1Department of Biology, Faculty of Science, Shahid Chamran University, Ahvaz, Iran
2Department of Parasitology and Medical Entomology, Tarbiat Modares University, Tehran
Human immunodeficiency virus type 1 (HIV-1) protease inhibitors comprise an important class of drugs used in HIV treatments. However, mutations of protease genes accelerated by low fidelity of reverse transcriptase yield drug resistant mutants of reduced affinities for the inhibitors. This problem is considered to be a serious barrier against HIV treatment for the foreseeable future. In this study, molecular dynamic simulation method was used to examine the combinational and additive effects of all known mutations involved in drug resistance against FDA approved inhibitors. Results showed that drug resistant mutations are not randomly distributed along the protease sequence; instead, they are localized on flexible or hot points of the protein chain. Substitution of more hydrophobic residues in flexible points of protease chains tends to increase the folding, lower the flexibility and decrease the active site area of the protease. The reduced affinities of HIV-1 protease for inhibitors seemed to be due to substantial decrease in the size of the active site and flap mobility. A correlation was found between the binding energy of inhibitors and their affinities for each mutant suggesting the distortion of the active site geometry in drug resistance by preventing effective fitting of inhibitors into the enzymes' active site. To overcome the problem of drug resistance of HIV-1 protease, designing inhibitors of variable functional groups and configurations is proposed.
1.Katz RA, Skalka AM. The retroviral enzymes. Annu Rev Biochem 1994;63:133-173.
2.Lee T, Laco GS, Torbett BE, Fox HS, Lerner DL, Elder JH, Wong CH. Analysis of the S3 and S3' subsite specificities of feline immunodeficiency virus (FIV) protease: development of a broad-based protease inhibitor efficacious against FIV, SIV, and HIV in vitro and ex vivo. Proc Natl Acad Sci USA 1998;95:939-944.
3.Tozzini V, McCammon JA. A coarse grained model for the dynamics of flap opening in HIV-1 protease. Chem Phys Lett 2005;413:123-128.
4.Tozzini V, Trylska J, Chang CE, McCammon JA. Flap opening dynamics in HIV-1 protease explored with a coarse-grained model. J Struct Biol 2007;157:606-615.
5.Mao Y. Dynamical basis for drug resistance of HIV-1 protease. BMC Struct Biol 2001;11:31.
6.De Meyer S, Azijn H, Surleraux D, Jochmans D, Tahri A, Pauwels R, Wigerinck P, de Béthune MP. TMC114, a novel human immunodeficiency virus type 1 protease inhibitor active against protease inhibitor-resistant viruses, including a broad range of clinical isolates. Antimicrob Agents Chemother 2005;6:2314-2321.
7.Koh Y, Nakata H, Maeda K, Ogata H, Bilcer G, Devasamudram T, Kincaid JF, Boross P, Wang YF, Tie Y, Volarath P, Gaddis L, Harrison RW, Weber IT, Ghosh AK, Mitsuya H. Novel bis-tetrahydrofuranylurethane-containing nonpeptidic protease inhibitor (PI) UIC-94017 (TMC114) with potent activity against multi-PI-resistant human immunodeficiency virus in vitro. Antimicrob Agents Chemother 2003;47:3123-3129.
9.Surleraux DL, Tahri A, Verschueren WG, Pille GM, de Kock HA, Jonckers TH, Peeters A, De Meyer S, Azijn H, Pauwels R, de Bethune MP, King NM, Prabu-Jeyabalan M, Schiffer CA, Wigerinck PB. Discovery and selection of TMC114, a next generation HIV-1 protease inhibitor. J Med Chem 2005;48:1813-1822.
10.Mager PP. The active site of HIV-1 protease. Med Res Rev 2001;4:348-353.
11.Mahalingam B, Boross P, Wang YF, Louis JM, Fischer CC, Tozser J, Harrison RW, Weber IT. Combining mutations in HIV-1 protease to understand mechanisms of resistance. Proteins 2002;48:107-116.
12.Vergne L, Peeters M, Mpoudi-Ngole E, Bourgeois A, Liegeois F, Toure-Kane C, Mboup S, Mulanga-Kabeya C, Saman E, Jourdan J, Reynes J, Delaporte E. Genetic diversity of protease and reverse transcriptase sequences in non-subtype-B human immunodeficiency virus type 1 strains: evidence of many minor drug resistance mutations in treatment-naive patients. J Clin Microbiol 2000;11:3919-3925.
13.Brik A, Wong CH. HIV-1 protease: mechanism and drug discovery. Org Biomol Chem 2003;1:5-14.
14.Coffin JM. HIV population dynamics in vivo: implications for genetic variation, pathogenesis, and therapy. Science 1995;267:483-489.
15.Freire E. Overcoming HIV-1 resistance to protease inhibitors. Drug Discov Today 2006;3:281-286.
16.Zennou V, Mammano F, Paulous S, Mathez D, Clavel F. Loss of viral fitness associated with multiple Gag and Gag-Pol processing defects in human immunodeficiency virus type 1 variants selected for resistance to protease inhibitors in vivo. J Virol 1998;72:3300-3306.
17.Dauber DS, Ziermann R, Parkin N, Maly DJ, Mahrus S, Harris JL, Ellman JA, Petropoulos C, Craik CS. Altered substrate specificity of drug-resistant human immunodeficiency virus type 1 protease. J Virol 2002;76:1359-1368.
18.Ridky TW, Kikonyogo A, Leis J, Gulnik S, Copeland T, Erickson J, Wlodawer A, Kurinov I, Harrison RW, Weber IT. Drug-resistant HIV-1 proteases identify enzyme residues important for substrate selection and catalytic rate. Biochemistry 1998;37: 13835-13845.
19.Xie D, Gulnik S, Gustchina E, Yu B, Shao W, Qoronfleh W, Nathan A, Erickson JW. Drug resistance mutations can effect dimer stability of HIV-1 protease at neutral pH. Protein Sci 1999;8:1702-1707.
20.Lee T, Le V, Lim D, Lin YC, Morris GM, Wong AL, Olson AJ, Elder JH, Wong CH. Development of a new type of protease inhibitor, Efficacious against FIV and HIV variants. J. Am. Chem. Soc 1999;121:1145-1155.
21.Ohtaka H, Schön A, Freire E. Multidrug resistance to HIV-1 protease inhibition requires cooperative coupling between distal mutations. Biochemistry 2003;42: 13659-13666.
22.Ohtaka H, Velázquez-Campoy A, Xie D, Freire E. Overcoming drug resistance in HIV-1 chemotherapy: the binding thermodynamics of Amprenavir and TMC-126 to wild-type and drug-resistant mutants of the HIV-1 protease. Protein Sci 2002;11: 1908-1916.
23.Stiffin RM, Sullivan SM, Carlson GM, Holyoak T. Differential inhibition of cytosolic PEPCK by substrate analogues. Kinetic and structural characterization of inhibitor recognition. Biochemistry 2008;47:2099-2109.
24.Johnson VA, Brun-Vezinet F, Clotet B, Günthard HF, Kuritzkes DR, Pillay D, Schapiro JM, Richman DD. Update of the drug resistance mutations in HIV-1: Spring 2008. Top HIV Med 2008;16:62-68.
25.Dayer MR, Ghayour O, Dayer MS. Mechanism of the bell-shaped profile of ribonuclease a activity: molecular dynamic approach. Protein J 2012;31:573-579.
26.Dayer MR, Dayer MS. Whiskers-less HIV-protease: a possible Way for HIV-1 deactivation. J Biomed Sci 2013;20:67
27.Weber IT, Agniswamy J. HIV-1 Protease: Structural Perspectives on Drug Resistance. Viruses 2009;1:1110-1136.
28.Macindoe G, Mavridis L, Venkatraman V, Devignes MD, Ritchie DW. HexServer: an FFT-based protein docking server powered by graphics processors. Nucleic Acids Res 2010;38:445-449.
29.Ghosh AK, Chapsal BD, Weber IT, Mitsuya H. Design of HIV protease inhibitors targeting protein backbone: an effective strategy for combating drug resistance. Acc Chem Res 2008;41:78-86.
30.Kyte J, Doolittle R. A simple method for displaying the hydropathic character of a protein. J Mol Biol 1982;157:105-132.
31.Ali A, Bandaranayake RM, Cai Y, King NM, Kolli M, Mittal S, Murzycki JF, Nalam MN, Nalivaika EA, Ozen A, Prabu-Jeyabalan MM, Thayer K, Schiffer CA. Molecular Basis for Drug Resistance in HIV-1 Protease. Viruses 2010;2:2509-2535.
32.Perryman AL, Lin JH, McCammon JA. HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: possible contributions to drug resistance and a potential new target site for drugs. Protein Sci 2004;13:1108-1123.
33.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.
34.Prabu-Jeyabalan M, Nalivaika EA, Romano K, Schiffer CA. Mechanism of substrate recognition by drug-resistant human immunodeficiency virus type 1 protease variants revealed by a novel structural intermediate. J Virol 2006;80:3607-3616.
35.Collins JR, Burt SK, Erickson JW. Flap opening in HIV-1 protease simulated by activated molecular dynamics. Nat Struct Biol 1995;2:334-338.
36.Mahalingam B, Louis JM, Hung J, Harrison RW, Weber IT. Structural implications of drug-resistant mutants of HIV-1 protease: high-resolution crystal structures of the mutant protease/substrate analogue complexes. Proteins 2001;43:455-464.
37.Katoh E, Louis JM, Yamazaki T, Gronenborn AM, Torchia DA, Ishima R. A solution NMR study of the binding kinetics and the internal dynamics of an HIV-1 protease-substrate complex. Protein Sci 2003;12:1376-1385.
38.Kurt N, Scott WR, Schiffer CA, Haliloglu T. Cooperative fluctuations of unliganded and substrate-bound HIV-1 protease: a structure-based analysis on a variety of conformations from crystallography and molecular dynamic simulations. Proteins 2003;51:409-422.
39.Nijhuis M, van Maarseveen NM, Lastere S, Schipper P, Coakley E, Glass B, Rovenska M, de Jong D, Chappey C, Goedegebuure IW, Heilek-Snyder G, Dulude D, Cammack N, Brakier-Gingras L, Konvalinka J, Parkin N, Kräusslich HG, Brun-Vezinet F, Boucher CA. A novel substrate-based HIV-1 protease inhibitor drug resistance mechanism. PLoS Med 2007;4:e36.