Effects of HIV-1 protease on cellular functions and their potential applications in antiretroviral therapy

Cell & Bioscience

Richard Y Zhao¹  Joseph Nkeze³  Hailiu Yang² 

[1] Institute of Human Virology, University of Maryland School of Medicine, 10 South Pine Street, MSTF 700, Baltimore, MD, 21201-1192, USA;University of Maryland School of Medicine, Baltimore, MD, USA;Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, USA

关键词: Cell-based high-throughput screening;    Fission yeast;    Antiretroviral therapy;    Allosteric inhibitor;    Structure-based design;    HIV-1 protease;   

Others  :  793205
DOI  :  10.1186/2045-3701-2-32

 received in 2012-08-10, accepted in 2012-08-31,  发布年份 2012

【 摘 要 】

Human Immunodeficiency Virus Type 1 (HIV-1) protease inhibitors (PIs) are the most potent class of drugs in antiretroviral therapies. However, viral drug resistance to PIs could emerge rapidly thus reducing the effectiveness of those drugs. Of note, all current FDA-approved PIs are competitive inhibitors, i.e., inhibitors that compete with substrates for the active enzymatic site. This common inhibitory approach increases the likelihood of developing drug resistant HIV-1 strains that are resistant to many or all current PIs. Hence, new PIs that move away from the current target of the active enzymatic site are needed. Specifically, allosteric inhibitors, inhibitors that prohibit PR enzymatic activities through non-competitive binding to PR, should be sought. Another common feature of current PIs is they were all developed based on the structure-based design. Drugs derived from a structure-based strategy may generate target specific and potent inhibitors. However, this type of drug design can only target one site at a time and drugs discovered by this method are often associated with strong side effects such as cellular toxicity, limiting its number of target choices, efficacy, and applicability. In contrast, a cell-based system may provide a useful alternative strategy that can overcome many of the inherited shortcomings associated with structure-based drug designs. For example, allosteric PIs can be sought using a cell-based system without considering the site or mechanism of inhibition. In addition, a cell-based system can eliminate those PIs that have strong cytotoxic effect. Most importantly, a simple, economical, and easy-to-maintained eukaryotic cellular system such as yeast will allow us to search for potential PIs in a large-scaled high throughput screening (HTS) system, thus increasing the chances of success. Based on our many years of experience in using fission yeast as a model system to study HIV-1 Vpr, we propose the use of fission yeast as a possible surrogate system to study the effects of HIV-1 protease on cellular functions and to explore its utility as a HTS system to search for new PIs to battle HIV-1 resistant strains.

【 授权许可】

   
2012 Yang et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

【 参考文献 】

• [1]WHO: Global HIV/AIDS Response: Epidemic update and health sector progress towards Universal Access. In Progress Report 2011. World Health Organization (WHO), Geneva, Switzerland; 2011:1-224.
• [2]Logsdon BC, Vickrey JF, Martin P, Proteasa G, Koepke JI, Terlecky SR, Wawrzak Z, Winters MA, Merigan TC, Kovari LC: Crystal structures of a multidrug-resistant human immunodeficiency virus type 1 protease reveal an expanded active-site cavity. J Virol 2004, 78:3123-3132.
• [3]Palmer S, Shafer RW, Merigan TC: Highly drug-resistant HIV-1 clinical isolates are cross-resistant to many antiretroviral compounds in current clinical development. Aids 1999, 13:661-667.
• [4]Rhee SY, Taylor J, Fessel WJ, Kaufman D, Towner W, Troia P, Ruane P, Hellinger J, Shirvani V, Zolopa A, Shafer RW: HIV-1 protease mutations and protease inhibitor cross-resistance. Antimicrob Agents Chemother 2010, 54:4253-4261.
• [5]Imamichi T: Action of anti-HIV drugs and resistance: reverse transcriptase inhibitors and protease inhibitors. Curr Pharm Des 2004, 10:4039-4053.
• [6]Dayam R, Neamati N: Small-molecule HIV-1 integrase inhibitors: the 2001–2002 update. Curr Pharm Des 2003, 9:1789-1802.
• [7]Neamati N, Marchand C, Pommier Y: HIV-1 integrase inhibitors: past, present, and future. Adv Pharmacol 2000, 49:147-165.
• [8]Pommier Y, Marchand C, Neamati N: Retroviral integrase inhibitors year 2000: update and perspectives. Antiviral Res 2000, 47:139-148.
• [9]Brik A, Wong CH: HIV-1 protease: mechanism and drug discovery. Org Biomol Chem 2003, 1:5-14.
• [10]Hoggard PG, Owen A: The mechanisms that control intracellular penetration of the HIV protease inhibitors. J Antimicrob Chemother 2003, 51:493-496.
• [11]Perez MA, Fernandes PA, Ramos MJ: Substrate recognition in HIV-1 protease: a computational study. J Phys Chem B 2010, 114:2525-2532.
• [12]Pettit SC, Clemente JC, Jeung JA, Dunn BM, Kaplan AH: Ordered processing of the human immunodeficiency virus type 1 GagPol precursor is influenced by the context of the embedded viral protease. J Virol 2005, 79:10601-10607.
• [13]Krausslich HG, Ingraham RH, Skoog MT, Wimmer E, Pallai PV, Carter CA: Activity of purified biosynthetic proteinase of human immunodeficiency virus on natural substrates and synthetic peptides. Proc Natl Acad Sci U S A 1989, 86:807-811.
• [14]De Oliveira T, Engelbrecht S, Janse van Rensburg E, Gordon M, Bishop K, Zur Megede J, Barnett SW, Cassol S: Variability at human immunodeficiency virus type 1 subtype C protease cleavage sites: an indication of viral fitness? J Virol 2003, 77:9422-9430.
• [15]Barrie KA, Perez EE, Lamers SL, Farmerie WG, Dunn BM, Sleasman JW, Goodenow MM: Natural variation in HIV-1 protease, Gag p7 and p6, and protease cleavage sites within gag/pol polyproteins: amino acid substitutions in the absence of protease inhibitors in mothers and children infected by human immunodeficiency virus type 1. Virology 1996, 219:407-416.
• [16]Ridky TW, Cameron CE, Cameron J, Leis J, Copeland T, Wlodawer A, Weber IT, Harrison RW: Human immunodeficiency virus, type 1 protease substrate specificity is limited by interactions between substrate amino acids bound in adjacent enzyme subsites. J Biol Chem 1996, 271:4709-4717.
• [17]Pearl LH, Taylor WR: A structural model for the retroviral proteases. Nature 1987, 329:351-354.
• [18]Piana S, Carloni P, Rothlisberger U: Drug resistance in HIV-1 protease: Flexibility-assisted mechanism of compensatory mutations. Protein Sci 2002, 11:2393-2402.
• [19]Todd MJ, Freire E: The effect of inhibitor binding on the structural stability and cooperativity of the HIV-1 protease. Proteins 1999, 36:147-156.
• [20]Todd MJ, Semo N, Freire E: The structural stability of the HIV-1 protease. J Mol Biol 1998, 283:475-488.
• [21]Toth G, Borics A: Flap opening mechanism of HIV-1 protease. J Mol Graph Model 2006, 24:465-474.
• [22]Velazquez-Campoy A, Muzammil S, Ohtaka H, Schon A, Vega S, Freire E: Structural and thermodynamic basis of resistance to HIV-1 protease inhibition: implications for inhibitor design. Curr Drug Targets Infect Disord 2003, 3:311-328.
• [23]Luque I, Freire E: Structural stability of binding sites: consequences for binding affinity and allosteric effects. Proteins 2000, Suppl 4:63-71.
• [24]Lapatto R, Blundell T, Hemmings A, Overington J, Wilderspin A, Wood S, Merson JR, Whittle PJ, Danley DE, Geoghegan KF, et al.: X-ray analysis of HIV-1 proteinase at 2.7 A resolution confirms structural homology among retroviral enzymes. Nature 1989, 342:299-302.
• [25]Spinelli S, Liu QZ, Alzari PM, Hirel PH, Poljak RJ: The three-dimensional structure of the aspartyl protease from the HIV-1 isolate BRU. Biochimie 1991, 73:1391-1396.
• [26]Wlodawer A, Miller M, Jaskolski M, Sathyanarayana BK, Baldwin E, Weber IT, Selk LM, Clawson L, Schneider J, Kent SB: Conserved folding in retroviral proteases: crystal structure of a synthetic HIV-1 protease. Science 1989, 245:616-621.
• [27]Louis JM, Dyda F, Nashed NT, Kimmel AR, Davies DR: Hydrophilic peptides derived from the transframe region of Gag-Pol inhibit the HIV-1 protease. Biochemistry 1998, 37:2105-2110.
• [28]Prabu-Jeyabalan M, Nalivaika E, Schiffer CA: How does a symmetric dimer recognize an asymmetric substrate? A substrate complex of HIV-1 protease. J Mol Biol 2000, 301:1207-1220.
• [29]Coffin JM: HIV population dynamics in vivo: implications for genetic variation, pathogenesis, and therapy. Science 1995, 267:483-489.
• [30]Miller M, Schneider J, Sathyanarayana BK, Toth MV, Marshall GR, Clawson L, Selk L, Kent SB, Wlodawer A: Structure of complex of synthetic HIV-1 protease with a substrate-based inhibitor at 2.3 A resolution. Science 1989, 246:1149-1152.
• [31]Rick SW, Erickson JW, Burt SK: Reaction path and free energy calculations of the transition between alternate conformations of HIV-1 protease. Proteins 1998, 32:7-16.
• [32]Scott WR, Schiffer CA: Curling of flap tips in HIV-1 protease as a mechanism for substrate entry and tolerance of drug resistance. Structure 2000, 8:1259-1265.
• [33]Collins JR, Burt SK, Erickson JW: Flap opening in HIV-1 protease simulated by 'activated' molecular dynamics. Nat Struct Biol 1995, 2:334-338.
• [34]Levy JA: Pathogenesis of human immunodeficiency virus infection. Microbiol Rev 1993, 57:183-289.
• [35]Voss TG, Fermin CD, Levy JA, Vigh S, Choi B, Garry RF: Alteration of intracellular potassium and sodium concentrations correlates with induction of cytopathic effects by human immunodeficiency virus. J Virol 1996, 70:5447-5454.
• [36]Blanco R, Carrasco L, Ventoso I: Cell killing by HIV-1 protease. J Biol Chem 2003, 278:1086-1093.
• [37]Ventoso I, Navarro J, Munoz MA, Carrasco L: Involvement of HIV-1 protease in virus-induced cell killing. Antiviral Res 2005, 66:47-55.
• [38]Shoeman RL, Honer B, Stoller TJ, Kesselmeier C, Miedel MC, Traub P, Graves MC: Human immunodeficiency virus type 1 protease cleaves the intermediate filament proteins vimentin, desmin, and glial fibrillary acidic protein. Proc Natl Acad Sci U S A 1990, 87:6336-6340.
• [39]Shoeman RL, Huttermann C, Hartig R, Traub P: Amino-terminal polypeptides of vimentin are responsible for the changes in nuclear architecture associated with human immunodeficiency virus type 1 protease activity in tissue culture cells. Mol Biol Cell 2001, 12:143-154.
• [40]Konvalinka J, Litterst MA, Welker R, Kottler H, Rippmann F, Heuser AM, Krausslich HG: An active-site mutation in the human immunodeficiency virus type 1 proteinase (PR) causes reduced PR activity and loss of PR-mediated cytotoxicity without apparent effect on virus maturation and infectivity. J Virol 1995, 69:7180-7186.
• [41]Tomasselli AG, Hui JO, Adams L, Chosay J, Lowery D, Greenberg B, Yem A, Deibel MR, Zurcher-Neely H, Heinrikson RL: Actin, troponin C, Alzheimer amyloid precursor protein and pro-interleukin 1 beta as substrates of the protease from human immunodeficiency virus. J Biol Chem 1991, 266:14548-14553.
• [42]Shoeman RL, Sachse C, Honer B, Mothes E, Kaufmann M, Traub P: Cleavage of human and mouse cytoskeletal and sarcomeric proteins by human immunodeficiency virus type 1 protease. Actin, desmin, myosin, and tropomyosin. Am J Pathol 1993, 142:221-230.
• [43]Honer B, Shoeman RL, Traub P: Human immunodeficiency virus type 1 protease microinjected into cultured human skin fibroblasts cleaves vimentin and affects cytoskeletal and nuclear architecture. J Cell Sci 1991, 100(Pt 4):799-807.
• [44]Strack PR, Frey MW, Rizzo CJ, Cordova B, George HJ, Meade R, Ho SP, Corman J, Tritch R, Korant BD: Apoptosis mediated by HIV protease is preceded by cleavage of Bcl-2. Proc Natl Acad Sci U S A 1996, 93:9571-9576.
• [45]Korant BD, Strack P, Frey MW, Rizzo CJ: A cellular anti-apoptosis protein is cleaved by the HIV-1 protease. Adv Exp Med Biol 1998, 436:27-29.
• [46]Elmore S: Apoptosis: a review of programmed cell death. Toxicol Pathol 2007, 35:495-516.
• [47]Vlahakis SR: Cell Death In HIV Infection: gp120. In Cell Death During HIV Infection. Edited by Badley AD. CRC Press, Taylor and Francis Group, Florida; 2006:95-108.
• [48]Cory S, Huang DC, Adams JM: The Bcl-2 family: roles in cell survival and oncogenesis. Oncogene 2003, 22:8590-8607.
• [49]Rapp UR, Rennefahrt U, Troppmair J: Bcl-2 proteins: master switches at the intersection of death signaling and the survival control by Raf kinases. Biochim Biophys Acta 2004, 1644:149-158.
• [50]Nie Z, Bren GD, Vlahakis SR, Schimnich AA, Brenchley JM, Trushin SA, Warren S, Schnepple DJ, Kovacs CM, Loutfy MR, Douek DC, Badley AD: Human immunodeficiency virus type 1 protease cleaves procaspase 8 in vivo. J Virol 2007, 81:6947-6956.
• [51]Nie Z, Phenix BN, Lum JJ, Alam A, Lynch DH, Beckett B, Krammer PH, Sekaly RP, Badley AD: HIV-1 protease processes procaspase 8 to cause mitochondrial release of cytochrome c, caspase cleavage and nuclear fragmentation. Cell Death Differ 2002, 9:1172-1184.
• [52]Nie Z, Bren GD, Rizza SA, Badley AD: HIV Protease Cleavage of Procaspase 8 is Necessary for Death of HIV-Infected Cells. Open Virol J 2008, 2:1-7.
• [53]Sainski AM, Natesampillai S, Cummins NW, Bren GD, Taylor J, Saenz DT, Poeschla EM, Badley AD: The HIV-1-specific protein Casp8p41 induces death of infected cells through Bax/Bak. J Virol 2011, 85:7965-7975.
• [54]Nakagawa F, Lodwick RK, Smith CJ, Smith R, Cambiano V, Lundgren JD, Delpech V, Phillips AN: Projected life expectancy of people with HIV according to timing of diagnosis. Aids 2012, 26:335-343.
• [55]Hartman TL, Buckheit RW Jr: The Continuing Evolution of HIV-1 Therapy: Identification and Development of Novel Antiretroviral Agents Targeting Viral and Cellular Targets. Mol Biol Int 2012, 2012:401965.
• [56]Vlahakis SR, Bennett SA, Whitehead SN, Badley AD: HIV protease inhibitors modulate apoptosis signaling in vitro and in vivo. Apoptosis 2007, 12:969-977.
• [57]Rizza SA, Badley AD: HIV protease inhibitors impact on apoptosis. Med Chem 2008, 4:75-79.
• [58]FDA-Approved Anti-HIV Medications. http://www.aidsinfo.nih.gov/contentfiles/ApprovedMedstoTreatHIV_FS_en.pdf webcite
• [59]Anderson J, Schiffer C, Lee SK, Swanstrom R: Viral protease inhibitors. Handb Exp Pharmacol 2009, 189:85-110.
• [60]Chang MW, Giffin MJ, Muller R, Savage J, Lin YC, Hong S, Jin W, Whitby LR, Elder JH, Boger DL, Torbett BE: Identification of broad-based HIV-1 protease inhibitors from combinatorial libraries. Biochem J 2010, 429:527-532.
• [61]Agniswamy J, Shen CH, Aniana A, Sayer JM, Louis JM, Weber IT: HIV-1 protease with 20 mutations exhibits extreme resistance to clinical inhibitors through coordinated structural rearrangements. Biochemistry 2012, 51:2819-2828.
• [62]Judd DA, Nettles JH, Nevins N, Snyder JP, Liotta DC, Tang J, Ermolieff J, Schinazi RF, Hill CL: Polyoxometalate HIV-1 protease inhibitors. A new mode of protease inhibition. J Am Chem Soc 2001, 123:886-897.
• [63]Moskovitz BL: Clinical trial of tolerance of HPA-23 in patients with acquired immune deficiency syndrome. Antimicrob Agents Chemother 1988, 32:1300-1303.
• [64]Flutsch A, Schroeder T, Grutter MG, Patzke GR: HIV-1 protease inhibition potential of functionalized polyoxometalates. Bioorg Med Chem Lett 2011, 21:1162-1166.
• [65]Ghosh AK, Chapsal BD, Parham GL, Steffey M, Agniswamy J, Wang YF, Amano M, Weber IT, Mitsuya H: Design of HIV-1 protease inhibitors with C3-substituted hexahydrocyclopentafuranyl urethanes as P2-ligands: synthesis, biological evaluation, and protein-ligand X-ray crystal structure. J Med Chem 2011, 54:5890-5901.
• [66]Ghosh AK, Chapsal BD, Steffey M, Agniswamy J, Wang YF, Amano M, Weber IT, Mitsuya H: Substituent effects on P2-cyclopentyltetrahydrofuranyl urethanes: design, synthesis, and X-ray studies of potent HIV-1 protease inhibitors. Bioorg Med Chem Lett 2012, 22:2308-2311.
• [67]Bouras A, Boggetto N, Benatalah Z, de Rosny E, Sicsic S, Reboud-Ravaux M: Design, synthesis, and evaluation of conformationally constrained tongs, new inhibitors of HIV-1 protease dimerization. J Med Chem 1999, 42:957-962.
• [68]Shultz MD, Ham YW, Lee SG, Davis DA, Brown C, Chmielewski J: Small-molecule dimerization inhibitors of wild-type and mutant HIV protease: a focused library approach. J Am Chem Soc 2004, 126:9886-9887.
• [69]Bowman MJ, Byrne S, Chmielewski J: Switching between allosteric and dimerization inhibition of HIV-1 protease. Chem Biol 2005, 12:439-444.
• [70]Bowman MJ, Chmielewski J: Novel strategies for targeting the dimerization interface of HIV protease with cross-linked interfacial peptides. Biopolymers 2002, 66:126-133.
• [71]Shultz MD, Bowman MJ, Ham YW, Zhao X, Tora G, Chmielewski J: Small-Molecule Inhibitors of HIV-1 Protease Dimerization Derived from Cross-Linked Interfacial Peptides This work was supported by NIH (GM52739) and NSF (9457372-CHE). Angew Chem Int Ed Engl 2000, 39:2710-2713.
• [72]Hwang YS, Chmielewski J: Development of low molecular weight HIV-1 protease dimerization inhibitors. J Med Chem 2005, 48:2239-2242.
• [73]Cheng TJ, Brik A, Wong CH, Kan CC: Model system for high-throughput screening of novel human immunodeficiency virus protease inhibitors in Escherichia coli. Antimicrob Agents Chemother 2004, 48:2437-2447.
• [74]Cheng YS, Lo KH, Hsu HH, Shao YM, Yang WB, Lin CH, Wong CH: Screening for HIV protease inhibitors by protection against activity-mediated cytotoxicity in Escherichia coli. J Virol Methods 2006, 137:82-87.
• [75]Lindsten K, Uhlikova T, Konvalinka J, Masucci MG, Dantuma NP: Cell-based fluorescence assay for human immunodeficiency virus type 1 protease activity. Antimicrob Agents Chemother 2001, 45:2616-2622.
• [76]Fuse T, Watanabe K, Kitazato K, Kobayashi N: Establishment of a new cell line inducibly expressing HIV-1 protease for performing safe and highly sensitive screening of HIV protease inhibitors. Microbes Infect 2006, 8:1783-1789.
• [77]Hu K, Clement JF, Abrahamyan L, Strebel K, Bouvier M, Kleiman L, Mouland AJ: A human immunodeficiency virus type 1 protease biosensor assay using bioluminescence resonance energy transfer. J Virol Methods 2005, 128:93-103.
• [78]Cheng YS, Yin FH, Foundling S, Blomstrom D, Kettner CA: Stability and activity of human immunodeficiency virus protease: comparison of the natural dimer with a homologous, single-chain tethered dimer. Proc Natl Acad Sci U S A 1990, 87:9660-9664.
• [79]Patterson CE, Seetharam R, Kettner CA, Cheng YS: Human immunodeficiency virus type 1 and type 2 protease monomers are functionally interchangeable in the dimeric enzymes. J Virol 1992, 66:1228-1231.
• [80]Takegawa K, Tohda H, Sasaki M, Idiris A, Ohashi T, Mukaiyama H, Giga-Hama Y, Kumagai H: Production of heterologous proteins using the fission-yeast (Schizosaccharomyces pombe) expression system. Biotechnol Appl Biochem 2009, 53:227-235.
• [81]Zhao Y, Lieberman HB: Schizosaccharomyces pombe: a model for molecular studies of eukaryotic genes. DNA Cell Biol 1995, 14:359-371.
• [82]Giga-Hama Y, Kumagai H: Expression system for foreign genes using the fission yeast Schizosaccharomyces pombe. Biotechnol Appl Biochem 1999, 30(Pt 3):235-244.
• [83]Lu Q, Bauer JC, Greener A: Using Schizosaccharomyces pombe as a host for expression and purification of eukaryotic proteins. Gene 1997, 200:135-144.
• [84]Zhao Y, Elder RT: Yeast perspectives on HIV-1 VPR. Front Biosci 2000, 5:D905-916.
• [85]Li G, Bukrinsky M, Zhao RY: HIV-1 viral protein R (Vpr) and its interactions with host cell. Curr HIV Res 2009, 7:178-183.
• [86]Zhao RY, Elder RT: Viral infections and cell cycle G2/M regulation. Cell Res 2005, 15:143-149.
• [87]Zhao Y, Cao J, O'Gorman MR, Yu M, Yogev R: Effect of human immunodeficiency virus type 1 protein R (vpr) gene expression on basic cellular function of fission yeast Schizosaccharomyces pombe. J Virol 1996, 70:5821-5826.
• [88]Zhao RY, Bukrinsky M, Elder RT: HIV-1 viral protein R (Vpr) & host cellular responses. Indian J Med Res 2005, 121:270-286.
• [89]Zhao RY, Elder RT, Bukrinsky M: Interactions of HIV-1 viral protein R with host cell proteins. Adv Pharmacol 2007, 55:233-260.
• [90]Huard S, Chen M, Burdette KE, Fenyvuesvolgyi C, Yu M, Elder RT, Zhao RY: HIV-1 Vpr-induced cell death in Schizosaccharomyces pombe is reminiscent of apoptosis. Cell Res 2008, 18:961-973.
• [91]Benko Z, Elder R, Liang D, Zhao R: Fission yeast as a HTS platform for molecular probes of HIV-1 Vpr-induced cell death. Int J High Throughput Screen 2010, 1:151-162.