WO2010040136A4 - Selection of hiv vaccine antigens by use of intrapatient sequence variation to identify mutations in the hiv envelope glycoprotein that affect the binding of broadly neutralizing antibodies - Google Patents

Selection of hiv vaccine antigens by use of intrapatient sequence variation to identify mutations in the hiv envelope glycoprotein that affect the binding of broadly neutralizing antibodies Download PDF

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Publication number
WO2010040136A4
WO2010040136A4 PCT/US2009/059583 US2009059583W WO2010040136A4 WO 2010040136 A4 WO2010040136 A4 WO 2010040136A4 US 2009059583 W US2009059583 W US 2009059583W WO 2010040136 A4 WO2010040136 A4 WO 2010040136A4
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WIPO (PCT)
Prior art keywords
hiv
amino acid
neutralization
envelope glycoprotein
vaccine composition
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PCT/US2009/059583
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French (fr)
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WO2010040136A2 (en
WO2010040136A3 (en
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Phillip W. Berman
Sara O'rourke
William Scott
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The Regents Of The University Of California
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Publication of WO2010040136A2 publication Critical patent/WO2010040136A2/en
Publication of WO2010040136A3 publication Critical patent/WO2010040136A3/en
Publication of WO2010040136A4 publication Critical patent/WO2010040136A4/en
Priority to US13/079,472 priority Critical patent/US9782472B2/en
Priority to US15/694,388 priority patent/US10201603B2/en

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    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/70Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving virus or bacteriophage
    • C12Q1/701Specific hybridization probes
    • C12Q1/702Specific hybridization probes for retroviruses
    • C12Q1/703Viruses associated with AIDS
    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07KPEPTIDES
    • C07K14/00Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/005Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from viruses
    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/569Immunoassay; Biospecific binding assay; Materials therefor for microorganisms, e.g. protozoa, bacteria, viruses
    • G01N33/56983Viruses
    • G01N33/56988HIV or HTLV
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00Medicinal preparations containing antigens or antibodies
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2740/00Reverse transcribing RNA viruses
    • C12N2740/00011Details
    • C12N2740/10011Retroviridae
    • C12N2740/16011Human Immunodeficiency Virus, HIV
    • C12N2740/16111Human Immunodeficiency Virus, HIV concerning HIV env
    • C12N2740/16122New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes
    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2500/00Screening for compounds of potential therapeutic value

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  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Virology (AREA)
  • Immunology (AREA)
  • Organic Chemistry (AREA)
  • Engineering & Computer Science (AREA)
  • Molecular Biology (AREA)
  • General Health & Medical Sciences (AREA)
  • Biochemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Zoology (AREA)
  • Hematology (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Wood Science & Technology (AREA)
  • Analytical Chemistry (AREA)
  • Physics & Mathematics (AREA)
  • Urology & Nephrology (AREA)
  • Microbiology (AREA)
  • AIDS & HIV (AREA)
  • Genetics & Genomics (AREA)
  • Biomedical Technology (AREA)
  • Medicinal Chemistry (AREA)
  • Tropical Medicine & Parasitology (AREA)
  • Gastroenterology & Hepatology (AREA)
  • Cell Biology (AREA)
  • General Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Food Science & Technology (AREA)
  • General Physics & Mathematics (AREA)
  • Pathology (AREA)
  • Peptides Or Proteins (AREA)
  • Medicines Containing Antibodies Or Antigens For Use As Internal Diagnostic Agents (AREA)

Abstract

Selection of HIV vaccine antigens by use of intrapatient sequence variation to identify mutations in the HIV envelope glycoprotein that affect the binding of broadly neutralizing antibodies and polypeptides identified by these methods.

Claims

AMENDED CLAIMS received by the International Bureau on 17 July 2010 (17.07.2010).
1. A method of analyzing intra-patient HIV virus variation to identify specific amino acid residues of the HIV envelope glycoproteins that affect sensitivity or resistance to broadly neutralizing antibodies, the method comprising the steps of:
i) providing a plurality of individual subjects who are seropositive for HIV antibodies and taking a biological sample from each subject, wherein the sample contains a multiplicity of HIV viruses with closely related genomes, wherein all subjects had been infected with HIV no more than one year before, and no less than one month before sample collection,
ii) amplifying the env genes of the multiplicity of viruses to produce a library of different env genes,
iii) cloning the amplified env genes into a plasmid shuttle vector that allows the plasmid to replicate in both bacteria and mammalian cells,
iv) transforming bacterial cells with the shuttle vector and plating out the transformed bacterial cells onto a selective medium so that bacteria containing the shuttle vector plasmid containing the cloned envelope gene are selectable,
v) selecting individual colonies at random and preparing plasmid DNA from each colony selected and analyzing the plasmid DNA by restriction digestion so as to identify plasmids containing the full length HlV envelope gene, which plasmids are used to produce pseudoviruses,
vi) co-transfecting mammalian cells with the env-containing vector and simultaneously with a plasmid containing a defective HIV provirus plasmid where the coding sequence of the env gene has been replaced with the coding sequence of a marker gene, and culturing the co-transfected mammalian cells in a culture medium, to produce pseudovirions containing the amplified env genes, which pseudovirions are released into the cell culture medium, vii) harvesting the supernatant from the cell culture medium, wherein the supernatant contains pseudoviruses from the transfected cells, and wherein each supernatant contains a stock of pseudovirus resulting from a single purified expression plasmid,
viii) testing the pseudovirion from the selected colonies to determine infectivity by culturing the pseudovirions with cells capable of being infected by HTV, wherein infectivity is measured by the degree of expression of the marker gene,
ix) selecting pseudovirions that exhibit high infectivity, and testing the selected pseudovirions for sensitivity or resistance to neutralization by one or more broadly neutralizing antibodies,
x) selecting pairs of plasmids from the same individual wherein each pair contains at least one neutralization resistant and at least one neutralization sensitive pseudovirus,
xi) sequencing the envelope genes identified from sensitive and resistant pseudovirus pairs,
xii) comparing the nucleotide sequences of the envelope genes of the neutralization sensitive and resistant pairs thereby identifying specific amino acid differences between the pairs and identifying polymorphisms that may affect sensitivity or resistance to neutralization by broadly neutralizing antibodies,
xiii) at each amino acid residue that differs between the neutralization sensitive and neutralization resistant envelope genes, site-by-site replacement of amino acids from the is performed, substituting one amino acid at a time from neutralization sensitive sequence into the neutralization resistant sequence,
xiv) each new construct is used to create a pseudotype virus which is tested for neutralization sensitivity so as to identify specific amino acid residues of the HlV envelope glycoproteins that affect sensitivity or resistance to broadly neutralizing antibodies.
2. The method of claim 1 wherein all subjects had been infected with HIV 109 days +/- 58 days before specimen collection.
3. A vaccine composition comprising an HIV envelope glycoprotein wherein a glutamine residue at a site identifiable as being homologous to position 655 of SEQ ID No.l is replaced by a substitute amino acid such that the amino acid substitution disrupts an inter- molecular hydrogen-bonded ring structure between the N36 and C34 helices of the gp41 trimer.
4. The vaccine composition of claim 3 wherein possession of the HIV envelope glycoprotein confers greater neutralization sensitivity upon an HIV virus when it is exposed to 2F5 or 4E10 monoclonal antibodies, Enfuvirtide or CD4-lgG, than would be provided by another HIV envelope glycoprotein identical in all respects except for the substitution of the glutamine residue.
5. The vaccine composition of claims 3 or 4 wherein the substitute amino acid is arginine.
6. The vaccine composition of claims 3 or 4 wherein the substitute amino acid is Lysine, Serine or Glutamic acid.
7. The vaccine composition of claims 3 or 4 wherein the HIV envelope glycoprotein has at least 60% sequence identity to SEQ ID No.l.
8. The composition of claims 3 or 4 wherein the HIV envelope glycoprotein comprises a fusion protein that includes a non-HIV signal sequence and a flag epitope.
9. The vaccine composition of claims 3 or 4 wherein the HIV envelope glycoprotein has had a furin cleavage site deleted.
10. The vaccine composition of claims 3 or 4 wherein the HIV envelope glycoprotein comprises a full length gplόO wherein a glutamine residue at a site identifiable as being homologous to position 655 of SEQ ID No.l is replaced by arginine.
11. The vaccine composition of claims 3 or 4 wherein the polypeptide comprises a truncated form of the envelope protein lacking the gp41 transmembrane domain and cytoplasmic tail.
12. A polynucleotide encoding an HIV envelope glycoprotein wherein a glutamine residue at a site identifiable as being homologous to position 655 of SEQ ID No.1 is replaced by a substitute amino acid such that the amino acid substitution disrupts an inter-molecular ring structure between the N36 and C34 helices of the gp41 trimer.
13. The polynucleotide of claim 14 formulated in an vector as a DNA vaccine.
14. A method for inhibiting the fusion of an HlV virus to a host cell, the method comprising exposing the HlV virus to a compound that disrupts the hydrogen-bonded ring structure between the N36 and C34 helices of gp41.
15. A method for increasing the immunogenicity of HIV envelope proteins the method comprising exposing the HlV virus to a compound that disrupts the hydrogen bonded ring structure between the N36 and C34 helices of gp41.
16. The method of claims 14 or 15 wherein the compound is a small molecule.
17. The method of claims 14 or 15 wherein the compound is an antibody.
18. An isolated antibody which specifically binds to the HlV envelope glycoprotein of the vaccine composition of claim 3.
19. an isolated antibody which specifically binds to the HIV envelope glycoprotein of the vaccine composition of claim 4.
PCT/US2009/059583 2008-10-04 2009-10-05 Selection of hiv vaccine antigens by use of intrapatient sequence variation to identify mutations in the hiv envelope glycoprotein that affect the binding of broadly neutralizing antibodies WO2010040136A2 (en)

Priority Applications (2)

Application Number Priority Date Filing Date Title
US13/079,472 US9782472B2 (en) 2008-10-04 2011-04-04 Therapeutic compositions and methods for treating HIV including identification and manipulation of particular domains associated with immunogenicity
US15/694,388 US10201603B2 (en) 2008-10-04 2017-09-01 Therapeutic compositions and methods for treating HIV including identification and manipulation of particular domains associated with immunogenicity

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US19511208P 2008-10-04 2008-10-04
US61/195,112 2008-10-04

Related Parent Applications (1)

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PCT/US2010/053637 Continuation-In-Part WO2011050222A2 (en) 2008-10-04 2010-10-22 Therapeutic compositions that disrupt the hydrogen bonded ring structure in gp41 and methods for treating hiv

Related Child Applications (1)

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US13/079,472 Continuation-In-Part US9782472B2 (en) 2008-10-04 2011-04-04 Therapeutic compositions and methods for treating HIV including identification and manipulation of particular domains associated with immunogenicity

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WO2010040136A3 WO2010040136A3 (en) 2010-07-15
WO2010040136A4 true WO2010040136A4 (en) 2010-09-02

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Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN107132066A (en) * 2017-04-28 2017-09-05 皖能马鞍山发电有限公司 A kind of coal sample takes control optimization method

Families Citing this family (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20150065381A1 (en) * 2013-09-05 2015-03-05 International Aids Vaccine Initiative Methods of identifying novel hiv-1 immunogens
CA2982376A1 (en) * 2015-05-28 2016-12-01 Immunomedics, Inc. T20 constructs for anti-hiv (human immunodeficiency virus) therapy and/or vaccines
CN114736930A (en) * 2022-04-30 2022-07-12 南京医科大学 Screening method and application of virus protein escape neutralizing antibody

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Publication number Priority date Publication date Assignee Title
US6841657B2 (en) * 1997-04-17 2005-01-11 Whitehead Institute For Biomedical Research Inhibitors of HIV membrane fusion
FR2829150B1 (en) * 2001-09-06 2004-09-03 Bio Merieux ENV MUTE GENE ENCODING HIV-1 GLYPOPROTEIN AND APPLICATIONS
WO2004072099A2 (en) * 2003-02-11 2004-08-26 The United States Of America As Represented By The Secretary Of Health And Human Services, Nih Novel peptide inhibitor of hiv fusion that disrupts the internal trimeric coiled-coil of gp41

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN107132066A (en) * 2017-04-28 2017-09-05 皖能马鞍山发电有限公司 A kind of coal sample takes control optimization method

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