Structural and dynamical properties of different protonated states of mutant HIV-1 protease complexed with the saquinavir inhibitor studied by molecular dynamics simulations

Journal of Molecular Graphics and Modelling

Volumn 25, Issue 3, 2006, Pages 324-332

  Aruksakunwong, Ornjira ^a   Wittayanarakul, Kitiyaporn ^a   Sompornpisut, Pornthep ^a   Sanghiran, Vannajan ^b   Parasuk, Vudthichai ^a   Hannongbua, Supot ^a  

^a CHULALONGKORN UNIVERSITY   (Thailand)

^b CHIANG MAI UNIVERSITY   (Thailand)

Author keywords

HIV 1 protease; Molecular dynamics simulations; Mutation; Protonation state; Saquinavir

Indexed keywords

COMPUTER SIMULATION; DRUG DOSAGE; ENZYMES; HYDROGEN BONDS; MOLECULAR DYNAMICS; MUTAGENESIS;

HIV-1 PROTEASE; INTERACTION ENERGY; MUTATION; PROTONATION STATE; SAQUINAVIR;

BIOCHEMISTRY;

BRINASE; HYDROGEN; PROTEINASE INHIBITOR; SAQUINAVIR;

AQUEOUS SOLUTION; ARTICLE; CATALYSIS; CONFORMATION; HUMAN IMMUNODEFICIENCY VIRUS 1; HYDROGEN BOND; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTON TRANSPORT; SIMULATION; STATISTICAL SIGNIFICANCE;

BINDING SITES; CATALYSIS; COMPUTER SIMULATION; HIV PROTEASE; HIV PROTEASE INHIBITORS; HYDROGEN BONDING; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PLIABILITY; PROTEIN BINDING; PROTONS; SAQUINAVIR; STRUCTURE-ACTIVITY RELATIONSHIP;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 33750990766     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2006.01.004     Document Type: Article

References (24)

1. CDC. First report of AIDS. MMWR 30 (1981) 250-252
2. Mahalingam B., Louis J.M., Hung J., Harrison R.W., and Weber I.T. Structural implications of drug-resistant mutants of HIV-1 protease: high-resolution crystal structures of the mutant protease/substrate analogue complexes. Proteins 43 (2001) 455-464
3. Skalova T., Hasek J., Dohnalek J., Petrokova H., Buchtelova E., Duskova J., Soucek M., Majer P., Uhlikova T., and Konvalinka J. An ethylenamine inhibitor binds tightly to both wild type and mutant HIV-1 proteases. Structure and energy study. J. Med. Chem. 46 (2003) 1636-1644
4. Hong L., Zhang X.C., Hartsuck J.A., and Tang J. Crystal structure of an in vivo HIV-1 protease mutant in complex with saquinavir: insights into the mechanisms of drug resistance. Protein Sci. 9 (2000) 1898-1904
5. Shafer R.W., Hsu P., Patick A.K., Craig C., and Brendel V. Identification of biased amino acid substitution patterns in human immunodeficiency virus type 1 isolates from patients treated with protease inhibitors. J. Virol. 73 (1999) 6197-6202
6. Shuman C.F., Markgren P.-O., Hämäläinen M., and Danielson U.H. Elucidation of HIV-1 protease resistance by characterization of interaction kinetics between inhibitors and enzyme variants. Antiviral Res. 58 (2003) 235-242
7. Kantor R., Fessel W.J., Zolopa A.R., Israelski D., Shulman N., Montoya J.G., Harbour M., Schapiro J.M., and Shafer W.R. Evolution of primary protease inhibitor resistance mutations during protease inhibitor salvage therapy. Antimicrob. Agents Chemother. 46 (2002) 1086-1092
8. Wlodawer A., and Erickson J.W. Structure-based inhibitors of HIV-1 protease. Annu. Rev. Biochem. 62 (1933) 543-585
9. Ermolieff J., Lin X., and Tang J. Kinetic properties of saquinavir-resistant mutants of human immunodeficiency virus type 1 protease and their implications in drug resistance in vivo. Biochemistry 36 (1997) 12364-12370
10. Piana S., Sebastiani D., Carloni P., and Parrinello M. Ab initio molecular dynamics-based assignment of the protonation state of pepstatin A/HIV-1 protease cleavage site. J. Am. Chem. Soc. 123 (2001) 8730-8737
11. Smith R., Brereton I.M., Chai R.Y., and Kent S.B. Ionization states of the catalytic residues in HIV-1 protease. Nat. Struct. Biol. 3 (1996) 946-950
12. Nam K.-Y., Chang B.H., Han C.K., Ahn S.G., and No K.T. Investigation of the protonated state of HIV-1 protease active site. Bull. Korean Chem. Soc. 24 (2003) 817-823
13. Zhu Z., Schuster D.I., and Tuckerman M.E. Molecular dynamics study of the connection between flap closing and binding of fullerene-based inhibitors of the HIV-1 protease. Biochemistry 42 (2003) 1326-1333
14. Krohn A., Redshaw S., Ritchie J.C., Graves B.J., and Hatada M.H. Novel binding mode of highly potent HIV-proteinase inhibitors incorporating the (R)-hydroxyethylamine isostere. J. Med. Chem. 34 (1991) 3340-3342
15. Wang W.A.K.P.A. Computational study of protein specificity: the molecular basis of HIV-1 protease drug resistance. PNAS 98 (2001) 14937-14942
16. Case D.A., Pearlman J.C.D., Cheatham III T., Wang J., Ross W., Simmerling C., Merz T.D.T., Stanton R., Cheng A., Vincent J., Crowley M., Gohlke V.T.H., Radmer R., Duan Y., Pitera J., Massova I., Seibel G., Weiner U.C.S.P., and Kollman P.A. AMBER 7 (2002), University of California, San Francisco, CA
17. Wittayanarakul K., Aruksakunwong O., Saen-oon S., Chantratita W., Parasuk V., Sompornpisut P., and Hannongbua S. Insights into saquinavir resistance in the G48V HIV-1 protease: quantum calculations and molecular dynamic simulations. Biophys. J. 88 (2005) 867-879
18. Jorgensen W.L., Chandrasekhar J., and Madura J.D. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79 (1983) 926-935
19. Bayly C.I., Cieplak P., Cornell W.D., and Kollman P.A. A well-behaved electrostatic potential based method using charge restraints for determining atom-centered charges: the RESP model. J. Phys. Chem. 97 (1993) 10269
20. Ryckaert J.P., Ciccotti G., and Berendsen H.J.C. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 23 (1977) 327-341
21. Berendsen H.J.C., Postma J.P.M., Gunsteren W.F.V., DiNola A., and Haak J.R. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81 (1984) 3684-3690
22. M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman, V.G.J.A.M. Zakrzewski Jr., R.E. Stratmann, J.C. Burant, S. Dapprich, J.M. Millam, A.D. Daniels, K.N. Kudin, M.C. Strain, O. Farkas, J. Tomasi, V. Barone, M. Cossi, R. Cammi, B. Mennucci, C. Pomelli, C. Adamo, S. Clifford, J. Ochterski, G.A. Petersson, P.Y. Ayala, Q. Cui, K. Morokuma, D.K. Malick, A.D. Rabuck, K. Raghavachari, J.B. Foresman, J. Cioslowski, J.V. Ortiz, A.G. Baboul, B.B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. Gomperts, R.L. Martin, D.J. Fox, T. Keith, M.A. Al-Laham, C.Y. Peng, A. Nanayakkara, C. Gonzalez, M. Challacombe, P.M.W. Gill, B. Johnson, W. Chen, M.W. Wong, J.L. Andres, C. Gonzalez, M. Head-Gordon, E.S. Replogle, J.A. Pople, Gaussian 98 Program (Revision A.7). Journal, 1998.
23. Won Y. Binding free energy simulations of the HIV-1 protease and hydroxyethylene isostere inhibitors. Bull. Korean Chem. Soc. 21 (2000) 1207-1212
24. Wittayanarakul K., Aruksakunwong O., Sompornpisut P., Sanghiran-Lee V., Parasuk V., Pinitglang S., and Hannongbua S. Structure, dynamics and solvation of HIV-1 protease/saquinavir complex in aqueous solution and their contributions to drug resistance: molecular dynamic simulations. J. Chem. Inf. Model. 45 (2005) 300-308