176
Views
2
CrossRef citations to date
0
Altmetric
Research Articles

Relative assessment of different statistical instruments and measures for the prediction of promising outcomes using docking, virtual screening and ADMET analysis against HIV-RT

ORCID Icon, ORCID Icon, ORCID Icon, , ORCID Icon & ORCID Icon
Pages 7680-7692 | Received 25 Oct 2020, Accepted 04 Mar 2021, Published online: 29 Mar 2021

References

  • Accelrys Software Inc. (2012). Discovery Studio Modeling Environment, Release 3.1. Accelrys Software Inc.
  • Andrew, R. L., Brian, K. S., & Catherine, E. P. (2006). Docking and scoring perspective, prediction of protein-ligand interactions. Docking and scoring: Successes and gaps. Journal of Medicinal Chemistry, 49, 5851–5855.
  • Antonio, C., Sabrina, P., Sandra, P., Maurizio, F., Paolo, L. C., & Roberta, L. (2009). Activity and molecular modeling of a new small molecule active against NNRTI-resistant HIV-1 mutants. European Journal of Medicinal Chemistry, 44(12), 5117–5122.
  • Case, D. A., Belfon, K., Ben-Shalom, I. Y., Brozell, S. R., Cerutti, D. S., Cheatham, T. E., III, Cruzeiro, V. W. D., Darden, T. A., Duke, R. E., Giambasu, G., Gilson, M. K., Gohlke, H., Goetz, A. W., Harris, R., Izadi, S., Izmailov, S. A., Kasavajhala, K., Kovalenko, A., Krasny, R., … Kollman, P. A. (2020). AMBER 2020. University of California.
  • Chemical Computing Group Inc. (2008). Molecular operating environment version 09.
  • Chen, M., Elise, A. S. T. K. V., & Fatih, M. U. (2000). Structure-based drug design of non-nucleoside inhibitors for wild-type and drug-resistant HIV reverse transcriptase. Biochemical Pharmacology, 60, 1251–1265.
  • Claudio, N. C., & Ruben, A. A. (2004). Protein flexibility in ligand docking and virtual screening to protein kinases. Journal of Molecular Biology, 337, 209–225.
  • Corbeil, C. R., Englebienne, P., & Moitessier, N. (2007). Docking ligands in to flexible and solvated macromolecules. Journal of Chemical Information and Modeling, 47(2), 435–449.
  • Dimitar, P. H., Tudor, I., & Oprea, J. G, (2007). Virtual screening applications: A study of ligand-based methods and different structure representations in four different scenarios. Journal of Computer-Aided Molecular Design, 21, 617–640.
  • Fonteh, P. N. (2012). GOLD compounds with anti-HIV and immunomodulatory activity, Chapter 3, compound properties, GOLD compounds: Structure and drug likeness, University of Pretoria [Doctoral thesis].
  • Galina, N. N., Krista, A. D. F., & Vinay, K. P. (2010). Novel molecular mechanism of dual resistance to nucleoside and nonnucleoside reverse transcriptase inhibitors. Journal of virology, 84, 5238–5249.
  • Giuseppe, C., Elena, M., Monica, F., Vito, N., Giovanni, G., Ettore, N., Anna, R., Giovanni, M., Silvio, S., Giuseppe, C., Alberto, B., Emanuela, F., Ilaria, U., Francesca, B., Stefano, M., Massimiliano, C., X., Angelo, N., & Silvio, C. (1999). Pyrrolobenzoxazepinone derivatives as non-nucleoside HIV-1 RT inhibitors: Further structure-activity relationship studies and identification of more potent broad-spectrum HIV-1 RT inhibitors with antiviral activity. Journal of Medicinal Chemistry, 42, 4462–4470.
  • Giuseppe, C., Francesca, A., Monica, F., Elena, M., Anna, R., Silvia, A., Vito, N., Antonio, G., Giovanni, G., Ettore, N., Giovanni, M., Silvio, S., Alberto, B., Laura, V., Barbara, B., Marcella, C., Francesca, B., Stefano, M., Massimiliano, C., Giovanna, G., & Silvio, C. (2001). Quinoxalinylethylpyridylthioureas (QXPTs) as potent non-nucleoside HIV-1 reverse transcriptase (RT) inhibitors. Further SAR studies and identification of a novel orally bioavailable hydrazine-based antiviral agent. Journal of Medicinal Chemistry, 44, 305–315.
  • Halim, S. A., Abdalla, O. M., Mesaik, M. A., Wadood, A., & Kontoyianni, M. (2013). Identification of novel Interleukin-2 inhibitors through computational approaches. Molecular Diversity, 17, 345–355. https://doi.org/10.1007/s11030-013-9431-4
  • Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38. https://doi.org/10.1016/0263-7855(96)00018-5
  • Johannes, K., Patrick, M., Simona, D., Gerhard, W., & Thierry, L. (2008). Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection—What can we learn from earlier mistakes? Journal of Computer-Aided Molecular Design, 22, 213–228.
  • Jones, G., Willett, P., Glen, R. C., Leach, A. R., & Taylor, R. (1997). Development and validation of a genetic algorithm for flexible docking. Journal of Molecular Biology, 267(3), 727–748.
  • Kirschberg, T. A., Balakrishnan, M., Huang, W., Hluhanich, R., Kutty, N., Liclican, A. C., McColl, D. J., Squires, N. H., & Lansdon, E. B. (2008). Triazole derivatives as non-nucleoside inhibitors of HIV-1 reverse transcriptase-structure-activity relationships and crystallographic analysis. Bioorganic & Medicinal Chemistry Letters, 18(3), 1131–1134. https://doi.org/10.1016/j.bmcl.2007.11.127
  • Miyamoto, S., & Kollman, P. A. (1992). Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models. Journal of Computational Chemistry, 13(8), 952–962. https://doi.org/10.1002/jcc.540130805
  • Murugesan, S., Swastika, G., & Giovanni, M. (2010). Synthesis, evaluation and molecular modelling studies of some novel 3-(3,4-dihydroisoquinolin-2(1H)-yl)-N-(substituted-phenyl)propanamides as HIV-1 non-nucleoside reverse transcriptase inhibitors. Journal of Chemical Sciences, 122(2), 169–176. https://doi.org/10.1007/s12039-010-0018-7
  • Mysinger, M., Carchia, M., Irwin, J., & Shoichet, B. (2012). Directory of useful decoys enhanced (DUD-E): Better ligands and decoys for better benchmarking. Journal of Medicinal Chemistry, 55(14), 6582–6594. https://doi.org/10.1021/jm300687e
  • Nicolas, S. C., N. Alpay, T., & Ivet, B. (2004). Conformational changes in HIV-1 reverse transcriptase induced by nonnucleoside reverse transcriptase inhibitor binding. Current HIV Research, 2, 323–332.
  • Nisachon, K., Nitirat, C., Arunee, T., Patchreenart, S., Kiattawee, C., Pornpan, P., Supa, H., & Supanna, T. (2009). Dipyridodiazepinone derivatives; synthesis and anti HIV-1 activity. Beilstein Journal of Organic Chemistry, 5, 1–6.
  • OpenEye Scientific Software. (2009). FRED 2.2.4, Documentation released on 2009.
  • OpenEye Scientific Software. (2020). OEDocking FRED version 3.0.0, Filter 2.1.1. OMEGA, Release 2.4.6.
  • Rajender, K., & Prabha, G. (2010). Active site binding interactions of β-carboline derivative for HIV reverse transcriptase, protease and integrase. International Journal of Drug Discovery, 2, 51–55.
  • Ravindra, K., Rawal, K., Ashutosh, K., Mohammad, I. S., & Setu, B. K. (2007). Molecular docking studies on 4-thiazolidinones as HIV-1 RT inhibitors. Journal of Molecular Modeling, 13, 155–161.
  • RCSB PDB. (2005). University of New Jersey, Department of Chemistry and Chemical Biology.
  • Rick, G., Nagarajan, P., Daniel, W. Z., Glen, E. K., Igor, A. T., William, G. R., Catherine, A. S., John, W. E., & Stanley, K. B. (1996). All-atom models for the non-nucleoside binding site of HIV-1 reverse transcriptase complexed with inhibitors: A 3D QSAR approach. Journal of Medicinal Chemistry, 39, 1645–1650.
  • Rino, R., Simona, F., Fabrizio, M., Antonella, B., & Silvio, M. (2005). HIV-reverse transcriptase inhibition: Inclusion of ligand-induced fit by cross-docking studies. Journal of Medicinal Chemistry, 48, 200–212.
  • Roe, D. R., & Cheatham, T. E. (2013). III PTRAJ and CPPTRAJ: Software for processing and analysis of molecular dynamics trajectory data. Journal of Chemical Theory and Computation, 9(7), 3084–3095. https://doi.org/10.1021/ct400341p
  • Saparpakorn, P., Hannongbua, S., & Rognan, D. (2006). Design of nevirapine derivatives insensitive to the K103N and Y181C HIV-1 reverse transcriptase mutants. SAR and QSAR in Environmental Research, 17(2), 183–194. https://doi.org/10.1080/10659360600636147
  • SlidePlayer. (2006). Molecular Docking Using GOLD, Tommi Suvitaiva, Seppo Virtanen, S-114.2500, Basics for Biosystems of the Cell.
  • Tripos Associates. (2003). SYBYL molecular modeling software version 6.9.
  • Tripos Inc. (2006). Cscore: Rank the affinity of compounds bound to a target with consensus scoring. Sybyl version 7.3.
  • Truchon, J. F., & Bayly, C. I. (2007). Evaluating virtual screening methods: Good and bad metrics for the “early recognition” problem. Journal of Chemical Information and Modeling, 47, 488–508.
  • Wei, Z., Kirk, E. H., Stephen, W. W., Richard, E. L., & James, M. B. (2009). A statistical framework to evaluate virtual screening. BMC Bioinformatics, 10, 1–13. https://doi.org/10.1186/1471-2105-10-225
  • Yasser, B., Ihab, M. A. M., Ahmad, Q., Amal, G. A. B., & Mutasem, O. T. (2009). In silico screening for non-nucleoside HIV-1 reverse transcriptase inhibitors using physicochemical filters and high-throughput docking followed by in vitro evaluation. Chemical Biology and Drug Design, 74, 258–265.
  • Zaheer, U. H., Reaz, U., & Sana, G. (2011). Optimization of structure based virtual screening protocols against thymidine monophosphate kinase inhibitors as antitubercular agents. Molecular Informatics, 30(10), 851–862.
  • Zhigang, Z., & Jeffry, D. M. (2004). CoMFA 3D-QSAR analysis of HIV-1 RT nonnucleoside inhibitors, TIBO derivatives based on docking conformation and alignment. Journal of Chemical Information and Computer Science, 44, 2167–2178.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.