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Research Articles

Insilico drug designing for COVID-19: an approach of high-throughput virtual screening, molecular, and essential dynamics simulations

ORCID Icon, ORCID Icon & ORCID Icon
Pages 7394-7407 | Received 03 Aug 2020, Accepted 25 Feb 2021, Published online: 10 Mar 2021

References

  • Al-Osail, A. M., & Al-Wazzah, M. J. (2017). The history and epidemiology of Middle East respiratory syndrome corona virus. Multidisciplinary Respiratory Medicine, 12, 20. https://doi.org/10.1186/s40248-017-0101-8
  • Anand, K., Ziebuhr, J., Wadhwani, P., Mesters, J. R., & Hilgenfeld, R. (2003). Coronavirus main proteinase (3CLpro) structure: Basis for design of anti-SARS drugs. Science (New York, N.Y.), 300(5626), 1763–1767. https://doi.org/10.1126/science.1085658
  • Angelini, M. M., Akhlaghpour, M., Neuman, B. W., & Buchmeier, M. J. (2013). Severe acute respiratory syndrome coronavirus nonstructural proteins 3, 4, and 6 induce double-membrane vesicles. mBio, 4(4), e00524-13. https://doi.org/10.1128/mBio.00524-13
  • Berendsen, H. J., & Hayward, S. (2000). Collective protein dynamics in relation to function. Current Opinion in Structural Biology, 10(2), 165–169. https://doi.org/10.1016/S0959-440X(00)00061-0
  • Bhardwaj, V. K., Singh, R., Sharma, J., Rajendran, V., Purohit, R., & Kumar, S. (2020a). Identification of bioactive molecules from Tea plant as SARS-CoV-2 main protease inhibitors. Journal of Biomolecular Structure and Dynamics, 1–13. https://doi.org/10.1080/07391102.2020.1766572.
  • Bhardwaj, V. K., Singh, R., Sharma, J., Das, P., & Purohit, R. (2020b). Structural based study to identify new potential inhibitors for dual specificity tyrosine-phosphorylation-regulated kinase. Computer Methods and Programs in Biomedicine, 194, 105494. https://doi.org/10.1016/j.cmpb.2020.105494
  • Chen, Y. C. (2015). Beware of docking!. Trends in Pharmacological Science, 36(2), 78–95. https://doi.org/10.1016/j.tips.2014.12.001
  • Chorin, E., Dai, M., Shulman, E., Wadhwani, L., Bar-Cohen, R., Barbhaiya, C., Aizer, A., Holmes, D., Bernstein, S., Spinelli, M., Park, D. S., Chinitz, L. A., & Jankelson, L. (2020). The QT interval in patients with COVID-19 treated with hydroxychloroquine and azithromycin. Nature Medicine, 26(6), 808–809. https://doi.org/10.1038/s41591-020-0888-2
  • Daina, A., Michielin, O., & Zoete, V. (2017). SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Scientific Reports, 7, 42717. https://doi.org/10.1038/srep42717
  • Dong, Y. W., Liao, M. L., Meng, X. L., & Somero, G. N. (2018). Structural flexibility and protein adaptation to temperature: Molecular dynamics analysis of malate dehydrogenases of marine molluscs. Proceedings of the National Academy of Sciences of the United States of America, 115(6), 1274–1279. https://doi.org/10.1073/pnas.1718910115
  • Durrant, J. D., & McCammon, J. A. (2011). Molecular dynamics simulations and drug discovery. BMC Biology, 9, 71. https://doi.org/10.1186/1741-7007-9-71
  • Elfiky, A. A. (2020). Ribavirin, remdesivir, sofosbuvir, galidesivir, and tenofovir against SARS-CoV-2 RNA dependent RNA polymerase (RdRp): A molecular docking study. Life Sci, 253, 117592. https://doi.org/10.1016/j.lfs.2020.117592
  • Guex, N., & Peitsch, M. C. (1996). Swiss-PdbViewer: A fast and easy-to-use PDB viewer for Macintosh and PC. Protein Data Bank Quarterly Newsletter, 77, 7.
  • Guo, Y. R., Cao, Q. D., Hong, Z. S., Tan, Y. Y., Chen, S. D., Jin, H. J., Tan, K. S., Wang, D. Y., & Yan, Y. (2020). The origin, transmission and clinical therapies on coronavirus disease 2019 (COVID-19) outbreak—An update on the status. Military Medical Research, 7(1), 11. https://doi.org/10.1186/s40779-020-00240-0
  • Hess, B., Bekker, H., Berendsen, H. J., & Fraaije, J. G. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18(12), 1463–1472. https://doi.org/10.1002/(SICI)1096-987X(199709)18:12. https://doi.org/10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
  • 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
  • Huang, B. (2009). MetaPocket: A meta approach to improve protein ligand binding site prediction. Omics: A Journal of Integrative Biology, 13(4), 325–330. https://doi.org/10.1089/omi.2009.0045
  • Irwin, J. J., & Shoichet, B. K. (2005). ZINC-a free database of commercially available compounds for virtual screening. Journal of Chemical Information and Modeling, 45(1), 177–182. https://doi.org/10.1021/ci049714+
  • Jin, Z., Du, X., Xu, Y., Deng, Y., Liu, M., Zhao, Y., Zhang, B., Li, X., Zhang, L., Peng, C., Duan, Y., Yu, J., Wang, L., Yang, K., Liu, F., Jiang, R., Yang, X., You, T., Liu, X., … Yang, H. (2020). Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors. Nature, 582(7811), 289–293. https://doi.org/10.1038/s41586-020-2223-y
  • Kabsch, W., & Sander, C. (1983). Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22(12), 2577–2637. https://doi.org/10.1002/bip.360221211
  • Kamaraj, B., & Purohit, R. (2016). Mutational analysis on membrane associated transporter protein (MATP) and their structural consequences in oculocutaeous albinism type 4 (OCA4) – A molecular dynamics approach. Journal of Cellular Biochemistry, 117(11), 2608–2619. https://doi.org/10.1002/jcb.25555
  • Kumar, R., & Saran, S. (2018). Structure, molecular dynamics simulation, and docking studies of Dictyostelium discoideum and human STRAPs. Journal of Cellular Biochemistry, 119(9), 7177–7191. https://doi.org/10.1002/jcb.26840
  • Kumar, R., Maurya, R., & Saran, S. (2017). Identification of novel inhibitors of the translationally controlled tumor protein (TCTP): Insights from molecular dynamics. Molecular bioSystems, 13(3), 510–524. https://doi.org/10.1039/c6mb00850j
  • Kumar, R., Maurya, R., & Saran, S. (2019). Introducing a simple model system for binding studies of known and novel inhibitors of AMPK: A therapeutic target for prostate cancer. Journal of Biomolecular Structure & Dynamics, 37(3), 781–795. https://doi.org/10.1080/07391102.2018.1441069
  • Kumar, R., Kumar, R., Tanwar, P., Deo, S. V. S., Mathur, S., Agarwal, U., & Hussain, S. (2020). Structural and conformational changes induced by missense variants in the zinc finger domains of GATA3 involved in breast cancer. RSC Advances, 10(65), 39640–39653. https://doi.org/10.1039/D0RA07786K
  • Kumari, R., Kumar, R., Open Source Drug Discovery Consortium., & Lynn, A. (2014). g_mmpbsa-a GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information and Modeling, 54(7), 1951–1962. https://doi.org/10.1021/ci500020m
  • Laskowski, R. A., & Swindells, M. B. (2011). LigPlot+: Multiple ligand-protein interaction diagrams for drug discovery. Journal of Chemical Information and Modeling, 51(10), 2778–2786. https://doi.org/10.1021/ci200227u
  • Lipinski, C. A. (2004). Lead- and drug-like compounds: The rule-of-five revolution. Drug Discovery Today: Technologies, 1(4), 337–341. https://doi.org/10.1016/j.ddtec.2004.11.007
  • Liu, J., Cao, R., Xu, M., Wang, X., Zhang, H., Hu, H., Li, Y., Hu, Z., Zhong, W., & Wang, M. (2020). Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro. Cell Discovery, 6, 16. https://doi.org/10.1038/s41421-020-0156-0
  • Lüthy, R., Bowie, J. U., & Eisenberg, D. (1992). Assessment of protein models with three-dimensional profiles. Nature, 356(6364), 83–85. https://doi.org/10.1038/356083a0
  • McNicholas, S., Potterton, E., Wilson, K. S., & Noble, M. E. (2011). Presenting your structures: The CCP4mg molecular-graphics software. Acta Crystallogr D: Biol Crystallogr, 67(Pt 4), 386–394. https://doi.org/10.1107/S0907444911007281
  • Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30(16), 2785–2791. https://doi.org/10.1002/jcc.21256
  • Mukherjee, G., & Jayaram, B. (2013). A rapid identification of hit molecules for target proteins via physico-chemical descriptors. Physical Chemistry Chemical Physics: PCCP, 15(23), 9107–9116. https://doi.org/10.1039/c3cp44697b
  • O'Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., & Hutchison, G. R. (2011). Open Babel: An open chemical toolbox. Journal of Cheminformatics, 3(1), 33. https://doi.org/10.1186/1758-2946-3-33
  • Oostenbrink, C., Villa, A., Mark, A. E., & van Gunsteren, W. F. (2004). A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6. Journal of Computational Chemistry, 25(13), 1656–1676. https://doi.org/10.1002/jcc.20090
  • Rajendran, V., Gopalakrishnan, C., & Sethumadhavan, R. (2018). Pathological role of a point mutation (T315I) in BCR-ABL1 protein—A computational insight. Journal of Cellular Biochemistry, 119(1), 918–925. https://doi.org/10.1002/jcb.26257
  • Rose, P. W., Beran, B., Bi, C., Bluhm, W. F., Dimitropoulos, D., Goodsell, D. S., Prlic, A., Quesada, M., Quinn, G. B., Westbrook, J. D., Young, J., Yukich, B., Zardecki, C., Berman, H. M., & Bourne, P. E. (2011). The RCSB Protein Data Bank: Redesigned web site and web services. Nucleic Acids Research, 39 (Database issue), D392–D401. https://doi.org/10.1093/nar/gkq1021
  • Rothan, H. A., & Byrareddy, S. N. (2020). The epidemiology and pathogenesis of coronavirus disease (COVID-19) outbreak. Journal of Autoimmunity, 109, 102433. https://doi.org/10.1016/j.jaut.2020.102433
  • Schüttelkopf, A. W., & van Aalten, D. M. (2004). PRODRG: A tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallographica Section D: Biological Crystallography, 60(Pt 8), 1355–1363. https://doi.org/10.1107/S0907444904011679
  • Shen, J., Cheng, F., Xu, Y., Li, W., & Tang, Y. (2010). Estimation of ADME properties with substructure pattern recognition. Journal of Chemical Information and Modeling, 50(6), 1034–1041. https://doi.org/10.1021/ci100104j
  • Simmerling, C., Strockbine, B., & Roitberg, A. E. (2002). All-atom structure prediction and folding simulations of a stable protein. Journal of the American Chemical Society, 124(38), 11258–11259. https://doi.org/10.1021/ja0273851
  • Sinha, N., & Balayla, G. (2020). Hydroxychloroquine and covid-19. Postgraduate Medical Journal, 96(1139), 550–555. postgradmedj-2020-137785. Advance online publication. https://doi.org/10.1136/postgradmedj-2020-137785
  • Ton, A. T., Gentile, F., Hsing, M., Ban, F., & Cherkasov, A. (2020). Rapid identification of potential inhibitors of SARS-CoV-2 main protease by deep docking of 1.3 Billion compounds. Molecular Informatics, 39(8), 2000028. 10.1002/minf.202000028. Advance online publication. https://doi.org/10.1002/minf.202000028
  • Trott, O., & Olson, A. J. (2010). 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
  • Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26(16), 1701–1718. https://doi.org/10.1002/jcc.20291
  • Wang, C., Horby, P. W., Hayden, F. G., & Gao, G. F. (2020). A novel coronavirus outbreak of global health concern. The Lancet, 395(10223), 470–473. https://doi.org/10.1016/S0140-6736(20)30185-9
  • Wiederstein, M., & Sippl, M. J. (2007). ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Research, 35(Web Server issue), W407–W410. https://doi.org/10.1093/nar/gkm290
  • Xu, R. H., He, J. F., Evans, M. R., Peng, G. W., Field, H. E., Yu, D. W., Lee, C. K., Luo, H. M., Lin, W. S., Lin, P., Li, L. H., Liang, W. J., Lin, J. Y., & Schnur, A. (2004). Epidemiologic clues to SARS origin in China. Emerging Infectious Diseases, 10(6), 1030–1037. https://doi.org/10.3201/eid1006.030852
  • Zhao, H., & Caflisch, A. (2015). Molecular dynamics in drug design. European Journal of Medicinal Chemistry, 91, 4–14. https://doi.org/10.1016/j.ejmech.2014.08.004

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