Molecular docking and simulation studies of synthetic protease inhibitors against COVID-19: a computational study

References

• Bhardwaj, V. K., Singh, R., Sharma, J., Rajendran, V., Purohit, R., & Kumar, S. (2021). Identification of bioactive molecules from tea plant as SARS-CoV-2 main protease inhibitors. Journal of Biomolecular Structure & Dynamics, 39(10), 3449–3458. https://doi.org/10.1080/07391102.2020.1766572
   PubMed Web of Science ®Google Scholar
• Biovia, D. S. (2017). Discovery studio visualizer (p. 936). San Diego: Dassault Systèmes.
   Google Scholar
• Case, D. A., Cerutti, D. S., Cheatham, T. E., III, Darden, T. A., Duke, R. E., Giese, T. J., Gohlke, H., Goetz, A. W., Greene, D., & Homeyer, N. (2017). AMBER 2017. University of California.
   Google Scholar
• Chen, J., Yang, M., Yi, C., Shi, S., & Zhang, Q.-Z. (2009). Molecular dynamics simulation and free energy calculations of symmetric fluoro-substituted diol-based HIV-1 protease inhibitors. Journal of Molecular Structure: THEOCHEM, 899, 1–8. https://www.sciencedirect.com/science/article/pii/S0166128008007057 https://doi.org/10.1016/j.theochem.2008.11.029
   Web of Science ®Google Scholar
• Chen, Y. W., Yiu, C.-P B., & Wong, K.-Y. (2020). Prediction of the SARS-CoV-2 (2019-nCoV) 3C-like protease (3CL pro) structure: Virtual screening reveals velpatasvir, ledipasvir, and other drug repurposing candidates. F1000Research, 9, 129. https://doi.org/10.12688/f1000research.22457.2
   PubMedGoogle Scholar
• Clementz, M. A., Chen, Z., Banach, B. S., Wang, Y., Sun, L., Ratia, K., Baez-Santos, Y. M., Wang, J., Takayama, J., Ghosh, A. K., Li, K., Mesecar, A. D., & Baker, S. C. (2010). Deubiquitinating and interferon antagonism activities of coronavirus papain-like proteases. Journal of Virology, 84(9), 4619–4629. https://doi.org/10.1128/JVI.02406-09
   PubMed Web of Science ®Google Scholar
• Deng, S.-Q., & Peng, H.-J. (2020). Characteristics of and public health responses to the coronavirus disease 2019 outbreak in China. Journal of Clinical Medicine, 9(2), 575. https://doi.org/10.3390/jcm9020575
   PubMed Web of Science ®Google Scholar
• Gamez, P. (2014). The anion–π interaction: Naissance and establishment of a peculiar supramolecular bond. RSC Publishing. https://pubs.rsc.org/fi/content/articlehtml/2014/qi/c3qi00055a
   Google Scholar
• Hassanipour, S., Arab-Zozani, M., Amani, B., Heidarzad, F., Fathalipour, M., & Martinez-de-Hoyo, R. (2021). The efficacy and safety of Favipiravir in treatment of COVID-19: A systematic review and meta-analysis of clinical trials. Scientific Reports, 11(1), 11022. https://doi.org/10.1038/s41598-021-90551-6
   PubMed Web of Science ®Google Scholar
• Hilgenfeld, R. (2014). From SARS to MERS: Crystallographic studies on coronaviral proteases enable antiviral drug design. The FEBS Journal, 281(18), 4085–4096. https://doi.org/10.1111/febs.12936
   PubMed Web of Science ®Google Scholar
• Hollingsworth, S. A., & Dror, R. O. (2018). Molecular dynamics simulation for all. Neuron, 99(6), 1129–1143. https://doi.org/10.1016/j.neuron.2018.08.011
   PubMed Web of Science ®Google Scholar
• 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
   PubMedGoogle Scholar
• Ivashchenko, A. A., Dmitriev, K. A., Vostokova, N. V., Azarova, V. N., Blinow, A. A., Egorova, A. N., Gordeev, I. G., Ilin, A. P., Karapetian, R. N., Kravchenko, D. V., Lomakin, N. V., Merkulova, E. A., Papazova, N. A., Pavlikova, E. P., Savchuk, N. P., Simakina, E. N., Sitdekov, T. A., Smolyarchuk, E. A., Tikhomolova, E. G., Yakubova, E. V., & Ivachtchenko, A. V. (2021). AVIFAVIR for treatment of patients with moderate coronavirus disease 2019 (COVID-19): Interim results of a phase II/III multicenter randomized clinical trial. Clinical Infectious Diseases, 73(3), 531–534. https://doi.org/10.1093/cid/ciaa1176
   PubMed Web of Science ®Google Scholar
• Jadhav, P. K., Ala, P., Woerner, F. J., Chang, C.-H., Garber, S. S., Anton, E. D., & Bacheler, L. T. (1997). Cyclic urea amides: HIV-1 protease inhibitors with low nanomolar potency against both wild type and protease inhibitor resistant mutants of HIV. Journal of Medicinal Chemistry, 40(2), 181–191. https://doi.org/10.1021/jm960586t
   PubMed Web of Science ®Google Scholar
• Jo, S., Kim, T., Iyer, V. G., & Im, W. (2008). CHARMM-GUI: A web-based graphical user interface for CHARMM. Journal of Computational Chemistry, 29(11), 1859–1865. https://doi.org/10.1002/jcc.20945
   PubMed Web of Science ®Google Scholar
• Khedri, M., Maleki, R., Dahri, M., Sadeghi, M. M., Rezvantalab, S., Santos, H. A., & Shahbazi, M.-A. (2021). Engineering of 2D nanomaterials to trap and kill SARS-CoV-2: A new insight from multi-microsecond atomistic simulations. Drug Delivery and Translational Research, 11, 1–15. https://doi.org/10.1007/s13346-021-01054-w
   PubMedGoogle Scholar
• Lauer, S. A., Grantz, K. H., Bi, Q., Jones, F. K., Zheng, Q., Meredith, H. R., Azman, A. S., Reich, N. G., & Lessler, J. (2020). The incubation period of coronavirus disease 2019 (COVID-19) from publicly reported confirmed cases: Estimation and application. Annals of Internal Medicine, 172(9), 577–582. https://doi.org/10.7326/M20-0504
   PubMed Web of Science ®Google Scholar
• Lee, J., Cheng, X., Swails, J. M., Yeom, M. S., Eastman, P. K., Lemkul, J. A., Wei, S., Buckner, J., Jeong, J. C., Qi, Y., Jo, S., Pande, V. S., Case, D. A., Brooks, C. L., MacKerell, A. D., Klauda, J. B., & Im, W. (2016). CHARMM-GUI input generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM simulations using the CHARMM36 additive force field. Journal of Chemical Theory and Computation, 12(1), 405–413. https://doi.org/10.1021/acs.jctc.5b00935
   PubMed Web of Science ®Google Scholar
• Lee, J., Hitzenberger, M., Rieger, M., Kern, N. R., Zacharias, M., & Im, W. (2020). CHARMM-GUI supports the Amber force fields. Journal of Chemical Physics, 153(3), 035103. https://doi.org/10.1063/5.0012280
   PubMed Web of Science ®Google Scholar
• Lu, R., Zhao, X., Li, J., Niu, P., Yang, B., Wu, H., Wang, W., Song, H., Huang, B., Zhu, N., Bi, Y., Ma, X., Zhan, F., Wang, L., Hu, T., Zhou, H., Hu, Z., Zhou, W., Zhao, L., Chen, J., … Tan, W. (2020). Genomic characterisation and epidemiology of 2019 novel coronavirus: Implications for virus origins and receptor binding. The Lancet, 395, P565–P574. https://www.sciencedirect.com/science/article/pii/S0140673620302518
   PubMed Web of Science ®Google Scholar
• Lokhande, K. B., Doiphode, S., Vyas, R., & Swamy, K. V. (2021). Molecular docking and simulation studies on SARS-CoV-2 M pro reveals Mitoxantrone, Leucovorin, Birinapant, and Dynasore as potent drugs against COVID-19. Journal of Biomolecular Structure & Dynamics, 39(18), 7294–7212. https://doi.org/10.1080/07391102.2020.1805019
   PubMed Web of Science ®Google Scholar
• Lu, S., Wang, J., Chitsaz, F., Derbyshire, M. K., Geer, R. C., Gonzales, N. R., Gwadz, M., Hurwitz, D. I., Marchler, G. H., Song, J. S., Thanki, N., Yamashita, R. A., Yang, M., Zhang, D., Zheng, C., Lanczycki, C. J., & Marchler-Bauer, A. (2020). CDD/SPARCLE: The conserved domain database in 2020. Nucleic Acids Research, 48(D1), D265–D268. https://doi.org/10.1093/nar/gkz991
   PubMed Web of Science ®Google Scholar
• Modi, P., Patel, S., & Chhabria, M. (2019). Structure-based design, synthesis and biological evaluation of a newer series of pyrazolo[1,5-a]pyrimidine analogues as potential anti-tubercular agents. Bioorganic Chemistry, 87, 240–251. https://doi.org/10.1016/j.bioorg.2019.02.044
   PubMed Web of Science ®Google Scholar
• Motta, M., Sylvester, S., Callaghan, T., & Lunz-Trujillo, K. (2021). Encouraging COVID-19 vaccine uptake through effective health communication. Frontiers in Political Science, 3, 1. https://doi.org/10.3389/fpos.2021.630133
   Google Scholar
• Mühlman, A., Classon, B., Hallberg, A., & Samuelsson, B. (2001). Synthesis of Potent C(2)-symmetric, diol-based hiv-1 protease inhibitors. Investigation of thioalkyl and thioaryl P1/P1' substituents. Journal of Medicinal Chemistry, 44(21), 3402–3406. https://doi.org/10.1021/jm0011169
   PubMed Web of Science ®Google Scholar
• Murphy, J., Vallières, F., Bentall, R. P., Shevlin, M., McBride, O., Hartman, T. K., McKay, R., Bennett, K., Mason, L., Gibson-Miller, J., Levita, L., Martinez, A. P., Stocks, T. V. A., Karatzias, T., & Hyland, P. (2021). Psychological characteristics associated with COVID-19 vaccine hesitancy and resistance in Ireland and the United Kingdom. Nature Communications, 12(1), 1–15. https://doi.org/10.1038/s41467-020-20226-9
   PubMed Web of Science ®Google Scholar
• Nugiel, D. A., Jacobs, K., Cornelius, L., Chang, C.-H., Jadhav, P. K., Holler, E. R., Klabe, R. M., Bacheler, L. T., Cordova, B., Garber, S., Reid, C., Logue, K. A., Gorey-Feret, L. J., Lam, G. N., Erickson-Viitanen, S., & Seitz, S. P. (1997). Improved P1/P1' substituents for cyclic urea based HIV-1 protease inhibitors: Synthesis, structure-activity relationship, and X-ray crystal structure analysis. Journal of Medicinal Chemistry, 40(10), 1465–1474. https://doi.org/10.1021/jm960839i
   PubMed Web of Science ®Google Scholar
• Örtqvist, P., Peterson, S. D., Kerblom, E., Gossas, T., Sabnis, Y. A., Fransson, R., Lindeberg, G., Helena Danielson, U., Karlén, A., & Sandström, A. (2007). Phenylglycine as a novel P2 scaffold in hepatitis C virus NS3 protease inhibitors. Bioorganic & Medicinal Chemistry, 15(3), 1448–1474. https://doi.org/10.1016/j.bmc.2006.11.003
   PubMed Web of Science ®Google Scholar
• Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera – A visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. https://doi.org/10.1002/jcc.20084
   PubMed Web of Science ®Google Scholar
• Phillips, J. C., Hardy, D. J., Maia, J. D. C., Stone, J. E., Ribeiro, J. V., Bernardi, R. C., Buch, R., Fiorin, G., Hénin, J., Jiang, W., McGreevy, R., Melo, M. C. R., Radak, B. K., Skeel, R. D., Singharoy, A., Wang, Y., Roux, B., Aksimentiev, A., Luthey-Schulten, Z., … Tajkhorshid, E. (2020). Scalable molecular dynamics on CPU and GPU architectures with NAMD. The Journal of Chemical Physics, 153(4), 044130. https://doi.org/10.1063/5.0014475
   PubMed Web of Science ®Google Scholar
• Pillaiyar, T., Meenakshisundaram, S., & Manickam, M. (2020). Recent discovery and development of inhibitors targeting coronaviruses. Drug Discovery Today, 25, 668–688. https://www.sciencedirect.com/science/article/pii/S1359644620300416
   PubMed Web of Science ®Google Scholar
• Ritchie, T. J., & Macdonald, S. J. F. (2009). The impact of aromatic ring count on compound developability – Are too many aromatic rings a liability in drug design? Drug Discovery Today, 14(21–22), 1011–1020. https://doi.org/10.1016/j.drudis.2009.07.014
   PubMed Web of Science ®Google Scholar
• Smith, T., Bushek, J., LeClaire, A., & Prosser, T. (2020). COVID-19 drug therapy‏. Repository.Phb.Ac.Id‏. http://repository.phb.ac.id/776/1/COVID-19-Drug-Therapy_5.14.2020.pdf
   Google Scholar
• Sohrabi, C., Alsafi, Z., O’Neill, N., Khan, M., Kerwan, A., Al-Jabir, A., Iosifidis, C., & Agha, R. (2020). World Health Organization declares global emergency: A review of the 2019 novel coronavirus (COVID-19). International Journal of Surgery, 76, 71–76. https://www.sciencedirect.com/science/article/pii/S1743919120301977
   PubMed Web of Science ®Google Scholar
• Sousa, S. F., Fernandes, P. A., & Ramos, M. J. (2006). Protein-ligand docking: Current status and future challenges. Proteins, 65(1), 15–26. https://doi.org/10.1002/prot.21082
   PubMed Web of Science ®Google Scholar
• Stanzione, F., Giangreco, I., & Cole, J. C. (2021). Use of molecular docking computational tools in drug discovery, Progress in Medicinal Chemistry, 60, 273–343. https://doi.org/10.1016/bs.pmch.2021.01.004
   PubMedGoogle Scholar
• Su, H.-X., Yao, S., Zhao, W.-F., Li, M.-J., Liu, J., Shang, W.-J., Xie, H., Ke, C.-Q., Hu, H.-C., Gao, M.-N., Yu, K.-Q., Liu, H., Shen, J.-S., Tang, W., Zhang, L.-K., Xiao, G.-F., Ni, L., Wang, D.-W., Zuo, J.-P., … Xu, Y.-C. (2020). Anti-SARS-CoV-2 activities in vitro of Shuanghuanglian preparations and bioactive ingredients. Acta Pharmacologica Sinica, 41(9), 1167–1177. https://doi.org/10.1038/s41401-020-0483-6
   PubMed Web of Science ®Google Scholar
• Taha, M., Ismail, N., Khan, A., Adnan Ali Shah, S., Anwar, A., Ahsan Halim, S., Qaiser Fatmi, M., Imran, S., Rahim, F., & Mohammed Khan, K. (2015). Synthesis of novel derivatives of oxindole, their urease inhibition and molecular docking studies. Bioorganic & Medicinal Chemistry Letters, 25, 3285–3289. https://www.sciencedirect.com/science/article/pii/S0960894X15005430
   PubMed Web of Science ®Google Scholar
• Trott, O., & Olson, A. J. (2009). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455–461. https://doi.org/10.1002/jcc.21334
   Web of Science ®Google Scholar
• Wang, E., Sun, H., Wang, J., Wang, Z., Liu, H., Zhang, J. Z. H., & Hou, T. (2019). End-point binding free energy calculation with MM/PBSA and MM/GBSA: Strategies and applications in drug design. Chemical Reviews, 119(16), 9478–9508. https://doi.org/10.1021/acs.chemrev.9b00055
   PubMed Web of Science ®Google Scholar
• WHO. (2021). Coronavirus disease (COVID-19) situation dashboard. World Health Organization Website.
   Google Scholar
• Williams, T., Kelley, C., Bröker, H., Cunningham, R., Denholm, D., Elber, G., Fearick, R., Grammes, C., Hart, L., Hecking, L., Juhász, P., Koenig, T., Kotz, D., Ed Kubaitis, Lang, R., Lecomte, T., Lehmann, A., Mai, A., Märkisch, B., Merritt, E. A., … Zellner, J. (2012). gnuplot 4.6. Gnuplot.Info. http://www.gnuplot.info/docs_4.6/gnuplot-ja.pdf
   Google Scholar