoxanthine, 0.4 pM aminopterin, 16 pM thymidine (HAT Media Supplement, Sigma), and 7 pg/ml ouabain (Sigma) and cultured in 384-well plates for 18 days before screening hybridomas for antibody production by ELISA. After fusion with HMMA2.5 myeloma cells, hybridomas producing ZIKV E-specific antibodies were cloned biologically by single-cell fluorescence-activated cell sorting. Hybridomas were expanded in post-fusion medium (ClonaCell-HY Medium E, STEMCELL Technologies) until 50% confluent in 75-cm2 flasks (Coming).
For antibody production, cells from one 75-cm2 flask were collected with a cell scraper and expanded to four 225-cm2 flasks (Coming) in serum-free medium (Hybridoma-SFM, Life Technologies). After 21 days, supernatants were clarified by centrifugation and filtered using 0.45-pm pore size filter devices. HiTrap Protein G or HiTrap MabSelectSure columns (GE Healthcare Life Sciences) were used to purify antibodies from filtered supernatants.
Sequence analysis of antibody variable region genes. Total cellular RNA was extracted from pelleted cells from hybridoma clones, and an RT-PCR reaction was performed using mixtures of primers designed to amplify all heavy-chain or light-chain antibody variable regions (Nelson et al, 2014). The generated PCR products were purified using AMPure XP magnetic beads (Beckman Coulter) and sequenced directly using an ABI3700 automated DNA sequencer. The variable region sequences of the heavy and light chains were analyzed using the IMGT/V -Quest program (Brochet et al. , 2008; Gui dicell & Lefranc, 2011).
ELISA and half-maximal effective concentration (ECso) binding analysis. Wells of microtiter plates were coated with purified, recombinant ectodomain of ZIKV E, Dill, Dill LRM (Dill containing A310E and T335K mutations in the lateral ridge of Dill) or Dill of related flaviviruses DENV2 or WNV and incubated at 4°C overnight. In ELISA studies with purified mAbs, the inventor used recombinant ZIKV E protein ectodomain with His6 tag produced in Sf9 insect cells (Meridian Life Sciences R01635). Plates were blocked with 5% skim milk in PBS-T for 1 hr. B cell culture supernatants or purified antibodies were added to the wells and incubated for 1 hr at ambient temperature. The bound antibodies were detected using goat anti-human IgG (g-specific) conjugated with alkaline phosphatase (Southern Biotech) and pNPP disodium salt hexahydrate substrate (Sigma). In ELISAs that assessed binding of mAbs to Dill and Dill LRM, the inventor used previously described murine mAbs ZV-2 and ZV-54 (Zhao et al. , 2016) as controls. A goat anti-mouse IgG conjugated with alkaline phosphatase (Southern Biotech) was used for detection of these antibodies. Color development was monitored at 405 nm in a spectrophotometer (Biotek). For determining half- maximal effective concentration binding (EC50), microtiter plates were coated with ZIKV E or E-FLM that eliminated interaction of fusion-loop specific antibodies. Purified antibodies were diluted serially and applied to the plates. Bound antibodies were detected as above. A non linear regression analysis was performed on the resulting curves using Prism (GraphPad) to calculate ECso values. ELISA for detection of human antibodies in murine tissues. Fetal head and placental tissues were collected at E13.5 from groups treated with ZIKV-117 or PBS (as a negative control), homogenized in PBS (250 pl) and stored at -20°C. ELISA plates were coated with ZIKV E protein, and thawed, clarified tissue homogenates were applied undiluted in triplicate. Bound antibodies were detected using goat anti -human IgG (Fc-specific) antibody conjugated with alkaline phosphatase. The quantity of antibody was determined by comparison with a standard curve constructed using purified ZIKV-117 in a dilution series.
Biolayer interferometry competition binding assay. His6-tagged ZIKV E protein was immobilized on anti-His coated biosensor tips (Pall) for 2 min on an Octet Red biosensor instrument. After measuring the baseline signal in kinetics buffer (PBS, 0.01% BSA, and 0.002% Tween 20) for 1 min, biosensor tips were immersed into the wells containing first antibody at a concentration of 10 pg/ml for 7 min. Biosensors then were immersed into wells containing a second mAh at a concentration of 10 pg/ml for 7 min. The signal obtained for binding of the second antibody in the presence of the first antibody was expressed as a percent of the uncompeted binding of the second antibody that was derived independently. The antibodies were considered competing if the presence of first antibody reduced the signal of the second antibody to less than 30% of its maximal binding and non-competing if the signal was greater than 70%. A level of 30 -70% was considered intermediate competition.
Shotgun mutagenesis epitope mapping. Epitope mapping was performed by shotgun mutagenesis essentially as described previously (Davidson & Doranz, 2014. A ZIKV prM/E protein expression construct (strain ZikaSPH20l5) was subjected to high-throughput alanine scanning mutagenesis to generate a comprehensive mutation library. Each residue within prM/E was changed to alanine, with alanine codons mutated to serine. In total, 672 ZIKV prM/E mutants were generated (100% coverage), sequence confirmed, and arrayed into 384- well plates. Each ZIKV prM/E mutant was transfected into HEK-293T cells and allowed to express for 22 h. Cells were fixed in 4% (v/v) paraformaldehyde (Electron Microscopy Sciences), and permeabilized with 0.1% (w/v) saponin (Sigma- Aldrich) in PBS plus calcium and magnesium (PBS++). Cells were incubated with purified mAbs diluted in PBS++, 10% normal goat serum (NGS) (Sigma), and 0.1% saponin. Primary antibody screening concentrations were determined using an independent immunofluorescence titration curve against WT ZIKV prM/E to ensure that signals were within the linear range of detection. Antibodies were detected using 3.75 pg/ml of AlexaFluor488-conjugated secondary antibody (Jackson ImmunoResearch Laboratories) in 10% NGS/0.l% saponin. Cells were washed three times with PBS++/0.l% saponin followed by two washes in PBS. Mean cellular fluorescence was detected using a high-throughput flow cytometer (HTFC, Intellicyt). Antibody reactivity against each mutant prM/E clone was calculated relative to WT prM/E protein reactivity by subtracting the signal from mock-transfected controls and normalizing to the signal from WT prM/E-transfected controls. Mutations within clones were identified as critical to the mAh epitope if they did not support reactivity of the test MAb but supported reactivity of other ZIKV antibodies. This counter-screen strategy facilitates the exclusion of prM/E mutants that are locally misfolded or have an expression defect.
Vertebrate animal studies ethics statement. This study was carried out in accordance with the recommendations in the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health. The protocols were approved by the Institutional Animal Care and Use Committee at the Washington University School of Medicine (Assurance number A3381-01). Inoculations were performed under anesthesia induced and maintained with ketamine hydrochloride and xylazine, and all efforts were made to minimize animal suffering.
Viruses and cells. ZIKV strain H/PF/2013 (French Polynesia, 2013) was obtained from X. de Lamballerie (Aix Marseille Universite). ZIKV Brazil Paraiba 2015 was provided by S. Whitehead (Bethesda) and originally obtained from P.F.C. Vasconcelos (Instituto Evandro Cargas). ZIKV MR 766 (Uganda, 1947), Malaysia P6740 (1966), and Dakar 41519 (Senegal, 1982) were provided by the World Reference Center or Emerging Viruses and Arboviruses (R. Tesh, University of Texas Medical Branch). Nicaraguan DENV strains (DENV-l 1254-4, DENV-2 172-08, DENV-3 N2845-09, and DENV-4 N703-99) were provided generously by E. Harris (University of California, Berkeley). Virus stocks were propagated in C6/36 Aedes albopictus cells (DENV) or Vero cells (ZIKV). ZIKV Dakar 41519 (ZIKV-Dakar) was passaged twice in vivo in Ragl 1 mice (M. Gorman and M. Diamond, unpublished data) to create a mouse-adapted strain. Virus stocks were titrated by focus-forming assay (FFA) on Vero cells.
Neutralization assays. Serial dilutions of mAbs were incubated with 102 FFU of different ZIKV strains (MR 766, Dakar 41519, Malaysia P6740, H/PF/2013, or Brazil Paraiba 2015) for 1 hr at 37 °C. The mAb-virus complexes were added to Vero cell monolayers in 96- well plates for 90 min at 37°C. Subsequently, cells were overlaid with 1% (w/v) methylcellulose in MEM supplemented with 4% heat-inactivated FBS. Plates were fixed 40 h later with 1% PFA in PBS for 1 hr at room temperature. The plates were incubated sequentially with 500 ng/ml mouse anti-ZIKV (ZV-16, E. Fernandez and M. Diamond, unpublished) and HRP-conjugated goat anti-mouse IgG in PBS supplemented with 0.1% (w/v) saponin (Sigma) and 0.1% BSA. ZIKV-infected cell foci were visualized using TrueBlue peroxidase substrate (KPL) and quantitated on an ImmunoSpot 5.0.37 macroanalyzer (Cellular Technologies).
MAb binding to ZIKV- or DENV-infected cells. C6/36 Aedes albopictus cells were inoculated with a MOI 0.01 of ZIKV (H/PF/2013) or different DENV serotypes (Nicaraguan strains DENV-l 1254-4, DENV-2 172-08, DENV-3 N2845-09, DENV-4 N703-99). At 120 hr post infection, cells were fixed with 4% PFA diluted in PBS for 20 min at room temperature and permeabilized with HBSS supplemented with 10 mM HEPES, 0.1% saponin and 0.025% NaN3 for 10 min at room temperature. Fifty -thousand cells were transferred to U-bottom plates and incubated for 30 min at 4°C with 5 pg/ml of anti-ZIKV human mAbs or negative (hCHK- 152)12; or positive (hE60) (Williams el al, 2013) isotype controls. After washing, cells were incubated with Alexa Fluor 647-conjugated goat anti-human IgG (Invitrogen) at 1:500, fixed in 1% PFA in PBS, processed on MACSQuant Analyzed (Miltenyi Biotec), and analyzed using FlowJo software (Tree Star).
Recombinant antibody expression and purification. Total RNA was extracted from hybridoma cells and genes encoding the VH and VL domains were amplified in RT-PCR using IgExp primers (Thornburg el al. , 2016). The PCR products were directly cloned into antibody expression vectors containing the constant domains of WT gammal chain, LALA mutant (a leucine (L) to alanine (A) substitution at positions 234 and 235) gammal chain for the VH domains, and WT kappa chain for the VL domain in an isothermal amplification reaction (Gibson reaction) (Gibson et al. , 2009). Plasmids encoding the heavy and light chain were transfected into 293F cells and full-length recombinant IgG was secreted into transfected cell supernatants. Supernatants were collected and IgG purified using Protein G chromatography and eluted into PBS. The functional abrogation of the binding of the LALA variant IgG was confirmed in an ELISA binding assay with recombinant human FcyRI. The binding of ZIKV- 117 WT or LALA antibody to FcyRI was evaluated, in comparison with the binding pattern of control antibodies (human mAh CKV063 (Fong et al, 2014); LALA-mutated IgG).
Adult mouse lethal protection experiments. C57BL/6J male mice (4- to 5-week-old, Jackson Laboratories) were inoculated with 103 FFU of mouse-adapted ZIKV Dakar by subcutaneous route in the footpad. One-day prior to infection, mice were treated with 2 mg anti-Ifnarl mAh (MAR1-5A3, Leinco Technologies) by intraperitoneal injection. ZIKV- specific human mAb (ZIKV- 117) or an isotype control (hCHK-l52) was administered as a single dose at day +1 (100 pg) or day +5 (250 pg) after infection via an intraperitoneal route. Animals were monitored for 21 days. Pregnant mouse protection experiments. WT C57BL/6J mice were bred in a specific pathogen-free facility at Washington University School of Medicine. WT dams prophylaxis studies. WT female and male mice were mated; at embryonic days E5.5, dams were treated with a single 250 pg dose of ZIKV mAh or isotype control by intraperitoneal injection as well as a 1 mg injection of anti-Ifnarl (MAR1-5A3). At E6.5, mice were inoculated with 103 FFU of mouse-adapted ZIKV Dakar 41519 by subcutaneous injection in the footpad. At E7.5, dams received a second 1 mg dose of anti-Ifnarl via an intraperitoneal route. WT dams, therapy. WT female and male mice were mated; at embryonic days E5.5, dams were treated with a 1 mg injection of anti-Ifnarl (MAR1-5A3). At E6.5, mice were inoculated with mouse-adapted 103 FFU of ZIKV Dakar 41519 by subcutaneous injection in the footpad. At E7.5, dams received a second 1 mg dose of anti-Ifnarl as well as a single 250 pg dose of ZIKV mAh or isotype control via an intraperitoneal route. All animals were sacrificed at E13.5, and placentas, fetuses and maternal tissues were harvested. Fetus size was measured as the crown-rump length x occipito-frontal diameter of the head.
Measurement of viral burden. ZIKV -infected tissues were weighed and homogenized with stainless steel beads in a Bullet Blender instrument (Next Advance) in 200 pL of PBS. Samples were clarified by centrifugation (2,000 x g for 10 min). All homogenized tissues from infected animals were stored at -20°C. Tissue samples and serum from ZIKV-infected mice were extracted with RNeasy 96 Kit (tissues) or Viral RNA Mini Kit (serum) (Qiagen). ZIKV RNA levels were determined by TaqMan one-step quantitative reverse transcriptase PCR (qRT-PCR) on an ABI7500 Fast Instrument using published primers and conditions (Lanciotti et ah, 2008). Viral burden was expressed on a logio scale as viral RNA equivalents per g or ml after comparison with a standard curve produced using serial 10-fold dilutions of ZIKV RNA.
Viral RNA in situ hybridization (ISH). RNA ISH was performed with RNAscope 2.5 (Advanced Cell Diagnostics) according to the manufacturer’s instructions. PFA-fixed paraffin embedded placental sections were deparaffmized by incubation for 60 min at 60°C. Endogenous peroxidases were quenched with H2O2 for 10 min at room temperature. Slides were boiled for 15 min in RNAscope Target Retrieval Reagents and incubated for 30 min in RNAscope Protease Plus before probe hybridization. The probe targeting ZIKV RNA was designed and synthesized by Advanced Cell Diagnostics (catalog no. 467771). Negative (targeting bacterial gene dapB) control probes were also obtained from Advanced Cell Diagnostics (catalog no. 310043). Tissues were counterstained with Gill’s hematoxylin and visualized with standard bright- field microscopy. Histology and immunohistochemistry. Harvested placentas were fixed in 10% neutral buffered formalin at room temperature and embedded in paraffin. At least three placentas from different litters with the indicated treatments were sectioned and stained with hematoxylin and eosin to assess morphology. Surface area and thickness of placenta and different layers were measured using Image J software. For immunofluorescence staining on mouse placentas, deparaffmized tissues were blocked in blocking buffer (1% BSA, 0.3% Triton, 1 c PBS) for 2 hr and incubated with anti-vimentin antibody (1:500, rabbit, Abeam ab92547). Secondary antibody conjugated with Alexa 488 (1:500 in PBS) was applied for 1 h at room temperature. Samples were counterstained with DAPI (4'6'-diamidino-2-phenilindole, 1 : 1,000 dilution).
Statistical analysis. All virological data were analyzed with GraphPad Prism software. Kaplan-Meier survival curves were analyzed by the log rank test, and viremia was compared using an ANOVA with a multiple comparisons test. A P value of < 0.05 indicated statistically significant differences.
Sequence analysis of antibody variable genes by 5' Rapid Amplification of cDNA Ends (5'RACE). The inventor developed a novel approach for analyzing full-length antibody heavy or light variable region gene sequences from antigen-specific hybridoma lines that have been cloned previously biologically by flow cytometric single-cell sorting. This approach uses 5' Rapid Amplification of cDNA Ends (5'RACE) and unique molecular identifiers (UMIs or ‘bar codes) introduced during the course of cDNA synthesis to control bottlenecks, minimize primer bias, and to eliminate PCR and sequencing errors. Analysis of the full-length antibody heavy or light chain cDNA variable region from the 5vUTR to the J gene segment (plus ~40 nucleotides more in order to preserve information on the antibody isotype that is encoded in the C gene segment) requires a sequencing length of -600-640 nucleotides. This length is almost feasible with paired-end sequencing using the 600- nucleotide MiSeq Illumina kit, which has enough reagents for up to 650 cycles (it is possible to increase the read length by 50 nucleotide to achieve paired reads overlap). However, the quality of Illumina sequencing rapidly decreases along the read length, which makes it challenging to obtain reliable sequence information in the middle of the variable segment. To overcome this challenge, the inventor used Pacific Bioscience long-read single-molecule real-time (SMRT) sequencing technology. Despite the moderately high error rate associated with SMRT technology, high quality sequences can be obtained easily by circular consensus sequencing (CCS) due to the random nature of the error profile. Additionally, grouping multiple sequencing reads from the same cDNA starting molecule (i.e., carrying the same UMI) results in a high-quality consensus read, which can be used to obtain high-quality sequence throughout the whole antibody heavy or light chain variable region. For example, if the Pacific Biosciences quality report states that there is a 1% chance that‘A’ at position X is erroneous, but there are four such reads covering the same original starting molecule, the resulting error probability is only 0.000001%. Therefore, the reliability of each nucleotide position drastically increases. Sequence analysis of the resulting data is performed with the IMGT/V-Quest tool of the International ImMunoGeneTics information system IMG), a publically available web-based tool. This combined 5'RACE/UMI/SMRT approach ensures maximal recovery and accuracy of nucleotide sequences encoding the mAbs isolated from human B cells that the inventor generated.
Protective and therapeutic efficacy of ZIKV-117 in nonhuman primates. A study was performed in 12 rhesus monkeys administered intravenous mAh ZIKV-117 (or an unrelated human IgG) at 10 mg/kg IV on Day -1 or +2, and then challenged with 106 viral particles (103 PFU) ZIKV Brazil strain on Day 0. The experimental groups were as follows: Group 1 : Sham (control antibody) on Day -1 (N=3), Group 2: ZIKV-117 on Day -1 (N=3), Group 3: Sham (control antibody) on Day +2 (N=3), Group 4: ZIKV-l 17 on Day +2 (N=3).
Example 2 - Results
The inventor sought to isolate neutralizing human mAbs with broad specificity against all ZIKV strains. To do this, they initially tested the serological response of human survivors who had been infected with African or Asian lineage strain ZIKV in diverse geographic locations. Serum from each subject contained antibodies that reacted by ELISA with ZIKV E protein and neutralized infection of a contemporary Asian isolate (H/PF/2013) from French Polynesia (FIGS. 1A-B). The inventor studied the B cells of Subject 1001 in detail. The frequency of B cells secreting antibodies to ZIKV E protein in the peripheral blood of Subject 1001 was 0.61% (FIG. 1C), when a threshold for detection of binding [absorbance at 405 nm (A405)] of 1.5 was used. They also tested the reactivity of antibodies with domain III (Dill) of the E protein from ZIKV, or the related dengue (DENV) or West Nile (WNV) viruses. Most of the ZIKV E reactive antibodies did not bind to Dill, and of those binding to Dill, most were ZIKV-specific (FIG. 1C). In a replicate of the assay performed with another aliquot of cells from the same subject (FIG. 1D), the frequency of ZIKV E-reactive B cell was 0.36%. Comparative binding to a WT ZIKV E or mutant (E-FLM) protein lacking the conserved fusion loop epitope in DII showed immunodominance (binding ~ 70% of mAbs) of the fusion loop. The inventor obtained 32 stable cloned hybridomas secreting antibodies that bound to ZIKV E protein from the cells of three donors (mAb ZIKV-195 from Subject 1011, mAbs ZIKV-204 and ZIKV-216 from Subject 973, and the remaining 29 mAbs from Subject 1001). All except one mAb belonged to IgGl isotype, with an equal distribution of light chain isotypes (FIG. 2A). Sanger sequencing of cDNA of the antibody variable gene regions revealed that each mAb represented an independently derived clone. The inventor determined the half maximal effective concentration for binding (EC50) to ZIKV E protein (FIGS. 2A and FIG. 5); most of the mAbs bound to E protein at low concentrations, with EC50 values generally below 100 ng/ml. Six of the 32 mAbs exhibited neutralizing activity, with FRNT50 values in the range of 0.9 to 420 ng/ml. They next determined how many antigenic sites were recognized by members of the panel using quantitative competition binding to ZIKV E protein. The inventor identified four major competition groups (designated A, B, C or D). Antibodies belonging to the largest group, Group A with 24 members, were directed against the fusion loop in DII as determined from the disparate binding patterns to E, Dill, or to E-FLM (FIG. 5). This group of fusion loop-specific mAbs had a single neutralizing clone (ZIKV-88), with moderate potency. Group B mAbs (ZIKV-l 16 and ZIKV- 161) neutralized ZIKV infection and bound to E, Dill, and E-FLM. Group C mAbs (ZIKV- 19 and ZIKV- 190) bound to E and E-FLM weakly but did not potently neutralize infection. Group D mAbs ZIKV- 195 and ZIKV-216 neutralized with moderate potency and were similar in binding to both E and E-FLM. The most potently inhibitory Group D mAb, ZIKV-l 17, bound to both E and E-FLM weakly. One antibody (ZIKV-216) competed with members of both Groups C and D and neutralized with moderate potency.
The inventor mapped the epitopes of representative mAbs from each competition group using a complete shotgun mutagenesis library (Davidson & Doranz, 2014) of ZIKV prM/E (Brazil Paraiba 2015 strain) protein variants in which each residue was changed individually to alanine (FIG. 2B and FIGS. 6A-C). Loss-of-binding analysis confirmed that Group A mAbs bound to the fusion loop in DII, whereas Group B mAbs bound Dill. Group B mAb ZIKV-l 16 bound an epitope involving residue K394 in the lateral ridge of Dill, which was confirmed in an ELISA showing reduced binding to a Dill protein with mutations A310E and T335K in the Dill lateral ridge [DIII-LR] (Zhao etal, 2016). The non-neutralizing clones comprising Group C mAbs bound DII, and the group D neutralizing mAbs bound to a unique epitope in DII not described previously for the closely related DENV (Screaton et al, 2015). The position of the residues affecting binding of ZIKV-l 17 suggests that on the virion this mAb may bind DII across two distinct dimers (at the“dimer-dimer” interface, FIG. 2C). The inventor was unable to isolate virus neutralization escape mutant viruses for ZIKV-117 despite six passages in cell culture under mAb selection pressure.
Of the 32 mAbs, six (ZIKV-88, ZIKV-116, ZIKV-161, ZIKV-195, ZIKV-216, and ZIKV-117) showed significant (< 1 pg/ml) neutralizing activity in vitro against ZIKV French Polynesia strain H/PF/2013. The FRNT50 values for the mAbs were as follows: Group A mAb ZIKV-88 (420 ng/ml), Group B mAbs ZIKV-l 16 (16 ng/ml) and ZIKV-161 (0.9 ng/ml), Group C/D mAb ZIKV-216 (16 ng/ml) and Group D mAbs ZIKV-195 (346 ng/ml) and ZIKV-l 17 (5 ng/ml). The inventor assessed whether Group B mAb ZIKV-l 16 and Group D mAb ZIKV-l 17 could inhibit diverse ZIKV strains encompassing the African, Asian, and American lineages. ZIKV-l 17 neutralized potently all ZIKV strains tested including two African (MR 766 and Dakar 41519), two Asian (Malaysia P6740 and H/PF/2013), and an American (Brazil Paraiba 2015) strain with FRNT50 values of 5 to 25 ng/ml (FIGS. 2D-E). In comparison, ZIKV-l 16 inhibited four of the five strains efficiently, but lost activity against MR 766, the original African strain (FIGS 2D-E). As recent studies have suggested that cross-reactive ZIKV- specific mAbs can enhance DENV infection in vivo (Stettler et al, 2016), the inventor tested whether these two ZIKV neutralizing mAbs could bind to DENV -infected C6/36 cells. ZIKV- 117 showed a type-specific pattern of binding as it failed to stain permeabilized cells infected with DENV-l, DENV-2, DENV-3, or DENV-4 or bind to purified WNV E protein (FIG. 7 and data not shown). In comparison, ZIKV-l 16 bound to cells infected with DENV1, DENV2, or DENV4, but did not bind to DENV2 Dill or WNV Dill in ELISA.
Recently, in vivo models of ZIKV pathogenesis and antibody prophylaxis have been reported in mice deficient in type I IFN signaling. To determine whether ZIKV-l 17 had therapeutic activity, the inventor treated 4- to 5-week-old WT male C57BL/6 mice at day -1 with anti-Ifnarl mAb, and then inoculated animals with 103 FFU of ZIKV -Dakar, an African strain that is pathogenic in mice. Subsequently, animals were treated with a single dose of ZIKV-l 17 or isotype control (hCHK-l52) (Pal et al, 2013), on day +1 (100 pg; 6.7 mg/kg) or day +5 (250 pg; 16.7 mg/kg). Animals treated with the non-binding isotype control (hCHK- 152) developed significant lethality compared to those receiving ZIKV-l 17 (FIG. 3A), which were protected even when administered only a single dose five days after virus inoculation.
The inventor and others have demonstrated intrauterine growth restriction, placental injury, and fetal demise following ZIKV infection of pregnant mice with deficiencies in type I IFN signaling (Mysorekar et al, 2016; Miner et al, 2016; Yockey et al, 2016). To assess the protective ability of ZIKV-l 17 during fetal development, WT pregnant dams were treated at day -1 (embryo day (E)5.5) with an anti-Ifnarl mAb. At the same time, these animals were administered vehicle control (PBS), 250 mg isotype control hCHK-l52, or 250 pg ZIKV-117 as prophylaxis. One day later, dams were infected subcutaneously with 103 FFU of ZIKV- Dakar. Fetuses at E13.5 from anti-Ifnarl mAh treated dams given PBS or hCHK-l52 showed high levels (e.g., -105 to 107 FFU equivalents/g) of viral RNA in the placenta and fetal brain (FIG. 3B). In comparison, mice treated with ZIKV-117 had markedly reduced levels of virus in the placenta and fetal brain (e.g., -10° to 103 FFU equivalents/g) (FIG. 3B). This phenotype was associated with transport of antibody across the maternal-fetal placental barrier such that levels (816 + 53 ng/ml for the placenta and 1,675 + 203 ng/ml for the fetal head) of human ZIKV E-specific IgG were detected (FIG. 8). It should be noted that the levels of neonatal Fc receptor (FcRn) in the placenta of mice are lower than other mammalian species (Kim el al, 2009), thus reduced levels of transport of maternal or exogenous IgG into the fetus is expected (Pentsuk & van der Laan, 2009). Although this factor could underestimate the therapeutic effect of exogenous anti-ZIKV IgG or maternal antibodies, the inventor achieved levels in placenta and fetal head that still were orders of magnitude above the FRNT50 value for ZIKV-l 17. Dams treated with ZIKV-l 17 also had lower levels of viral RNA in the maternal brain and serum (FIG. 3C).
Antibody-dependent enhancement (ADE) of infection of the closely related DENV is due to cross-reactive antibodies that fail to neutralize heterologous serotype infection and instead facilitate uptake and infection of FcyR-expressing myeloid cells (Morens, 1994). Because flavivirus antibodies can promote ADE in cell culture (Dejnirattisai el al, 2016; Charles and Christofferson, 2016) with unknown consequences in vivo, the inventor evaluated the protective efficacy of a recombinant form of ZIKV-l 17 IgG containing a leucine (L) to alanine (A) substitution at positions 234 and 235 (LALA) (Hessell et al, 2007), which lacked efficient binding to FcyR, retained interactions with FcRn (Hessell et al. , 2007), and neutralized ZIKV in vitro equivalently compared to the parent mAh (FIGS. 9A-B). The LALA variant of ZIKV-l 17 showed similar protective activity against infection of the placenta and fetus relative to the parent mAh (FIG. 3D). As the majority of the protection conferred by ZIKV-l 17 in the pregnancy model likely is due to neutralization and not Fc effector functions, LALA variants could be used without a loss in potency or risk of ADE from a future infection with a heterologous flavivirus such as DENV.
The inventor next assessed the post-exposure efficacy of ZIKV-l 17 during pregnancy. Mice treated with anti-Ifnarl mAh at E5.5 were infected with 103 FFU of ZIKV-Dakar at E6.5 and then given a single dose of PBS, 250 pg of hCHK-l52, or 250 pg of ZIKV-l 17 at E7.5. Compared to PBS or isotype control mAb treatment, administration of ZIKV-117 resulted in markedly reduced viral burden in the dams, the placenta, and fetus when measured at El 3.5 (FIGS. 3E-F).
The inventor also evaluated the consequences of ZIKV-117 administration on pathology in the placenta and fetus. The reduction in viral load mediated by ZIKV-117 was associated with decreased destruction of the placenta (as judged by labyrinth layer and overall placenta area), less trophoblast cell death, and increased body size of the fetus (FIGS. 4A-C) compared to fetuses of PBS- or hCHK-l52-treated dams. When administered as prophylaxis, ZIKV-117 fully protected against ZIKV -induced placental insufficiency and intrauterine growth restriction, as the placental area and fetal size from infected dams treated with anti- ZIKV mAb were similar to that of uninfected placentas. In situ hybridization revealed an almost complete absence of viral RNA in the junctional zone and decidua of the placenta in animals treated with ZIKV-117 compared to staining observed in PBS or hCHK-l52-treated controls (FIG. 4D). The inventor also observed vascular damage associated with ZIKV infection of the placenta (Miner et al, 2016), characterized as diminished vimentin staining of fetal endothelial cells, which was rescued by ZIKV-117 to levels similar to those in uninfected placentas (FIG. 4E). The histopathological data suggests that ZIKV-117 treatment can reduce the ability of ZIKV to cross the fetal endothelial cell barrier, and thereby prevent vertical transmission and improve placental health and fetal outcome.
Finally, the inventor determined the protective and therapeutic efficacy of ZIKV-117 against ZIKV Brazil strain challenge in rhesus monkeys. The antibody was 100% effective when used in protective or therapeutic experiments (FIG. 10).
TABLE 5 - Research Subjects with Time and Place of Infection
Figure imgf000087_0002
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y BD, KobyBneki K€, Chllsort Foy JL, B!fvleh BJ, Travassos da Rosa A, B bdo AD Lan o!l RS, Tesh RB. Probable nonwectonbome transmission of Zta vtes, Colorado, USA. Enrn infmt Dm, 2011 ;17:880-2.
Example 3 - Discussion
These studies reveal a number of features of humoral immunity to ZIKV. First, following infection, a subset of human B cells encode mAbs that neutralize ZIKV in vitro with high potency, the most potent with FRNT50 values <10 ng/ml. Second, the human B cell response is directed against multiple antigenic sites on ZIKV E protein, predominantly against the fusion loop in DII, and other structural features in DII and Dill, results that agree with a recent study 10. The most inhibitory antibodies recognized antigenic sites in Dill (lateral ridge) and in DII at a unique site not reported to be targeted by DENV antibodies, located at the dimer- dimer interface of the E protein. The most potent neutralizing antibodies exhibited a breadth of inhibitory activity against strains from Africa, Asia, and the Americas. Treatment of ZIKV- infected male mice with mAh ZIKV-117 showed strong post-exposure therapeutic activity in vivo. Even a single ZIKV-117 dose given five days after infection protected against lethal ZIKV infection, a timeline that was similar to the most protective antibodies reported against other flaviviruses (Oliphant el al, 2005). Prophylaxis or post-exposure therapy of pregnant mice with ZIKV-117 reduced infection in the mothers, and in placental and fetal tissues. To the inventor’s knowledge, this is the first evidence showing that an antiviral agent can prevent or control ZIKV infection in pregnancy. Accordingly, ZIKV-117 or human antibodies with similar profiles, could be developed as a preventive or treatment measure during pregnancy for at-risk humans. By defining key epitopes on the E protein associated with antibody-mediated protection, these studies also inform vaccine efforts to design new epitope-based immunogens that elicit highly protective antibody responses against ZIKV.
TABLE 1 - NUCLEOTIDE SEQUENCES FOR ANTIBODY VARIABLE REGIONS
Clone Variable Sequence Region SEQ
ID NO:
ZIKV- GAGGTGAAGCTGGTGGAGTCTGGGAGAGGCCTAGTTCGGCCTG 1 116 GGGGGTCCCTGAGACTCTCTTGTGCAGCCTCTGGATTCACCTTT
Heavy AGCAACTATGCCATGAGCTGGGTCCGCCAGGGTCCAGGGATGG
GAC T GGAGT GGGT CT C A AC GAT C ACT GC C GAT AGT GAT AGC A A ATATTACGTGGACTCTGTGAAGGGCCGGTTCACCATCTCCAGA GACAATTCCAAGGACACATTATTTCTACACATGACCAGCCTGA GAGCCGAAGACACGGCCGTTTACTACTGTGCGAAAGATCGCCT CTCTC GGGGGGT C GGGGAGTT AT AT GAC TC GT GGGGC C AGGGA ACGCTGGTCATCGTCTCCTCA
ZIKV- GACATACAGATGACCCAGTCTCCTTCCACCCTGTCTGCATCTGT 2 116 AGGAGAC AGAGTCACCATCACTTGCCGGGCC AGCCAGAGTATT
Light GAT GTCT GGTT GGC CT GGT AT C AGC AG A AGC C AGGGA A AGC C C
CTAAACTCCTGATGTATAAGACGTCTACTTTACAAACTGGGGT CCCATCAAGATTCAGCGGCAGTGGATCTGGGACAGAATTCACT CTCACCATCAGCAGCCTGCAGACTGATGATTTTGC AACTT ATTA CTGCCAAAAGTACGATAGTTATCCGTGGACGTTCGGCCCAGGG AC C AAGGT GGAAATC AAA
ZIKV- C AGGT GC AACT GGT GGAGT CT GGGGGAGGCGT GGT C CGGCCTG 3 117 GGGGGTCCCTCAGACTCTCCTGTGCAGCGTCTGGATTCACCTTC heavy AAAAACTATGGCATCCACTGGGTCCGCCAGGCTCCAGGCAAGG
GGC C GGAGT GGGT GGC ATTT GT AC GGT AT GAT GGA A AT A AC A A GTACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGA GACAATGCCAAGAACACGCTGTCTCTGCAAATGAACAGCCTGA GAGTTGAAGACACGGCTGTCTATTTCTGTGCGAGGGATCCTGA AACTTTCGGGGGGTTTGACTACTGGGGCCAGGGAACCCTGGTC ACCGTCTCCTCA
ZIKV- GAAACAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTC 4 117 CAGGGGAAAGAGGCACCCTCTCCTGCAGGGCC AGTGAGAGTG light TT AGC AGC AACTT GGCCT GGT ACC AGC AGAAAC CT GGC AAGGC
TCCCCGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGT AT C CC AGAC AGGTT C AGT GGC AGT GGGTCTGGGAC AGAGTT C A CTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTAT TACTGTCAGCAGTATTATTACTCGCCTCGAACGTTCGGCCAAG GGACCAAGGTGGAAGTCAAA TABLE 2 - PROTEIN SEQUENCES FOR ANTIBODY VARIABLE REGIONS
Clone Variable Sequence SEQ ID
NO.
ZIKV- EVKLVESGRGLVRPGGSLRLSCAASGFTFSNYAMSWVRQGPGMG 5 116 LEWVSTITADSDSKYYVDSVKGRFTISRDNSKDTLFLHMTSLRAE heavy DT AV YY C AKDRLS RGV GEL YD S W GQGTL VI V S S
ZIKV- DIQMTQSPSTLSASVGDRVTITCRASQSIDVWLAWYQQKPGKAPK 6
116 LLMYKTSTLQTGVPSRFSGSGSGTEFTLTISSLQTDDFATYYCQKY light D S YP WTF GPGTKVEIK
ZIKV- QV QLVESGGGVVRPGGSLRLSC AASGFTFKNY GIHWVRQAPGKG 7
117 PEWVAFVRYDGNNKYYADSVKGRFTISRDNAKNTLSLQMNSLR heavy VEDTAVYF CARDPETFGGFDYWGQGTLVTV S S
ZIKV- ETVMTQSPATLSVSPGERGTLSCRASESVSSNLAWYQQKPGKAPR 8
117 LLIYGASTRATGIPDRFSGSGSGTEFTLTISSLQSEDFAVYYCQQYY light YSPRTFGQGTKVEVK
Figure imgf000090_0002
Figure imgf000090_0001
All of the compositions and methods disclosed and claimed herein can be made and executed without undue experimentation in light of the present disclosure. While the compositions and methods of this disclosure have been described in terms of preferred embodiments, it will be apparent to those of skill in the art that variations may be applied to the compositions and methods and in the steps or in the sequence of steps of the method described herein without departing from the concept, spirit and scope of the disclosure. More specifically, it will be apparent that certain agents which are both chemically and physiologically related may be substituted for the agents described herein while the same or similar results would be achieved. All such similar substitutes and modifications apparent to those skilled in the art are deemed to be within the spirit, scope and concept of the disclosure as defined by the appended claims.
VII. REFERENCES
The following references, to the extent that they provide exemplary procedural or other details supplementary to those set forth herein, are specifically incorporated herein by reference.
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Claims

WHAT IS CLAIMED IS:
1. A method of detecting a Zika virus infection in a subject comprising:
(a) contacting a sample from said subject with an antibody or antibody fragment having clone-paired heavy and light chain sequences from Table 2; and
(b) detecting Zika virus in said sample by binding of said antibody or antibody fragment to a Zika virus antigen in said sample.
2. The method of claim 1, wherein said sample is a body fluid.
3. The method of claims 1-2, wherein said sample is blood, sputum, tears, saliva, mucous or serum, semen, cervical or vaginal secretions, amniotic fluid, placental tissues, urine, exudate, transudate, tissue scrapings or feces.
4. The method of claims 1-3, wherein detection comprises ELISA, RIA, lateral flow assay or Western blot.
5. The method of claims 1-4, further comprising performing steps (a) and (b) a second time and determining a change in Zika virus antigen levels as compared to the first assay.
6. The method of claims 1-5, wherein the antibody or antibody fragment is encoded by clone-paired variable sequences as set forth in Table 1.
7. The method of claims 1-6, wherein the antibody fragment is a recombinant scFv (single chain fragment variable) antibody, Fab fragment, F(ab')2 fragment, or Fv fragment.
8. A method of treating a subject infected with Zika virus or reducing the likelihood of infection of a subject at risk of contracting Zika virus, comprising delivering to said subject an antibody or antibody fragment having clone-paired heavy and light chain sequences from Table 2.
9. The method of claim 8, the antibody or antibody fragment is encoded by clone-paired light and heavy chain variable sequences as set forth in Table 1.
10. The method of claims 8-9, wherein the antibody fragment is a recombinant scFv (single chain fragment variable) antibody, Fab fragment, F(ab')2 fragment, or Fv fragment.
11. The method of claims 8-9, wherein said antibody is an IgG, or a recombinant IgG antibody or antibody fragment comprising an Fc portion mutated to alter (eliminate or enhance) FcR interactions, to increase half-life and/or increase therapeutic efficacy, such as a LALA, N297, GASD/ALIE, YTE or LS mutation or glycan modified to alter (eliminate or enhance) FcR interactions such as enzymatic or chemical addition or removal of glycans or expression in a cell line engineered with a defined glycosylating pattern, in particular wherein the antibody or antibody fragment comprises both LALA and YTE mutations.
12. The method of claims 8-9, wherein said antibody is a chimeric antibody or a bispecific antibody.
13. The method of claims 8-12, wherein said antibody or antibody fragment is
administered prior to infection or after infection.
14. The method of claims 8-13, wherein said subj ect is a pregnant female, a sexually active female, or a female undergoing fertility treatments.
15. The method of claims 8-14, wherein delivering comprises antibody or antibody fragment administration, or genetic delivery with an RNA or DNA sequence or vector encoding the antibody or antibody fragment.
16. A monoclonal antibody, wherein the antibody or antibody fragment is characterized by clone-paired heavy and light chain sequences from Table 2.
17. The monoclonal antibody of claim 16, wherein said antibody or antibody fragment is encoded by light and heavy chain variable sequences according to clone-paired sequences from Table 1.
18. The monoclonal antibody of claims 16-17, wherein the antibody fragment is a recombinant scFv (single chain fragment variable) antibody, Fab fragment, F(ab’)2 fragment, or Fv fragment.
19. The monoclonal antibody of claims 16-17, wherein said antibody is a chimeric antibody, or is bispecific antibody.
20. The monoclonal antibody of claims 16-17, wherein said antibody is an IgG, or a recombinant IgG antibody or antibody fragment comprising an Fc portion mutated to alter (eliminate or enhance) FcR interactions, to increase half-life and/or increase therapeutic efficacy, such as a LALA, N297, GASD/ALIE, YTE or LS mutation or glycan modified to alter (eliminate or enhance) FcR interactions such as enzymatic or chemical addition or removal of glycans or expression in a cell line engineered with a defined glycosylating pattern, in particular wherein the antibody or antibody fragment comprises both LALA and YTE mutations.
21. The monoclonal antibody of claims 16-17, wherein said antibody or antibody fragment further comprises a cell penetrating peptide and/or is an intrabody.
22. A hybridoma or engineered cell encoding an antibody or antibody fragment wherein the antibody or antibody fragment is characterized by clone-paired heavy and light chain sequences from Table 2.
23. The hybridoma or engineered cell of claim 22, wherein said antibody or antibody fragment is encoded by light and heavy chain variable sequences according to clone- paired sequences from Table 1.
24. The hybridoma or engineered cell of claims 22-23, wherein the antibody fragment is a recombinant scFv (single chain fragment variable) antibody, Fab fragment, F(ab')2 fragment, or Fv fragment.
25. The hybridoma or engineered cell of claims 22-23, wherein said antibody is a chimeric antibody or a bispecific antibody.
26. The hybridoma or engineered cell of claims 22-23, wherein said antibody is an IgG, or a recombinant IgG antibody or antibody fragment comprising an Fc portion mutated to alter (eliminate or enhance) FcR interactions, to increase half-life and/or increase therapeutic efficacy, such as a LALA, N297, GASD/ALIE, YTE or LS mutation or glycan modified to alter (eliminate or enhance) FcR interactions such as enzymatic or chemical addition or removal of glycans or expression in a cell line engineered with a defined glycosylating pattern, in particular wherein the antibody or antibody fragment comprises both LALA and YTE mutations.
27. The hybridoma or engineered cell of claims 22-23, wherein said antibody or antibody fragment further comprises a cell penetrating peptide and/or is an intrabody.
28. A vaccine formulation comprising one or more antibodies or antibody fragments characterized by clone-paired heavy and light chain sequences from Table 2.
29. The vaccine formulation of claim 28, wherein at least one of said antibodies or antibody fragments is encoded by light and heavy chain variable sequences according to clone- paired sequences from Table 1.
30. The vaccine formulation of claims 28-29, wherein at least one of said antibody fragments is a recombinant scFv (single chain fragment variable) antibody, Fab fragment, F(ab')2 fragment, or Fv fragment.
31. The vaccine formulation of claims 28-29, wherein at least one of said antibodies is a chimeric antibody or is bispecific antibody.
32. The vaccine formulation of claims 28-29, wherein said antibody is an IgG, or a recombinant IgG antibody or antibody fragment comprising an Fc portion mutated to alter (eliminate or enhance) FcR interactions, to increase half-life and/or increase therapeutic efficacy, such as a LALA, N297, GASD/ALIE, YTE or LS mutation or glycan modified to alter (eliminate or enhance) FcR interactions such as enzymatic or chemical addition or removal of glycans or expression in a cell line engineered with a defined glycosylating pattern, in particular wherein the antibody or antibody fragment comprises both LALA and YTE mutations.
33. The vaccine formulation of claims 28-29, wherein at least one of said antibodies or antibody fragments further comprises a cell penetrating peptide and/or is an intrabody.
34. A vaccine formulation comprising one or more expression vectors encoding a first antibody or antibody fragment according to claims 16-21.
35. The vaccine formulation of claim 34, wherein said expression vector(s) is/are Sindbis virus or VEE vector(s).
36. The vaccine formulation of claims 34-35, formulated for delivery by needle injection, jet injection, or electroporation.
37. The vaccine formulation of claim 34, further comprising one or more expression vectors encoding for a second antibody or antibody fragment, such as a distinct antibody or antibody fragment of claims 16-21.
38. A method of protecting the health of a placenta and/or fetus of a pregnant a subject infected with or at risk of infection with Zika virus comprising delivering to said subj ect an antibody or antibody fragment having clone-paired heavy and light chain sequences from Table 2.
39. The method of claim 38, the antibody or antibody fragment is encoded by clone-paired light and heavy chain variable sequences as set forth in Table 1.
40. The method of claims 38-39, wherein the antibody fragment is a recombinant scFv (single chain fragment variable) antibody, Fab fragment, F(ab')2 fragment, or Fv fragment.
41. The method of claims 38-39, wherein said antibody is an IgG, or a recombinant IgG antibody or antibody fragment comprising an Fc portion mutated to alter (eliminate or enhance) FcR interactions, to increase half-life and/or increase therapeutic efficacy, such as a LALA, N297, GASD/ALIE, YTE or LS mutation or glycan modified to alter (eliminate or enhance) FcR interactions such as enzymatic or chemical addition or removal of glycans or expression in a cell line engineered with a defined glycosylating pattern, in particular wherein the antibody or antibody fragment comprises both LALA and YTE mutations.
42. The method of claims 38-39 wherein said antibody is a chimeric antibody or a bispecific antibody.
43. The method of claims 38-42, wherein said antibody or antibody fragment is
administered prior to infection or after infection.
44. The method of claims 38-43, wherein said subject is a pregnant female, a sexually active female, or a female undergoing fertility treatments.
45. The method of claims 38-44, wherein delivering comprises antibody or antibody fragment administration, or genetic delivery with an RNA or DNA sequence or vector encoding the antibody or antibody fragment.
46. The method of claims 38-45, wherein the antibody or antibody fragment increases the size of the placenta as compared to an untreated control.
47. The method of claims 38-45, wherein the antibody or antibody fragment reduces viral load and/or pathology of the fetus as compared to an untreated control.
48. A method of determining the antigenic integrity, correct conformation and/or correct sequence of a Zika virus antigen comprising:
(a) contacting a sample comprising said antigen with a first antibody or antibody fragment having clone-paired heavy and light chain sequences from Table 2; and
(b) determining antigenic integrity, correct conformation and/or correct sequence of said antigen by detectable binding of said first antibody or antibody fragment to said antigen.
49. The method of claim 48, wherein said sample comprises recombinantly produced antigen.
50. The method of claim 48, wherein said sample comprises a vaccine formulation or vaccine production batch.
51. The method of claims 48-50, wherein detection comprises ELISA, RIA, western blot, a biosensor using surface plasmon resonance or biolayer interferometry, or flow cytometric staining.
52. The method of claims 48-51, wherein the first antibody or antibody fragment is encoded by clone-paired variable sequences as set forth in Table 1.
53. The method of claims 48-52, wherein the first antibody fragment is a recombinant scFv (single chain fragment variable) antibody, Fab fragment, F(ab')2 fragment, or Fv fragment.
54. The method of claims 48-53, further comprising performing steps (a) and (b) a second time to determine the antigenic stability of the antigen over time.
55. The method of claims 48-54, further comprising: (c) contacting a sample comprising said antigen with a second antibody or antibody fragment having clone-paired heavy and light chain sequences from Table 2; and
(d) determining antigenic integrity of said antigen by detectable binding of said second antibody or antibody fragment to said antigen.
56. The method of claim 55, wherein the second antibody or antibody fragment is encoded by clone-paired variable sequences as set forth in Table 1.
57. The method of claims 55-56, wherein the second antibody fragment is a recombinant ScFv (single chain fragment variable) antibody, Fab fragment, F(ab')2 fragment, or Fv fragment.
58. The method of claims 55-57, further comprising performing steps (c) and (d) a second time to determine the antigenic stability of the antigen over time.
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