Computational investigation of potential inhibitors of novel coronavirus 2019 through structure-based virtual screening, molecular dynamics and density functional theory studies

References

• Amanat, F., & Krammer, F. (2020). SARS-CoV-2 vaccines: Status Report. Immunity, 52(4), 583–589. https://doi.org/10.1016/j.immuni.2020.03.007
   PubMed Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Belouzard, S., Millet, J. K., Licitra, B. N., & Whittaker, G. R. (2012). Mechanisms of coronavirus cell entry mediated by the viral spike protein. Viruses, 4(6), 1011–1033. https://doi.org/10.3390/v4061011
   PubMed Web of Science ®Google Scholar
• Bochevarov, A. D., Harder, E., Hughes, T. F., Greenwood, J. R., Braden, D. A., Philipp, D. M., Rinaldo, D., Halls, M. D., Zhang, J., & Friesner, R. A. (2013). Jaguar: A high-performance quantum chemistry software program with strengths in life and materials sciences. International Journal of Quantum Chemistry, 113(18), 2110–2142. https://doi.org/10.1002/qua.24481
   Web of Science ®Google Scholar
• Boopathi, S., Poma, A. B., & Kolandaivel, P. (2020). Novel 2019 coronavirus structure, mechanism of action, antiviral drug promises and rule out against its treatment. Journal of Biomolecular Structure and Dynamics, 1–10. https://doi.org/10.1080/07391102.2020.1758788
   Web of Science ®Google Scholar
• Chang, C., Lo, S.-C., Wang, Y.-S., & Hou, M.-H. (2016). Recent insights into the development of therapeutics against coronavirus diseases by targeting N protein. Drug Discovery Today, 21(4), 562–572. https://doi.org/10.1016/j.drudis.2015.11.015
   PubMed Web of Science ®Google Scholar
• Guo, Z., Mohanty, U., Noehre, J., Sawyer, T. K., Sherman, W., & Krilov, G. (2010). Probing the alpha-helical structural stability of stapled p53 peptides: molecular dynamics simulations and analysis. Chemical Biology & Drug Design, 75(4), 348–359. https://doi.org/10.1111/j.1747-0285.2010.00951.x
   PubMed Web of Science ®Google Scholar
• Gupta, M. K., Vemula, S., Donde, R., Gouda, G., Behera, L., & Vadde, R. (2020). In-silico approaches to detect inhibitors of the human severe acute respiratory syndrome coronavirus envelope protein ion channel. Journal of Biomolecular Structure and Dynamics, 1–11. https://doi.org/10.1080/07391102.2020.1751300
   PubMedGoogle Scholar
• Hajduk, P. J., Huth, J. R., & Tse, C. (2005). Predicting protein druggability. Drug Discovery Today, 10(23-24), 1675–1682. https://doi.org/10.1016/S1359-6446(05)03624-X
   PubMed Web of Science ®Google Scholar
• Halgren, T. A. (2009). Identifying and characterizing binding sites and assessing druggability. Journal of Chemical Information and Modeling, 49(2), 377–389. https://doi.org/10.1021/ci800324m
   PubMed Web of Science ®Google Scholar
• Halgren, T. (2007). New method for fast and accurate binding-site identification and analysis. Chemical Biology & Drug Design, 69(2), 146–148. https://doi.org/10.1111/j.1747-0285.2007.00483.x
   PubMed Web of Science ®Google Scholar
• Hasan, A., Paray, B. A., Hussain, A., Qadir, F. A., Attar, F., Aziz, F. M., Sharifi, M., Derakhshankhah, H., Rasti, B., Mehrabi, M., & Shahpasand, K. Saboury, A. A, & Falahati, M. (2020). A review on the cleavage priming of the spike protein on coronavirus by angiotensin-converting enzyme-2 and furin. Journal of Biomolecular Structure and Dynamics, https://doi.org/10.1080/07391102.2020.1754293
   Web of Science ®Google Scholar
• Kar, S., & Roy, K. (2013). How far can virtual screening take us in drug discovery? Expert Opinion on Drug Discovery, 8(3), 245–261. https://doi.org/10.1517/17460441.2013.761204
   PubMed Web of Science ®Google Scholar
• Kirchdoerfer, R. N., Cottrell, C. A., Wang, N., Pallesen, J., Yassine, H. M., Turner, H. L., Corbett, K. S., Graham, B. S., McLellan, J. S., & Ward, A. B. (2016). Pre-fusion structure of a human coronavirus spike protein. Nature, 531(7592), 118–121. https://doi.org/10.1038/nature17200
   PubMed Web of Science ®Google Scholar
• Kumar, N., Mishra, S. S., Sharma, C. S., Singh, H. P., & Kalra, S. (2018). In silico binding mechanism prediction of benzimidazole based corticotropin releasing factor-1 receptor antagonists by quantitative structure activity relationship, molecular docking and pharmacokinetic parameters calculation. Journal of Biomolecular Structure & Dynamics, 36(7), 1691–1712. PMC]
   PubMed Web of Science ®Google Scholar
• Li, F. (2016). Structure, Function, and Evolution of Coronavirus Spike Proteins. Annual Review of Virology, 3(1), 237–261. https://doi.org/10.1146/annurev-virology-110615-042301
   PubMed Web of Science ®Google Scholar
• Lin, S.-M., Lin, S.-C., Hsu, J.-N., Chang, C.-K., Chien, C.-M., Wang, Y.-S., Wu, H.-Y., Jeng, U.-S., Kehn-Hall, K., & Hou, M.-H. (2020). Structure-based stabilization of non-native protein-protein interactions of coronavirus nucleocapsid proteins in antiviral drug design. Journal of Medicinal Chemistry, 63(6), 3131–3141. https://doi.org/10.1021/acs.jmedchem.9b01913
   PubMed Web of Science ®Google Scholar
• Masters, P. S. (2006). The molecular biology of coronaviruses. Advances in Virus Research, 66, 193–292. https://doi.org/10.1016/s0065-3527(06)66005-3
   PubMed Web of Science ®Google Scholar
• Muralidharan, N., Sakthivel, R., Velmurugan, D., & Gromiha, M. M. (2020). Computational studies of drug repurposing and synergism of lopinavir, oseltamivir and ritonavir binding with SARS-CoV-2 protease against COVID-19. Journal of Biomolecular Structure and Dynamics, https://doi.org/10.1080/07391102.2020.1752802
   PubMed Web of Science ®Google Scholar
• Rollinger, J. M., Stuppner, H., & Langer, T. (2008). Virtual screening for the discovery of bioactive natural products. Natural Compounds as Drugs, I, 211–249. https://doi.org/10.1007/978-3-7643-8117-2_6
   Google Scholar
• Sarma, P., Shekhar, N., Prajapat, M., Avti, P., Kaur, H., Kumar, S., Singh, S., Kumar, H., & Prakash, A., Dhibar, D. P. & Medhi, B. (2020 ) In-silico homology assisted identification of inhibitor of RNA binding against 2019-nCoV N-protein (N terminal domain). Journal of Biomolecular Structure and Dynamics, https://doi.org/10.1080/07391102.2020.1753580
   Google Scholar
• Shekhar, M. S., Venkatachalam, T., Sharma, C. S., Pratap Singh, H., Kalra, S., & Kumar, N. (2019). Computational investigation of binding mechanism of substituted pyrazinones targeting corticotropin releasing factor-1 receptor deliberated for anti-depressant drug design. Journal of Biomolecular Structure & Dynamics, 37(12), 3226–3244. https://doi.org/10.1080/07391102.2018.1513379
   PubMed Web of Science ®Google Scholar
• Su, P.-C., Tsai, C.-C., Mehboob, S., Hevener, K. E., & Johnson, M. E. (2015). Comparison of radii sets, entropy, QM methods, and sampling on MM-PBSA, MM-GBSA, and QM/MM-GBSA ligand binding energies of F. tularensis enoyl-ACP reductase (FabI)). Journal of Computational Chemistry, 36(25), 1859–1873. https://doi.org/10.1002/jcc.24011
   PubMed Web of Science ®Google Scholar
• Tahir Khan, M., Ali, A., Wang, Muhammad Irfan, Q., Khan, A., Zeb, M. T., Zhang, Y.-J., Chinnasamy, S., & Wei, D.-Q. (2020). Marine natural compounds as potents inhibitors against the main protease of SARS-CoV-2. A molecular dynamic study. Journal of Biomolecular Structure and Dynamics, https://doi.org/10.1080/07391102.2020.1769733
   Google Scholar
• Van Hemert, M. J., van den Worm, S. H. E., Knoops, K., Mommaas, A. M., Gorbalenya, A. E., & Snijder, E. J. (2008). SARS-coronavirus replication/transcription complexes are membrane-protected and need a host factor for activity in vitro. PLoS Pathogens, 4(5), e1000054. https://doi.org/10.1371/journal.ppat.1000054
   PubMed Web of Science ®Google Scholar
• Venugopal, P. P., Das, B. K., Soorya, E., & Chakraborty, D. (2020). Effect of hydrophobic and hydrogen bonding interactions on the potency of ß‐alanine analogs of G‐protein coupled glucagon receptor inhibitors. Proteins: Structure, Function, and Bioinformatics, 88(2), 327–344. https://doi.org/10.1002/prot.25807
   PubMed Web of Science ®Google Scholar
• Walls, A. C., Park, Y.-J., Tortorici, M. A., Wall, A., McGuire, A. T., & Veesler, D. (2020). Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein. Cell, 181(2), 281–292.e6. https://doi.org/10.1016/j.cell.2020.02.058
   PubMed Web of Science ®Google Scholar
• Yang, H., Bartlam, M., & Rao, Z. (2006). Drug design targeting the main protease, the Achilles' heel of coronaviruses. Current Pharmaceutical Design, 12(35), 4573–4590. https://doi.org/10.2174/138161206779010369
   PubMed Web of Science ®Google Scholar
• Zumla, A., Chan, J. F. W., Azhar, E. I., Hui, D. S. C., & Yuen, K.-Y. (2016). Coronaviruses – drug discovery and therapeutic options. Nature Reviews. Drug Discovery, 15(5), 327–347. https://doi.org/10.1038/nrd.2015.37
   PubMed Web of Science ®Google Scholar