Functional conservation of HIV-1 Gag: implications for rational drug design

Retrovirology

Kristof Theys³  Anne-Mieke Vandamme⁵  Arnout Voet²  Soo-Yon Rhee⁴  Jens Verheyen¹  Guangdi Li³ 

[1] Institute of Virology, University hospital, University Duisburg-Essen, Essen, Germany;Zhang IRU, RIKEN Institute Laboratories, Hirosawa 2-1, Wako-shi, Saitama, Japan;Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium;Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA;Centro de Malária e Outras Doenças Tropicais and Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal

关键词: Amino acid conservation;    Natural polymorphism;    Drug binding site;    Nucleocapsid;    Capsid;    Matrix;    Gag inhibitor;    HIV subtype;   

Others  :  806644
DOI  :  10.1186/1742-4690-10-126

 received in 2013-07-14, accepted in 2013-10-21,  发布年份 2013

【 摘 要 】

Background

HIV-1 replication can be successfully blocked by targeting gag gene products, offering a promising strategy for new drug classes that complement current HIV-1 treatment options. However, naturally occurring polymorphisms at drug binding sites can severely compromise HIV-1 susceptibility to gag inhibitors in clinical and experimental studies. Therefore, a comprehensive understanding of gag natural diversity is needed.

Findings

We analyzed the degree of functional conservation in 10862 full-length gag sequences across 8 major HIV-1 subtypes and identified the impact of natural variation on known drug binding positions targeted by more than 20 gag inhibitors published to date. Complete conservation across all subtypes was detected in 147 (29%) out of 500 gag positions, with the highest level of conservation observed in capsid protein. Almost half (41%) of the 136 known drug binding positions were completely conserved, but all inhibitors were confronted with naturally occurring polymorphisms in their binding sites, some of which correlated with HIV-1 subtype. Integration of sequence and structural information revealed one drug binding pocket with minimal genetic variability, which is situated at the N-terminal domain of the capsid protein.

Conclusions

This first large-scale analysis of full-length HIV-1 gag provided a detailed mapping of natural diversity across major subtypes and highlighted the considerable variation in current drug binding sites. Our results contribute to the optimization of gag inhibitors in rational drug design, given that drug binding sites should ideally be conserved across all HIV-1 subtypes.

【 授权许可】

   
2013 Li et al.; licensee BioMed Central Ltd.

【 图 表 】

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【 参考文献 】

• [1]Engelman A, Cherepanov P: The structural biology of HIV-1: mechanistic and therapeutic insights. Nat Rev Microbiol 2012, 10:279-290.
• [2]Waheed AA, Freed EO: HIV type 1 Gag as a target for antiviral therapy. AIDS Res Hum Retroviruses 2012, 28:54-75.
• [3]Bocanegra R, Rodriguez-Huete A, Fuertes MA, Del Alamo M, Mateu MG: Molecular recognition in the human immunodeficiency virus capsid and antiviral design. Virus Res 2012, 169:388-410.
• [4]Dau B, Holodniy M: Novel targets for antiretroviral therapy: clinical progress to date. Drugs 2009, 69:31-50.
• [5]Salzwedel K, Martin DE, Sakalian M: Maturation inhibitors: a new therapeutic class targets the virus structure. AIDS Rev 2007, 9:162-172.
• [6]Hemelaar J, Gouws E, Ghys PD, Osmanov S: Isolation W-UNfH, Characterisation: Global trends in molecular epidemiology of HIV-1 during 2000–2007. AIDS 2011, 25:679-689.
• [7]Gaschen B, Taylor J, Yusim K, Foley B, Gao F, Lang D, Novitsky V, Haynes B, Hahn BH, Bhattacharya T, Korber B: Diversity considerations in HIV-1 vaccine selection. Science 2002, 296:2354-2360.
• [8]Adamson CS, Sakalian M, Salzwedel K, Freed EO: Polymorphisms in Gag spacer peptide 1 confer varying levels of resistance to the HIV- 1 maturation inhibitor bevirimat. Retrovirology 2010, 7:36. BioMed Central Full Text
• [9]Blair WS, Pickford C, Irving SL, Brown DG, Anderson M, Bazin R, Cao J, Ciaramella G, Isaacson J, Jackson L, et al.: HIV capsid is a tractable target for small molecule therapeutic intervention. PLoS Pathog 2010, 6:e1001220.
• [10]Smith PF, Ogundele A, Forrest A, Wilton J, Salzwedel K, Doto J, Allaway GP, Martin DE: Phase I and II study of the safety, virologic effect, and pharmacokinetics/pharmacodynamics of single-dose 3-o-(3',3'-dimethylsuccinyl)betulinic acid (bevirimat) against human immunodeficiency virus infection. Antimicrob Agents Chemother 2007, 51:3574-3581.
• [11]Nguyen AT, Feasley CL, Jackson KW, Nitz TJ, Salzwedel K, Air GM, Sakalian M: The prototype HIV-1 maturation inhibitor, bevirimat, binds to the CA-SP1 cleavage site in immature Gag particles. Retrovirology 2011, 8:101. BioMed Central Full Text
• [12]Lu W, Salzwedel K, Wang D, Chakravarty S, Freed EO, Wild CT, Li F: A single polymorphism in HIV-1 subtype C SP1 is sufficient to confer natural resistance to the maturation inhibitor bevirimat. Antimicrob Agents Chemother 2011, 55:3324-3329.
• [13]Goudreau N, Lemke CT, Faucher AM, Grand-Maitre C, Goulet S, Lacoste JE, Rancourt J, Malenfant E, Mercier JF, Titolo S, Mason SW: Novel inhibitor binding site discovery on HIV-1 capsid N-terminal domain by NMR and X-ray crystallography. ACS Chem Biol 2013.
• [14]Bartonova V, Igonet S, Sticht J, Glass B, Habermann A, Vaney MC, Sehr P, Lewis J, Rey FA, Krausslich HG: Residues in the HIV-1 capsid assembly inhibitor binding site are essential for maintaining the assembly-competent quaternary structure of the capsid protein. J Biol Chem 2008, 283:32024-32033.
• [15]Lemke CT, Titolo S, von Schwedler U, Goudreau N, Mercier JF, Wardrop E, Faucher AM, Coulombe R, Banik SS, Fader L, et al.: Distinct effects of two HIV-1 capsid assembly inhibitor families that bind the same site within the N-terminal domain of the viral CA protein. J Virol 2012, 86:6643-6655.
• [16]Schiffner T, Sattentau QJ, Dorrell L: Development of prophylactic vaccines against HIV-1. Retrovirology 2013, 10:72. BioMed Central Full Text
• [17]Stephenson KE, Barouch DH: A global approach to HIV-1 vaccine development. Immunol Rev 2013, 254:295-304.
• [18]Rhee SY, Liu TF, Kiuchi M, Zioni R, Gifford RJ, Holmes SP, Shafer RW: Natural variation of HIV-1 group M integrase: implications for a new class of antiretroviral inhibitors. Retrovirology 2008, 5:74. BioMed Central Full Text
• [19]Yufenyuy EL, Aiken C: The NTD-CTD intersubunit interface plays a critical role in assembly and stabilization of the HIV-1 capsid. Retrovirology 2013, 10:29. BioMed Central Full Text
• [20]Zhang H, Curreli F, Zhang X, Bhattacharya S, Waheed AA, Cooper A, Cowburn D, Freed EO, Debnath AK: Antiviral activity of alpha-helical stapled peptides designed from the HIV-1 capsid dimerization domain. Retrovirology 2011, 8:28. BioMed Central Full Text
• [21]Goudreau N, Coulombe R, Faucher AM, Grand-Maitre C, Lacoste JE, Lemke CT, Malenfant E, Bousquet Y, Fader L, Simoneau B, et al.: Monitoring binding of HIV-1 capsid assembly inhibitors using (19)F ligand-and (15)N protein-based NMR and X-ray crystallography: early hit validation of a benzodiazepine series. ChemMedChem 2013, 8:405-414.
• [22]Thomas JA, Gorelick RJ: Nucleocapsid protein function in early infection processes. Virus Res 2008, 134:39-63.
• [23]Zentner I, Sierra LJ, Fraser AK, Maciunas L, Mankowski MK, Vinnik A, Fedichev P, Ptak RG, Martin-Garcia J, Cocklin S: Identification of a small-molecule inhibitor of HIV-1 assembly that targets the phosphatidylinositol (4,5)-bisphosphate binding site of the HIV-1 matrix protein. ChemMedChem 2013, 8:426-432.
• [24]Alfadhli A, McNett H, Eccles J, Tsagli S, Noviello C, Sloan R, Lopez CS, Peyton DH, Barklis E: Analysis of small molecule ligands targeting the HIV-1 matrix protein-RNA binding site. J Biol Chem 2013, 288:666-676.
• [25]Frahm N, Kaufmann DE, Yusim K, Muldoon M, Kesmir C, Linde CH, Fischer W, Allen TM, Li B, McMahon BH, et al.: Increased sequence diversity coverage improves detection of HIV-specific T cell responses. J Immunol 2007, 179:6638-6650.
• [26]Snoeck J, Fellay J, Bartha I, Douek DC, Telenti A: Mapping of positive selection sites in the HIV-1 genome in the context of RNA and protein structural constraints. Retrovirology 2011, 8:87. BioMed Central Full Text
• [27]Zentner I, Sierra LJ, Maciunas L, Vinnik A, Fedichev P, Mankowski MK, Ptak RG, Martin-Garcia J, Cocklin S: Discovery of a small-molecule antiviral targeting the HIV-1 matrix protein. Bioorg Med Chem Lett 2013, 23:1132-1135.
• [28]Fun A, Wensing AM, Verheyen J, Nijhuis M: Human immunodeficiency virus Gag and protease: partners in resistance. Retrovirology 2012, 9:63. BioMed Central Full Text
• [29]Gouy M, Guindon S, Gascuel O: SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol 2010, 27:221-224.
• [30]Rose PP, Korber BT: Detecting hypermutations in viral sequences with an emphasis on G –> A hypermutation. Bioinformatics 2000, 16:400-401.
• [31]Pineda-Pena AC, Faria NR, Imbrechts S, Libin P, Abecasis AB, Deforche K, Gomez-Lopez A, Camacho RJ, de Oliveira T, Vandamme AM: Automated subtyping of HIV-1 genetic sequences for clinical and surveillance purposes: Performance evaluation of the new REGA version 3 and seven other tools. Infect Genet Evol 2013.
• [32]Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The protein data bank. Nucleic Acids Res 2000, 28:235-242.
• [33]Zhang Z, Li Y, Lin B, Schroeder M, Huang B: Identification of cavities on protein surface using multiple computational approaches for drug binding site prediction. Bioinformatics 2011, 27:2083-2088.
• [34]Brocchieri L, Karlin S: Conservation among HSP60 sequences in relation to structure, function, and evolution. Protein Sci 2000, 9:476-486.