Study on the drug resistance and the binding mode of HIV-1 integrase with LCA inhibitor

Karplus M, Petsko G A. Molecular dynamics simulations in biology. Nature, 1990, 347: 631–639 Smith L J, Dobson C M, van Gunsteren W F. Side chain conforma-tional disorder in a molten globule: Molecular dynamics simulations of human alpha-lactalbumin. J Mol Biol, 1999, 286: 1567–1580 Blaney J M, Dixon J S. A good ligand is hard to find: Automated docking methods. Perspectives in Drug Discovery and Design, 1993, 1: 301–319 Lengauer T, Rarey M. Computational methods for biomolecular docking. Curr Opin Struct Biol, 1996, 6: 402–406 Engelman A, Mizuuchi K, Craigie R. HIV-1 DNA integration: Mechanism of viral DNA cleavage and DNA strand transfer. Cell, 1991, 67: 1211–1221 Zheng R, Jenkins T M, Craigie R. Zinc folds the N-terminal domain of HIV-1 integrase promotes multimerization, and enhances catalytic activity. Proc Natl Acad Sci, 1996, 93: 13659–13664 Lee S P, Xiao J, Knutson J R, Lewis M S, Han M K. Zn2+ promotes the self-association of human immunodeficiency virus type-1 integrase in vitro. Biochemistry, 1997, 36: 173–180 Engelman A, Craigie R. Identification of conserved amino acid residues critical for human immunodeficiency virus type 1 integrase function in vitro. J Virol, 1992, 66: 6361–6369 Kulkosky J, Jones K S, Katz R A, Mack J P, Skalka A M. Residues critical for retroviral integrative recombination in a region that is highly conserved among retroviral/retrotransposon integrases and bacterial insertion sequence transposases. Mol Cell Biol, 1992, 12: 2331–2338 Polard P, Chandler M. Bacterial transposases and retroviral integrases. Mol Microbiol, 1995, 15: 13–23 Engelman A, Hickman A B, Craigie R. The core and carboxyl-terminal domains of the integrase protein of human immunodeficiency virus type 1 each contribute to nonspecific DNA binding. J Virol, 1994, 68: 5911–5917 Vink C, Oude Groeneger A M, Plasterk R H. Identification of the catalytic and DNA-binding region of the human immunodeficiency virus type I integrase protein. Nucleic Acids Res, 1993, 21: 1419–1425 Chow S A, Vincent K A, Ellison V, Brown P O. Reversal of integration and DNA splicing mediated by integrase of human immunodeficiency virus. Science, 1992, 255: 723–726 Bushman F D, Engelman A, Palmer I, Wingfield P, Craigie R. Domains of the integrase protein of human immunodeficiency virus type 1 responsible for polynucleotidyl transfer and zinc binding. Proc Natl Acad Sci, 1993, 90: 3428–3432 Robinson W E Jr, Reinicke M G, Abdel-Malek S, Jia Q, Chow S A. Inhibitors of HIV-1 replication that inhibit HIV integrase. Proc Natl Acad Sci, 1996, 93: 6326–6331 King P J, Lee D J, Reinke R A, Victoria J G, Beale K, Robinson W E Jr. Human immunodeficiency virus type 1 integrase containing a glycine to serine mutation at position 140 is attenuated for catalysis and resistant to integrase inhibitors. Virology, 2003, 306: 147–161 King P J, Robinson W E Jr. Resistance to the anti-human immunodeficiency virus type 1 compound L-chicoric acid results from a single mutation at amino acid 140 of integrase. J Virol, 1998, 72: 8420–8424 Goldgur Y, Craigie R, Cohen G H, Fujiwara T, Yoshinaga T, Fujishita T, Sugimoto H, Enodo T, Murai H, Davies D R. Structure of the HIV-1 integrase catalytic domain complexed with an inhibitor: A platform for antiviral drug design. Proc Natl Acad Sci, 1999, 96: 13040–13043 Sotriffer C A, Ni H, McCammon A. Active site binding modes of HIV-1 integrase inhibitors. J Med Chem, 2000, 43: 4109–4117 Liu C L, Li C H, Chen W Z, Wang C X. Study on interaction between HIV-1 and its dicaffeoyl inhibitors through molecular modeling approach. Acta Phys Chim Sin (in Chinese), 2005, 21(11): 1229–1234 Morris G M, Goodsell D S, Halliday R S, Huey R, Hart W E, Belew R K, Olson A J. Automated docking using a lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem, 1998, 19: 1639–1662 Weiner S J, Kollman P A, Case D A, Singh U C, Ghio C, Algona G, Profeta S Jr, Weiner P. A new force field for molecular mechanical simulation of nucleic acids and proteins. J Am Chem Soc, 1984, 106: 765–784 Weiner S J, Kollman P A, Nguyen D T, Case D A. An all atom force field for simulations of proteins and nucleic acids. J Comput Chem, 1986, 7: 230–252 Homans S W. A molecular mechanical force field for the conformational analysis of oligosaccharides: Comparison of theoretical and crystal structures of man alpha 1–3man beta 1–4glcnac. Biochemistry, 1990, 29: 9110–9118 Cornell W D, Cieplak P, Bayly C I, Gould I R, Merz K M Jr, Ferguson D M, Spellmeyer D C, Fox T, Cald well J W, Kollman P A. A second generation force field for the simulation of proteins and nucleic acids. J Am Chem Soc, 1995, 117: 5179–5197 Wang J M, Cieplak P, Kollman P A. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules. J Comput Chem, 2000, 21: 1049–1074 Kollman P A, Massova I, Reyes C, Kohn B, Huo S, Chong L, Lee M, Lee T, Duan Y, Wang W, Donini O, Cieplak P, Srinirasan J, Case D A, Cheatham T E. Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. Acc Chem Res, 2000, 33: 889–897 Wang W, Donini O, Reyes C, Kollman P A. Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions. Annu Rev Biophys Biomol Struct, 2001, 30: 211–243 Goldgur Y, Dyda F, Hickman A B, Jenkins T M, Craigie R, Daries D R. Three new structures of the core domain of HIV-1 integrase: An active site that binds magnesium. Proc Natl Acad Sci, 1998, 95: 9150–9154 Wang J, Wolf R M, Caldwell J W, Kollman P A, Case D A. Development and testing of a general amber force field. J Comput Chem, 2004, 25: 1157–1174 Jorgensen W L, Chandrasekhar J, Madura J D, Impey R W, Klein M L. Comparison of simple potential functions for simulating liquid water. J Chem Phys, 1983, 79: 926–935 Ryckaert J P, Ciccotti G, Berendsen H J C. Numerical integration of the cartesian equations of motion of a system with constrains: Molecular dynamics of n-alkanes. J Comput Phys, 1977, 23(3): 327–341 Tsui V, Case D A. Theory and applications of the generalized born solvation model in macromolecular simulations. Biopolymers: Nucleic Acid Sciences, 2001, 56: 275–291 Simonson T. Macromolecular electrostatics: continuum models and their growing pains. Curr Opin Struct Biol, 2001, 11: 243–252 Bashford D, Case D A. Generalized born models of macromolecular salvation effects. Ann Rev Phys Chem, 2000, 51: 129–152 Still W C, Tempczyk A, Hawley R C, Hendrickson T. A general treatment of solvation for molecular mechanics. J Am Chem Soc, 1990, 112: 6127–6129 Weiser J, Shenkin P S, Still W C. Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO). J Comput Chem, 1999, 20: 217–230 Heuer T S, Brown P O. Mapping features of HIV-1 integrase near selected sites on viral and target DNA molecules in an active enzyme-DNA complex by photo-cross-linking. Biochemistry, 1997, 36: 10655–10665 Esposito D, Craigie R. Sequence specificity of viral end DNA binding by HIV-1 integrase reveals critical regions for protein-DNA interaction. EMBO J, 1998, 17: 5832–5843 Wang C X, Shi Y Y, Zhou F, Wang L. Thermodynamic integration calculations of binding free energy difference for gly 169 mutation in subtilisin BPN. Proteins, 1993, 15: 5–9 Kong R, Tan J J, Ma X H, Chen W Z, Wang C X. Prediction of the binding mode between BMS-378806 and HIV-1 gp120 by docking and molecular dynamics simulation. Biochim Biophys Acta, 2006, 1764(4): 766–772 Asante A E, Skalka A M. HIV-1 integrase: Structural organization, conformational changes, and catalysis. Adv Virus Res, 1999, 52: 351–369 Wlodawer A. Crystal structures of catalytic core domains of retroviral integrases and role of divalent cations in enzymatic activity. Adv Virus Res, 1999, 52: 335–350 Jenkins T M, Esposito D, Engelman A, Craigie R. Critical contacts between HIV-1 integrase and viral DNA identified by structure based analysis and photo-cross-linking. EMBO J, 1997, 16: 6849–6859 Wang J Y, Ling H, Yang W, Craigie R. Structure of a two domain fragment of HIV-1 integrase: implications for domain organization in the intact protein. EMBO J, 2001, 20: 7333–7343