Phages and HIV-1: From display to interplay

International Journal of Molecular Sciences

Volumn 13, Issue 4, 2012, Pages 4727-4794

  Delhalle, Sylvie ^a   Schmit, Jean Claude ^a,b   Chevigné, Andy ^a  

^a LUXEMBOURG INSTITUTE OF HEALTH   (Luxembourg)

^b CENTRE HOSPITALIER DE LUXEMBOURG   (Luxembourg)

Author keywords

CCR5; CXCR4; Epitope mapping; Gp120; Gp41; HIV 1; HIV 1 inhibitor; HIV 1 vaccine; Mimotopes; Phage display

Indexed keywords

ANTIVIRUS AGENT; CHEMOKINE RECEPTOR CCR4; CHEMOKINE RECEPTOR CCR5; EPITOPE; GAG PROTEIN; GLYCOPROTEIN GP 120; HUMAN IMMUNODEFICIENCY VIRUS PROTEINASE; HUMAN IMMUNODEFICIENCY VIRUS VACCINE; IMMUNOGLOBULIN G; INTEGRASE; MONOCLONAL ANTIBODY; NEUTRALIZING ANTIBODY; POLYCLONAL ANTIBODY; CCR5 PROTEIN, HUMAN; CHEMOKINE RECEPTOR CXCR4; CXCR4 PROTEIN, HUMAN; GLYCOPROTEIN GP 41; GP120 PROTEIN, HUMAN IMMUNODEFICIENCY VIRUS 1; GP41 PROTEIN, HUMAN IMMUNODEFICIENCY VIRUS 1; PEPTIDE LIBRARY; VIRUS ANTIBODY;

ANTIBODY SPECIFICITY; ARTICLE; BINDING AFFINITY; BINDING SITE; BIOPANNING; CONFORMATIONAL TRANSITION; ENZYME SPECIFICITY; EPITOPE MAPPING; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS INFECTED PATIENT; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; IMMUNE SYSTEM; LIFE EXPECTANCY; MEMBRANE FUSION; NONHUMAN; PHAGE DISPLAY; PROTEIN DOMAIN; RECEPTOR BINDING; VACCINATION; VIRUS CAPSID; VIRUS ENTRY; VIRUS NEUTRALIZATION; VIRUS NUCLEOCAPSID; VIRUS REPLICATION; VIRUS STRAIN; ACQUIRED IMMUNE DEFICIENCY SYNDROME; BACTERIOPHAGE; CELL SURFACE DISPLAY; GENETICS; IMMUNOLOGY; PEPTIDE LIBRARY; PROCEDURES;

ACQUIRED IMMUNODEFICIENCY SYNDROME; ANTIBODIES, MONOCLONAL; ANTIBODIES, NEUTRALIZING; ANTIBODIES, VIRAL; BACTERIOPHAGES; BINDING SITES; CELL SURFACE DISPLAY TECHNIQUES; EPITOPE MAPPING; EPITOPES; HIV ENVELOPE PROTEIN GP120; HIV ENVELOPE PROTEIN GP41; HIV-1; PEPTIDE LIBRARY; RECEPTORS, CCR5; RECEPTORS, CXCR4;

EID: 84860198022     PISSN: None     EISSN: 14220067     Source Type: Journal    
DOI: 10.3390/ijms13044727     Document Type: Article

References (220)

1. Gottlieb, M.S.; Schroff, R.; Schanker, H.M.; Weisman, J.D.; Fan, P.T.; Wolf, R.A.; Saxon, A. Pneumocystis carinii pneumonia and mucosal candidiasis in previously healthy homosexual men: Evidence of a new acquired cellular immunodeficiency. N. Engl. J. Med. 1981, 305, 1425-1431.
2. Barre-Sinoussi, F.; Chermann, J.C.; Rey, F.; Nugeyre, M.T.; Chamaret, S.; Gruest, J.; Dauguet, C.; Axler-Blin, C.; Vezinet-Brun, F.; Rouzioux, C. et al. Isolation of a t-lymphotropic retrovirus from a patient at risk for acquired immune deficiency syndrome (AIDS). Science 1983, 220, 868-871.
3. Naeger, L.K.; Struble, K.A.; Murray, J.S.; Birnkrant, D.B. Running a tightrope: Regulatory challenges in the development of antiretrovirals. Antiviral Res. 2010, 85, 232-240.
4. Kilby, J.M.; Hopkins, S.; Venetta, T.M.; DiMassimo, B.; Cloud, G.A.; Lee, J.Y.; Alldredge, L.; Hunter, E.; Lambert, D.; Bolognesi, D. et al. Potent suppression of HIV-1 replication in humans by T-20, a peptide inhibitor of gp41-mediated virus entry. Nat. Med. 1998, 4, 1302-1307.
5. Dorr, P.; Westby, M.; Dobbs, S.; Griffin, P.; Irvine, B.; Macartney, M.; Mori, J.; Rickett, G.; Smith-Burchnell, C.; Napier, C. et al. Maraviroc (uk-427,857), a potent, orally bioavailable, and selective small-molecule inhibitor of chemokine receptor CCR5 with broad-spectrum anti-human immunodeficiency virus type 1 activity. Antimicrob. Agents Chemother. 2005, 49, 4721-4732.
6. Summa, V.; Petrocchi, A.; Matassa, V.G.; Gardelli, C.; Muraglia, E.; Rowley, M.; Paz, O.G.; Laufer, R.; Monteagudo, E.; Pace, P. 4,5-dihydroxypyrimidine carboxamides and N-alkyl-5-hydroxypyrimidinone carboxamides are potent, selective HIV integrase inhibitors with good pharmacokinetic profiles in preclinical species. J. Med. Chem. 2006, 49, 6646-6649.
7. Tozzi, V.; Bellagamba, R.; Castiglione, F.; Amendola, A.; Ivanovic, J.; Nicastri, E.; Libertone, R.; D'Offizi, G.; Liuzzi, G.; Gori, C. et al. Plasma HIV RNA decline and emergence of drug resistance mutations among patients with multiple virologic failures receiving resistance testing-guided haart. AIDS Res. Hum. Retrovir. 2008, 24, 787-796.
8. Dragic, T. An overview of the determinants of CCR5 and CXCR4 co-receptor function. J. Gen. Virol. 2001, 82, 1807-1814.
9. Pantophlet, R.; Wang, M.; Aguilar-Sino, R.O.; Burton, D.R. The human immunodeficiency virus type 1 envelope spike of primary viruses can suppress antibody access to variable regions. J. Virol. 2009, 83, 1649-1659.
10. Mahalanabis, M.; Jayaraman, P.; Miura, T.; Pereyra, F.; Chester, E.M.; Richardson, B.; Walker, B.; Haigwood, N.L. Continuous viral escape and selection by autologous neutralizing antibodies in drug-naive human immunodeficiency virus controllers. J. Virol. 2009, 83, 662-672.
11. Overbaugh, J.; Morris, L. The antibody response against HIV-1. Cold Spring Harb. Perspect. Med. 2012, 2, a007039.
12. Smith, G.P. Filamentous fusion phage: Novel expression vectors that display cloned antigens on the virion surface. Science 1985, 228, 1315-1317.
13. Beghetto, E.; Gargano, N. Lambda-display: A powerful tool for antigen discovery. Molecules 2011, 16, 3089-3105.
14. Parmley, S.F.; Smith, G.P. Antibody-selectable filamentous fd phage vectors: Affinity purification of target genes. Gene 1988, 73, 305-318.
15. Poropatich, K.; Sullivan, D.J., Jr. Human immunodeficiency virus type 1 long-term non-progressors: The viral, genetic and immunological basis for disease non-progression. J. Gen. Virol. 2011, 92, 247-268.
16. Gorny, M.K.; Xu, J.Y.; Gianakakos, V.; Karwowska, S.; Williams, C.; Sheppard, H.W.; Hanson, C.V.; Zolla-Pazner, S. Production of site-selected neutralizing human monoclonal antibodies against the third variable domain of the human immunodeficiency virus type 1 envelope glycoprotein. Proc. Natl. Acad. Sci. USA 1991, 88, 3238-3242.
17. Keller, P.M.; Arnold, B.A.; Shaw, A.R.; Tolman, R.L.; van Middlesworth, F.; Bondy, S.; Rusiecki, V.K.; Koenig, S.; Zolla-Pazner, S.; Conard, P. et al. Identification of HIV vaccine candidate peptides by screening random phage epitope libraries. Virology 1993, 193, 709-716.
18. Boots, L.J.; McKenna, P.M.; Arnold, B.A.; Keller, P.M.; Gorny, M.K.; Zolla-Pazner, S.; Robinson, J.E.; Conley, A.J. Anti-human immunodeficiency virus type 1 human monoclonal antibodies that bind discontinuous epitopes in the viral glycoproteins can identify mimotopes from recombinant phage peptide display libraries. AIDS Res. Hum. Retrovir. 1997, 13, 1549-1559.
19. Jellis, C.L.; Cradick, T.J.; Rennert, P.; Salinas, P.; Boyd, J.; Amirault, T.; Gray, G.S. Defining critical residues in the epitope for a HIV-neutralizing monoclonal antibody using phage display and peptide array technologies. Gene 1993, 137, 63-68.
20. Moore, J.P.; Trkola, A.; Korber, B.; Boots, L.J.; Kessler, J.A., 2nd; McCutchan, F.E.; Mascola, J.; Ho, D.D.; Robinson, J.; Conley, A.J. A human monoclonal antibody to a complex epitope in the V3 region of gp120 of human immunodeficiency virus type 1 has broad reactivity within and outside clade b. J. Virol. 1995, 69, 122-130.
21. Grihalde, N.D.; Chen, Y.C.; Golden, A.; Gubbins, E.; Mandecki, W. Epitope mapping of anti-HIV and anti-HCV monoclonal antibodies and characterization of epitope mimics using a filamentous phage peptide library. Gene 1995, 166, 187-195.
22. Laisney, I.L.; Benjamin, H.; Gefter, M.; Strosberg, A.D. Permissive residues within the minimal epitopes of neutralizing monoclonal antibodies to the V3 loop of HIV-1. Eur. J. Immunol. 1996, 26, 1634-1640.
23. Conley, A.J.; Kessler, J.A., 2nd; Boots, L.J.; Tung, J.S.; Arnold, B.A.; Keller, P.M.; Shaw, A.R.; Emini, E.A. Neutralization of divergent human immunodeficiency virus type 1 variants and primary isolates by iam-41-2f5, an anti-gp41 human monoclonal antibody. Proc. Natl. Acad. Sci. USA 1994, 91, 3348-3352.
24. Menendez, A.; Chow, K.C.; Pan, O.C.; Scott, J.K. Human immunodeficiency virus type 1-neutralizing monoclonal antibody 2F5 is multispecific for sequences flanking the DKW core epitope. J. Mol. Biol. 2004, 338, 311-327.
25. Palacios-Rodriguez, Y.; Gazarian, T.; Huerta, L.; Gazarian, K. Constrained peptide models from phage display libraries highlighting the cognate epitope-specific potential of the anti-HIV-1 mab 2f5. Immunol. Lett. 2011, 136, 80-89.
26. Stern, B.; Denisova, G.; Buyaner, D.; Raviv, D.; Gershoni, J.M. Helical epitopes determined by low-stringency antibody screening of a combinatorial peptide library. FASEB J. 1997, 11, 147-153.
27. Gomez-Roman, V.R.; Cao, C.; Bai, Y.; Santamaria, H.; Acero, G.; Manoutcharian, K.; Weiner, D.B.; Ugen, K.E.; Gevorkian, G. Phage-displayed mimotopes recognizing a biologically active anti-HIV-1 gp120 murine monoclonal antibody. J. Acquir. Immune Defic. Syndr. 2002, 31, 147-153.
28. Zwick, M.B.; Bonnycastle, L.L.; Menendez, A.; Irving, M.B.; Barbas, C.F., 3rd; Parren, P.W.; Burton, D.R.; Scott, J.K. Identification and characterization of a peptide that specifically binds the human, broadly neutralizing anti-human immunodeficiency virus type 1 antibody b12. J. Virol. 2001, 75, 6692-6699.
29. Bonnycastle, L.L.; Mehroke, J.S.; Rashed, M.; Gong, X.; Scott, J.K. Probing the basis of antibody reactivity with a panel of constrained peptide libraries displayed by filamentous phage. J. Mol. Biol. 1996, 258, 747-762.
30. Dorgham, K.; Dogan, I.; Bitton, N.; Parizot, C.; Cardona, V.; Debre, P.; Hartley, O.; Gorochov, G. Immunogenicity of HIV type 1 gp120 CD4 binding site phage mimotopes. AIDS Res. Hum. Retrovir. 2005, 21, 82-92.
31. Enshell-Seijffers, D.; Denisov, D.; Groisman, B.; Smelyanski, L.; Meyuhas, R.; Gross, G.; Denisova, G.; Gershoni, J.M. The mapping and reconstitution of a conformational discontinuous b-cell epitope of HIV-1. J. Mol. Biol. 2003, 334, 87-101.
32. Wilkinson, R.A.; Evans, J.R.; Jacobs, J.M.; Slunaker, D.; Pincus, S.H.; Pinter, A.; Parkos, C.A.; Burritt, J.B.; Teintze, M. Peptides selected from a phage display library with an HIV-neutralizing antibody elicit antibodies to HIV gp120 in rabbits, but not to the same epitope. AIDS Res. Hum. Retrovir. 2007, 23, 1416-1427.
33. Ferrer, M.; Sullivan, B.J.; Godbout, K.L.; Burke, E.; Stump, H.S.; Godoy, J.; Golden, A.; Profy, A.T.; van Schravendijk, M.R. Structural and functional characterization of an epitope in the conserved C-terminal region of HIV-1 gp120. J. Pept. Res. 1999, 54, 32-42.
34. Menendez, A.; Calarese, D.A.; Stanfield, R.L.; Chow, K.C.; Scanlan, C.N.; Kunert, R.; Katinger, H.; Burton, D.R.; Wilson, I.A.; Scott, J.K. A peptide inhibitor of HIV-1 neutralizing antibody 2G12 is not a structural mimic of the natural carbohydrate epitope on gp120. FASEB J. 2008, 22, 1380-1392.
35. Rusche, J.R.; Javaherian, K.; McDanal, C.; Petro, J.; Lynn, D.L.; Grimaila, R.; Langlois, A.; Gallo, R.C.; Arthur, L.O.; Fischinger, P.J. et al. Antibodies that inhibit fusion of human immunodeficiency virus-infected cells bind a 24-amino acid sequence of the viral envelope, gp120. Proc. Natl. Acad. Sci. USA 1988, 85, 3198-3202.
36. Javaherian, K.; Langlois, A.J.; McDanal, C.; Ross, K.L.; Eckler, L.I.; Jellis, C.L.; Profy, A.T.; Rusche, J.R.; Bolognesi, D.P.; Putney, S.D. et al. Principal neutralizing domain of the human immunodeficiency virus type 1 envelope protein. Proc. Natl. Acad. Sci. USA 1989, 86, 6768-6772.
37. Scott, C.F., Jr.; Silver, S.; Profy, A.T.; Putney, S.D.; Langlois, A.; Weinhold, K.; Robinson, J.E. Human monoclonal antibody that recognizes the v3 region of human immunodeficiency virus gp120 and neutralizes the human T-lymphotropic virus type IIIMN strain. Proc. Natl. Acad. Sci. USA 1990, 87, 8597-8601.
38. Muster, T.; Steindl, F.; Purtscher, M.; Trkola, A.; Klima, A.; Himmler, G.; Ruker, F.; Katinger, H. A conserved neutralizing epitope on gp41 of human immunodeficiency virus type 1. J. Virol. 1993, 67, 6642-6647.
39. Denisova, G.; Stern, B.; Raviv, D.; Zwickel, J.; Smorodinsky, N.I.; Gershoni, J.M. Humoral immune response to immunocomplexed HIV envelope glycoprotein 120. AIDS Res. Hum. Retrovir. 1996, 12, 901-909.
40. Burton, D.R.; Barbas, C.F., 3rd; Persson, M.A.; Koenig, S.; Chanock, R.M.; Lerner, R.A. A large array of human monoclonal antibodies to type 1 human immunodeficiency virus from combinatorial libraries of asymptomatic seropositive individuals. Proc. Natl. Acad. Sci. USA 1991, 88, 10134-10137.
41. Barbas, C.F., 3rd; Bjorling, E.; Chiodi, F.; Dunlop, N.; Cababa, D.; Jones, T.M.; Zebedee, S.L.; Persson, M.A.; Nara, P.L.; Norrby, E. et al. Recombinant human fab fragments neutralize human type 1 immunodeficiency virus in vitro. Proc. Natl. Acad. Sci. USA 1992, 89, 9339-9343.
42. Bublil, E.M.; Yeger-Azuz, S.; Gershoni, J.M. Computational prediction of the cross-reactive neutralizing epitope corresponding to the [corrected] monclonal [corrected] antibody b12 specific for HIV-1 gp120. FASEB J. 2006, 20, 1762-1774.
43. Rizzuto, C.D.; Wyatt, R.; Hernandez-Ramos, N.; Sun, Y.; Kwong, P.D.; Hendrickson, W.A.; Sodroski, J. A conserved HIV gp120 glycoprotein structure involved in chemokine receptor binding. Science 1998, 280, 1949-1953.
44. Moore, J.P.; McCutchan, F.E.; Poon, S.W.; Mascola, J.; Liu, J.; Cao, Y.; Ho, D.D. Exploration of antigenic variation in gp120 from clades a through f of human immunodeficiency virus type 1 by using monoclonal antibodies. J. Virol. 1994, 68, 8350-8364.
45. Thali, M.; Moore, J.P.; Furman, C.; Charles, M.; Ho, D.D.; Robinson, J.; Sodroski, J. Characterization of conserved human immunodeficiency virus type 1 gp120 neutralization epitopes exposed upon gp120-CD4 binding. J. Virol. 1993, 67, 3978-3988.
46. Scanlan, C.N.; Pantophlet, R.; Wormald, M.R.; Ollmann Saphire, E.; Stanfield, R.; Wilson, I.A.; Katinger, H.; Dwek, R.A.; Rudd, P.M.; Burton, D.R. The broadly neutralizing anti-human immunodeficiency virus type 1 antibody 2G12 recognizes a cluster of α1→2 mannose residues on the outer face of gp120. J. Virol. 2002, 76, 7306-7321.
47. Trkola, A.; Purtscher, M.; Muster, T.; Ballaun, C.; Buchacher, A.; Sullivan, N.; Srinivasan, K.; Sodroski, J.; Moore, J.P.; Katinger, H. Human monoclonal antibody 2G12 defines a distinctive neutralization epitope on the gp120 glycoprotein of human immunodeficiency virus type 1. J. Virol. 1996, 70, 1100-1108.
48. Sanders, R.W.; Venturi, M.; Schiffner, L.; Kalyanaraman, R.; Katinger, H.; Lloyd, K.O.; Kwong, P.D.; Moore, J.P. The mannose-dependent epitope for neutralizing antibody 2G12 on human immunodeficiency virus type 1 glycoprotein gp120. J. Virol. 2002, 76, 7293-7305.
49. Scala, G.; Chen, X.; Liu, W.; Telles, J.N.; Cohen, O.J.; Vaccarezza, M.; Igarashi, T.; Fauci, A.S. Selection of HIV-specific immunogenic epitopes by screening random peptide libraries with HIV-1-positive sera. J. Immunol. 1999, 162, 6155-6161.
50. Chen, X.; Scala, G.; Quinto, I.; Liu, W.; Chun, T.W.; Justement, J.S.; Cohen, O.J.; van Cott, T.C.; Iwanicki, M.; Lewis, M.G. et al. Protection of rhesus macaques against disease progression from pathogenic SHIV-89.6PD by vaccination with phage-displayed HIV-1 epitopes. Nat. Med. 2001, 7, 1225-1231.
51. Enshell-Seijffers, D.; Smelyanski, L.; Vardinon, N.; Yust, I.; Gershoni, J.M. Dissection of the humoral immune response toward an immunodominant epitope of HIV: A model for the analysis of antibody diversity in HIV+ individuals. FASEB J. 2001, 15, 2112-2120.
52. Palacios-Rodriguez, Y.; Gazarian, T.; Rowley, M.; Majluf-Cruz, A.; Gazarian, K. Collection of phage-peptide probes for HIV-1 immunodominant loop-epitope. J. Microbiol. Methods 2007, 68, 225-235.
53. Humbert, M.; Antoni, S.; Brill, B.; Landersz, M.; Rodes, B.; Soriano, V.; Wintergerst, U.; Knechten, H.; Staszewski, S.; von Laer, D. et al. Mimotopes selected with antibodies from HIV-1-neutralizing long-term non-progressor plasma. Eur. J. Immunol. 2007, 37, 501-515.
54. Humbert, M.; Rasmussen, R.A.; Ong, H.; Kaiser, F.M.; Hu, S.L.; Ruprecht, R.M. Inducing cross-clade neutralizing antibodies against HIV-1 by immunofocusing. PLoS One 2008, 3, doi:10.1371/journal.pone.0003937.
55. Dieltjens, T.; Heyndrickx, L.; Willems, B.; Gray, E.; Van Nieuwenhove, L.; Grupping, K.; Vanham, G.; Janssens, W. Evolution of antibody landscape and viral envelope escape in an HIV-1 CRF02_AG infected patient with 4E10-like antibodies. Retrovirology 2009, 6, doi:10.1186/1742-4690-6-113.
56. Dieltjens, T.; Willems, B.; Coppens, S.; Van Nieuwenhove, L.; Humbert, M.; Dietrich, U.; Heyndrickx, L.; Vanham, G.; Janssens, W. Unravelling the antigenic landscape of the HIV-1 subtype a envelope of an individual with broad cross-neutralizing antibodies using phage display peptide libraries. J. Virol. Methods 2010, 169, 95-102.
57. Gupta, S.; Arora, K.; Sampath, A.; Singh, S.S.; Gupta, A.; Chaudhary, V.K. Mapping of HIV-1 gag epitopes recognized by polyclonal antibodies using gene-fragment phage display system. Prep. Biochem. Biotechnol. 2001, 31, 185-200.
58. Berman, H.M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T.N.; Weissig, H.; Shindyalov, I.N.; Bourne, P.E. The protein data bank. Nucleic. Acids Res. 2000, 28, 235-242.
59. Schreiber, A.; Humbert, M.; Benz, A.; Dietrich, U. 3d-epitope-explorer (3dex): Localization of conformational epitopes within three-dimensional structures of proteins. J. Comput. Chem. 2005, 26, 879-887.
60. Song, R.J.; Chenine, A.L.; Rasmussen, R.A.; Ruprecht, C.R.; Mirshahidi, S.; Grisson, R.D.; Xu, W.; Whitney, J.B.; Goins, L.M.; Ong, H. et al. Molecularly cloned SHIV-1157IPD3N4: A highly replication- competent, mucosally transmissible R5 simian-human immunodeficiency virus encoding HIV cladecenv. J. Virol. 2006, 80, 8729-8738.
61. O'Connor, K.H.; Konigs, C.; Rowley, M.J.; Irving, J.A.; Wijeyewickrema, L.C.; Pustowka, A.; Dietrich, U.; Mackay, I.R. Requirement of multiple phage displayed peptide libraries for optimal mapping of a conformational antibody epitope on CCR5. J. Immunol. Methods 2005, 299, 21-35.
62. Konigs, C.; Rowley, M.J.; Thompson, P.; Myers, M.A.; Scealy, M.; Davies, J.M.; Wu, L.; Dietrich, U.; Mackay, C.R.; Mackay, I.R. Monoclonal antibody screening of a phage-displayed random peptide library reveals mimotopes of chemokine receptor CCR5: Implications for the tertiary structure of the receptor and for an N-terminal binding site for HIV-1 gp120. Eur. J. Immunol. 2000, 30, 1162-1171.
63. Meta, A.; Torigoe, N.; Ito, Y.; Arakaki, R.; Nakashima, H.; Sugimura, K. Inhibition of M-tropic HIV-1 infection by the fd phage-gene 3 protein with MIP-1α-binding activity. Mol. Immunol. 1999, 36, 1249-1254.
64. Khurana, S.; Kennedy, M.; King, L.R.; Golding, H. Identification of a linear peptide recognized by monoclonal antibody 2D7 capable of generating CCR5-specific antibodies with human immunodeficiency virus-neutralizing activity. J. Virol. 2005, 79, 6791-6800.
65. Poloni, F.; Puddu, P.; Moretti, F.; Flego, M.; Romagnoli, G.; Tombesi, M.; Capone, I.; Chersi, A.; Felici, F.; Cianfriglia, M. Identification of a LFA-1 region involved in the HIV-1-induced syncytia formation through phage-display technology. Eur. J. Immunol. 2001, 31, 57-63.
66. Wu, L.; LaRosa, G.; Kassam, N.; Gordon, C.J.; Heath, H.; Ruffing, N.; Chen, H.; Humblias, J.; Samson, M.; Parmentier, M. et al. Interaction of chemokine receptor CCR5 with its ligands: Multiple domains for HIV-1 gp120 binding and a single domain for chemokine binding. J. Exp. Med. 1997, 186, 1373-1381.
67. Wu, L.; Paxton, W.A.; Kassam, N.; Ruffing, N.; Rottman, J.B.; Sullivan, N.; Choe, H.; Sodroski, J.; Newman, W.; Koup, R.A. et al. CCR5 levels and expression pattern correlate with infectability by macrophage-tropic HIV-1, in vitro. J. Exp. Med. 1997, 185, 1681-1691.
68. Pantaleo, G.; Butini, L.; Graziosi, C.; Poli, G.; Schnittman, S.M.; Greenhouse, J.J.; Gallin, J.I.; Fauci, A.S. Human immunodeficiency virus (HIV) infection in CD4+ t lymphocytes genetically deficient in LFA-1: LFA-1 is required for HIV-mediated cell fusion but not for viral transmission. J. Exp. Med. 1991, 173, 511-514.
69. Barbas, C.F., 3rd; Collet, T.A.; Amberg, W.; Roben, P.; Binley, J.M.; Hoekstra, D.; Cababa, D.; Jones, T.M.; Williamson, R.A.; Pilkington, G.R. et al. Molecular profile of an antibody response to HIV-1 as probed by combinatorial libraries. J. Mol. Biol. 1993, 230, 812-823.
70. Bera, T.K.; Kennedy, P.E.; Berger, E.A.; Barbas, C.F., 3rd; Pastan, I. Specific killing of HIV-infected lymphocytes by a recombinant immunotoxin directed against the HIV-1 envelope glycoprotein. Mol. Med. 1998, 4, 384-391.
71. Yang, W.P.; Green, K.; Pinz-Sweeney, S.; Briones, A.T.; Burton, D.R.; Barbas, C.F. 3rd. CDR walking mutagenesis for the affinity maturation of a potent human anti-HIV-1 antibody into the picomolar range. J. Mol. Biol. 1995, 254, 392-403.
72. Barbas, C.F., 3rd; Hu, D.; Dunlop, N.; Sawyer, L.; Cababa, D.; Hendry, R.M.; Nara, P.L.; Burton, D.R. In vitro evolution of a neutralizing human antibody to human immunodeficiency virus type 1 to enhance affinity and broaden strain cross-reactivity. Proc. Natl. Acad. Sci. USA 1994, 91, 3809-3813.
73. Ditzel, H.J.; Binley, J.M.; Moore, J.P.; Sodroski, J.; Sullivan, N.; Sawyer, L.S.; Hendry, R.M.; Yang, W.P.; Barbas, C.F., 3rd; Burton, D.R. Neutralizing recombinant human antibodies to a conformational V2- and CD4-binding site-sensitive epitope of HIV-1 gp120 isolated by using an epitope-masking procedure. J. Immunol. 1995, 154, 893-906.
74. Nishiyama, Y.; Karle, S.; Planque, S.; Taguchi, H.; Paul, S. Antibodies to the superantigenic site of HIV-1 gp120: Hydrolytic and binding activities of the light chain subunit. Mol. Immunol. 2007, 44, 2707-2718.
75. Karle, S.; Planque, S.; Nishiyama, Y.; Taguchi, H.; Zhou, Y.X.; Salas, M.; Lake, D.; Thiagarajan, P.; Arnett, F.; Hanson, C.V. et al. Cross-clade HIV-1 neutralization by an antibody fragment from a lupus phage display library. AIDS 2004, 18, 329-331.
76. Koh, W.W.; Steffensen, S.; Gonzalez-Pajuelo, M.; Hoorelbeke, B.; Gorlani, A.; Szynol, A.; Forsman, A.; Aasa-Chapman, M.M.; de Haard, H.; Verrips, T. et al. Generation of a family-specific phage library of llama single chain antibody fragments that neutralize HIV-1. J. Biol. Chem. 2010, 285, 19116-19124.
77. Forsman, A.; Beirnaert, E.; Aasa-Chapman, M.M.; Hoorelbeke, B.; Hijazi, K.; Koh, W.; Tack, V.; Szynol, A.; Kelly, C.; McKnight, A. et al. Llama antibody fragments with cross-subtype human immunodeficiency virus type 1 (HIV-1)-neutralizing properties and high affinity for HIV-1 gp120. J. Virol. 2008, 82, 12069-12081.
78. Krykbaev, R.; McKeating, J.; Jones, I. Mutant CD4 molecules with improved binding to HIV envelope protein gp120 selected by phage display. Virology 1997, 234, 196-202.
79. Thompson, J.; Pope, T.; Tung, J.S.; Chan, C.; Hollis, G.; Mark, G.; Johnson, K.S. Affinity maturation of a high-affinity human monoclonal antibody against the third hypervariable loop of human immunodeficiency virus: Use of phage display to improve affinity and broaden strain reactivity. J. Mol. Biol. 1996, 256, 77-88.
80. Ditzel, H.J.; Parren, P.W.; Binley, J.M.; Sodroski, J.; Moore, J.P.; Barbas, C.F., 3rd; Burton, D.R. Mapping the protein surface of human immunodeficiency virus type 1 gp120 using human monoclonal antibodies from phage display libraries. J. Mol. Biol. 1997, 267, 684-695.
81. Ferrer, M.; Harrison, S.C. Peptide ligands to human immunodeficiency virus type 1 gp120 identified from phage display libraries. J. Virol. 1999, 73, 5795-5802.
82. Moulard, M.; Phogat, S.K.; Shu, Y.; Labrijn, A.F.; Xiao, X.; Binley, J.M.; Zhang, M.Y.; Sidorov, I.A.; Broder, C.C.; Robinson, J. et al. Broadly cross-reactive HIV-1-neutralizing human monoclonal fab selected for binding to gp120-CD4-CCR5 complexes. Proc. Natl. Acad. Sci. USA 2002, 99, 6913-6918.
83. Dervillez, X.; Klaukien, V.; Durr, R.; Koch, J.; Kreutz, A.; Haarmann, T.; Stoll, M.; Lee, D.; Carlomagno, T.; Schnierle, B. et al. Peptide ligands selected with cd4-induced epitopes on native dualtropic HIV-1 envelope proteins mimic extracellular coreceptor domains and bind to HIV-1 gp120 independently of coreceptor usage. J. Virol. 2010, 84, 10131-10138.
84. Zwick, M.B.; Labrijn, A.F.; Wang, M.; Spenlehauer, C.; Saphire, E.O.; Binley, J.M.; Moore, J.P.; Stiegler, G.; Katinger, H.; Burton, D.R. et al. Broadly neutralizing antibodies targeted to the membrane-proximal external region of human immunodeficiency virus type 1 glycoprotein gp41. J. Virol. 2001, 75, 10892-10905.
85. Nelson, J.D.; Brunel, F.M.; Jensen, R.; Crooks, E.T.; Cardoso, R.M.; Wang, M.; Hessell, A.; Wilson, I.A.; Binley, J.M.; Dawson, P.E. et al. An affinity-enhanced neutralizing antibody against the membrane-proximal external region of human immunodeficiency virus type 1 gp41 recognizes an epitope between those of 2F5 and 4E10. J. Virol. 2007, 81, 4033-4043.
86. Welch, B.D.; VanDemark, A.P.; Heroux, A.; Hill, C.P.; Kay, M.S. Potent D-peptide inhibitors of HIV-1 entry. Proc. Natl. Acad. Sci. USA 2007, 104, 16828-16833.
87. Welch, B.D.; Francis, J.N.; Redman, J.S.; Paul, S.; Weinstock, M.T.; Reeves, J.D.; Lie, Y.S.; Whitby, F.G.; Eckert, D.M.; Hill, C.P. et al. Design of a potent d-peptide HIV-1 entry inhibitor with a strong barrier to resistance. J. Virol. 2010, 84, 11235-11244.
88. Eckert, D.M.; Malashkevich, V.N.; Hong, L.H.; Carr, P.A.; Kim, P.S. Inhibiting HIV-1 entry: Discovery of D-peptide inhibitors that target the gp41 coiled-coil pocket. Cell 1999, 99, 103-115.
89. Miller, M.D.; Geleziunas, R.; Bianchi, E.; Lennard, S.; Hrin, R.; Zhang, H.; Lu, M.; An, Z.; Ingallinella, P.; Finotto, M. et al. A human monoclonal antibody neutralizes diverse HIV-1 isolates by binding a critical gp41 epitope. Proc. Natl. Acad. Sci. USA 2005, 102, 14759-14764.
90. Eckert, D.M.; Kim, P.S. Design of potent inhibitors of HIV-1 entry from the gp41 N-peptide region. Proc. Natl. Acad. Sci. USA 2001, 98, 11187-11192.
91. Liu, Y.; Regula, L.K.; Stewart, A.; Lai, J.R. Synthetic fab fragments that bind the HIV-1 gp41 heptad repeat regions. Biochem. Biophys. Res. Commun. 2011, 413, 611-615.
92. Huang, J.H.; Liu, Z.Q.; Liu, S.; Jiang, S.; Chen, Y.H. Identification of the HIV-1 gp41 core-binding motif-HXXNPF. FEBS Lett. 2006, 580, 4807-4814.
93. Huang, J.H.; Yang, H.W.; Liu, S.; Li, J.; Jiang, S.; Chen, Y.H. The mechanism by which molecules containing the HIV gp41 core-binding motif hxxnpf inhibit HIV-1 envelope glycoprotein-mediated syncytium formation. Biochem. J. 2007, 403, 565-571.
94. Louis, J.M.; Bewley, C.A.; Gustchina, E.; Aniana, A.; Clore, G.M. Characterization and HIV-1 fusion inhibitory properties of monoclonal fabs obtained from a human non-immune phage library selected against diverse epitopes of the ectodomain of HIV-1 gp41. J. Mol. Biol. 2005, 353, 945-951.
95. Gustchina, E.; Louis, J.M.; Lam, S.N.; Bewley, C.A.; Clore, G.M. A monoclonal fab derived from a human nonimmune phage library reveals a new epitope on gp41 and neutralizes diverse human immunodeficiency virus type 1 strains. J. Virol. 2007, 81, 12946-12953.
96. Gustchina, E.; Louis, J.M.; Frisch, C.; Ylera, F.; Lechner, A.; Bewley, C.A.; Clore, G.M. Affinity maturation by targeted diversification of the CDR-H2 loop of a monoclonal fab derived from a synthetic naive human antibody library and directed against the internal trimeric coiled-coil of gp41 yields a set of fabs with improved HIV-1 neutralization potency and breadth. Virology 2009, 393, 112-119.
97. Gustchina, E.; Bewley, C.A.; Clore, G.M. Sequestering of the prehairpin intermediate of gp41 by peptide N36Mut(e,g) potentiates the human immunodeficiency virus type 1 neutralizing activity of monoclonal antibodies directed against the N-terminal helical repeat of gp41. J. Virol. 2008, 82, 10032-10041.
98. Nelson, J.D.; Kinkead, H.; Brunel, F.M.; Leaman, D.; Jensen, R.; Louis, J.M.; Maruyama, T.; Bewley, C.A.; Bowdish, K.; Clore, G.M. et al. Antibody elicited against the gp41 N-heptad repeat (NHR) coiled-coil can neutralize HIV-1 with modest potency but non-neutralizing antibodies also bind to NHR mimetics. Virology 2008, 377, 170-183.
99. Zhang, M.Y.; Vu, B.K.; Choudhary, A.; Lu, H.; Humbert, M.; Ong, H.; Alam, M.; Ruprecht, R.M.; Quinnan, G.; Jiang, S. et al. Cross-reactive human immunodeficiency virus type 1-neutralizing human monoclonal antibody that recognizes a novel conformational epitope on gp41 and lacks reactivity against self-antigens. J. Virol. 2008, 82, 6869-6879.
100. Choudhry, V.; Zhang, M.Y.; Sidorov, I.A.; Louis, J.M.; Harris, I.; Dimitrov, A.S.; Bouma, P.; Cham, F.; Choudhary, A.; Rybak, S.M. et al. Cross-reactive HIV-1 neutralizing monoclonal antibodies selected by screening of an immune human phage library against an envelope glycoprotein (gp140) isolated from a patient (R2) with broadly HIV-1 neutralizing antibodies. Virology 2007, 363, 79-90.
101. Zhang, M.Y.; Choudhry, V.; Sidorov, I.A.; Tenev, V.; Vu, B.K.; Choudhary, A.; Lu, H.; Stiegler, G.M.; Katinger, H.W.; Jiang, S. et al. Selection of a novel gp41-specific HIV-1 neutralizing human antibody by competitive antigen panning. J. Immunol. Methods 2006, 317, 21-30.
102. BouHamdan, M.; Xue, Y.; Baudat, Y.; Hu, B.; Sire, J.; Pomerantz, R.J.; Duan, L.X. Diversity of HIV-1 Vpr interactions involves usage of the WXXF motif of host cell proteins. J. Biol. Chem. 1998, 273, 8009-8016.
103. Krichevsky, A.; Graessmann, A.; Nissim, A.; Piller, S.C.; Zakai, N.; Loyter, A. Antibody fragments selected by phage display against the nuclear localization signal of the HIV-1 Vpr protein inhibit nuclear import in permeabilized and intact cultured cells. Virology 2003, 305, 77-92.
104. Desjobert, C.; de Soultrait, V.R.; Faure, A.; Parissi, V.; Litvak, S.; Tarrago-Litvak, L.; Fournier, M. Identification by phage display selection of a short peptide able to inhibit only the strand transferreaction catalyzed by human immunodeficiency virus type 1 integrase. Biochemistry 2004, 43, 13097-13105.
105. Pilkington, G.R.; Duan, L.; Zhu, M.; Keil, W.; Pomerantz, R.J. Recombinant human Fab antibody fragments to HIV-1 Rev and Tat regulatory proteins: Direct selection from a combinatorial phage display library. Mol. Immunol. 1996, 33, 439-450.
106. Bai, J.; Sui, J.; Zhu, R.Y.; Tallarico, A.S.; Gennari, F.; Zhang, D.; Marasco, W.A. Inhibition of Tat-mediated transactivation and HIV-1 replication by human anti-hCyclinT1 intrabodies. J. Biol. Chem. 2003, 278, 1433-1442.
107. Kolb, G.; Boiziau, C. Selection by phage display of peptides targeting the HIV-1 Tar element. RNA Biol. 2005, 2, 28-33.
108. Lener, D.; Benarous, R.; Calogero, R.A. Use of a constrain phage displayed-peptide library for the isolation of peptides binding to HIV-1 nucleocapsid protein (NCp7). FEBS Lett. 1995, 361, 85-88.
109. Pustowka, A.; Dietz, J.; Ferner, J.; Baumann, M.; Landersz, M.; Konigs, C.; Schwalbe, H.; Dietrich, U. Identification of peptide ligands for target RNA structures derived from the HIV-1 packaging signal ψ by screening phage-displayed peptide libraries. ChemBioChem 2003, 4, 1093-1097.
110. Dietz, J.; Koch, J.; Kaur, A.; Raja, C.; Stein, S.; Grez, M.; Pustowka, A.; Mensch, S.; Ferner, J.; Moller, L. et al. Inhibition of HIV-1 by a peptide ligand of the genomic RNA packaging signal ψ. ChemMedChem 2008, 3, 749-755.
111. Park, M.Y.; Kwon, J.; Lee, S.; You, J.; Myung, H. Selection and characterization of peptides specifically binding to HIV-1 ψ (ψ) RNA. Virus Res. 2004, 106, 77-81.
112. Yoshikawa, M.; Mukai, Y.; Tsunoda, S.; Tsutsumi, Y.; Yoshioka, Y.; Okada, N.; Nakagawa, S. Modifying the antigen-immunization schedule improves the variety of monoclonal antibodies obtained from immune-phage antibody libraries against HIV-1 Nef and Vif. J. Biosci. Bioeng. 2011, 111, 597-599.
113. Bouchet, J.; Basmaciogullari, S.E.; Chrobak, P.; Stolp, B.; Bouchard, N.; Fackler, O.T.; Chames, P.; Jolicoeur, P.; Benichou, S.; Baty, D. Inhibition of the nef regulatory protein of HIV-1 by a single-domain antibody. Blood 2011, 117, 3559-3568.
114. Nunoya, J.; Nakashima, T.; Kawana-Tachikawa, A.; Kiyotani, K.; Ito, Y.; Sugimura, K.; Iwamoto, A. Short communication: Generation of recombinant monoclonal antibodies against an immunodominant HLA-A*2402-restricted HIV type 1 CTL epitope. AIDS Res. Hum. Retrovir. 2009, 25, 897-904.
115. Yang, S.; Sun, Y.; Zhang, H. The multimerization of human immunodeficiency virus type I Vif protein: A requirement for Vif function in the viral life cycle. J. Biol. Chem. 2001, 276, 4889-4893.
116. Yang, B.; Gao, L.; Li, L.; Lu, Z.; Fan, X.; Patel, C.A.; Pomerantz, R.J.; DuBois, G.C.; Zhang, H. Potent suppression of viral infectivity by the peptides that inhibit multimerization of human immunodeficiency virus type 1 (HIV-1) Vif proteins. J. Biol. Chem. 2003, 278, 6596-6602.
117. Ohba, H.; Soga, T.; Tomozawa, T.; Nishikawa, Y.; Yasuda, A.; Kojima, A.; Kurata, T.; Chiba, J. An immunodominant neutralization epitope on the "thumb" subdomain of human immunodeficiency virus type 1 reverse transcriptase revealed by phage display antibodies. J. Gen. Virol. 2001, 82, 813-820.
118. Chiba, J.; Yamaguchi, A.; Suzuki, Y.; Nakano, M.; Zhu, W.; Ohba, H.; Saito, A.; Shinagawa, H.; Yamakawa, Y.; Kobayashi, T. et al. A novel neutralization epitope on the -thumb{norm of matrix} subdomain of human immunodeficiency virus type 1 reverse transcriptase revealed by a monoclonal antibody. J. Gen. Virol. 1996, 77 (Pt 12), 2921-2929.
119. Herschhorn, A.; Admon, A.; Hizi, A. Recombinant human antibodies against the reverse transcriptase of human immunodeficiency virus type-1. Biochim. Biophys. Acta 2003, 1648, 154-163.
120. Jensen, A.; Jensen, T.H.; Kjems, J. HIV-1 Rev nuclear export signal binding peptides isolated by phage display. J. Mol. Biol. 1998, 283, 245-254.
121. Vercruysse, T.; Pawar, S.; de Borggraeve, W.; Pardon, E.; Pavlakis, G.N.; Pannecouque, C.; Steyaert, J.; Balzarini, J.; Daelemans, D. Measuring cooperative Rev protein-protein interactions on rev responsive RNA by fluorescence resonance energy transfer. RNA Biol. 2011, 8, 316-324.
122. Vercruysse, T.; Pardon, E.; Vanstreels, E.; Steyaert, J.; Daelemans, D. An intrabody based on a llama single-domain antibody targeting the N-terminal α-helical multimerization domain of HIV-1 Rev prevents viral production. J. Biol. Chem. 2010, 285, 21768-21780.
123. Stahl, S.J.; Watts, N.R.; Rader, C.; DiMattia, M.A.; Mage, R.G.; Palmer, I.; Kaufman, J.D.; Grimes, J.M.; Stuart, D.I.; Steven, A.C. et al. Generation and characterization of a chimeric rabbit/human fab for co-crystallization of HIV-1 Rev. J. Mol. Biol. 2010, 397, 697-708.
124. Sticht, J.; Humbert, M.; Findlow, S.; Bodem, J.; Muller, B.; Dietrich, U.; Werner, J.; Krausslich, H.G. A peptide inhibitor of HIV-1 assembly in vitro. Nat. Struct. Mol. Biol. 2005, 12, 671-677.
125. Huang, L.; Zhang, L.; Chen, C.H. Potential drug targets on the HIV-1 envelope glycoproteins, gp120 and gp41. Curr. Pharm. Des. 2003, 9, 1453-1462.
126. Kadow, J.; Wang, H.G.; Lin, P.F. Small-molecule HIV-1 gp120 inhibitors to prevent HIV-1 entry: An emerging opportunity for drug development. Curr. Opin. Investig. Drugs 2006, 7, 721-726.
127. Koefoed, K.; Farnaes, L.; Wang, M.; Svejgaard, A.; Burton, D.R.; Ditzel, H.J. Molecular characterization of the circulating anti-HIV-1 gp120-specific b cell repertoire using antibody phage display libraries generated from pre-selected HIV-1 gp120 binding PBLs. J. Immunol. Methods 2005, 297, 187-201.
128. Parren, P.W.; Gauduin, M.C.; Koup, R.A.; Poignard, P.; Fisicaro, P.; Burton, D.R.; Sattentau, Q.J. Relevance of the antibody response against human immunodeficiency virus type 1 envelope to vaccine design. Immunol. Lett. 1997, 57, 105-112.
129. Bermas, B.L.; Petri, M.; Berzofsky, J.A.; Waisman, A.; Shearer, G.M.; Mozes, E. Binding of glycoprotein 120 and peptides from the HIV-1 envelope by autoantibodies in mice with experimentally induced systemic lupus erythematosus and in patients with the disease. AIDS Res. Hum. Retrovir. 1994, 10, 1071-1077.
130. Zhou, Y.X.; Karle, S.; Taguchi, H.; Planque, S.; Nishiyama, Y.; Paul, S. Prospects for immunotherapeutic proteolytic antibodies. J. Immunol. Methods 2002, 269, 257-268.
131. Paul, S.; Tramontano, A.; Gololobov, G.; Zhou, Y.X.; Taguchi, H.; Karle, S.; Nishiyama, Y.; Planque, S.; George, S. Phosphonate ester probes for proteolytic antibodies. J. Biol. Chem. 2001, 276, 28314-28320.
132. Paul, S.; Karle, S.; Planque, S.; Taguchi, H.; Salas, M.; Nishiyama, Y.; Handy, B.; Hunter, R.; Edmundson, A.; Hanson, C. Naturally occurring proteolytic antibodies: Selective immunoglobulin m-catalyzed hydrolysis of HIV gp120. J. Biol. Chem. 2004, 279, 39611-39619.
133. Paul, S.; Nishiyama, Y.; Planque, S.; Taguchi, H. Theory of proteolytic antibody occurrence. Immunol. Lett. 2006, 103, 8-16.
134. Gao, Q.S.; Sun, M.; Rees, A.R.; Paul, S. Site-directed mutagenesis of proteolytic antibody light chain. J. Mol. Biol. 1995, 253, 658-664.
135. Hamers-Casterman, C.; Atarhouch, T.; Muyldermans, S.; Robinson, G.; Hamers, C.; Songa, E.B.; Bendahman, N.; Hamers, R. Naturally occurring antibodies devoid of light chains. Nature 1993, 363, 446-448.
136. Vanlandschoot, P.; Stortelers, C.; Beirnaert, E.; Ibanez, L.I.; Schepens, B.; Depla, E.; Saelens, X. Nanobodies(r): New ammunition to battle viruses. Antiviral Res. 2011, 92, 389-407.
137. Biorn, A.C.; Cocklin, S.; Madani, N.; Si, Z.; Ivanovic, T.; Samanen, J.; van Ryk, D.I.; Pantophlet, R.; Burton, D.R.; Freire, E. et al. Mode of action for linear peptide inhibitors of HIV-1 gp120 interactions. Biochemistry 2004, 43, 1928-1938.
138. Garg, R.; Juncadella, I.J.; Ramamoorthi, N.; Ashish; Ananthanarayanan, S.K.; Thomas, V.; Rincon, M.; Krueger, J.K.; Fikrig, E.; Yengo, C.M. et al. Cutting edge: CD4 is the receptor for the tick saliva immunosuppressor, Salp15. J. Immunol. 2006, 177, 6579-6583.
139. Juncadella, I.J.; Garg, R.; Bates, T.C.; Olivera, E.R.; Anguita, J. The ixodes scapularis salivary protein, Salp15, prevents the association of HIV-1 gp120 and CD4. Biochem. Biophys. Res. Commun. 2008, 367, 41-46.
140. Llorente, M.; Sanchez-Palomino, S.; Manes, S.; Lucas, P.; Kremer, L.; de Alboran, I.M.; Toran, J.L.; Alcami, J.; Del Real, G.; Martinez, A.C. Natural human antibodies retrieved by phage display libraries from healthy donors: Polyreactivity and recognition of human immunodeficiency virus type 1gp120 epitopes. Scand. J. Immunol. 1999, 50, 270-279.
141. Berberian, L.; Valles-Ayoub, Y.; Sun, N.; Martinez-Maza, O.; Braun, J. A VH clonal deficit in human immunodeficiency virus-positive individuals reflects a B-cell maturational arrest. Blood 1991, 78, 175-179.
142. David, D.; Demaison, C.; Bani, L.; Zouali, M.; Theze, J. Selective variations in vivo of VH3 and VH1 gene family expression in peripheral B cell igM, igD and igG during HIV infection. Eur. J. Immunol. 1995, 25, 1524-1528.
143. Toran, J.L.; Kremer, L.; Sanchez-Pulido, L.; de Alboran, I.M.; del Real, G.; Llorente, M.; Valencia, A.; de Mon, M.A.; Martinez, A.C. Molecular analysis of HIV-1 gp120 antibody response using isotype igM and igG phage display libraries from a long-term non-progressor HIV-1-infected individual. Eur. J. Immunol. 1999, 29, 2666-2675.
144. Toran, J.L.; Sanchez-Pulido, L.; Kremer, L.; del Real, G.; Valencia, A.; Martinez, A.C. Improvement in affinity and HIV-1 neutralization by somatic mutation in the heavy chain first complementarity-determining region of antibodies triggered by HIV-1 infection. Eur. J. Immunol. 2001, 31, 128-137.
145. Chen, W.; Zhu, Z.; Liao, H.; Quinnan, G.V., Jr.; Broder, C.C.; Haynes, B.F.; Dimitrov, D.S. Cross-reactive human igm-derived monoclonal antibodies that bind to HIV-1 envelope glycoproteins. Viruses 2010, 2, 547-565.
146. Chen, W.; Streaker, E.D.; Russ, D.E.; Feng, Y.; Prabakaran, P.; Dimitrov, D.S. Characterization of germline antibody libraries from human umbilical cord blood and selection of monoclonal antibodies to viral envelope glycoproteins: Implications for mechanisms of immune evasion and design of vaccine immunogens. Biochem. Biophys. Res. Commun. 2012, 417, 1164-1169.
147. Zhu, Z.; Qin, H.R.; Chen, W.; Zhao, Q.; Shen, X.; Schutte, R.; Wang, Y.; Ofek, G.; Streaker, E.; Prabakaran, P. et al. Cross-reactive HIV-1-neutralizing human monoclonal antibodies identified from a patient with 2F5-like antibodies. J. Virol. 2011, 85, 11401-11408.
148. Matthews, T.; Salgo, M.; Greenberg, M.; Chung, J.; DeMasi, R.; Bolognesi, D. Enfuvirtide: The first therapy to inhibit the entry of HIV-1 into host CD4 lymphocytes. Nat. Rev. Drug Discov. 2004, 3, 215-225.
149. Schumacher, T.N.; Mayr, L.M.; Minor, D.L., Jr.; Milhollen, M.A.; Burgess, M.W.; Kim, P.S. Identification of D-peptide ligands through mirror-image phage display. Science 1996, 271, 1854-1857.
150. Root, M.J.; Kay, M.S.; Kim, P.S. Protein design of an HIV-1 entry inhibitor. Science 2001, 291, 884-888.
151. Fellouse, F.A.; Li, B.; Compaan, D.M.; Peden, A.A.; Hymowitz, S.G.; Sidhu, S.S. Molecular recognition by a binary code. J. Mol. Biol. 2005, 348, 1153-1162.
152. Luftig, M.A.; Mattu, M.; di Giovine, P.; Geleziunas, R.; Hrin, R.; Barbato, G.; Bianchi, E.; Miller, M.D.; Pessi, A.; Carfi, A. Structural basis for HIV-1 neutralization by a gp41 fusion intermediate-directed antibody. Nat. Struct. Mol. Biol. 2006, 13, 740-747.
153. Lu, M.; Ji, H.; Shen, S. Subdomain folding and biological activity of the core structure from human immunodeficiency virus type 1 gp41: Implications for viral membrane fusion. J. Virol. 1999, 73, 4433-4438.
154. Knappik, A.; Ge, L.; Honegger, A.; Pack, P.; Fischer, M.; Wellnhofer, G.; Hoess, A.; Wolle, J.; Pluckthun, A.; Virnekas, B. Fully synthetic human combinatorial antibody libraries (HuCAL) based on modular consensus frameworks and cdrs randomized with trinucleotides. J. Mol. Biol. 2000, 296, 57-86.
155. Louis, J.M.; Nesheiwat, I.; Chang, L.; Clore, G.M.; Bewley, C.A. Covalent trimers of the internal N-terminal trimeric coiled-coil of gp41 and antibodies directed against them are potent inhibitors of HIV envelope-mediated cell fusion. J. Biol. Chem. 2003, 278, 20278-20285.
156. Louis, J.M.; Bewley, C.A.; Clore, G.M. Design and properties of N(CCG)-gp41, a chimeric gp41 molecule with nanomolar HIV fusion inhibitory activity. J. Biol. Chem. 2001, 276, 29485-29489.
157. Bewley, C.A.; Louis, J.M.; Ghirlando, R.; Clore, G.M. Design of a novel peptide inhibitor of HIV fusion that disrupts the internal trimeric coiled-coil of gp41. J. Biol. Chem. 2002, 277, 14238-14245.
158. Montefiori, D.C.; Pantaleo, G.; Fink, L.M.; Zhou, J.T.; Zhou, J.Y.; Bilska, M.; Miralles, G.D.; Fauci, A.S. Neutralizing and infection-enhancing antibody responses to human immunodeficiency virus type 1 in long-term nonprogressors. J. Infect. Dis. 1996, 173, 60-67.
159. Agostini, I.; Navarro, J.M.; Rey, F.; Bouhamdan, M.; Spire, B.; Vigne, R.; Sire, J. The human immunodeficiency virus type 1 Vpr transactivator: Cooperation with promoter-bound activator domains and binding to TFIIB. J. Mol. Biol. 1996, 261, 599-606.
160. Stewart, S.A.; Poon, B.; Jowett, J.B.; Chen, I.S. Human immunodeficiency virus type 1 Vpr induces apoptosis following cell cycle arrest. J. Virol. 1997, 71, 5579-5592.
161. Cohen, E.A.; Dehni, G.; Sodroski, J.G.; Haseltine, W.A. Human immunodeficiency virus Vpr product is a virion-associated regulatory protein. J. Virol. 1990, 64, 3097-3099.
162. Cohen, E.A.; Terwilliger, E.F.; Jalinoos, Y.; Proulx, J.; Sodroski, J.G.; Haseltine, W.A. Identification of HIV-1 Vpr product and function. J. Acquir. Immune Defic. Syndr. 1990, 3, 11-18.
163. Bouhamdan, M.; Benichou, S.; Rey, F.; Navarro, J.M.; Agostini, I.; Spire, B.; Camonis, J.; Slupphaug, G.; Vigne, R.; Benarous, R. et al. Human immunodeficiency virus type 1 Vpr protein binds to the Uracil DNA glycosylase DNA repair enzyme. J. Virol. 1996, 70, 697-704.
164. Refaeli, Y.; Levy, D.N.; Weiner, D.B. The glucocorticoid receptor type II complex is a target of the HIV-1 Vpr gene product. Proc. Natl. Acad. Sci. USA 1995, 92, 3621-3625.
165. Wang, L.; Mukherjee, S.; Jia, F.; Narayan, O.; Zhao, L.J. Interaction of virion protein Vpr of human immunodeficiency virus type 1 with cellular transcription factor sp1 and trans-activation of viral long terminal repeat. J. Biol. Chem. 1995, 270, 25564-25569.
166. Nissim, A.; Hoogenboom, H.R.; Tomlinson, I.M.; Flynn, G.; Midgley, C.; Lane, D.; Winter, G. Antibody fragments from a "single" pot phage display library as immunochemical reagents. EMBO J. 1994, 13, 692-698.
167. Garber, M.E.; Wei, P.; Jones, K.A. HIV-1 tat interacts with cyclin t1 to direct the p-TEFb CTD kinase complex to TAR RNA. Cold Spring Harb. Symp. Quant. Biol. 1998, 63, 371-380.
168. Druillennec, S.; Dong, C.Z.; Escaich, S.; Gresh, N.; Bousseau, A.; Roques, B.P.; Fournie-Zaluski, M.C. A mimic of HIV-1 nucleocapsid protein impairs reverse transcription and displays antiviral activity. Proc. Natl. Acad. Sci. USA 1999, 96, 4886-4891.
169. Druillennec, S.; Caneparo, A.; de Rocquigny, H.; Roques, B.P. Evidence of interactions between the nucleocapsid protein ncp7 and the reverse transcriptase of HIV-1. J. Biol. Chem. 1999, 274, 11283-11288.
170. Frankel, A.D.; Young, J.A. HIV-1: Fifteen proteins and an RNA. Annu. Rev. Biochem. 1998, 67, 1-25.
171. Cimarelli, A.; Sandin, S.; Hoglund, S.; Luban, J. Basic residues in human immunodeficiency virus type 1 nucleocapsid promote virion assembly via interaction with RNA. J. Virol. 2000, 74, 3046-3057.
172. Hashiguchi, S.; Nakashima, T.; Nitani, A.; Yoshihara, T.; Yoshinaga, K.; Ito, Y.; Maeda, Y.; Sugimura, K. Human Fc epsilon rialpha-specific human single-chain Fv (ScFv) antibody with antagonistic activity toward igE/Fc epsilon Rialpha-binding. J. Biochem. 2003, 133, 43-49.
173. Gargano, N.; Biocca, S.; Bradbury, A.; Cattaneo, A. Human recombinant antibody fragments neutralizing human immunodeficiency virus type 1 reverse transcriptase provide an experimental basis for the structural classification of the DNA polymerase family. J. Virol. 1996, 70, 7706-7712.
174. Heaphy, S.; Finch, J.T.; Gait, M.J.; Karn, J.; Singh, M. Human immunodeficiency virus type 1 regulator of virion expression, Rev, forms nucleoprotein filaments after binding to a purine-rich "Bubble" Located within the Rev-responsive region of viral mRNAs. Proc. Natl. Acad. Sci. USA 1991, 88, 7366-7370.
175. De Haard, J.J.; Kazemier, B.; Oudshoorn, P.; Boender, P.; van Gemen, B.; Koolen, M.J.; van der Groen, G.; Hoogenboom, H.R.; Arends, J.W. Selection of human anti-human immunodeficiency virus type 1 envelope single-chain antibodies from a peripheral blood cell-based phage repertoire. J. Gen. Virol. 1998, 79 (Pt 12), 2883-2894.
176. Khurana, S.; Needham, J.; Mathieson, B.; Rodriguez-Chavez, I.R.; Catanzaro, A.T.; Bailer, R.T.; Kim, J.; Polonis, V.; Cooper, D.A.; Guerin, J. et al. Human immunodeficiency virus (HIV) vaccine trials: A novel assay for differential diagnosis of HIV infections in the face of vaccine-generated antibodies. J. Virol. 2006, 80, 2092-2099.
177. Vyroubalova, E.C.; Hartley, O.; Mermod, N.; Fisch, I. Identification of peptide ligands to the chemokine receptor CCR5 and their maturation by gene shuffling. Mol. Immunol. 2006, 43, 1573-1578.
178. Wang, F.Y.; Zhang, T.Y.; Luo, J.X.; He, G.A.; Gu, Q.L.; Xiao, F. Selection of CC chemokine receptor 5-binding peptide from a phage display peptide library. Biosci. Biotechnol. Biochem. 2006, 70, 2035-2041.
179. Mirzabekov, T.; Kontos, H.; Farzan, M.; Marasco, W.; Sodroski, J. Paramagnetic proteoliposomes containing a pure, native, and oriented seven-transmembrane segment protein, CCR5. Nat. Biotechnol. 2000, 18, 649-654.
180. Zhang, Y.; Pool, C.; Sadler, K.; Yan, H.P.; Edl, J.; Wang, X.; Boyd, J.G.; Tam, J.P. Selection of active ScFv to g-protein-coupled receptor CCR5 using surface antigen-mimicking peptides. Biochemistry 2004, 43, 12575-12584.
181. Chevigne, A.; Fischer, A.; Mathu, J.; Counson, M.; Beaupain, N.; Plesseria, J.M.; Schmit, J.C.; Deroo, S. Selection of a CXCR4 antagonist from a human heavy chain CDR3-derived phage library. FEBS J. 2011, 278, 2867-2878.
182. Huang, Y.; Paxton, W.A.; Wolinsky, S.M.; Neumann, A.U.; Zhang, L.; He, T.; Kang, S.; Ceradini, D.; Jin, Z.; Yazdanbakhsh, K. et al. The role of a mutant CCR5 allele in HIV-1 transmission and disease progression. Nat. Med. 1996, 2, 1240-1243.
183. Steinberger, P.; Sutton, J.K.; Rader, C.; Elia, M.; Barbas, C.F. 3rd. Generation and characterization of a recombinant human CCR5-specific antibody. A phage display approach for rabbit antibody humanization. J. Biol. Chem. 2000, 275, 36073-36078.
184. Hartley, O.; Dorgham, K.; Perez-Bercoff, D.; Cerini, F.; Heimann, A.; Gaertner, H.; Offord, R.E.; Pancino, G.; Debre, P.; Gorochov, G. Human immunodeficiency virus type 1 entry inhibitors selected on living cells from a library of phage chemokines. J. Virol. 2003, 77, 6637-6644.
185. Gaertner, H.; Cerini, F.; Escola, J.M.; Kuenzi, G.; Melotti, A.; Offord, R.; Rossitto-Borlat, I.; Nedellec, R.; Salkowitz, J.; Gorochov, G. et al. Highly potent, fully recombinant anti-HIV chemokines: Reengineering a low-cost microbicide. Proc. Natl. Acad. Sci. USA 2008, 105, 17706-17711.
186. Jahnichen, S.; Blanchetot, C.; Maussang, D.; Gonzalez-Pajuelo, M.; Chow, K.Y.; Bosch, L.; de Vrieze, S.; Serruys, B.; Ulrichts, H.; Vandevelde, W. et al. CXCR4 nanobodies (VHH-based single variable domains) potently inhibit chemotaxis and HIV-1 replication and mobilize stem cells. Proc. Natl. Acad. Sci. USA 2010, 107, 20565-20570.
187. Ellmark, P.; Andersson, H.; Abayneh, S.; Fenyo, E.M.; Borrebaeck, C.A. Identification of a strongly activating human anti-CD40 antibody that suppresses HIV type 1 infection. AIDS Res. Hum. Retrovir. 2008, 24, 367-373.
188. Ellmark, P.; Ottosson, C.; Borrebaeck, C.A.; Malmborg Hager, A.C.; Furebring, C. Modulation of the CD40-CD40 ligand interaction using human anti-CD40 single-chain antibody fragments obtained from the n-coder phage display library. Immunology 2002, 106, 456-463.
189. Garbelli, A.; Beermann, S.; di Cicco, G.; Dietrich, U.; Maga, G. A motif unique to the human dead-box protein DDX3 is important for nucleic acid binding, ATP hydrolysis, RNA/DNA unwinding and HIV-1 replication. PLoS One 2011, 6, doi:10.1371/journal.pone.0019810.
190. Chevigne, A.; Fievez, V.; Schmit, J.C.; Deroo, S. Engineering and screening the N-terminus of chemokines for drug discovery. Biochem. Pharmacol. 2011, 82, 1438-1456.
191. Tamamura, H.; Fujii, N. The therapeutic potential of CXCR4 antagonists in the treatment of HIV infection, cancer metastasis and rheumatoid arthritis. Expert Opin. Ther. Targets 2005, 9, 1267-1282.
192. Steen, A.; Schwartz, T.W.; Rosenkilde, M.M. Targeting CXCR4 in HIV cell-entry inhibition. Mini Rev. Med. Chem. 2009, 9, 1605-1621.
193. Deroo, S.; Fischer, A.; Beaupain, N.; Counson, M.; Boutonnet, N.; Pletinckx, J.; Loverix, S.; Beirnaert, E.; de Haard, H.; Schmit, J.C. et al. Non-immunized natural human heavy chain CDR3 repertoires allow the isolation of high affinity peptides mimicking a human influenza hemagglutinin epitope. Mol. Immunol. 2008, 45, 1366-1373.
194. Rubinstein, D.B.; Leblanc, P.; Wright, D.G.; Guillaume, T.; Strotchevoi, A.; Boosalis, M. Anti-CD34+ fabs generated against hematopoietic stem cells in HIV-derived combinatorial immunoglobulin library suggest antigen-selected autoantibodies. Mol. Immunol. 1998, 35, 955-964.
195. Abayneh, S.A.; Ellmark, P.; Karlsson, U.; Andersson, H.; Borrebaeck, C.A.; Karlsson, I.; Fenyo, E.M. Sensitivity of HIV type 1 primary isolates to human anti-CD40 antibody-mediated suppression is related to coreceptor use. AIDS Res. Hum. Retrovir. 2008, 24, 447-452.
196. Matthews, D.J.; Wells, J.A. Substrate phage: Selection of protease substrates by monovalent phage display. Science 1993, 260, 1113-1117.
197. Beck, Z.Q.; Lin, Y.C.; Elder, J.H. Molecular basis for the relative substrate specificity of human immunodeficiency virus type 1 and feline immunodeficiency virus proteases. J. Virol. 2001, 75, 9458-9469.
198. Beck, Z.Q.; Hervio, L.; Dawson, P.E.; Elder, J.H.; Madison, E.L. Identification of efficiently cleaved substrates for HIV-1 protease using a phage display library and use in inhibitor development. Virology 2000, 274, 391-401.
199. Schechter, I.; Berger, A. On the size of the active site in proteases. I. Papain. Biochem. Biophys. Res. Commun. 1967, 27, 157-162
200. Tozser, J.; Weber, I.T.; Gustchina, A.; Blaha, I.; Copeland, T.D.; Louis, J.M.; Oroszlan, S. Kinetic and modeling studies of s3-s3' subsites of HIV proteinases. Biochemistry 1992, 31, 4793-4800.
201. Kleinschmidt, W.J.; Douthart, R.J.; Murphy, E.B. Interferon production by t4 coliphage. Nature 1970, 228, 27-30.
202. Clark, J.R.; March, J.B. Bacterial viruses as human vaccines? Expert Rev. Vaccines 2004, 3, 463-476.
203. Jepson, C.D.; March, J.B. Bacteriophage lambda is a highly stable DNA vaccine delivery vehicle. Vaccine 2004, 22, 2413-2419.
204. Minenkova, O.O.; Ilyichev, A.A.; Kishchenko, G.P.; Petrenko, V.A. Design of specific immunogens using filamentous phage as the carrier. Gene 1993, 128, 85-88.
205. De Berardinis, P.; Sartorius, R.; Fanutti, C.; Perham, R.N.; Del Pozzo, G.; Guardiola, J. Phage display of peptide epitopes from HIV-1 elicits strong cytolytic responses. Nat. Biotechnol. 2000, 18, 873-876.
206. Di Marzo Veronese, F.; Willis, A.E.; Boyer-Thompson, C.; Appella, E.; Perham, R.N. Structural mimicry and enhanced immunogenicity of peptide epitopes displayed on filamentous bacteriophage. The V3 loop of HIV-1 gp120. J. Mol. Biol. 1994, 243, 167-172.
207. Cano, A.; Viveros, M.; Acero, G.; Govezensky, T.; Munguia, M.E.; Gonzalez, E.; Soto, L.; Gevorkian, G.; Manoutcharian, K. Antigenic properties of phage displayed peptides comprising disulfide-bonded loop of the immunodominant region of HIV-1 gp41. Immunol. Lett. 2004, 95, 207-212.
208. Majumdar, S.; Hajduczki, A.; Mendez, A.S.; Weiss, G.A. Phage display of functional, full-length human and viral membrane proteins. Bioorg. Med. Chem. Lett. 2008, 18, 5937-5940.
209. Perham, R.N.; Terry, T.D.; Willis, A.E.; Greenwood, J.; di Marzo Veronese, F.; Appella, E. Engineering a peptide epitope display system on filamentous bacteriophage. FEMS Microbiol. Rev. 1995, 17, 25-31.
210. Ren, Z.; Black, L.W. Phage T4 SOC and HOC display of biologically active, full-length proteins on the viral capsid. Gene 1998, 215, 439-444.
211. Peabody, D.S.; Manifold-Wheeler, B.; Medford, A.; Jordan, S.K.; do Carmo Caldeira, J.; Chackerian, B. Immunogenic display of diverse peptides on virus-like particles of RNA phage MS2. J. Mol. Biol. 2008, 380, 252-263.
212. Mattiacio, J.; Walter, S.; Brewer, M.; Domm, W.; Friedman, A.E.; Dewhurst, S. Dense display of HIV-1 envelope spikes on the lambda phage scaffold does not result in the generation of improved antibody responses to HIV-1 Env. Vaccine 2011, 29, 2637-2647.
213. Ren, Z.J.; Lewis, G.K.; Wingfield, P.T.; Locke, E.G.; Steven, A.C.; Black, L.W. Phage display of intact domains at high copy number: A system based on soc, the small outer capsid protein of bacteriophage T4. Protein Sci. 1996, 5, 1833-1843.
214. Pedroza-Roldan, C.; Charles-Nino, C.; Saavedra, R.; Govezensky, T.; Vaca, L.; Avaniss-Aghajani, E.; Gevorkian, G.; Manoutcharian, K. Variable epitope library-based vaccines: Shooting moving targets. Mol. Immunol. 2009, 47, 270-282.
215. Sathaliyawala, T.; Rao, M.; Maclean, D.M.; Birx, D.L.; Alving, C.R.; Rao, V.B. Assembly of human immunodeficiency virus (HIV) antigens on bacteriophage T4: A novel in vitro approach to construct multicomponent HIV vaccines. J. Virol. 2006, 80, 7688-7698.
216. Caldeira Jdo, C.; Medford, A.; Kines, R.C.; Lino, C.A.; Schiller, J.T.; Chackerian, B.; Peabody, D.S. Immunogenic display of diverse peptides, including a broadly cross-type neutralizing human papillomavirus l2 epitope, on virus-like particles of the RNA bacteriophage PP7. Vaccine 2010, 28, 4384-4393.
217. Charles-Nino, C.; Pedroza-Roldan, C.; Viveros, M.; Gevorkian, G.; Manoutcharian, K. Variable epitope libraries: New vaccine immunogens capable of inducing broad human immunodeficiency virus type 1-neutralizing antibody response. Vaccine 2011, 29, 5313-5321.
218. Ishii, T.; Yanagida, M. The two dispensable structural proteins (soc and hoc) of the T4 phage capsid; their purification and properties, isolation and characterization of the defective mutants, and their binding with the defective heads in vitro. J. Mol. Biol. 1977, 109, 487-514.
219. Zhu, P.; Liu, J.; Bess, J., Jr.; Chertova, E.; Lifson, J.D.; Grise, H.; Ofek, G.A.; Taylor, K.A.; Roux, K.H. Distribution and three-dimensional structure of AIDS virus envelope spikes. Nature 2006, 441, 847-852.
220. Deroo, S.; Muller, C.P. Antigenic and immunogenic phage displayed mimotopes as substitute antigens: Applications and limitations. Comb. Chem. High Throughput Screen. 2001, 4, 75-110