Identifying inhibitors of NSP16-NSP10 of SARS-CoV-2 from large databases

References

• Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindahl, E. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1–2, 19–25. https://doi.org/10.1016/j.softx.2015.06.001
   Google Scholar
• Ali, A., & Vijayan, R. (2020). Dynamics of the ACE2–SARS-CoV-2/SARS-CoV spike protein interface reveal unique mechanisms. Scientific Reports, 10(1), 14214. https://doi.org/10.1038/s41598-020-71188-3
   PubMed Web of Science ®Google Scholar
• Arya, R., Kumari, S., Pandey, B., Mistry, H., Bihani, S. C., Das, A., Prashar, V., Gupta, G. D., Panicker, L., & Kumar, M. (2021). Structural insights into SARS-CoV-2 proteins. Journal of Molecular Biology, 433(2), 166725. https://doi.org/10.1016/j.jmb.2020.11.024
   PubMed Web of Science ®Google Scholar
• Bartholomew-Biggs, M. (2005). The steepest descent method. In: Nonlinear optimization with financial applications (pp. 51–64). Springer. https://doi.org/10.1007/0-387-24149-3_5
   Google Scholar
• Bhowmik, D., Nandi, R., Jagadeesan, R., Kumar, N., Prakash, A., & Kumar, D. (2020). Identification of potential inhibitors against SARS-CoV-2 by targeting proteins responsible for envelope formation and virion assembly using docking based virtual screening, and pharmacokinetics approaches. Infection, Genetics and Evolution, 84, 104451. https://doi.org/10.1016/j.meegid.2020.104451
   PubMed Web of Science ®Google Scholar
• Bobiļeva, O., Bobrovs, R., Kaņepe, I., Patetko, L., Kalniņš, G., Šišovs, M., Bula, A. L., Gri Nberga, S., Borodušķis, M. R., Ramata-Stunda, A., Rostoks, N., Jirgensons, A., Ta Rs, K., & Jaudzems, K. (2021). Potent SARS-CoV-2 mRNA cap methyltransferase inhibitors by bioisosteric replacement of methionine in SAM cosubstrate. ACS Medicinal Chemistry Letters, 12(7), 1102–1107. https://doi.org/10.1021/acsmedchemlett.1c00140
   PubMed Web of Science ®Google Scholar
• Bolton, E. E., Wang, Y., Thiessen, P. A., & Bryant, S. H. (2008). Chapter 12 - PubChem: Integrated platform of small molecules and biological activities. Annual Reports in Computational Chemistry, 4, 217–241. https://doi.org/10.1016/S1574-1400(08)00012-1
   Google Scholar
• Bouvet, M., Debarnot, C., Imbert, I., Selisko, B., Snijder, E. J., Canard, B., & Decroly, E. (2010). In vitro reconstitution of SARS-coronavirus mRNA cap methylation. PLoS Pathogens, 6(4), e1000863. https://doi.org/10.1371/journal.ppat.1000863
   PubMed Web of Science ®Google Scholar
• Bussi, G., Donadio, D., & Parrinello, M. (2007). Canonical sampling through velocity rescaling. The Journal of Chemical Physics, 126(1), 014101. https://doi.org/10.1063/1.2408420
   PubMed Web of Science ®Google Scholar
• Coronaviridae Study Group of the International Committee on Taxonomy of Viruses. (2020). The species severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2. Nature Microbiology, 5(4), 536–544. https://doi.org/10.1038/s41564-020-0695-z
   PubMed Web of Science ®Google Scholar
• Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: AnN⋅log(N) method for Ewald sums in large systems. The Journal of Chemical Physics, 98(12), 10089–10092. https://doi.org/10.1063/1.464397
   Web of Science ®Google Scholar
• El Hassab, M. A., Ibrahim, T. M., Al-Rashood, S. T., Alharbi, A., Eskandrani, R. O., & Eldehna, W. M. (2021). In silico identification of novel SARS-COV-2 2'-O-methyltransferase (nsp16) inhibitors: structure-based virtual screening, molecular dynamics simulation and MM-PBSA approaches. Journal of Enzyme Inhibition and Medicinal Chemistry, 36(1), 727–736. https://doi.org/10.1080/14756366.2021.1885396
   PubMed Web of Science ®Google Scholar
• El Hassab, M. A., Ibrahim, T. M., Shoun, A. A., Al-Rashood, S. T., Alkahtani, H. M., Alharbi, A., Eskandrani, R. O., & Eldehna, W. M. (2021). In silico identification of potential SARS COV-2 2'-O-methyltransferase inhibitor: fragment-based screening approach and MM-PBSA calculations. RSC Advances, 11(26), 16026–16033. https://doi.org/10.1039/d1ra01809d
   PubMed Web of Science ®Google Scholar
• Elfiky, A. A. (2021). SARS-CoV-2 RNA dependent RNA polymerase (RdRp) targeting: an in silico perspective. Journal of Biomolecular Structure & Dynamics, 39(9), 3204–3212. https://doi.org/10.1080/07391102.2020.1761882
   PubMed Web of Science ®Google Scholar
• Encinar, J. A., & Menendez, J. A. (2020). Potential drugs targeting early innate immune evasion of SARS-coronavirus 2 via 2’-O-methylation of viral RNA. Viruses, 12(5), 525. https://doi.org/10.3390/v12050525
   PubMed Web of Science ®Google Scholar
• AIDS Antiviral Screen Data. (Sep 08, 2021). https://wiki.nci.nih.gov/display/NCIDTPdata/AIDS+Antiviral+Screen+Data
   Google Scholar
• Gasteiger’s group (2004). AIDS Antiviral Screen Data. Available from https://wiki.nci.nih.gov/display/NCIDTPdata/AIDS+Antiviral+Screen+Data
   Google Scholar
• Gibson, C. T., Carnally, S., & Roberts, C. J. (2007). Attachment of carbon nanotubes to atomic force microscope probes. Ultramicroscopy, 107(10–11), 1118–1122. https://doi.org/10.1016/j.ultramic.2007.02.045
   PubMed Web of Science ®Google Scholar
• Group, R. C., Horby, P., Lim, W. S., Emberson, J. R., Mafham, M., Bell, J. L., Linsell, L., Staplin, N., Brightling, C., & Ustianowski, A. (2021). Dexamethasone in hospitalized patients with Covid-19. The New England Journal of Medicine, 384(8), 693–704. https://doi.org/10.1056/NEJMoa2021436
   PubMed Web of Science ®Google Scholar
• Grubmuller, H., Heymann, B., & Tavan, P. (1996). Ligand binding: molecular mechanics calculation of the streptavidin-biotin rupture force. Science (New York, NY), 271(5251), 997–999. https://doi.org/10.1126/science.271.5251.997
   Google Scholar
• He, R., Adonov, A., Traykova-Adonova, M., Cao, J., Cutts, T., Grudesky, E., Deschambaul, Y., Berry, J., Drebot, M., & Li, X. (2004). Potent and selective inhibition of SARS coronavirus replication by aurintricarboxylic acid. Biochemical and Biophysical Research Communications, 320(4), 1199–1203. https://doi.org/10.1016/j.bbrc.2004.06.076
   PubMed Web of Science ®Google Scholar
• Hockney, R., Goel, S., & Eastwood, J. (1974). Quiet high-resolution computer models of a plasma. Journal of Computational Physics, 14(2), 148–158. https://doi.org/10.1016/0021-9991(74)90010-2
   Web of Science ®Google Scholar
• Hu, X., Zhou, Z., Li, F., Xiao, Y., Wang, Z., Xu, J., Dong, F., Zheng, H., & Yu, R. (2021). The study of antiviral drugs targeting SARS-CoV-2 nucleocapsid and spike proteins through large-scale compound repurposing. Heliyon, 7(3), e06387. https://doi.org/10.1016/j.heliyon.2021.e06387
   PubMed Web of Science ®Google Scholar
• Huang, Y., Yang, C., Xu, X. F., Xu, W., & Liu, S. W. (2020). Structural and functional properties of SARS-CoV-2 spike protein: Potential antivirus drug development for COVID-19. Acta Pharmacologica Sinica, 41(9), 1141–1149. https://doi.org/10.1038/s41401-020-0485-4
   PubMed Web of Science ®Google Scholar
• Hub, J. S., de Groot, B. L., & van der Spoel, D. (2010). g_wham—A free weighted histogram analysis implementation including robust error and autocorrelation estimates. Journal of Chemical Theory and Computation, 6(12), 3713–3720. https://doi.org/10.1021/ct100494z
   Web of Science ®Google Scholar
• Hummer, G., & Szabo, A. (2001). Free energy reconstruction from nonequilibrium single-molecule pulling experiments. Proceedings of the National Academy of Sciences of the United States of America, 98(7), 3658–3661. https://doi.org/10.1073/pnas.071034098
   PubMed Web of Science ®Google Scholar
• Huy, P. D. Q., & Li, M. S. (2014). Binding of fullerenes to amyloid beta fibrils: Size matters. Physical Chemistry Chemical Physics, 16(37), 20030–20040. https://doi.org/10.1039/C4CP02348J
   Google Scholar
• Jakalian, A., Bush, B. L., Jack, D. B., & Bayly, C. I. (2000). Fast, efficient generation of high‐quality atomic charges. AM1‐BCC model: I. Method. Journal of Computational Chemistry, 21(2), 132–146. https://doi.org/10.1002/jcc.10128
   Web of Science ®Google Scholar
• Jarzynski, C. (1997). Nonequilibrium equality for free energy differences. Physical Review Letters, 78(14), 2690–2693. https://doi.org/10.1103/PhysRevLett.78.2690
   Web of Science ®Google Scholar
• Jayk Bernal, A., Gomes da Silva, M. M., Musungaie, D. B., Kovalchuk, E., Gonzalez, A., Delos Reyes, V., Martín-Quirós, A., Caraco, Y., Williams-Diaz, A., Brown, M. L., Du, J., Pedley, A., Assaid, C., Strizki, J., Grobler, J. A., Shamsuddin, H. H., Tipping, R., Wan, H., Paschke, A., … De Anda, C. (2022). Molnupiravir for oral treatment of covid-19 in nonhospitalized patients. New England Journal of Medicine, 386(6), 509–520. https://doi.org/10.1056/NEJMoa2116044
   PubMed Web of Science ®Google Scholar
• Jiang, S., Hillyer, C., & Du, L. (2020). Neutralizing antibodies against SARS-CoV-2 and other human coronaviruses. Trends in Immunology, 41(5), 355–359. https://doi.org/10.1016/j.it.2020.03.007
   PubMed Web of Science ®Google Scholar
• Jiang, Y., Liu, L., Manning, M., Bonahoom, M., Lotvola, A., Yang, Z., & Yang, Z. Q. (2022). Structural analysis, virtual screening and molecular simulation to identify potential inhibitors targeting 2'-O-ribose methyltransferase of SARS-CoV-2 coronavirus. Journal of Biomolecular Structure & Dynamics, 40(3), 1331–1346. https://doi.org/10.1080/07391102.2020.1828172
   PubMed Web of Science ®Google Scholar
• Jimenez-Alberto, A., Ribas-Aparicio, R. M., Aparicio-Ozores, G., & Castelan-Vega, J. A. (2020). Virtual screening of approved drugs as potential SARS-CoV-2 main protease inhibitors. Computational Biology and Chemistry, 88, 107325. https://doi.org/10.1016/j.compbiolchem.2020.107325
   PubMed Web of Science ®Google Scholar
• Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics, 79(2), 926–935. https://doi.org/10.1063/1.445869
   Web of Science ®Google Scholar
• Kadioglu, O., Saeed, M., Greten, H. J., & Efferth, T. (2021). Identification of novel compounds against three targets of SARS CoV-2 coronavirus by combined virtual screening and supervised machine learning. Computers in Biology and Medicine, 133, 104359. https://doi.org/10.1016/j.compbiomed.2021.104359
   PubMed Web of Science ®Google Scholar
• Khamsi, R. (2021). Rogue antibodies could be driving severe COVID-19. Nature, 590(7844), 29–31. https://doi.org/10.1038/d41586-021-00149-1
   PubMed Web of Science ®Google Scholar
• Kim, D., Lee, J. Y., Yang, J. S., Kim, J. W., Kim, V. N., & Chang, H. (2020). The architecture of SARS-CoV-2 transcriptome. Cell, 181(4), 914–921. https://doi.org/10.1016/j.cell.2020.04.011
   PubMed Web of Science ®Google Scholar
• Kozielski, F., Sele, C., Talibov, V. O., Lou, J., Dong, D., Wang, Q., Shi, X., Nyblom, M., Rogstam, A., Krojer, T., Fisher, Z., & Knecht, W. (2022). Identification of fragments binding to SARS-CoV-2 nsp10 reveals ligand-binding sites in conserved interfaces between nsp10 and nsp14/nsp16. RSC Chemical Biology, 3(1), 44–55. https://doi.org/10.1039/D1CB00135C
   PubMedGoogle Scholar
• Krafcikova, P., Silhan, J., Nencka, R., & Boura, E. (2020). Structural analysis of the SARS-CoV-2 methyltransferase complex involved in RNA cap creation bound to sinefungin. Nature Communications, 11(1), 3717. https://doi.org/10.1038/s41467-020-17495-9
   PubMed Web of Science ®Google Scholar
• Kumar, S., Rosenberg, J. M., Bouzida, D., Swendsen, R. H., & Kollman, P. A. (1992). THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method. Journal of Computational Chemistry, 13(8), 1011–1021. https://doi.org/10.1002/jcc.540130812
   Web of Science ®Google Scholar
• Liang, J., Pitsillou, E., Burbury, L., Hung, A., & Karagiannis, T. C. (2021). In silico investigation of potential small molecule inhibitors of the SARS-CoV-2 nsp10-nsp16 methyltransferase complex. Chemical Physics Letters, 774, 138618. https://doi.org/10.1016/j.cplett.2021.138618
   PubMed Web of Science ®Google Scholar
• Lindorff-Larsen, K., Piana, S., Palmo, K., Maragakis, P., Klepeis, J. L., Dror, R. O., & Shaw, D. E. (2010). Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins, 78(8), 1950–1958. https://doi.org/10.1002/prot.22711
   PubMed Web of Science ®Google Scholar
• Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (2012). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews, 64, 4–17. https://doi.org/10.1016/j.addr.2012.09.019
   Web of Science ®Google Scholar
• Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (1997). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews, 23(1–3), 3–25. https://doi.org/10.1016/S0169-409X(96)00423-1
   Web of Science ®Google Scholar
• Ma, C., Sacco, M. D., Xia, Z., Lambrinidis, G., Townsend, J. A., Hu, Y., Meng, X., Szeto, T., Ba, M., Zhang, X., Gongora, M., Zhang, F., Marty, M. T., Xiang, Y., Kolocouris, A., Chen, Y., & Wang, J. (2021). Discovery of SARS-CoV-2 papain-like protease inhibitors through a combination of high-throughput screening and a FlipGFP-based reporter assay. ACS Central Science, 7(7), 1245–1260. https://doi.org/10.1021/acscentsci.1c00519
   PubMed Web of Science ®Google Scholar
• Mai, B. K., & Li, M. S. (2011). Neuraminidase inhibitor R-125489–A promising drug for treating influenza virus: steered molecular dynamics approach. Biochemical and Biophysical Research Communications, 410(3), 688–691. https://doi.org/10.1016/j.bbrc.2011.06.057
   PubMed Web of Science ®Google Scholar
• Mai, B. K., Viet, M. H., & Li, M. S. (2010). Top leads for swine influenza A/H1N1 virus revealed by steered molecular dynamics approach. Journal of Chemical Information and Modeling, 50(12), 2236–2247. https://doi.org/10.1021/ci100346s
   PubMed Web of Science ®Google Scholar
• Malik, A., Kohli, M., Jacob, N. A., Kayal, A., Raj, T. K., Kulkarni, N., & Chandramohan, V. (2021). In silico screening of phytochemical compounds and FDA drugs as potential inhibitors for NSP16/10 5' methyl transferase activity. Journal of Biomolecular Structure and Dynamics, 1–13. https://doi.org/10.1080/07391102.2021.2005680
   Google Scholar
• Maurya, S. K., Maurya, A. K., Mishra, N., & Siddique, H. R. (2020). Virtual screening, ADME/T, and binding free energy analysis of anti-viral, anti-protease, and anti-infectious compounds against NSP10/NSP16 methyltransferase and main protease of SARS CoV-2. Journal of Receptor and Signal Transduction Research, 40(6), 605–612. https://doi.org/10.1080/10799893.2020.1772298
   PubMed Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Nallagatla, S. R., Toroney, R., & Bevilacqua, P. C. (2008). A brilliant disguise for self RNA: 5'-end and internal modifications of primary transcripts suppress elements of innate immunity. RNA Biology, 5(3), 140–144. https://doi.org/10.4161/rna.5.3.6839
   PubMed Web of Science ®Google Scholar
• Nencka, R., Silhan, J., Klima, M., Otava, T., Kocek, H., Krafcikova, P., & Boura, E. (2022). Coronaviral RNA-methyltransferases: function, structure and inhibition. Nucleic Acids Research, 50(2), 635–650. https://doi.org/10.1093/nar/gkab1279
   PubMed Web of Science ®Google Scholar
• Nguyen, H. L., Thai, N. Q., Truong, D. T., & Li, M. S. (2020). Remdesivir strongly binds to both RNA-dependent RNA polymerase and main protease of SARS-CoV-2: Evidence from molecular simulations. The Journal of Physical Chemistry B, 124(50), 11337–11348. https://doi.org/10.1021/acs.jpcb.0c07312
   PubMed Web of Science ®Google Scholar
• NIAID Division of AIDS Anti-HIV/OI/TB Therapeutics Database. https://chemdb.niaid.nih.gov/
   Google Scholar
• Orfali, R., Rateb, M. E., Hassan, H. M., Alonazi, M., Gomaa, M. R., Mahrous, N., GabAllah, M., Kandeil, A., Perveen, S., Abdelmohsen, U. R., & Sayed, A. M. (2021). Sinapic acid suppresses SARS CoV-2 replication by targeting its envelope protein. Antibiotics (Basel), 10(4), 420. https://doi.org/10.3390/antibiotics10040420
   PubMed Web of Science ®Google Scholar
• Owen, D. R., Allerton, C. M. N., Anderson, A. S., Aschenbrenner, L., Avery, M., Berritt, S., Boras, B., Cardin, R. D., Carlo, A., Coffman, K. J., Dantonio, A., Di, L., Eng, H., Ferre, R., Gajiwala, K. S., Gibson, S. A., Greasley, S. E., Hurst, B. L., Kadar, E. P., … Zhu, Y. (2021). An oral SARS-CoV-2 M(pro) inhibitor clinical candidate for the treatment of COVID-19. Science (New York, NY), 374(6575), 1586–1593. https://doi.org/10.1126/science.abl4784
   Google Scholar
• Park, S., & Schulten, K. (2004). Calculating potentials of mean force from steered molecular dynamics simulations. The Journal of Chemical Physics, 120(13), 5946–5961. https://doi.org/10.1063/1.1651473
   PubMed Web of Science ®Google Scholar
• Parrinello, M., & Rahman, A. (1981). Polymorphic transitions in single crystals: A new molecular dynamics method. Journal of Applied Physics, 52(12), 7182–7190. https://doi.org/10.1063/1.328693
   Web of Science ®Google Scholar
• Perez-Lemus, G. R., Menendez, C. A., Alvarado, W., Bylehn, F., & de Pablo, J. J. (2022). Toward wide-spectrum antivirals against coronaviruses: Molecular characterization of SARS-CoV-2 NSP13 helicase inhibitors. Science Advances, 8(1), eabj4526. https://doi.org/10.1126/sciadv.abj4526
   PubMed Web of Science ®Google Scholar
• Rampogu, S., & Lee, K. W. (2021). Pharmacophore modelling-based drug repurposing approaches for SARS-CoV-2 therapeutics. Frontiers in Chemistry, 9, 636362. https://doi.org/10.3389/fchem.2021.636362
   PubMed Web of Science ®Google Scholar
• Rosas-Lemus, M., Minasov, G., Shuvalova, L., Inniss, N. L., Kiryukhina, O., Brunzelle, J., & Satchell, K. J. F. (2020). High-resolution structures of the SARS-CoV-2 2'-O-methyltransferase reveal strategies for structure-based inhibitor design. Science Signaling, 13(651) eabe1202. https://doi.org/10.1126/scisignal.abe1202
   Google Scholar
• Ruan, Z., Liu, C., Guo, Y., He, Z., Huang, X., Jia, X., & Yang, T. (2021). SARS-CoV-2 and SARS-CoV: Virtual screening of potential inhibitors targeting RNA-dependent RNA polymerase activity (NSP12). Journal of Medical Virology, 93(1), 389–400. https://doi.org/10.1002/jmv.26222
   PubMed Web of Science ®Google Scholar
• Sanner, M. F. (1999). Python: a programming language for software integration and development. Journal of Molecular Graphics & Modelling, 17(1), 57–61.
   PubMed Web of Science ®Google Scholar
• Selvaraj, C., Dinesh, D. C., Panwar, U., Abhirami, R., Boura, E., & Singh, S. K. (2021). Structure-based virtual screening and molecular dynamics simulation of SARS-CoV-2 Guanine-N7 methyltransferase (nsp14) for identifying antiviral inhibitors against COVID-19. Journal of Biomolecular Structure & Dynamics, 39(13), 4582–4593. https://doi.org/10.1080/07391102.2020.1778535
   PubMed Web of Science ®Google Scholar
• Sharma, A., Goyal, S., Yadav, A. K., Kumar, P., & Gupta, L. (2022). In-silico screening of plant-derived antivirals against main protease, 3CL(pro) and endoribonuclease, NSP15 proteins of SARS-CoV-2. Journal of Biomolecular Structure & Dynamics, 40(1), 86–100. https://doi.org/10.1080/07391102.2020.1808077
   PubMed Web of Science ®Google Scholar
• Skowronski, D. M., Astell, C., Brunham, R. C., Low, D. E., Petric, M., Roper, R. L., Talbot, P. J., Tam, T., & Babiuk, L. (2005). Severe acute respiratory syndrome (SARS): A year in review. Annual Review of Medicine, 56(1), 357–381. https://doi.org/10.1146/annurev.med.56.091103.134135
   PubMedGoogle Scholar
• Sousa da Silva, A. W., & Vranken, W. F. (2012). ACPYPE - AnteChamber PYthon Parser interfacE. BMC Research Notes, 5(1), 367. https://doi.org/10.1186/1756-0500-5-367
   PubMedGoogle Scholar
• Suan Li, M., & Khanh Mai, B. (2012). Steered molecular dynamics-a promising tool for drug design. Current Bioinformatics, 7(4), 342–351. https://doi.org/10.2174/157489312803901009
   Web of Science ®Google Scholar
• Thai, N. Q., Linh, H. N., Linh, H. Q., & Li, M. S. (2017). Protocol for fast screening of multi-target drug candidates: Application to Alzheimer's disease. Journal of Molecular Graphics & Modelling, 77, 121–129. https://doi.org/10.1016/j.jmgm.2017.08.002
   PubMed Web of Science ®Google Scholar
• Torrie, G. M., & Valleau, J. P. (1977). Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling. Journal of Computational Physics, 23(2), 187–199. https://doi.org/10.1016/0021-9991(77)90121-8
   Web of Science ®Google Scholar
• Tripathi, P. K., Upadhyay, S., Singh, M., Raghavendhar, S., Bhardwaj, M., Sharma, P., & Patel, A. K. (2020). Screening and evaluation of approved drugs as inhibitors of main protease of SARS-CoV-2. International Journal of Biological Macromolecules, 164(1), 2622–2631. https://doi.org/10.1016/j.ijbiomac.2020.08.166
   PubMedGoogle Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Viet, M.H., Siposova, K., Bednarikova, Z., Antosova, A., Nguyen, T. T., Gazova, Z., & Li, M. S. (2015). In silico a n d in vitro study of binding affinity of tripeptides to amyloid beta fibrils: Implications for Alzheimer’s disease . The Journal of Physical Chemistry B, 119(16), 5145–5155. https://doi.org/10.1021/acs.jpcb.5b00006
   Google Scholar
• Viswanathan, T., Arya, S., Chan, S.-H., Qi, S., Dai, N., Misra, A., Park, J.-G., Oladunni, F., Kovalskyy, D., Hromas, R. A., Martinez-Sobrido, L., & Gupta, Y. K. (2020). Structural basis of RNA cap modification by SARS-CoV-2. Nature Communications, 11(1), 3718. https://doi.org/10.1038/s41467-020-17496-8
   PubMed Web of Science ®Google Scholar
• Vuong, Q. V., Nguyen, T. T., & Li, M. S. (2015). A new method for navigating optimal direction for pulling ligand from binding pocket: Application to ranking binding affinity by steered molecular dynamics. Journal of Chemical Information and Modeling, 55(12), 2731–2738. https://doi.org/10.1021/acs.jcim.5b00386
   PubMed Web of Science ®Google Scholar
• Wang, J., Wang, W., Kollman, P. A., & Case, D. A. (2001). Antechamber: An accessory software package for molecular mechanical calculations. Journal of the American Chemical Society, 222, U403.
   Web of Science ®Google Scholar
• Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A., & Case, D. A. (2004). Development and testing of a general amber force field. Journal of Computational Chemistry, 25(9), 1157–1174. https://doi.org/10.1002/jcc.20035
   PubMed Web of Science ®Google Scholar
• Wang, Y., Zhang, D., Du, G., Du, R., Zhao, J., Jin, Y., Fu, S., Gao, L., Cheng, Z., Lu, Q., Hu, Y., Luo, G., Wang, K., Lu, Y., Li, H., Wang, S., Ruan, S., Yang, C., Mei, C., … Wang, C. (2020). Remdesivir in adults with severe COVID-19: A randomised, double-blind, placebo-controlled, multicentre trial. Lancet (London, England), 395(10236), 1569–1578. https://doi.org/10.1016/S0140-6736(20)31022-9
   PubMed Web of Science ®Google Scholar
• White, M. A., Lin, W., & Cheng, X. (2020). Discovery of COVID-19 inhibitors targeting the SARS-CoV-2 Nsp13 helicase. The Journal of Physical Chemistry Letters, 11(21), 9144–9151. https://doi.org/10.1021/acs.jpclett.0c02421
   PubMed Web of Science ®Google Scholar
• WHO. (2021). Classification of omicron (B.1.1.529): SARS-CoV-2 variant of concern. https://www.who.int/news/item/26-11-2021-classification-of-omicron-(b.1.1.529)-sars-cov-2-variant-of-concern
   Google Scholar
• World Health Organization. (2020). Coronavirus disease 2019 (COVID-19): Situation report (Vol. 74). WHO.
   Google Scholar
• Yadav, R., Imran, M., Dhamija, P., Suchal, K., & Handu, S. (2021). Virtual screening and dynamics of potential inhibitors targeting RNA binding domain of nucleocapsid phosphoprotein from SARS-CoV-2. Journal of Biomolecular Structure & Dynamics, 39(12), 4433–4448. https://doi.org/10.1080/07391102.2020.1778536
   PubMed Web of Science ®Google Scholar