References
- Nguyen JT, Kato K, Kumada HO, et al. Maintaining potent HTLV-I protease inhibition without the P3-cap moiety in small tetrapeptidic inhibitors. Bioorg Med Chem Lett 2011;21:1832–7
- Kumada HO, Nguyen JT, Kakizawa T, et al. Development of [Ile(4)(0)]HTLV-I protease inhibition assay using novel fluorogenic and chromogenic substrate. J Pept Sci 2011;17:569–75
- Matsuoka M. Human T-cell leukemia virus type I (HTLV-I) infection and the onset of adult T-cell leukemia (ATL). Retrovirology 2005;2:27–40
- Renjifo B, Chou K, Soto Ramirez L, et al. Human T cell leukemia virus type I (HTLV-I) molecular genotypes and disease outcome. J Acquir Immune Defic Syndr Hum Retrovirol 1996;13:S146–53
- Tozser J, Weber IT. The protease of human T-cell leukemia virus type-1 is a potential therapeutic target. Curr Pharm Des 2007;13:1285–94
- Chen X, Tsiang M, Yu F, 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;380:504–19
- Hamasaki T, Toyama M, Aoyama H, et al. Selective inhibition of HTLV-1-infected cell proliferation by a novel tetramethylnaphthalene derivative. Anticancer Res 2012;31:2241–7
- Rowan AG, Bangham CR. Is there a role for HTLV-1-specific CTL in adult T-cell leukemia/lymphoma? Leuk Res Treatment 2012;8:2090–3219
- Demir A, Oguariri RM, Magis A, et al. Kinetic characterization of newly discovered inhibitors of various constructs of human T-cell leukemia virus-1 (HTLV-1) protease and their effect on HTLV-1-infected cells. Antivir Ther 2012;17:883–92
- Gulnik S, Erickson JW, Xie D. HIV protease: enzymes function and drug resistance. Vitam Horm 2000;58:213–56
- Kadas J, Weber IT, Bagossi P, et al. Narrow substrate specificity and sensitivity toward ligand-binding site mutations of human T-cell Leukemia virus type 1 protease. J Biol Chem 2004;25:27148–57
- Li M, Laco GS, Jaskolski M, et al. Crystal structure of human T cell leukemia virus protease, a novel target for anticancer drug design. Proc Natl Acad Sci USA 2005;102:18332–7
- Nguyen JT, Kato K, Hidaka K, et al. Design and synthesis of several small-size HTLV-I protease inhibitors with different hydrophilicity profiles. Bioorg Med Chem Lett 2011;21:2425–9
- Sperka T, Miklossy G, Tie Y, et al. Bovine leukemia virus protease: comparison with human T-lymphotropic virus and human immunodeficiency virus proteases. J Gen 2007;88:2052–63
- Alfonso Y, Monzote L. HIV Protease inhibitors: effect on the opportunistic protozoan parasites. Open Med Chem J 2011;5:40–50
- Rucker P, Horn AH, Meiselbach H, Sticht H. A comparative study of HIV-1 and HTLV-I protease structure and dynamics reveals a conserved residue interaction network. J Mol Model 2011;17:2693–705
- Epik version 2.3, Schrödinger, LLC, New York (NY); 2012
- Impact version 5.8, Schrödinger, LLC, New York (NY); 2012
- Prime version 2.3, Schrödinger, LLC, New York (NY); 2012
- Shafreen RM, Selvaraj C, Singh SK, Pandian SK. Exploration of fluoroquinolone resistance in Streptococcus pyogenes: comparative structure analysis of wild-type and mutant DNA gyrase. J Mol Recognit 2013;26:276–85
- LigPrep, version 2.6, Schrödinger, LLC, New York (NY); 2012
- Wu X, Ohrngren P, Ekegren JK, et al. Two-carbon-elongated HIV-1 protease inhibitors with a tertiary-alcohol-containing transition-state mimic. J Med Chem 2008;51:1053–7
- Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994;22:4673–80
- Pettersen EF, Goddard TD, Huang CC, et al. UCSF Chimera – a visualization system for exploratory research and analysis. J Comput Chem 2004;25:1605–12
- SiteMap, version 2.6, Schrödinger, LLC, New York (NY); 2012
- Das D, Koh Y, Tojo Y, et al. Prediction of potency of protease inhibitors using free energy simulations with polarizable quantum mechanics-based ligand charges and a hybrid water model. J Chem Inf Model 2009;49:2851–62
- Tripathi SK, Selvaraj C, Singh SK, Reddy KK. Molecular docking, QPLD, and ADME prediction studies on HIV-1 integrase leads. Med Chem Res 2012;21:4239–51
- Kalyaanamoorthy S, Chen YP. Quantum polarized ligand docking investigation to understand the significance of protonation states in histone deacetylase inhibitors. J Mol Graph Model 2013;44:44–53
- Chung JY, Hah JM, Cho AE. Correlation between performance of QM/MM docking and simple classification of binding sites. J Chem Inf Model 2009;49:2382–7
- Cho AE, Guallar V, Berne BJ, Friesner R. Importance of accurate charges in molecular docking: quantum mechanical/molecular mechanical (QM/MM) approach. J Comput Chem 2005;26:915–31
- Cho AE, Rinaldo D. Extension of QM/MM docking and its applications to metalloproteins. J Comput Chem 2009;30:2609–16
- Vijayalakshmi P, Selvaraj C, Singh SK, et al. Exploration of the binding of DNA binding ligands to Staphylococcal DNA through QM/MM docking and molecular dynamics simulation. J Biomol Struct Dyn 2013;31:561–71
- Mobley DL, Dill KA. Binding of small-molecule ligands to proteins: “what you see” is not always “what you get". Structure 2009;17:489–8
- Balaji B, Ramanathan M. Prediction of estrogen receptor beta ligands potency and selectivity by docking and MM-GBSA scoring methods using three different scaffolds. J Enzyme Inhib Med Chem 2012;27:832–44
- Tripathi SK, Singh SK, Singh P, et al. Exploring the selectivity of a ligand complex with CDK2/CDK1: a molecular dynamics simulation approach. J Mol Recognit 2012;25:504–12
- Selvaraj C, Singh SK, Tripathi SK, et al. In silico screening of indinavir-based compounds targeting proteolytic activity in HIV PR: binding pocket fit approach. Med Chem Res 2012;21:4060–8
- Pronk S, Pall S, Schulz R, et al. GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics 2013;29:845–54
- Schuttelkopf AW, van Aalten DM. PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr D Biol Crystallogr 2004;29:1355–63
- Van Der Spoel D, Lindahl E, Hess B, et al. GROMACS: fast, flexible, and free. J Comput Chem 2005;26:1701–18
- Fazil MH, Kumar S, Farmer R, et al. Binding efficiencies of carbohydrate ligands with different genotypes of cholera toxin B: molecular modeling, dynamics and docking simulation studies. J Mol Model 2012;18:1–10
- Shuker SB, Mariani VL, Herger BE, Dennison KJ. Understanding HTLV-I protease. Chem Biol 2003;10:373–80
- Singh P, Singh SK, Selvaraj SK, Singh RK. In silico study on HIV-PRIs substructures to terminate proteolytic activity in HTLV. J Biomol Struct Dyn 2013;31:127