164
Views
0
CrossRef citations to date
0
Altmetric
Research Articles

Atom-based 3D-QSAR and DFT analysis of 5‐substituted 2‐acylaminothiazole derivatives as HIV-1 latency-reversing agents

& ORCID Icon
Pages 6759-6774 | Received 14 Feb 2022, Accepted 05 Aug 2022, Published online: 16 Aug 2022

References

  • Athar, M., Lone, M. Y., Khedkar, V. M., & Jha, P. C. (2016). Pharmacophore model prediction, 3D-QSAR and molecular docking studies on vinyl sulfones targeting Nrf2-mediated gene transcription intended for anti-Parkinson drug design. Journal of Biomolecular Structure & Dynamics, 34(6), 1282–1297. https://doi.org/10.1080/07391102.2015.1077343.
  • Chandra, I., Prabhu, S. V., Nayak, C., & Singh, S. K. (2021). E-pharmacophore based screening to identify potential HIV-1 gp120 and CD4 interaction blockers for wild and mutant types. SAR and QSAR in Environmental Research, 32(5), 353–377. https://doi.org/10.1080/1062936X.2021.1901310.
  • Chavez, L., Calvanese, V., & Verdin, E. (2015). HIV latency is established directly and early in both resting and activated primary CD4 T cells. PLoS Pathogens, 11(6), e1004955. https://doi.org/10.1371/journal.ppat.1004955.
  • Chem. Axon. (2019). Available at, Marvin Sketch Version 19. 22 https://chemaxon.com/products/marvin.
  • Chirico, N., & Gramatica, P. (2011). Real external predictivity of QSAR models: How to evaluate it? Comparison of different validation criteria and proposal of using the concordance correlation coefficient. Journal of Chemical Information and Modeling, 51(9), 2320–2335. https://doi.org/10.1021/ci200211n
  • Colby, D., Trautmann, L., Pinyakorn, S., Leyre, L., Pagliuzza, A., Kroon, E., Rolland, M., Takata, H., Buranapraditkun, S., Intasan, J., Chomchey, N., Muir, R., Haddad, E., Tovanabutra, S., Ubolyam, S., Bolton, D., Fullmer, B., Gorelick, R., Fox, L., …, RV411 study group. (2018). Rapid HIV RNA rebound after antiretroviral treatment interruption in persons durably suppressed in Fiebig I acute HIV infection. Nature Medicine, 24(7), 923–926. https://doi.org/10.1038/s41591-018-0026-6.
  • Darcis, G., Kula, A., Bouchat, S., Fujinaga, K., Corazza, F., Ait-Ammar, A., Delacourt, N., Mélard, A., Kabeya, K., Vanhulle, C., Van Driessche, B., Gatot, J., Cherrier, T., Pianowski, L., Gama, L., Schwartz, C., Vila, J., Burny, A., Clumeck, N., … Van Lint, C. (2015). An in-depth comparison of latency-reversing agent combinations in various in vitro and ex vivo HIV-1 latency models identified bryostatin-1+ JQ1 and ingenol-B + JQ1 to potently reactivate viral gene expression. PLOS Pathogens, 11(7), e1005063. https://doi.org/10.1371/journal.ppat.1005063
  • Deeks, S. G., Overbaugh, J., Phillips, A., & Buchbinder, S. (2015). HIV infection. Nature Reviews. Disease Primers, 1, 15035. https://doi.org/10.1038/nrdp.2015.35.
  • Dessalew, N., & Singh, S. K. (2008). 3D-QSAR CoMFA and CoMSIA study on benzodipyrazoles as cyclin dependent kinase 2 inhibitors. Medicinal Chemistry (Shariqah (United Arab Emirates)), 4(4), 313–321. https://doi.org/10.2174/157340608784872244.
  • Egloff, S. (2021). CDK9 keeps RNA polymerase II on track. Cellular and Molecular Life Sciences : CMLS, 78(14), 5543–5567. https://doi.org/10.1007/s00018-021-03878-8.
  • El-Desoky, A., Eguchi, K., Kishimoto, N., Asano, T., Kato, H., Hitora, Y., Kotani, S., Nakamura, T., Tsuchiya, S., Kawahara, T., Watanabe, M., Wada, M., Nakajima, M., Watanabe, T., Misumi, S., & Tsukamoto, S. (2022). Isolation, synthesis, and structure-activity relationship study on daphnane and tigliane diterpenes as HIV latency-reversing agents. Journal of Medicinal Chemistry, 65(4), 3460–3472. https://doi.org/10.1021/acs.jmedchem.1c01973.
  • Gadaleta, D., Mangiatordi, G., Catto, M., Carotti, A., & Nicolotti, O. (2016). Applicability domain for QSAR models: Where theory meets reality. International Journal of Quantitative Structure-Property Relationships, 1(1), 45–63. https://doi.org/10.4018/IJQSPR.2016010102
  • Golbraikh, A., & Tropsha, A. (2002). Beware of Q2! Journal of Molecular Graphics & Modelling, 20(4), 269–276. https://doi.org/10.1016/S1093-3263(01)00123-1
  • Huang, X. S., Tian, R. R., Ma, M. D., Luo, R. H., Yang, L. M., Peng, G. H., Zhang, M., Dong, X. Q., & Zheng, Y. T. (2022). Bromodomain and extra-terminal inhibitor BMS-986158 reverses latent HIV-1 infection in vitro and ex vivo by increasing CDK9 phosphorylation and recruitment. Pharmaceuticals (Basel, 15(3), 338. https://doi.org/10.3390/ph15030338
  • Khan, M. A., Gupta, K. K., & Singh, S. K. (2020). A review on pharmacokinetics properties of antiretroviral drugs to treat HIV-1 infections. Current Computer-Aided Drug Design, 17, 1–15. https://doi.org/10.2174/1573409916666201006143007
  • Kim, Y., Anderson, J. L., & Lewin, S. R. (2018). Getting the “Kill” into “Shock and Kill”: Strategies to eliminate latent HIV. Cell Host & Microbe, 23(1), 14–26. https://doi.org/10.1016/j.chom.2017.12.004.
  • Lopes, J. R., Chiba, D. E., & Dos Santos, J. L. (2021). HIV latency reversal agents: A potential path for functional cure? European Journal of Medicinal Chemistry, 213, 113213. https://doi.org/10.1016/j.ejmech.2021.113213.
  • Margolis, D., Garcia, J., Hazuda, D., & Haynes, B. (2016). Latency reversal and viral clearance to cure HIV-1. Science (New York, N.Y.), 353(6297), aaf6517. https://doi.org/10.1126/science.aaf6517.
  • Mousseau, G., & Valente, S. (2017). Role of host factors on the regulation of tat-mediated HIV-1 transcription. Current Pharmaceutical Design, 23(28), 4079–4090. https://doi.org/10.2174/1381612823666170622104355.
  • Nayak, C., Chandra, I., & Singh, S. K. (2019). An in silico pharmacological approach toward the discovery of potent inhibitors to combat drug resistance HIV-1 protease variants. Journal of Cellular Biochemistry, 120(6), 9063–9081. https://doi.org/10.1002/jcb.28181.
  • Nguyen, W., Jacobson, J., Jarman, K., Sabroux, H. J., Harty, L., McMahon, J., Lewin, S., Purcell, D., & Sleebs, B. (2019). Identification of 5-substituted 2-acylaminothiazoles that activate tat-mediated transcription in HIV-1 latency models. Journal of Medicinal Chemistry, 62(10), 5148–5175. https://doi.org/10.1021/acs.jmedchem.9b00462.
  • Panwar, U., & Singh, S. K. (2021). Atom-based 3D-QSAR, molecular docking, DFT, and simulation studies of acylhydrazone, hydrazine, and diazene derivatives as IN-LEDGF/p75 inhibitors. Structural Chemistry, 32(1), 337–352. https://doi.org/10.1007/s11224-020-01628-3
  • Panwar, U., Chandra, I., Selvaraj, C., & Singh, S. K. (2019). Current computational approaches for the development of anti-HIV inhibitors: An overview. Current Pharmaceutical Design, 25(31), 3390–3405. https://doi.org/10.2174/1381612825666190911160244.
  • Prabhu, S. V., & Singh, S. K. (2018). Atom-based 3D-QSAR, induced fit docking, and molecular dynamics simulations study of thieno [2,3-b] pyridines negative allosteric modulators of mGluR5. Journal of Receptor and Signal Transduction Research, 38(3), 225–239. https://doi.org/10.1080/10799893.2018.1476542.
  • Reddy, K. K., Singh, S., Dessalew, N., Tripathi, S., & Selvaraj, C. (2012). Pharmacophore modelling and atom-based 3D-QSAR studies on N-methyl pyrimidones as HIV-1 integrase inhibitors. Journal of Enzyme Inhibition and Medicinal Chemistry, 27(3), 339–347. https://doi.org/10.3109/14756366.2011.590803.
  • Roos, K., Wu, C., Damm, W., Reboul, M., Stevenson, J. M., Lu, C., Dahlgren, M., Mondal, S., Chen, W., Wang, L., Abel, R., Friesner, R., & Harder, E. D. (2019). OPLS3e: Extending force field coverage for drug-like small molecules. Journal of Chemical Theory and Computation, 15(3), 1863–1874. https://doi.org/10.1021/acs.jctc.8b01026.
  • Roy, K., & Mitra, I. (2011). On various metrics used for validation of predictive QSAR models with applications in virtual screening and focused library design. Combinatorial Chemistry & High Throughput Screening, 14(6), 450–474. https://doi.org/10.2174/138620711795767893.
  • Roy, K., Das, R., Ambure, P., & Aher, R. (2016). Be aware of error measures. Further studies on validation of predictive QSAR models. Chemometrics and Intelligent Laboratory Systems, 152, 18–33. https://doi.org/10.1016/j.chemolab.2016.01.008
  • Schrödinger Release 2019-3. (2019a). LigPrep, Schrödinger. LLC.
  • Schrödinger Release 2019-3. (2019b). Epik, Schrödinger. LLC.
  • Schrödinger Release 2019-3: (2019c). ConfGen, Schrödinger. LLC.
  • Schrödinger Release 2019-3: (2019d). Jaguar, Schrödinger. LLC.
  • Schulze-Gahmen, U., & Hurley, J. (2018). Structural mechanism for HIV-1 TAR loop recognition by Tat and the super elongation complex. Proceedings of the National Academy of Sciences of the United States of America, 115(51), 12973–12978. https://doi.org/10.1073/pnas.1806438115.
  • Schulze-Gahmen, U., Echeverria, I., Stjepanovic, G., Bai, Y., Lu, H., Schneidman-Duhovny, D., Doudna, J., Zhou, Q., Sali, A., & Hurley, J. (2016). Insights into HIV-1 proviral transcription from integrative structure and dynamics of the Tat:AFF4:P-TEFb:TAR complex. eLife, 5, e15910. https://doi.org/10.7554/eLife.15910
  • Selvaraj, C., Selvaraj, G., Mohamed Ismail, R., Vijayakumar, R., Baazeem, A., Wei, D.-Q., & Singh, S. K. (2021). Interrogation of Bacillus anthracis SrtA active site loop forming open/close lid conformations through extensive MD simulations for understanding binding selectivity of SrtA inhibitors. Saudi Journal of Biological Sciences, 28(7), 3650–3659. https://doi.org/10.1016/j.sjbs.2021.05.009.
  • Selvaraj, C., Tripathi, S. K., Reddy, K. K., & Singh, S. K. (2011). Tool development for prediction of pIC50 values from the IC50 values-A pIC50 value calculator. Current Trends in Biotechnology and Pharmacy, 5, 1104–1109.
  • Shan, L., Deng, K., Gao, H., Xing, S., Capoferri, A., Durand, C., Rabi, A., Laird, G., Kim, M., Hosmane, N. N., Yang, H.-C., Zhang, H., Margolick, J., Li, L., Cai, W., Ke, R., Flavell, R., Siliciano, J., & Siliciano, R. (2017). Transcriptional reprogramming during effector-to-memory transition renders CD4+ T cells permissive for latent HIV-1 infection. Immunity, 47(4), 766–775. https://doi.org/10.1016/j.immuni.2017.09.014.
  • SIMCA Version 17 trial (2021). https://www.sartorius.com/en/products/process-analytical-technology/data-analytics-software/mvda-software/simca/simca-free-trial-download.
  • Singh, S. K., Dessalew, N., & Bharatam, P. V. (2006). 3D-QSAR CoMFA study on indenopyrazole derivatives as cyclin dependent kinase 4 (CDK4) and cyclin dependent kinase 2 (CDK2) inhibitors. European Journal of Medicinal Chemistry, 41(11), 1310–1319. https://doi.org/10.1016/j.ejmech.2006.06.010.
  • Søgaard, O., Graversen, M. E., Leth, S., Olesen, R., Brinkmann, C., Nissen, S., Kjaer, A. S., Schleimann, M. H., Denton, P. W., Hey-Cunningham, W., Koelsch, K., Pantaleo, G., Krogsgaard, K., Sommerfelt, M., Fromentin, R., Chomont, N., Rasmussen, T., Østergaard, L., & Tolstrup, M. (2015). The depsipeptide romidepsin reverses HIV-1 latency in vivo. PLOS Pathogens, 11(9), e1005142. https://doi.org/10.1371/journal.ppat.1005063
  • Spivak, A. M., & Planelles, V. (2016). HIV-1 eradication: Early trials (and tribulations). Trends in Molecular Medicine, 22(1), 10–27. https://doi.org/10.1016/j.molmed.2015.11.004.
  • Spivak, A., & Planelles, V. (2018). Novel latency reversal agents for HIV-1 cure. Annual Review of Medicine, 69, 421–436. https://doi.org/10.1146/annurev-med-052716-031710.
  • Thorlund, K., Horwitz, M., Fife, B., Lester, R., & Cameron, D. (2017). Landscape review of current HIV ‘kick and kill’cure research-some kicking, not enough killing. BMC Infectious Diseases, 17(1), 595. https://doi.org/10.1186/s12879-017-2683-3.
  • Tropsha, A. (2010). Best practices for QSAR model development, validation, and exploitation. Molecular Informatics, 29(6–7), 476–488. https://doi.org/10.1002/minf.201000061.
  • UNAIDS (Joint United Nations Programme on HIV/AIDS). (2021). Global HIV & AIDS statistics 2021 fact sheet. https://www.unaids.org/en/resources/fact-sheet (Accessed 17 Dec 2021).
  • Wang, C., Wang, H., Pan, Z., Wu, J., Guo, Y., Zhang, J., Xiang, Z., Lu, W., & Xue, Y. (2022). Polyphenol extracts from grape seeds and apple can reactivate latent HIV-1 transcription through promoting P-TEFb release from 7SK snRNP. Disease Markers, 2022, 6055347. https://doi.org/10.1155/2022/6055347.
  • Wong, M. E., Jaworowski, A., & Hearps, A. (2019). The HIV reservoir in monocytes and macrophages. Frontiers in Immunology, 10, 1435. https://doi.org/10.3389/fimmu.2019.01435
  • Xing, S., & Siliciano, R. F. (2013). Targeting HIV latency: Pharmacologic strategies toward eradication. Drug Discovery Today. 18(11–12), 541–551. https://doi.org/10.1016/j.drudis.2012.12.008.
  • Xternal Validation Plus 1.2 (2016). http://www.teqip.jdvu.ac.in/QSAR_Tools/DTCLab.

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.