Molecular dynamics and MM/GBSA-integrated protocol probing the correlation between biological activities and binding free energies of HIV-1 TAR RNA inhibitors

References

• Alonso, H. , Bliznyuk, A. A. , & Gready, J. E. (2006). Combining docking and molecular dynamic simulations in drug design. Medicinal Research Reviews , 26 , 531–568. doi:10.1002/med.20067
   PubMed Web of Science ®Google Scholar
• Andersen, H. C. (1983). Rattle: A “velocity” version of the shake algorithm for molecular dynamics calculations. Journal of Computational Physics , 52 , 24–34. doi:10.1016/0021-9991(83)90014-1
   Web of Science ®Google Scholar
• Aqvist, J. , Medina, C. , & Samuelsson, J. E. (1994). A new method for predicting binding affinity in computer-aided drug design. Protein Engineering, Design & Selection , 7 , 385–391. doi:10.1093/protein/7.3.385
   Web of Science ®Google Scholar
• Athanassiou, Z. , Dias, R. L. , Moehle, K. , Dobson, N. , Varani, G. , & Robinson, J. A. (2004). Structural mimicry of retroviral tat proteins by constrained β-hairpin peptidomimetics: Ligands with high affinity and selectivity for viral TAR RNA regulatory elements. Journal of the American Chemical Society , 126 , 6906–6913. doi:10.1021/ja0497680
   PubMed Web of Science ®Google Scholar
• Athanassiou, Z. , Patora, K. , Dias, R. L. , Moehle, K. , Robinson, J. A. , & Varani, G. (2007). Structure-guided peptidomimetic design leads to nanomolar beta-hairpin inhibitors of the Tat-TAR interaction of bovine immunodeficiency virus. Biochemistry , 46 , 741–751. doi:10.1021/bi0619371
   PubMed Web of Science ®Google Scholar
• Bardaro, M. F. , Shajani, Z. , Patora-Komisarska, K. , Robinson, J. A. , & Varani, G. (2009). How binding of small molecule and peptide ligands to HIV-1 TAR alters the RNA motional landscape. Nucleic Acids Research , 37 , 1529–1540. doi:10.1093/nar/gkn1074
   PubMed Web of Science ®Google Scholar
• Berendsen, H. J. C. , Grigera, J. R. , & Straatsma, T. P. (1987). The missing term in effective pair potentials. The Journal of Physical Chemistry , 91 , 6269–6271. doi:10.1021/j100308a038
   Web of Science ®Google Scholar
• Bieniasz, P. D. , Grdina, T. A. , Bogerd, H. P. , & Cullen, B. R. (1998). Recruitment of a protein complex containing Tat and cyclin T1 to TAR governs the species specificity of HIV-1 Tat. The EMBO Journal , 17 , 7056–7065. doi:10.1093/emboj/17.23.7056
   PubMed Web of Science ®Google Scholar
• Bieniasz, P. D. , Grdina, T. A. , Bogerd, H. P. , & Cullen, B. R. (1999). Recruitment of cyclin T1/P-TEFb to an HIV type 1 long terminal repeat promoter proximal RNA target is both necessary and sufficient for full activation of transcription. Proceedings of the National Academy of Sciences of the United States of America , 96 , 7791–7796. doi:10.1073/pnas.96.14.7791
   PubMed Web of Science ®Google Scholar
• Biswas, D. K. , Salas, T. R. , Wang, F. , Ahlers, C. M. , Dezube, B. J. , & Pardee, A. B. (1995). A Tat-induced auto-up-regulatory loop for superactivation of the human immunodeficiency virus type 1 promoter. Journal of Virology , 69 , 7437–7444.
   PubMed Web of Science ®Google Scholar
• Carlsson, J. , Boukharta, L. , & Aqvist, J. (2008). Combining Docking, molecular dynamics and the linear interaction energy method to predict binding modes and affinities for non-nucleoside inhibitors to HIV-1 reverse transcriptase. Journal of Medicinal Chemistry , 51 , 2648–2656. doi:10.1021/jm7012198
   PubMed Web of Science ®Google Scholar
• Chen, F. , Liu, H. , Sun, H. , Pan, P. , Li, Y. , Li, D. , & Hou, T. (2016). Assessing the performance of the MM/PBSA and MM/GBSA methods. 6. Capability to predict protein-protein binding free energies and re-rank binding poses generated by protein-protein docking. Physical Chemistry Chemical Physics , 18 , 22129–22139. doi:10.1039/c6cp03670h
   PubMed Web of Science ®Google Scholar
• Churcher, M. J. , Lamont, C. , Hamy, F. , Dingwall, C. , Green, S. M. , Lowe, A. D. , … Karn, J. (1993). High affinity binding of TAR RNA by the human immunodeficiency virus type-1 tat protein requires base-pairs in the RNA stem and amino acid residues flanking the basic region. Journal of Molecular Biology , 230 , 90–110. doi:10.1006/jmbi.1993.1128
   PubMed Web of Science ®Google Scholar
• Daelemans, D. , Schols, D. , Witvrouw, M. , Pannecouque, C. , Hatse, S. , van Dooren, S. , … VanDamme, A. M. (2000). A second target for the peptoid Tat/transactivation response element inhibitor CGP64222: Inhibition of human immunodeficiency virus replication by blocking CXC-chemokine receptor 4-mediated virus entry. Molecular Pharmacology , 57 , 116–124.
   PubMed Web of Science ®Google Scholar
• Davidson, A. , Leeper, T. C. , Athanassiou, Z. , Patora-Komisarska, K. , Karn, J. , Robinson, J. A. , & Varani, G. (2009). Simultaneous recognition of HIV-1 TAR RNA bulge and loop sequences by cyclic peptide mimics of Tat protein. Proceedings of the National Academy of Sciences of the United States of America , 106 , 11931–11936. doi:10.1073/pnas.0900629106
   PubMed Web of Science ®Google Scholar
• Davidson, A. , Patora-Komisarska, K. , Robinson, J. A. , & Varani, G. (2011). Essential structural requirements for specific recognition of HIV TAR RNA by peptide mimetics of Tat protein. Nucleic Acids Research , 39 , 248–256. doi:10.1093/nar/gkq713
   PubMed Web of Science ®Google Scholar
• Davis, B. , Afshar, M. , Varani, G. , Murchie, A. I. H. , Karn, J. , Lentzen, G. , … Aboul-Ela, F. (2004). Rational design of inhibitors of HIV-1 TAR RNA through the stabilisation of electrostatic “Hot Spots”. Journal of Molecular Biology , 336 , 343–356. doi:10.1016/j.jmb.2003.12.046
   PubMed Web of Science ®Google Scholar
• El-Sayed, W. A. , El-Essawy, F. A. , Ali, O. M. , Nasr, B. S. , Abdalla, M. M. , & Abdel-Rahman, A. A. (2010). Synthesis and antiviral evaluation of new 2, 5-disubstituted 1, 3, 4-oxadiazole derivatives and their acyclic nucleoside analogues. Monatshefte für Chemie – Chemical Monthly , 141 , 1021–1028. doi:10.1007/s00706-010-0360-y
   Google Scholar
• Ferrara, P. , Gohlke, H. , Price, D. J. , Klebe, G. , & Brooks III, C. L. (2004). Assessing scoring functions for protein−ligand interactions. Journal of Medicinal Chemistry , 47 , 3032–3047. doi:10.1021/jm030489h
   PubMed Web of Science ®Google Scholar
• Friesner, R. A. , Banks, J. L. , Murphy, R. B. , Halgren, T. A. , Klicic, J. J. , Mainz, D. T. , … Shenkin, P. S. (2004). Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. Journal of Medicinal Chemistry , 47 , 1739–1749. doi:10.1021/jm0306430
   PubMed Web of Science ®Google Scholar
• Friesner, R. A. , Murphy, R. B. , Repasky, M. P. , Frye, L. L. , Greenwood, J. R. , Halgren, T. A. , … Mainz, D. T. (2006). Extra Precision glide: Docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. Journal of Medicinal Chemistry , 49 , 6177–6196. doi:10.1021/jm051256o
   PubMed Web of Science ®Google Scholar
• Garber, M. E. , Wei, P. , KewalRamani, V. N. , Mayall, T. P. , Herrmann, C. H. , Rice, A. P. , … Jones, K. A. (1998). The interaction between HIV-1 Tat and human cyclin T1 requires zinc and a critical cysteine residue that is not conserved in the murine CycT1 protein. Genes & Development , 12 , 3512–3527. doi:10.1101/gad.12.22.3512
   PubMed Web of Science ®Google Scholar
• Gatignol, A. , Buckler-White, A. , Berkhout, B. , & Jeang, K. T. (1991). Characterization of a human TAR RNA-binding protein that activates the HIV-1 LTR. Science , 251 , 1597–1600. doi:10.1126/science.2011739
   PubMed Web of Science ®Google Scholar
• Gelman, M. A. , Richter, S. , Cao, H. , Umezawa, N. , Gellman, S. H. , & Rana, T. M. (2003). Selective binding of TAR RNA by a Tat-derived β-peptide. Organic Letters , 5 , 3563–3565. doi:10.1021/ol034977v
   PubMed Web of Science ®Google Scholar
• Gilbert, P. B. , McKeague, I. W. , Eisen, G. , Mullins, C. , Guéye-NDiaye, A. , Mboup, S. , & Kanki, P. J. (2003). Comparison of HIV-1 and HIV-2 infectivity from a prospective cohort study in Senegal. Statistics in Medicine , 22 , 573–593. doi:10.1002/sim.1342
   PubMed Web of Science ®Google Scholar
• Gohlke, H. , & Klebe, G. (2002). Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors. AngewandteChemie International Edition , 41 , 2644–2676. doi:10.1002/1521-3773(20020802)41:15<2644::AID-ANIE2644>3.0.CO;2-O
   PubMed Web of Science ®Google Scholar
• Gupta, M. K. , & Misra, K. (2014). Atom-based 3D-QSAR, molecular docking and molecular dynamics simulation assessment of inhibitors for thyroid hormone receptor α and β. Journal of Molecular Modeling , 20 , 2286. doi:10.1007/s00894-014-2286-5
   PubMed Web of Science ®Google Scholar
• Hamy, F. , Felder, E. R. , Heizmann, G. , Lazdins, J. , Aboul-ela, F. , Varani, G. , … Klimkait, T. (1997). An inhibitor of the Tat/TAR RNA interaction that effectively suppresses HIV-1 replication. Proceedings of the National Academy of Sciences of the United States of America , 94 , 3548–3553.
   PubMed Web of Science ®Google Scholar
• Hayes, J. M. , & Archontis, G. (2012). This is a chapter. In L. Wang (Ed.), Molecular dynamics-studies of synthetic and biological macromolecules: And MM-GB(PB)SA calculations of protein-ligand binding free energies (pp. 171–190). Rijeka: InTech.
   Google Scholar
• Hou, T. , & Yu, R. (2007). Molecular dynamics and free energy studies on the wild-type and double mutant HIV-1 protease complexed with amprenavir and two amprenavir-related inhibitors: Mechanism for binding and drug resistance. Journal of Medicinal Chemistry , 50 , 1177–1188. doi:10.1021/jm0609162
   PubMed Web of Science ®Google Scholar
• Hou, T. , Wang, J. , Li, Y. , & Wang, W. (2011a). 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 and Modeling , 51 , 69–82. doi:10.1021/ci100275a
   PubMed Web of Science ®Google Scholar
• Hou, T. , Wang, J. , Li, Y. , & Wang, W. (2011b). Assessing the performance of the MM/PBSA and MM/GBSA methods: II. The accuracy of ranking poses generated from docking. Journal of Computational Chemistry , 32 , 866–877. doi:10.1002/jcc.21666
   PubMed Web of Science ®Google Scholar
• Hou, T. , Li, N. , Li, Y. , & Wang, W. (2012). Characterization of domain-peptide interaction interface: Prediction of SH3 domain-mediated protein-protein interaction network in yeast by generic structure-based models. Journal of Proteome Research , 11 , 2982–2995. doi:10.1021/pr3000688
   PubMed Web of Science ®Google Scholar
• Huq, I. , Wang, X. , & Rana, T. M. (1997). Specific recognition of HIV-1 TAR RNA by a D-Tat peptide. Nature Structural Biology , 4 , 881–882. doi:10.1038/nsb1197-881
   PubMedGoogle Scholar
• Huq, I. , Ping, Y. H. , Tamilarasu, N. , & Rana, T. M. (1999). Controlling human immunodeficiency virus type 1 gene expression by unnatural peptides. Biochemistry , 38 , 5172–5177. doi:10.1021/bi982638h
   PubMed Web of Science ®Google Scholar
• Kalra, P. , Reddy, T. V. , & Jayaram, B. (2001). Free energy component analysis for drug design: A case study of HIV-1 protease−inhibitor binding. Journal of Medicinal Chemistry , 44 , 4325–4338. doi:10.1021/jm010175z
   PubMed Web of Science ®Google Scholar
• Kaminski, G. A. , & Friesner, R. A. (2001). Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. The Journal of Physical Chemistry B , 105 , 6474–6487. doi:10.1021/jp003919d
   Web of Science ®Google Scholar
• Kesavan, V. , Tamilarasu, N. , Cao, H. , & Rana, T. M. (2002). A new class of RNA-binding oligomers: Peptoid amide and ester analogues. Bioconjugate Chemistry , 13 , 1171–1175. doi:10.1021/bc0255642
   PubMed Web of Science ®Google Scholar
• Kirkwood, J. G. (1935). Statistical mechanics of fluid mixtures. The Journal of Chemical Physics , 3 , 300–313. doi:10.1063/1.1749657
   Web of Science ®Google Scholar
• Kollman, P. A. , Massova, I. , Reyes, C. , Kuhn, B. , Huo, S. , Chong, L. , … Cheatham III, T. E. (2000). Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. Accounts of Chemical Resesearch , 33 , 889–897. doi:10.1021/ar000033j
   PubMed Web of Science ®Google Scholar
• Kulinski, T. , Kulinska, K. , Sarzynska, J. , & Adamiak, R. W. (2005). Conformational dynamics of RNA hairpins-regulatory elements of the HIV-1 genome. Biophysical Journal ,. 88 , 402a–402a.
   Web of Science ®Google Scholar
• Lalonde, M. S. , Lobritz, M. A. , Ratcliff, A. , Chamanian, M. , Athanassiou, Z. , Tyagi, M. , … Arts, E. J. (2011). Inhibition of both HIV-1 reverse transcription and gene expression by a cyclic peptide that binds the Tat-transactivating response element (TAR) RNA. PLoS pathogens , 7 , e1002038. doi:10.1371/journal.ppat.1002038
   PubMed Web of Science ®Google Scholar
• Leeper, T. C. , Athanassiou, Z. , Dias, R. L. A. , Robinson, J. A. , & Varani, G. (2005). TAR RNA recognition by a cyclic peptidomimetic of tat protein. Biochemistry , 44 , 12362–12372. doi:10.1021/bi0510532
   PubMed Web of Science ®Google Scholar
• Li, J. , Abel, R. , Zhu, K. , Cao, Y. , Zhao, S. , & Friesner, R. A. (2011). The VSGB 2.0 model: A next generation energy model for high resolution protein structure modelling. Proteins , 79 , 2794–2812. doi:10.1002/prot.23106
   PubMed Web of Science ®Google Scholar
• Li, C. H. , Zuo, Z. C. , Su, J. G. , Xu, X. J. , & Wang, C. X. (2013). The interactions and recognition of cyclic peptide mimetics of Tat with HIV-1 TAR RNA: A molecular dynamics simulation study. Journal of Biomolecular Structure and Dynamics , 31 , 276–287. doi:10.1080/07391102.2012.698248
   PubMed Web of Science ®Google Scholar
• Lyne, P. D. , Lamb, M. L. , & Saeh, J. C. (2006). Accurate prediction of the relative potencies of members of a series of kinase inhibitors using molecular docking and MM-GBSA scoring. Journal of Medicinal Chemistry , 49 , 4805–4808. doi:10.1021/jm060522a
   PubMed Web of Science ®Google Scholar
• Mancebo, H. S. Y. , Lee, G. , Flygare, J. , Tomassini, J. , Luu, P. , Zhu, Y. , … Flores, O. (1997). P-TEFb kinase is required for HIV Tat transcriptional activation in vivo and in vitro. Genes & Development , 11 , 2633–2644. doi:10.1101/gad.11.20.2633
   PubMed Web of Science ®Google Scholar
• Meher, B. R. , & Wang, Y. (2012). Interaction of I50V mutant and I50L/A71V double mutant HIV-protease with inhibitor TMC114 (darunavir): molecular dynamics simulation and binding free energy studies. The Journal of Physical Chemistry B , 2012 (116), 1884–1900. doi:10.1021/jp2074804
   Web of Science ®Google Scholar
• Moehle, K. , Athanassiou, Z. , Patora, K. , Davidson, A. , Varani, G. , & Robinson, J. A. (2007). Design of beta-hairpin peptidomimetics that inhibit binding of alpha-helical HIV-1 Rev protein to the rev response element RNA. AngewandteChemie International Edition , 46 , 9101–9104. doi:10.1002/anie.200702801
   PubMed Web of Science ®Google Scholar
• Mu, Y. , & Stock, G. (2006). Conformational dynamics of RNA-peptide binding: A molecular dynamics simulation study. Biophysical Journal , 90 , 391–399. doi:10.1529/biophysj.105.069559
   PubMed Web of Science ®Google Scholar
• Munnaluri, R. , Sivan, S. K. , & Manga, V. (2015). Molecular docking and MM/GBSA integrated protocol for designing small molecule inhibitors against HIV-1 gp41. Medicinal Chemistry Research , 24 , 829–841. doi:10.1007/s00044-014-1185-8
   Web of Science ®Google Scholar
• Musselman, C. , Al-Hashimi, H. M. , & Andricioaei, I. (2007). iRED analysis of TAR RNA reveals motional coupling, long-range correlations, and a dynamical hinge. Biophysical Journal , 93 , 411–422. doi:10.1529/biophysj.107.104620
   PubMed Web of Science ®Google Scholar
• Nifosi, R. , Reyes, C. M. , & Kollman, P. A. (2000). Molecular dynamics studies of the HIV-1 TAR and its complex with argininamide. Nucleic Acids Research , 28 , 4944–4955. doi:10.1093/nar/28.24.4944
   PubMed Web of Science ®Google Scholar
• Peddi, S. R. , Sivan, S. K. , & Manga, V. (2016). An integrated molecular modeling approach for in silico design of new tetracyclic derivatives as ALK inhibitors. Journal of Receptors and Signal Transduction , 36 , 488–504. doi:10.3109/10799893.2015.1130057
   PubMed Web of Science ®Google Scholar
• Reyes, C. M. , Nifosi, R. , Frankel, A. D. , & Kollman, P. A. (2001). Molecular dynamics and binding specificity analysis of the bovine immunodeficiency virus BIV Tat-TAR complex. Biophysical Journal , 80 , 2833–2842. doi:10.1016/S0006-3495(01)76250-9
   PubMed Web of Science ®Google Scholar
• Richter, S. N. , & Palù, G. (2006). Inhibitors of HIV-1 Tat-mediated transactivation. Current Medicinal Chemistry , 13 , 1305–1315. doi:10.2174/092986706776872989
   PubMed Web of Science ®Google Scholar
• Rizzo, R. C. , Tirado-Rives, J. , & Jorgensen, W. L. (2001). Estimation of binding affinities for HEPT and nevirapine analogues with HIV-1 reverse transcriptase via Monte Carlo simulations. Journal of Medicinal Chemistry , 44 , 145–154. doi:10.1021/jm000255n
   PubMed Web of Science ®Google Scholar
• Runyon, S. T. , & Puglisi, J. D. (2003). Design of a cyclic peptide that targets a viral RNA. Journal of the American Chemical Society , 125 , 15704–15705. doi:10.1021/ja036344h
   PubMed Web of Science ®Google Scholar
• Schrödinger, LLC . (2010). Glide (5.6) . New York, NY . https://www.schrodinger.com.
   Google Scholar
• Shaw, D. E. (2014). Desmond (3.8) . New York, NY . http://www.deshawresearch.com.
   Google Scholar
• Srinivasan, J. , Miller, J. , Kollman, P. A. , & Case, D. A. (1998). Continuum solvent studies of the stability of RNA hairpin loops and helices. Journal of Biomolecular Structure and Dynamics , 16 , 671–682. doi:10.1080/07391102.1998.10508279
   PubMed Web of Science ®Google Scholar
• Srivani, P. , Srinivas, E. , Raghu, R. , & Sastry, G. N. (2007). Molecular modeling studies of pyridopurinone derivatives-potential phosphodiesterase 5 inhibitors. Journal of Molecular Graphics and Modelling , 26 , 378–390. doi:10.1016/j.jmgm.2007.01.007
   PubMed Web of Science ®Google Scholar
• Srivastava, H. K. , & Sastry, G. N. (2013). Efficient estimation of MMGBSA-based BEs for DNA and aromatic furan amidino derivatives. Journal of Biomolecular Structure and Dynamics , 31 , 522–537. doi:10.1080/07391102.2012.703071
   PubMed Web of Science ®Google Scholar
• Still, W. C. , Tempczyk, A. , Hawley, R. C. , & Hendrickson, T. (1990). Semianalytical treatment of solvation for molecular mechanics and dynamics. Journal of the American Chemical Society , 112 , 6127–6129. doi:10.1021/ja00172a038
   Web of Science ®Google Scholar
• 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. doi:10.1021/ja0779250
   PubMed Web of Science ®Google Scholar
• Strahan, G. D. , Keniry, M. A. , & Shafer, R. H. (1998). NMR structure refinement and dynamics of the K+-[d(G3T4G3)]2 quadruplex via particle mesh Ewald molecular dynamics simulations. Biophysical Journal , 75 , 968–981. doi:10.1016/S0006-3495(98)77585-X
   PubMed Web of Science ®Google Scholar
• Sun, H. , Li, Y. , Shen, M. , Tian, S. , Xu, L. , Pan, P. , … Hou, T. (2014). Assessing the performance of MM/PBSA and MM/GBSA methods. 5. Improved docking performance using high solute dielectric constant MM/GBSA and MM/PBSA rescoring. Physical Chemistry Chemical Physics , 16 , 22035–22045. doi:10.1039/c4cp03179b
   PubMed Web of Science ®Google Scholar
• Sun, H. , Li, Y. , Tian, S. , Xu, L. , & Hou, T. (2014). Assessing the performance of MM/PBSA and MM/GBSA methods. 4. Accuracies of MM/PBSA and MM/GBSA methodologies evaluated by various simulation protocols using PDBbind data set. Physical Chemistry Chemical Physics , 16 , 16719–16729. doi:10.1039/c4cp01388c
   PubMed Web of Science ®Google Scholar
• Takeuchi, H. , & Okazaki, K. (1990). Molecular dynamics simulation of diffusion of simple gas molecules in a short chain polymer. The Journal of Chemical Physics , 92 , 5643–5652. doi:10.1063/1.458496
   Web of Science ®Google Scholar
• The Gap Report . (2014). Joint United Nations programme on HIV/AIDS . Geneva: UNAIDS.
   Google Scholar
• Tzoupis, H. , Leonis, G. , Megariotis, G. , Supuran, C. T. , Mavromoustakos, T. , & Papadopoulos, M. G. (2012). Dual inhibitors for aspartic proteases HIV-1 PR and renin: Advancements in AIDS-hypertension-diabetes linkage via molecular dynamics, inhibition assays, and binding free energy calculations. Journal of Medicinal Chemistry , 55 , 5784–5796. doi:10.1021/jm300180r
   PubMed Web of Science ®Google Scholar
• Wang, Z. , Sun, H. , Yao, X. , Li, D. , Xu, L. , Li, Y. , … Hou, T. (2016). Comprehensive evaluation of ten docking programs on a diverse set of protein–ligand complexes: The prediction accuracy of sampling power and scoring power. Physical Chemistry Chemical Physics , 18 , 12964–12975. doi:10.1039/C6CP01555G
   PubMed Web of Science ®Google Scholar
• Warren, G. L. , Andrews, C. W. , Capelli, A. M. , Clarke, B. , LaLonde, J. , Lambert, M. H. , … Head, M. S. (2006). A critical assessment of docking programs and scoring functions. Journal of Medicinal Chemistry , 49 , 5912–5931. doi:10.1021/jm050362n
   PubMed Web of Science ®Google Scholar
• Wei, P. , Garber, M. E. , Fang, S. M. , Fischer, W. H. , & Jones, K. A. (1998). A novel CDK9-associated C-type cyclin interacts directly with HIV-1 Tat and mediates its high-affinity, loop specific binding to TAR RNA. Cell , 92 , 451–462. doi:10.1016/S0092-8674(00)80939-3
   PubMed Web of Science ®Google Scholar
• World Health Organization . (2015). Global Health Observatory (GHO) data . Retrieved from http://www.who.int/gho/hiv/en/
   Google Scholar
• Xu, L. , Sun, H. , Li, Y. , Wang, J. , & Hou, T. (2013). Assessing the performance of MM/PBSA and MM/GBSA methods. 3. The impact of force fields and ligand charge models. The Journal of Physical Chemistry B , 117 , 8408–8421. doi:10.1021/jp404160y
   PubMed Web of Science ®Google Scholar
• Yajima, S. , Shionoya, H. , Akagi, T. , & Hamasaki, K. (2006). Neamine derivatives having a nucleobase with a lysine or an arginine as a linker, their synthesis and evaluation as potential inhibitors for HIV TAR-Tat. Bioorganic & Medicinal Chemistry , 14 , 2799–2809. doi:10.1016/j.bmc.2005.11.056
   PubMed Web of Science ®Google Scholar
• Zhu, Y. , Pe’ery, T. , Peng, J. , Ramanathan, Y. , Marshall, N. , Marshall, T. , … Price, D. H. (1997). Transcription elongation factor P-TEFb is required for HIV-1 tat transactivation in vitro. Genes & Development , 11 , 2622–2632. doi:10.1101/gad.11.20.2622
   PubMed Web of Science ®Google Scholar
• Zwanzig, R. W. (1954). High-temperature equation of state by a perturbation method. I. Nonpolar gases. The Journal of Chemical Physics , 22 , 1420–1426. doi:10.1063/1.1740409
   Web of Science ®Google Scholar