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Research Articles

The conformational feasibility for the formation of reaching dimer in ASV and HIV integrase: a molecular dynamics study

ORCID Icon, , , , &
Pages 3469-3485 | Received 22 Jul 2016, Accepted 31 Oct 2016, Published online: 28 Nov 2016

References

  • Adamson, C. S., & Freed, E. O. (2010). Novel approaches to inhibiting HIV-1 replication. Antiviral Research, 85, 119–141.10.1016/j.antiviral.2009.09.009
  • Alian, A., Griner, S. L., Chiang, V., Tsiang, M., Jones, G., Birkus, G., … Stroud, R. M. (2009). Catalytically-active complex of HIV-1 integrase with a viral DNA substrate binds anti-integrase drugs. Proceedings of the National Academy of Sciences, 106, 8192–8197.10.1073/pnas.0811919106
  • Al-Mawsawi, L. Q., Al-Safi, R. I., & Neamati, N. (2008). Anti-infectives clinical progress of HIV-1 integrase inhibitors. Expert Opinion on Emerging Drugs, 13, 213–225.10.1517/14728214.13.2.213
  • Baker, N. A., Sept, D., Joseph, S., Holst, M. J., & McCammon, J. A. (2001). Electrostatics of nanosystems: Application to microtubules and the ribosome. Proceedings of the National Academy of Sciences, 98, 10037–10041.10.1073/pnas.181342398
  • Balasubramanian, S., Rajagopalan, M., & Ramaswamy, A. (2012). Structural dynamics of full-length retroviral integrase: A molecular dynamics analysis. Journal of Biomolecular Structure Dynamics, 29, 659–670.
  • Ballandras-Colas, A., Brown, M., Cook, N. J., Dewdney, T. G., Demeler, B., Cherepanov, P., … Engelman, A. N. (2016). Cryo-EM reveals a novel octameric integrase structure for betaretroviral intasome function. Nature, 530, 358–361.10.1038/nature16955
  • Bao, K. K., Wang, H., Miller, J. K., Erie, D. A., Skalka, A. M., & Wong, I. (2003). Functional oligomeric state of avian sarcoma virus integrase. Journal of Biological Chemistry, 278, 1323–1327.10.1074/jbc.C200550200
  • Bojja, R. S., Andrake, M. D., Merkel, G., Weigand, S., Dunbrack, Jr., R. L., & Skalka, A. M. (2013). Architecture and assembly of HIV integrase multimers in the absence of DNA substrates. Journal of Biological Chemistry, 288, 7373–7386.10.1074/jbc.M112.434431
  • Bojja, R. S., Andrake, M. D., Weigand, S., Merkel, G., Yarychkivska, O., Henderson, A., … Skalka, A. M. (2011). Architecture of a full-length retroviral integrase monomer and dimer, revealed by small angle X-ray scattering and chemical cross-linking. Journal of Biological Chemistry, 286, 17047–17059.10.1074/jbc.M110.212571
  • Bushman, F. D., & Craigie, R. (1990). Sequence requirements for integration of Moloney murine leukemia virus DNA in vitro. Journal of Virology, 64, 5645–5648.
  • Bushman, F. D., & Craigie, R. (1991). Activities of human immunodeficiency virus (HIV) integration protein in vitro: Specific cleavage and integration of HIV DNA. Proceedings of the National Academy of Sciences, 88, 1339–1343.10.1073/pnas.88.4.1339
  • Bushman, F. D., Fujiwara, T., & Craigie, R. (1990). Retroviral DNA integration directed by HIV integration protein in vitro. Science, 249, 1555–1558.10.1126/science.2171144
  • Bushman, F. D., & Wang, B. (1994). Rous sarcoma virus integrase protein: Mapping functions for catalysis and substrate binding. Journal of Virology, 68, 2215–2223.
  • Cai, M., Zheng, R., Caffrey, M., Craigie, R., Clore, G. M., & Gronenborn, A. M. (1997). Solution structure of the N-terminal zinc binding domain of HIV-1 integrase. Nature Structural Biology, 4, 567–577.10.1038/nsb0797-567
  • Case, D. A., Darden, T. A., Cheatham, I., Simmerling, T. E., Wang, J., Duke, C. L., … Kollman, P. A. (2010). AMBER 11. San Francisco, CA: University of California.
  • Casoni, A., Clerici, F., & Contini, A. (2013). Molecular dynamic simulation of mGluR5 amino terminal domain: essential dynamics analysis captures the agonist or antagonist behaviour of ligands. Journal of Molecular Graphics and Modelling, 41, 72–78.10.1016/j.jmgm.2013.02.002
  • Ceccherini-Silberstein, F., Malet, I., D’Arrigo, R., Antinori, A., Marcelin, A. G., & Perno, C. F. (2009). Characterization and structural analysis of HIV-1 integrase conservation. AIDS Reviews, 11, 17–29.
  • Chen, J. C., Krucinski, J., Miercke, L. J., Finer-Moore, J. S., Tang, A. H., Leavitt, A. D., & Stroud, R. M. (2000). 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, 97, 8233–8238.10.1073/pnas.150220297
  • Cheng, A. C., Coleman, R. G., Smyth, K. T., Cao, Q., Soulard, P., Caffrey, D. R., … Huang, E. S. (2007). Structure-based maximal affinity model predicts small-molecule druggability. Nature Biotechnology, 25, 71–75.10.1038/nbt1273
  • Cheng, Z., Zhang, Y., & Fu, W. (2010). QSAR study of carboxylic acid derivatives as HIV-1 Integrase inhibitors. European Journal of Medicinal Chemistry, 45, 3970–3980.10.1016/j.ejmech.2010.05.052
  • Cooper, D. A., Steigbigel, R. T., Gatell, J. M., Rockstroh, J. K., Katlama, C., Yeni, P., … Nguyen, B. Y. (2008). Subgroup and resistance analyses of raltegravir for resistant HIV-1 infection. New England Journal of Medicine, 359, 355–365.10.1056/NEJMoa0708978
  • Costantino, G., Entrena-Guadix, A., Macchiarulo, A., Gioiello, A., & Pellicciari, R. (2005). Molecular dynamics simulation of the ligand binding domain of farnesoid X receptor. Insights into helix-12 stability and coactivator peptide stabilization in response to agonist binding. Journal of Medicinal Chemistry, 48, 3251–3259.10.1021/jm049182o
  • DeLisi, C. (1980). The biophysics of ligand-receptor interactions. Quarterly Reviews of Biophysics, 13, 201–230.10.1017/S0033583500001657
  • Eijkelenboom, A. P., Lutzke, R. A., Boelens, R., Plasterk, R. H., Kaptein, R., & Hard, K. (1995). The DNA-binding domain of HIV-1 integrase has an SH3-like fold. Nature Structural Biology, 2, 807–810.10.1038/nsb0995-807
  • Eijkelenboom, A. P., Sprangers, R., Hard, K., Puras Lutzke, R. A., Plasterk, R. H., Boelens, R., & Kaptein, R. (1999). Refined solution structure of the c-terminal DNA-binding domain of human immunovirus-1 integrase. Proteins: Structure, Function, and Genetics, 36, 556–564.10.1002/(ISSN)1097-0134
  • Elcock, A. H., Gabdoulline, R. R., Wade, R. C., & McCammon, J. A. (1999). Computer simulation of protein–protein association kinetics: acetylcholinesterase-fasciculin. Journal of Molecular Biology, 291, 149–162.10.1006/jmbi.1999.2919
  • Ellison, V., Gerton, J., Vincent, K. A., & Brown, P. O. (1995). An essential interaction between distinct domains of HIV-1 integrase mediates assembly of the active multimer. Journal of Biological Chemistry, 270, 3320–3326.
  • Elsawy, K. M., Caves, L. S., & Twarock, R. (2010). The impact of viral RNA on the association rates of capsid protein assembly: Bacteriophage MS2 as a case study. Journal of Molecular Biology, 400, 935–947.10.1016/j.jmb.2010.05.037
  • ElSawy, K. M., Verma, C. S., Joseph, T. L., Lane, D. P., Twarock, R., & Caves, L. S. (2013). On the interaction mechanisms of a p53 peptide and nutlin with the MDM2 and MDMX proteins: A Brownian dynamics study. Cell Cycle, 12, 394–404.10.4161/cc.23511
  • Engelman, A., Bushman, F. D., & Craigie, R. (1993). Identification of discrete functional domains of HIV-1 integrase and their organization within an active multimeric complex. EMBO Journal, 12, 3269–3275.
  • Engelman, A., & Craigie, R. (1992). Identification of conserved amino acid residues critical for human immunodeficiency virus type 1 integrase function in vitro. Journal of Virology, 66, 6361–6369.
  • Engelman, A., Mizuuchi, K., & Craigie, R. (1991). HIV-1 DNA integration: Mechanism of viral DNA cleavage and DNA strand transfer. Cell, 67, 1211–1221.10.1016/0092-8674(91)90297-C
  • Ermak, D. L., & McCammon, J. A. (1978). Brownian dynamics with hydrodynamic interactions. The Journal of Chemical Physics, 69, 1352–1360.10.1063/1.436761
  • Fujiwara, T., & Craigie, R. (1989). Integration of mini-retroviral DNA: A cell-free reaction for biochemical analysis of retroviral integration. Proceedings of the National Academy of Sciences, 86, 3065–3069.10.1073/pnas.86.9.3065
  • Gabdoulline, R. R., & Wade, R. C. (1996). Effective charges for macromolecules in solvent. The Journal of Physical Chemistry, 100, 3868–3878.10.1021/jp953109f
  • Gabdoulline, R. R., & Wade, R. C. (1997). Simulation of the diffusional association of barnase and barstar. Biophysical Journal, 72, 1917–1929.10.1016/S0006-3495(97)78838-6
  • Gabdoulline, R. R., & Wade, R. C. (1998). Brownian dynamics simulation of protein–protein diffusional encounter. Methods, 14, 329–341.10.1006/meth.1998.0588
  • Garcia De La Torre, J., Huertas, M. L., & Carrasco, B. (2000). Calculation of hydrodynamic properties of globular proteins from their atomic-level structure. Biophysical Journal, 78, 719–730.10.1016/S0006-3495(00)76630-6
  • Gilson, M. K., & Zhou, H. X. (2007). Calculation of protein-ligand binding affinities. Annual Review of Biophysics and Biomolecular Structure, 36, 21–42.10.1146/annurev.biophys.36.040306.132550
  • Goff, S. P. (1992). Genetics of retroviral integration. Annual Review of Genetics, 26, 527–544.10.1146/annurev.ge.26.120192.002523
  • Goldgur, Y., Craigie, R., Cohen, G. H., Fujiwara, T., Yoshinaga, T., Fujishita, T., … Davies, D. R. (1999). Structure of the HIV-1 integrase catalytic domain complexed with an inhibitor: A platform for antiviral drug design. Proceedings of the National Academy of Sciences, 96, 13040–13043.10.1073/pnas.96.23.13040
  • Goldgur, Y., Dyda, F., Hickman, A. B., Jenkins, T. M., Craigie, R., & Davies, D. R. (1998). Three new structures of the core domain of HIV-1 integrase: An active site that binds magnesium. Proceedings of the National Academy of Sciences, 95, 9150–9154.10.1073/pnas.95.16.9150
  • Guiot, E., Carayon, K., Delelis, O., Simon, F., Tauc, P., Zubin, E., … Deprez, E. (2006). Relationship between the oligomeric status of HIV-1 integrase on DNA and enzymatic activity. Journal of Biological Chemistry, 281, 22707–22719.10.1074/jbc.M602198200
  • Gupta, P., Roy, N., & Garg, P. (2009). Docking-based 3D-QSAR study of HIV-1 integrase inhibitors. European Journal of Medicinal Chemistry, 44, 4276–4287.10.1016/j.ejmech.2009.07.010
  • Hare, S., Gupta, S. S., Valkov, E., Engelman, A., & Cherepanov, P. (2010). Retroviral intasome assembly and inhibition of DNA strand transfer. Nature, 464, 232–236.10.1038/nature08784
  • Hayward, S. (1999). Structural principles governing domain motions in proteins. Proteins, 36, 425–435.10.1002/(ISSN)1097-0134
  • Hayward, S., & Berendsen, H. J. (1998). Systematic analysis of domain motions in proteins from conformational change: New results on citrate synthase and T4 lysozyme. Proteins, 30, 144–154.10.1002/(ISSN)1097-0134
  • He, J., Xu, L., Zhang, S., Guan, J., Shen, M., Li, H., & Song, Y. (2013). Steered molecular dynamics simulation of the binding of the beta2 and beta3 regions in domain-swapped human cystatin C dimer. Journal of Molecular Modeling, 19, 825–832.10.1007/s00894-012-1609-7
  • Heuer, T. S., & Brown, P. O. (1998). Photo-cross-linking studies suggest a model for the architecture of an active human immunodeficiency virus type 1 integrase-DNA complex. Biochemistry, 37, 6667–6678.10.1021/bi972949c
  • Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A., & Simmerling, C. (2006). Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins: Structure, Function, and Bioinformatics, 65, 712–725.10.1002/prot.v65:3
  • Hornak, V., Okur, A., Rizzo, R. C., & Simmerling, C. (2006). HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations. Proceedings of the National Academy of Sciences, 103, 915–920.10.1073/pnas.0508452103
  • Hou, T., Wang, J., Li, Y., & Wang, W. (2010). Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations. Journal of Chemical Information Modeling, 51, 69–82. Retrieved from http://aidsinfo.nih.gov/guidelines
  • Hu, G., Wang, D., Liu, X., & Zhang, Q. (2010). A computational analysis of the binding model of MDM2 with inhibitors. Journal of Computer-Aided Molecular Design, 24, 687–697.10.1007/s10822-010-9366-0
  • Hu, G., Zhang, Q., & Chen, L. Y. (2011). Insights into scFv: Drug binding using the molecular dynamics simulation and free energy calculation. Journal of Molecular Modeling, 17, 1919–1926.10.1007/s00894-010-0892-4
  • Huggins, D. J., McKenzie, G. J., Robinson, D. D., Narvaez, A. J., Hardwick, B., Roberts-Thomson, M., … Payne, M. C. (2010). Computational analysis of phosphopeptide binding to the polo-box domain of the mitotic kinase PLK1 using molecular dynamics simulation. PLoS Comput Biol, 6, e1000880.
  • Janin, J. (1997). The kinetics of protein-protein recognition. Proteins, 28, 153–161.10.1002/(ISSN)1097-0134
  • Jaskolski, M., Alexandratos, J. N., Bujacz, G., & Wlodawer, A. (2009). Piecing together the structure of retroviral integrase, an important target in AIDS therapy. FEBS Journal, 276, 2926–2946.10.1111/ejb.2009.276.issue-11
  • Johnson, T. W., Tanis, S. P., Butler, S. L., Dalvie, D., Delisle, D. M., Dress, K. R., … Zhu, H. (2011). Design and synthesis of novel N-hydroxy-dihydronaphthyridinones as potent and orally bioavailable HIV-1 integrase inhibitors. Journal of Medicinal Chemistry, 54, 3393–3417.10.1021/jm200208d
  • Jones, K. S., Coleman, J., Merkel, G. W., Laue, T. M., & Skalka, A. M. (1992). Retroviral integrase functions as a multimer and can turn over catalytically. Journal of Biological Chemistry, 267, 16037–16040.
  • Jones, D. T., & Cozzetto, D. (2014). DISOPRED3: Precise disordered region predictions with annotated protein-binding activity. Bioinformatics, 31, 857–863.
  • Jorgensen, W. L., Chandrasekhar, J., Madura, J., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics, 79, 926–935.10.1063/1.445869
  • Katz, R. A., Merkel, G., Kulkosky, J., Leis, J., & Skalka, A. M. (1990). The avian retroviral IN protein is both necessary and sufficient for integrative recombination in vitro. Cell, 63, 87–95.10.1016/0092-8674(90)90290-U
  • Kim, J. H., Hartley, T. L., Curran, A. R., & Engelman, D. M. (2009). Molecular dynamics studies of the transmembrane domain of gp41 from HIV-1. Biochimica et Biophysica Acta (BBA) – Biomembranes, 1788, 1804–1812.10.1016/j.bbamem.2009.06.011
  • Krishnan, L., Li, X., Naraharisetty, H. L., Hare, S., Cherepanov, P., & Engelman, A. (2010). Structure-based modeling of the functional HIV-1 intasome and its inhibition. Proceedings of the National Academy of Sciences, 107, 15910–15915.10.1073/pnas.1002346107
  • Li, M., & Craigie, R. (2005). Processing of viral DNA ends channels the HIV-1 integration reaction to concerted integration. Journal of Biological Chemistry, 280, 29334–29339.10.1074/jbc.M505367200
  • Li, M., Mizuuchi, M., Burke, Jr., T. R., & Craigie, R. (2006). Retroviral DNA integration: Reaction pathway and critical intermediates. The EMBO Journal, 25, 1295–1304.10.1038/sj.emboj.7601005
  • Lins, R. D., Briggs, J. M., Straatsma, T. P., Carlson, H. A., Greenwald, J., Choe, S., & McCammon, J. A. (1999). Molecular dynamics studies on the HIV-1 integrase catalytic domain. Biophysical Journal, 76, 2999–3011.10.1016/S0006-3495(99)77453-9
  • Liu, S. Q., Liu, S. X., & Fu, Y. X. (2008). Molecular motions of human HIV-1 gp120 envelope glycoproteins. Journal of Molecular Modeling, 14, 857–870.10.1007/s00894-008-0327-7
  • Lodi, P. J., Ernst, J. A., Kuszewski, J., Hickman, A. B., Engelman, A., Craigie, R., … Gronenborn, A. M. (1995). Solution structure of the DNA binding domain of HIV-1 integrase. Biochemistry, 34, 9826–9833.10.1021/bi00031a002
  • Madrid, M., Jacobo-Molina, A., Ding, J., & Arnold, E. (1999). Major subdomain rearrangement in HIV-1 reverse transcriptase simulated by molecular dynamics. Proteins: Structure, Function, and Genetics, 35, 332–337.10.1002/(ISSN)1097-0134
  • Madrid, M., Lukin, J. A., Madura, J. D., Ding, J., & Arnold, E. (2001). Molecular dynamics of HIV-1 reverse transcriptase indicates increased flexibility upon DNA binding. Proteins: Structure, Function, and Genetics, 45, 176–182.10.1002/(ISSN)1097-0134
  • Mereghetti, P., Kokh, D., McCammon, J. A., & Wade, R. C. (2011). Diffusion and association processes in biological systems: Theory, computation and experiment. BMC Biophysics, 4, 1–6.10.1186/2046-1682-4-2
  • Miller, B. R., McGee, T. D., Swails, J. M., Homeyer, N., Gohlke, H., & Roitberg, A. E. (2012). MMPBSA.py: An efficient program for end-state free energy calculations. Journal of Chemical Theory and Computation, 8, 3314–3321.10.1021/ct300418h
  • Molteni, V., Greenwald, J., Rhodes, D., Hwang, Y., Kwiatkowski, W., Bushman, F. D., … Choe, S. (2001). Identification of a small-molecule binding site at the dimer interface of the HIV integrase catalytic domain. Acta Crystallographica Section D Biological Crystallography, 57, 536–544.10.1107/S0907444901001652
  • Moreno, S., Lopez Aldeguer, J., Arribas, J. R., Domingo, P., Iribarren, J. A., Ribera, E., … Pulido, F. (2010). The future of antiretroviral therapy: Challenges and needs. Journal of Antimicrobial Chemotherapy, 65, 827–835.10.1093/jac/dkq061
  • Neamati, N. (2011). HIV-1 Integrase inhibitor design: overview and historical perspectives. In N. Neamati (Eds.), HIV-1 integrase: Mechanism and inhibitor design (p. 165–196). Hoboken, NJ: John Wiley & Sons. doi: 10.1002/9781118015377.ch13
  • Northrup, S. H., Allison, S. A., & McCammon, J. A. (1984). Brownian dynamics simulation of diffusion-influenced bimolecular reactions. The Journal of Chemical Physics, 80, 1517–1524.10.1063/1.446900
  • Pang, X., Qin, S., & Zhou, H. X. (2011). Rationalizing 5000-fold differences in receptor-binding rate constants of four cytokines. Biophysical Journal, 101, 1175–1183.10.1016/j.bpj.2011.06.056
  • Plewe, M. B., Butler, S. L., Dress, K. R., Hu, Q., Johnson, T. W., Kuehler, J. E., … Zhang, J. (2009). Azaindole hydroxamic acids are potent HIV-1 integrase inhibitors. Journal of Medicinal Chemistry, 52, 7211–7219.10.1021/jm900862n
  • Podtelezhnikov, A. A., Gao, K., Bushman, F. D., & McCammon, J. A. (2003). Modeling HIV-1 integrase complexes based on their hydrodynamic properties. Biopolymers, 68, 110–120.10.1002/(ISSN)1097-0282
  • Pommier, Y., Johnson, A. A., & Marchand, C. (2005). Integrase inhibitors to treat HIV/Aids. Nature Reviews Drug Discovery, 4, 236–248.10.1038/nrd1660
  • Rastelli, G., Del Rio, A., Degliesposti, G., & Sgobba, M. (2010). Fast and accurate predictions of binding free energies using MM-PBSA and MM-GBSA. Journal of Computational Chemistry, 31, 797–810.
  • Sangeetha, B., Muthukumaran, R., & Amutha, R. (2014). The dynamics of interconverting D- and E-forms of the HIV-1 integrase N-terminal domain. European Biophysics Journal, 43, 485–498.10.1007/s00249-014-0979-4
  • Sangeetha, B., Muthukumaran, R., & Amutha, R. (2015). Structural dynamics of native and V260E mutant C-terminal domain of HIV-1 integrase. Journal of Computer-Aided Molecular Design, 29, 371–385.10.1007/s10822-015-9830-y
  • Serrao, E., Odde, S., Ramkumar, K., & Neamati, N. (2009). Raltegravir, elvitegravir, and metoogravir: the birth of ‘me-too’ HIV-1 integrase inhibitors. Retrovirology, 6, 25.10.1186/1742-4690-6-25
  • Sharma, H., Patil, S., Sanchez, T. W., Neamati, N., Schinazi, R. F., & Buolamwini, J. K. (2011). Synthesis, biological evaluation and 3D-QSAR studies of 3-keto salicylic acid chalcones and related amides as novel HIV-1 integrase inhibitors. Bioorganic & Medicinal Chemistry, 19, 2030–2045.10.1016/j.bmc.2011.01.047
  • Sherman, P. A., & Fyfe, J. A. (1990). Human immunodeficiency virus integration protein expressed in Escherichia coli possesses selective DNA cleaving activity. Proceedings of the National Academy of Sciences, 87, 5119–5123.10.1073/pnas.87.13.5119
  • Spaar, A., Dammer, C., Gabdoulline, R. R., Wade, R. C., & Helms, V. (2006). Diffusional encounter of barnase and barstar. Biophysical Journal, 90, 1913–1924.10.1529/biophysj.105.075507
  • Spaar, A., Flock, D., & Helms, V. (2009). Association of cytochrome c with membrane-bound cytochrome c oxidase proceeds parallel to the membrane rather than in bulk solution. Biophysical Journal, 96, 1721–1732.10.1016/j.bpj.2008.11.052
  • Stoica, I., Sadiq, S. K., & Coveney, P. V. (2008). Rapid and accurate prediction of binding free energies for saquinavir-bound HIV-1 proteases. Journal of the American Chemical Society, 130, 2639–2648.10.1021/ja0779250
  • Summa, V., Petrocchi, A., Bonelli, F., Crescenzi, B., Donghi, M., Ferrara, M., … Rowley, M. (2008). Discovery of raltegravir, a potent, selective orally bioavailable HIV-integrase inhibitor for the treatment of HIV-AIDS infection. Journal of Medicinal Chemistry, 51, 5843–5855.10.1021/jm800245z
  • Tanis, S. P., Plewe, M. B., Johnson, T. W., Butler, S. L., Dalvie, D., DeLisle, D., … Zhu, H. (2010). Azaindole N-methyl hydroxamic acids as HIV-1 integrase inhibitors-II. The impact of physicochemical properties on ADME and PK. Bioorganic & Medicinal Chemistry Letters, 20, 7429–7434.10.1016/j.bmcl.2010.10.022
  • Telvekar, V. N., & Patel, K. N. (2011). Pharmacophore development and docking studies of the HIV-1 integrase inhibitors derived from N-methylpyrimidones, dihydroxypyrimidines, and bicyclic pyrimidinones. Chemical Biology & Drug Design, 78, 150–160.10.1111/j.1747-0285.2011.01130.x
  • Vijayakumar, M., Wong, K. Y., Schreiber, G., Fersht, A. R., Szabo, A., & Zhou, H. X. (1998). Electrostatic enhancement of diffusion-controlled protein-protein association: comparison of theory and experiment on barnase and barstar. Journal of Molecular Biology, 278, 1015–1024.10.1006/jmbi.1998.1747
  • Villa, A., Wohnert, J., & Stock, G. (2009). Molecular dynamics simulation study of the binding of purine bases to the aptamer domain of the guanine sensing riboswitch. Nucleic Acids Research, 37, 4774–4786.10.1093/nar/gkp486
  • Volberding, P. A., & Deeks, S. G. (2010). Antiretroviral therapy and management of HIV infection. The Lancet, 376, 49–62.10.1016/S0140-6736(10)60676-9
  • Wang, J. Y., Ling, H., Yang, W., & Craigie, R. (2001). Structure of a two-domain fragment of HIV-1 integrase: implications for domain organization in the intact protein. The EMBO Journal, 20, 7333–7343.10.1093/emboj/20.24.7333
  • Weiser, J., Shenkin, P. S., & Still, W. C. (1999). Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO). Journal of Computational Chemistry, 20, 217–230.10.1002/(ISSN)1096-987X
  • Wielens, J., Crosby, I. T., & Chalmers, D. K. (2005). A three-dimensional model of the human immunodeficiency virus type 1 integration complex. Journal of Computer-Aided Molecular Design, 19, 301–317.10.1007/s10822-005-5256-2
  • Xue, W., Jin, X., Ning, L., Wang, M., Liu, H., & Yao, X. (2012). Exploring the molecular mechanism of cross-resistance to HIV-1 integrase strand transfer inhibitors by molecular dynamics simulation and residue interaction network analysis. Jouranl of Chemical Information and Modeling, 53, 210–222.
  • Xue, W., Liu, H., & Yao, X. (2011). Molecular mechanism of HIV-1 integrase-vDNA interactions and strand transfer inhibitor action: a molecular modeling perspective. Journal of Computational Chemistry, 33, 527–536.
  • Yin, Z., Shi, K., Banerjee, S., Pandey, K. K., Bera, S., Grandgenett, D. P., & Aihara, H. (2016). Crystal structure of the Rous sarcoma virus intasome. Nature, 530, 362–366.10.1038/nature16950
  • Yokoyama, M., Naganawa, S., Yoshimura, K., Matsushita, S., & Sato, H. (2012). Structural dynamics of HIV-1 envelope Gp120 outer domain with V3 loop. PLoS One, 7, e37530.10.1371/journal.pone.0037530

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