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Advances in Virology
Volume 2012 (2012), Article ID 548657, 13 pages
In Silico and In Vitro Comparison of HIV-1 Subtypes B and CRF02_AG Integrases Susceptibility to Integrase Strand Transfer Inhibitors
1LBPA, CNRS, LabEx LERMIT, Ecole Normale Supérieure de Cachan, 61 Avenue du Président Wilson, 94235 Cachan, France
2School of Life Science, East China Normal University, Shanghai 200062, China
3Laboratoire de Virologie, AP-HP, Hôpital Pitié-Salpêtrière, EA 2387, UPMC Université Paris VI, 75013 Paris, France
Received 3 January 2012; Revised 16 April 2012; Accepted 30 April 2012
Academic Editor: Domenico Genovese
Copyright © 2012 Xiaoju Ni et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
- P. O. Brown, “Integration of retroviral DNA,” Current Topics in Microbiology and Immunology, vol. 157, pp. 19–48, 1990.
- S. Y. Rhee, T. F. Liu, M. Kiuchi et al., “Natural variation of HIV-1 group M integrase: implications for a new class of antiretroviral inhibitors,” Retrovirology, vol. 5, article 74, 2008.
- J. Hemelaar, E. Gouws, P. D. Ghys, and S. Osmanov, “Global trends in molecular epidemiology of HIV-1 during 2000–2007,” AIDS, vol. 25, no. 5, pp. 679–689, 2011.
- L. Fischetti, O. Opare-Sem, D. Candotti, F. Sarkodie, H. Lee, and J. P. Allain, “Molecular epidemiology of HIV in Ghana: dominance of CRF02_AG,” Journal of Medical Virology, vol. 73, no. 2, pp. 158–166, 2004.
- L. Fischetti, O. Opare-Sem, D. Candotti, H. Lee, and J. P. Allain, “Higher viral load may explain the dominance of CRF02_AG in the molecular epidemiology of HIV in Ghana,” AIDS, vol. 18, no. 8, pp. 1208–1210, 2004.
- H. F. Njai, Y. Gali, G. Vanham et al., “The predominance of Human Immunodeficiency Virus type I (HIV-1) circulating recombinant form 02 (CRF02_AG) in West Central Africa may be related to its replicative fitness,” Retrovirology, vol. 3, article 40, 2006.
- L. F. A. MacHado, M. O. G. Ishak, A. C. R. Vallinoto et al., “Molecular epidemiology of HIV type 1 in Northern Brazil: identification of subtypes C and D and the introduction of CRF02-AG in the amazon region of Brazil,” AIDS Research and Human Retroviruses, vol. 25, no. 10, pp. 961–966, 2009.
- J. R. Ye, S. Q. Yu, H. Y. Lu, W. S. Wang, R. L. Xin, and Y. Zeng, “Genetic diversity of HIV type 1 isolated from newly diagnosed subjects (2006-2007) in Beijing, China,” AIDS Research and Human Retroviruses, vol. 28, no. 1, pp. 119–123, 2012.
- D. Descamps, M. L. Chaix, B. Montes et al., “Increasing prevalence of transmitted drug resistance mutations and non-B subtype circulation in antiretroviral-naive chronically HIV-infected patients from 2001 to 2006/2007 in France,” Journal of Antimicrobial Chemotherapy, vol. 65, no. 12, Article ID dkq380, pp. 2620–2627, 2010.
- J. L. Martínez-Cajas, N. Pant-Pai, M. B. Klein, and M. A. Wainberg, “Role of genetic diversity amongst HIV-1 non-B subtypes in drug resistance: a systematic review of virologic and biochemical evidence,” AIDS Reviews, vol. 10, no. 4, pp. 212–223, 2008.
- B. S. Taylor, M. E. Sobieszczyk, F. E. McCutchan, and S. M. Hammer, “Medical progress: the challenge of HIV-1 subtype diversity,” New England Journal of Medicine, vol. 358, no. 15, pp. 1590–1602, 2008.
- T. Bar-Magen, R. D. Sloan, V. H. Faltenbacher et al., “Comparative biochemical analysis of HIV-1 subtype B and C integrase enzymes,” Retrovirology, vol. 6, article 103, 2009.
- A. Low, N. Prada, M. Topper et al., “Natural polymorphisms of human immunodeficiency virus type 1 integrase and inherent susceptibilities to a panel of integrase inhibitors,” Antimicrobial Agents and Chemotherapy, vol. 53, no. 10, pp. 4275–4282, 2009.
- I. Malet, C. Soulie, L. Tchertanov et al., “Structural effects of amino acid variations between B and CRF02-AG HIV-1 integrases,” Journal of Medical Virology, vol. 80, no. 5, pp. 754–761, 2008.
- C. Fenollar-Ferrer, V. Carnevale, S. Raugei, and P. Carloni, “HIV-1 integrase-DNA interactions investigated by molecular modelling,” Computational and Mathematical Methods in Medicine, vol. 9, no. 3-4, pp. 231–243, 2008.
- A. I. Maïga, I. Malet, C. Soulie et al., “Genetic barriers for integrase inhibitor drug resistance in HIV type-1 B and CRF02_AG subtypes,” Antiviral Therapy, vol. 14, no. 1, pp. 123–129, 2009.
- E. Asante-Appiah and A. M. Skalka, “A metal-induced conformational change and activation of HIV-1 integrase,” Journal of Biological Chemistry, vol. 272, no. 26, pp. 16196–16205, 1997.
- J. F. Mouscadet, O. Delelis, A. G. Marcelin, and L. Tchertanov, “Resistance to HIV-1 integrase inhibitors: a structural perspective,” Drug Resistance Updates, vol. 13, no. 4-5, pp. 139–150, 2010.
- S. Hare, A. M. Vos, R. F. Clayton, J. W. Thuring, M. D. Cummings, and P. Cherepanov, “Molecular mechanisms of retroviral integrase inhibition and the evolution of viral resistance,” Proceedings of the National Academy of Sciences of the United States of America, vol. 107, no. 46, pp. 20057–20062, 2010.
- S. Hare, S. S. Gupta, E. Valkov, A. Engelman, and P. Cherepanov, “Retroviral intasome assembly and inhibition of DNA strand transfer,” Nature, vol. 464, no. 7286, pp. 232–236, 2010.
- Z. Yin and R. Craigie, “Modeling the HIV-1 intasome: a prototype view of the target of integrase inhibitors,” Viruses, vol. 2, no. 12, pp. 2777–2781, 2010.
- E. Guiot, K. Carayon, O. Delelis et al., “Relationship between the oligomeric status of HIV-1 integrase on DNA and enzymatic activity,” Journal of Biological Chemistry, vol. 281, no. 32, pp. 22707–22719, 2006.
- O. Delelis, I. Malet, L. Na et al., “The G140S mutation in HIV integrases from raltegravir-resistant patients rescues catalytic defect due to the resistance Q148H mutation,” Nucleic Acids Research, vol. 37, no. 4, pp. 1193–1201, 2009.
- C. Maurin, F. Bailly, E. Buisine et al., “Spectroscopic studies of diketoacids-metal interactions. A probing tool for the pharmacophoric intermetallic distance in the HIV-1 integrase active site,” Journal of Medicinal Chemistry, vol. 47, no. 22, pp. 5583–5586, 2004.
- A. S. Espeseth, P. Felock, A. Wolfe et al., “HIV-1 integrase inhibitors that compete with the target DNA substrate define a unique strand transfer conformation for integrase,” Proceedings of the National Academy of Sciences of the United States of America, vol. 97, no. 21, pp. 11244–11249, 2000.
- T. Kawasuji, T. Yoshinaga, A. Sato, M. Yodo, T. Fujiwara, and R. Kiyama, “A platform for designing HIV integrase inhibitors. Part 1: 2-Hydroxy-3-heteroaryl acrylic acid derivatives as novel HIV integrase inhibitor and modeling of hydrophilic and hydrophobic pharmacophores,” Bioorganic and Medicinal Chemistry, vol. 14, no. 24, pp. 8430–8445, 2006.
- E. Z. Loizidou, I. Kousiappa, C. D. Zeinalipour-Yazdi, D. A. M. C. Van De Vijver, and L. G. Kostrikis, “Implications of HIV-1 M group polymorphisms on integrase inhibitor efficacy and resistance: genetic and structural in silico analyses,” Biochemistry, vol. 48, no. 1, pp. 4–6, 2009.
- R. Hewer, T. Traut, J. Coates, and B. Williams, “Predicted modes of resistance and hypersensensivity confered by natural polymorphisms of HIV-1 integrase,” Antiviral Research, vol. 82, no. 2, article A24, 2009.
- A. Ali, R. M. Bandaranayake, Y. Cai et al., “Molecular basis for drug resistance in HIV-1 protease,” Viruses, vol. 2, no. 11, pp. 2509–2535, 2010.
- R. M. Bandaranayake, M. Kolli, N. M. King et al., “The effect of clade-specific sequence polymorphisms on HIV-1 protease activity and inhibitor resistance pathways,” Journal of Virology, vol. 84, no. 19, pp. 9995–10003, 2010.
- N. Eswar, B. John, N. Mirkovic et al., “Tools for comparative protein structure modeling and analysis,” Nucleic Acids Research, vol. 31, no. 13, pp. 3375–3380, 2003.
- M. A. Larkin, G. Blackshields, N. P. Brown et al., “Clustal W and Clustal X version 2.0,” Bioinformatics, vol. 23, no. 21, pp. 2947–2948, 2007.
- J. D. Thompson, D. G. Higgins, and T. J. Gibson, “CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice,” Nucleic Acids Research, vol. 22, no. 22, pp. 4673–4680, 1994.
- R. A. Friesner, J. L. Banks, R. B. Murphy et al., “Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy,” Journal of Medicinal Chemistry, vol. 47, no. 7, pp. 1739–1749, 2004.
- G. M. Morris, H. Ruth, W. Lindstrom et al., “Software news and updates AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility,” Journal of Computational Chemistry, vol. 30, no. 16, pp. 2785–2791, 2009.
- The PyMOL Molecular Grapics System, 2002.
- J. Y. Wang, H. Ling, W. Yang, and R. Craigie, “Structure of a two-domain fragment of HIV-1 integrase: implications for domain organization in the intact protein,” EMBO Journal, vol. 20, no. 24, pp. 7333–7343, 2002.
- J. C. H. Chen, J. Krucinski, L. J. W. Miercke et al., “Crystal structure of the HIV-1 integrase catalytic core and C-terminal domains: a model for viral DNA binding,” Proceedings of the National Academy of Sciences of the United States of America, vol. 97, no. 15, pp. 8233–8238, 2000.
- M. Y. Shen and A. Sali, “Statistical potential for assessment and prediction of protein structures,” Protein Science, vol. 15, no. 11, pp. 2507–2524, 2006.
- J. F. Mouscadet, R. Arora, J. André et al., “HIV-1 IN alternative molecular recognition of DNA induced by raltegravir resistance mutations,” Journal of Molecular Recognition, vol. 22, no. 6, pp. 480–494, 2009.
- S. Maignan, J. P. Guilloteau, Q. Zhou-Liu, C. Clément-Mella, and V. Mikol, “Crystal structures of the catalytic domain of HIV-1 integrase free and complexed with its metal cofactor: high level of similarity of the active site with other viral integrases,” Journal of Molecular Biology, vol. 282, no. 2, pp. 359–368, 1998.
- B. R. Brooks, C. L. Brooks, A. D. Mackerell et al., “CHARMM: the biomolecular simulation program,” Journal of Computational Chemistry, vol. 30, no. 10, pp. 1545–1614, 2009.
- A. Sali and T. L. Blundell, “Comparative protein modelling by satisfaction of spatial restraints,” Journal of Molecular Biology, vol. 234, no. 3, pp. 779–815, 1993.
- S. Hare, F. Di Nunzio, A. Labeja, J. Wang, A. Engelman, and P. Cherepanov, “Structural basis for functional tetramerization of lentiviral integrase,” PLoS Pathogens, vol. 5, no. 7, Article ID e1000515, 2009.
- L. Du, L. Shen, Z. Yu et al., “Hyrtiosal, from the marine sponge Hyrtios erectus, inhibits HIV-1 integrase binding to viral DNA by a new inhibitor binding site,” ChemMedChem, vol. 3, no. 1, pp. 173–180, 2008.
- R. Lu, H. Z. Ghory, and A. Engelman, “Genetic analyses of conserved residues in the carboxyl-terminal domain of human immunodeficiency virus type 1 integrase,” Journal of Virology, vol. 79, no. 16, pp. 10356–10368, 2005.
- R. A. Laskowski, M. W. Macarthur, D. S. Moss, and J. M. Thornton, “Procheck—a program to check the stereochemical quality of protein structures,” Journal of Applied Crystallography, vol. 26, pp. 283–291, 1993.
- S. M. Kerwin, “ChemBioOffice Ultra 2010 suite,” Journal of the American Chemical Society, vol. 132, no. 7, pp. 2466–2467, 2010.
- Gaussian 03, Gaussian, Wallingford, UK, 2003.
- H. Leh, P. Brodin, J. Bischerour et al., “Determinants of Mg2+-dependent activities of recombinant human immunodeficiency virus type 1 integrase,” Biochemistry, vol. 39, no. 31, pp. 9285–9294, 2000.
- I. Malet, O. Delelis, M. A. Valantin et al., “Mutations associated with failure of raltegravir treatment affect integrase sensitivity to the inhibitor in vitro,” Antimicrobial Agents and Chemotherapy, vol. 52, no. 4, pp. 1351–1358, 2008.
- J. Agapkina, M. Smolov, S. Barbe et al., “Probing of HIV-1 integrase/DNA interactions using novel analogs of viral DNA,” Journal of Biological Chemistry, vol. 281, no. 17, pp. 11530–11540, 2006.
- M. Smolov, M. Gottikh, V. Tashlitskii et al., “Kinetic study of the HIV-1 DNA 3′-end processing: single-turnover property of integrase,” FEBS Journal, vol. 273, no. 6, pp. 1137–1151, 2006.