Jundishapur Journal of Microbiology

Published by: Kowsar

Comparison of Newly Assembled Full Length HIV-1 Integrase With Prototype Foamy Virus Integrase: Structure-Function Prospective

Mohammad Reza Dayer 1 , *
Author Information
1 Department of Biology, Faculty of Science, Shahid Chamran University, Ahvaz, IR Iran
Article information
  • Jundishapur Journal of Microbiology: May 01, 2016, 9 (5); e29773
  • Published Online: February 15, 2016
  • Article Type: Research Article
  • Received: May 9, 2015
  • Revised: November 17, 2015
  • Accepted: November 30, 2015
  • DOI: 10.5812/jjm.29773

To Cite: Dayer M R. Comparison of Newly Assembled Full Length HIV-1 Integrase With Prototype Foamy Virus Integrase: Structure-Function Prospective, Jundishapur J Microbiol. 2016 ; 9(5):e29773. doi: 10.5812/jjm.29773.

Copyright © 2016, Ahvaz Jundishapur University of Medical Sciences. This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International License (http://creativecommons.org/licenses/by-nc/4.0/) which permits copy and redistribute the material just in noncommercial usages, provided the original work is properly cited.
1. Background
2. Objectives
3. Materials and Methods
4. Results
5. Discussion
  • 1. Xue W, Jin X, Ning L, Wang M, Liu H, Yao X. Exploring the molecular mechanism of cross-resistance to HIV-1 integrase strand transfer inhibitors by molecular dynamics simulation and residue interaction network analysis. J Chem Inf Model. 2013; 53(1): 210-22[DOI][PubMed]
  • 2. Feller L, Khammissa RAG., Wood NH, Meyerov R, Lemmer J. Insights into immunopathogenic mechanisms of HIV infection: high levels of immune activation and HIV fitness: communication corner. South African Dental Journal. 2008; 63(10): 552-7
  • 3. Hammer SM, Saag MS, Schechter M, Montaner JSG, Schooley RT, Jacobsen DM, et al. Treatment for Adult HIV Infection. Jama. 2006; 296(7): 827[DOI]
  • 4. Pommier Y, Johnson AA, Marchand C. Integrase inhibitors to treat HIV/AIDS. Nat Rev Drug Discov. 2005; 4(3): 236-48[DOI][PubMed]
  • 5. Savarino A. A historical sketch of the discovery and development of HIV-1 integrase inhibitors. Expert Opin Investig Drugs. 2006; 15(12): 1507-22[DOI][PubMed]
  • 6. DeJesus E, Berger D, Markowitz M, Cohen C, Hawkins T, Ruane P, et al. Antiviral activity, pharmacokinetics, and dose response of the HIV-1 integrase inhibitor GS-9137 (JTK-303) in treatment-naive and treatment-experienced patients. J Acquir Immune Defic Syndr. 2006; 43(1): 1-5[DOI][PubMed]
  • 7. Markowitz M, Morales-Ramirez JO, Nguyen BY, Kovacs CM, Steigbigel RT, Cooper DA, et al. Antiretroviral activity, pharmacokinetics, and tolerability of MK-0518, a novel inhibitor of HIV-1 integrase, dosed as monotherapy for 10 days in treatment-naive HIV-1-infected individuals. J Acquir Immune Defic Syndr. 2006; 43(5): 509-15[DOI][PubMed]
  • 8. Johnson BC, Metifiot M, Pommier Y, Hughes SH. Molecular dynamics approaches estimate the binding energy of HIV-1 integrase inhibitors and correlate with in vitro activity. Antimicrob Agents Chemother. 2012; 56(1): 411-9[DOI][PubMed]
  • 9. Nowotny M. Retroviral integrase superfamily: the structural perspective. EMBO Rep. 2009; 10(2): 144-51[DOI][PubMed]
  • 10. Rice PAP, Baker TA. Comparative architecture of transposase and integrase complexes. Nat Struct Mol Biol. 2001; 8(4): 302-7[PubMed]
  • 11. Chen X, Tsiang M, Yu F, Hung M, Jones GS, Zeynalzadegan A, et al. Modeling, analysis, and validation of a novel HIV integrase structure provide insights into the binding modes of potent integrase inhibitors. J Mol Biol. 2008; 380(3): 504-19[DOI][PubMed]
  • 12. Jayappa KD, Ao Z, Yang M, Wang J, Yao X. Identification of critical motifs within HIV-1 integrase required for importin alpha3 interaction and viral cDNA nuclear import. J Mol Biol. 2011; 410(5): 847-62[DOI][PubMed]
  • 13. Agapkina J, Smolov M, Barbe S, Zubin E, Zatsepin T, Deprez E, et al. Probing of HIV-1 integrase/DNA interactions using novel analogs of viral DNA. J Biol Chem. 2006; 281(17): 11530-40[DOI][PubMed]
  • 14. Grobler JA, Stillmock K, Hu B, Witmer M, Felock P, Espeseth AS, et al. Diketo acid inhibitor mechanism and HIV-1 integrase: implications for metal binding in the active site of phosphotransferase enzymes. Proc Natl Acad Sci. 2002; 99(10): 6661-6
  • 15. Marchand C, Johnson AA, Karki RG, Pais GCG, Zhang X, Cowansage K, et al. Metal-dependent inhibition of HIV-1 integrase by β-diketo acids and resistance of the soluble double-mutant (F185K/C280S). Mol Pharmacol. 2003; 64(3): 600-9[PubMed]
  • 16. Chen JCH, Krucinski J, Miercke LJW, Finer-Moore JS, Tang AH, Leavitt AD, et al. Crystal structure of the HIV-1 integrase catalytic core and C-terminal domains: a model for viral DNA binding. Proc Natl Acad Sci. 2000; 97(15): 8233-8
  • 17. Craigie R. HIV integrase, a brief overview from chemistry to therapeutics. J Biol Chem. 2001; 276(26): 23213-6[DOI][PubMed]
  • 18. Nomura Y, Masuda T, Kawai G. Structural analysis of a mutant of the HIV-1 integrase zinc finger domain that forms a single conformation. J Biochem. 2006; 139(4): 753-9[DOI][PubMed]
  • 19. Almerico A, Tutone M, Ippolito M, Lauria A. Molecular Modelling and QSAR in the Discovery of HIV-1 Integrase Inhibitors. Curr Comput Aided Drug Des. 2007; 3(3): 214-33[DOI]
  • 20. Dicker IB, Samanta HK, Li Z, Hong Y, Tian Y, Banville J, et al. Changes to the HIV long terminal repeat and to HIV integrase differentially impact HIV integrase assembly, activity, and the binding of strand transfer inhibitors. J Biol Chem. 2007; 282(43): 31186-96[DOI][PubMed]
  • 21. Huang M, Grant GH, Richards WG. Binding modes of diketo-acid inhibitors of HIV-1 integrase: a comparative molecular dynamics simulation study. J Mol Graph Model. 2011; 29(7): 956-64[DOI][PubMed]
  • 22. Pommier Y, Marchand C, Neamati N. Retroviral integrase inhibitors year 2000: update and perspectives. Antiviral Research. 2000; 47(3): 139-48[DOI]
  • 23. Metifiot M, Marchand C, Maddali K, Pommier Y. Resistance to integrase inhibitors. Viruses. 2010; 2(7): 1347-66[PubMed]
  • 24. Hazuda DJ, Felock P, Witmer M, Wolfe A, Stillmock K, Grobler JA, et al. Inhibitors of strand transfer that prevent integration and inhibit HIV-1 replication in cells. Science. 2000; 287(5453): 646-50[PubMed]
  • 25. Zhuang L, Wai JS, Embrey MW, Fisher TE, Egbertson MS, Payne LS, et al. Design and synthesis of 8-hydroxy-[1,6]naphthyridines as novel inhibitors of HIV-1 integrase in vitro and in infected cells. J Med Chem. 2003; 46(4): 453-6[DOI][PubMed]
  • 26. Marchand C, Zhang X, Pais GC, Cowansage K, Neamati N, BurkeTR Jr., et al. Structural determinants for HIV-1 integrase inhibition by beta-diketo acids. J Biol Chem. 2002; 277(15): 12596-603[DOI][PubMed]
  • 27. Zouhiri F, Mouscadet JF, Mekouar K, Desmaele D, Savoure D, Leh H, et al. Structure-activity relationships and binding mode of styrylquinolines as potent inhibitors of HIV-1 integrase and replication of HIV-1 in cell culture. J Med Chem. 2000; 43(8): 1533-40[PubMed]
  • 28. Chen JCH, Krucinski J, Miercke LJW, Finer-Moore JS, Tang AH, Leavitt AD, et al. Crystal structure of the HIV-1 integrase catalytic core and C-terminal domains: a model for viral DNA binding. Proc Acad Sci. 2000; 97(15): 8233-8[PubMed]
  • 29. Cherepanov P, Ambrosio ALB, Rahman S, Ellenberger T, Engelman A. Structural basis for the recognition between HIV-1 integrase and transcriptional coactivator p75. Proc Natl Acad Sci. 2005; 102(48): 17308-13
  • 30. Yuan P, Gupta K, Van Duyne GD. Tetrameric structure of a serine integrase catalytic domain. Structure. 2008; 16(8): 1275-86[DOI]
  • 31. Goldgur Y, Craigie R, Cohen GH, Fujiwara T, Yoshinaga T, Fujishita T, et al. Structure of the HIV-1 integrase catalytic domain complexed with an inhibitor: a platform for antiviral drug design. Proc Natl Acad Sci. 1999; 96(23): 13040-3
  • 32. Wielens J, Headey SJ, Jeevarajah D, Rhodes DI, Deadman J, Chalmers DK, et al. Crystal structure of the HIV-1 integrase core domain in complex with sucrose reveals details of an allosteric inhibitory binding site. FEBS Lett. 2010; 584(8): 1455-62[DOI][PubMed]
  • 33. Wang JY, 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(24): 7333-43[DOI][PubMed]
  • 34. Cherepanov P, Sun ZY, Rahman S, Maertens GN, Wagner G, Engelman A. Solution structure of the HIV-1 integrase-binding domain in LEDGF/p75. Nat.Struct Mol Biol. 2005; 12(6): 526-32
  • 35. Métifiot M, Maddali K, Johnson BC, Hare S, Smith SJ, Zhao XZ, et al. Activities, crystal structures, and molecular dynamics of dihydro-1 H-isoindole derivatives, inhibitors of HIV-1 integrase. ACS chemical biology. 2012; 8(1): 209-17[DOI]
  • 36. Hare S, Gupta S, Valkov E, Engelman A, Cherepanov P. Retroviral intasome assembly and inhibition of DNA strand transfer. Nature. 2010; 464(7286): 232-6[DOI]
  • 37. Maertens GN, Hare S, Cherepanov P. The mechanism of retroviral integration from X-ray structures of its key intermediates. Nature. 2010; 468(7321): 326-9[DOI]
  • 38. Hare S, Vos AM, Clayton RF, Thuring JW, Cummings MD, Cherepanov P. Molecular mechanisms of retroviral integrase inhibition and the evolution of viral resistance. Nat Struct Mol Biol. 2010; 107(46): 20057-62[DOI]
  • 39. 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(7): 2099-109[DOI][PubMed]
  • 40. Guex N, Peitsch MC. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis. 1997; 18(15): 2714-23[DOI][PubMed]
  • 41. Johnson VA, Brun-Vezinet F, Clotet B, Gunthard HF, Kuritzkes DR, Pillay D, et al. Update of the drug resistance mutations in HIV-1: Spring 2008. Top HIV Med. 2008; 16(1): 62-8
  • 42. Dayer MR, Dayer MS. Whiskers-less HIV-protease: a possible way for HIV-1 deactivation. J Biomed Sci. 2013; 20: 67[DOI][PubMed]
  • 43. Kirk W, Kurian E, Wessels W. Photophysics of ANS. V. Decay modes of ANS in proteins: the IFABP-ANS complex. Biophys Chem. 2007; 125(1): 50-8[DOI][PubMed]
  • 44. Konkle ME, Muellner SK, Schwander AL, Dicus MM, Pokhrel R, Britt RD, et al. Effects of pH on the Rieske protein from Thermus thermophilus: a spectroscopic and structural analysis. Biochemistry. 2009; 48(41): 9848-57[DOI][PubMed]
  • 45. Sheng C, Ji H, Miao Z, Che X, Yao J, Wang W, et al. Homology modeling and molecular dynamics simulation of N-myristoyltransferase from protozoan parasites: active site characterization and insights into rational inhibitor design. J Comput Aided Mol Des. 2009; 23(6): 375-89[DOI][PubMed]
  • 46. 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; 38-9[DOI][PubMed]
  • 47. Dayer MR, Dayer MS, Ghayour O. Dynamic Behavior of Rat Phosphoenolpyruvate Carboxykinase Inhibitors: New Mechanism for Enzyme Inhibition. The Protein Journal. 2013; 32(4): 253-8[DOI]
  • 48. Yang XG, Luo RY, Feng ZP. Using amino acid and peptide composition to predict membrane protein types. Biochem Biophys Res Commun. 2007; 353(1): 164-9[DOI][PubMed]
Creative Commons License Except where otherwise noted, this work is licensed under Creative Commons Attribution Non Commercial 4.0 International License .
Readers' Comments