Binding properties of selective inhibitors of P323L mutated RdRp of SARS-CoV-2: a combined molecular screening, docking and dynamics simulation study

References

• Arba, M., Wahyudi, S. T., Brunt, D. J., Paradis, N., & Wu, C. (2021). Mechanistic insight on the remdesivir binding to RNA-dependent RNA polymerase (RdRp) of SARS-cov-2. Computers in Biology and Medicine, 129(, 104156. https://doi.org/10.1016/j.compbiomed.2020.104156
   PubMed Web of Science ®Google Scholar
• Ashour, H. M., Elkhatib, W. F., Rahman, M. M., & Elshabrawy, H. A. (2020). Insights into the recent 2019 novel coronavirus (Sars-coV-2) in light of past human coronavirus outbreaks. Pathogens, 9(3), 186. https://doi.org/10.3390/pathogens9030186
   PubMed Web of Science ®Google Scholar
• Beigel, J. H., Tomashek, K. M., Dodd, L. E., Mehta, A. K., Zingman, B. S., Kalil, A. C., Hohmann, E., Chu, H. Y., Luetkemeyer, A., Kline, S., Lopez de Castilla, D., Finberg, R. W., Dierberg, K., Tapson, V., Hsieh, L., Patterson, T. F., Paredes, R., Sweeney, D. A., Short, W. R., … Lane, H. C. (2020). Remdesivir for the treatment of Covid-19—Final Report. The New England Journal of Medicine, 383(19), 1813–1826. https://doi.org/10.1056/nejmoa2007764
   PubMed Web of Science ®Google Scholar
• Biswas, S. K., & Mudi, S. R. (2020). Spike protein D614G and RdRp P323L: The SARS-CoV-2 mutations associated with severity of COVID-19. Genomics & Informatics, 18(4), e44. https://doi.org/10.5808/GI.2020.18.4.e44
   PubMedGoogle Scholar
• Corman, V. M., Muth, D., Niemeyer, D., & Drosten, C. (2018). Hosts and sources of endemic human coronaviruses. Advances in Virus Research, 100, 163–188. https://doi.org/10.1016/bs.aivir.2018.01.001
   PubMed Web of Science ®Google Scholar
• Cosar, B., Karagulleoglu, Z. Y., Unal, S., Ince, A. T., Uncuoglu, D. B., Tuncer, G., Kilinc, B. R., Ozkan, Y. E., Ozkoc, H. C., Demir, I. N., Eker, A., Karagoz, F., Simsek, S. Y., Yasar, B., Pala, M., Demir, A., Atak, I. N., Mendi, A. H., Bengi, V. U., … Demir-Dora, D. (2022). SARS-CoV-2 mutations and their viral variants. Cytokine & Growth Factor Reviews, 63, 10–22. https://doi.org/10.1016/j.cytogfr.2021.06.001
   PubMed Web of Science ®Google Scholar
• Cui, J., Li, F., & Shi, Z. L. (2019). Origin and evolution of pathogenic coronaviruses. Nature Reviews. Microbiology, 17(3), 181–192. https://doi.org/10.1038/s41579-018-0118-9
   PubMed Web of Science ®Google Scholar
• DeLano, W. L. (2002). Pymol: An open-source molecular graphics tool. CCP4 Newsletter on Protein Crystallography, 40, 82–92. http://www.ccp4.ac.uk/newsletters/newsletter40/11_pymol.pdf
   Google Scholar
• Eskier, D., Karakülah, G., Suner, A., & Oktay, Y. (2020). RdRp mutations are associated with SARS-CoV-2 genome evolution. PeerJ, 8, e9587. https://doi.org/10.7717/peerj.9587
   PubMed Web of Science ®Google Scholar
• Genheden, S., & Ryde, U. (2015). The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opinion on Drug Discovery, 10(5), 449–461. https://doi.org/10.1517/17460441.2015.1032936
   PubMed Web of Science ®Google Scholar
• Halgren, T. A., Murphy, R. B., Friesner, R. A., Beard, H. S., Frye, L. L., Pollard, W. T., & Banks, J. L. (2004). Glide: A new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. Journal of Medicinal Chemistry, 47(7), 1750–1759. https://doi.org/10.1021/jm030644s
   PubMed Web of Science ®Google Scholar
• Hou, T., Wang, J., Li, Y., & Wang, W. (2011). Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations. Journal of Chemical Information and Modeling, 51(1), 69–82. https://doi.org/10.1021/ci100275a
   PubMed Web of Science ®Google Scholar
• Kumar, D. T., Shaikh, N., Kumar S, U., Doss C, G. P., & Zayed, H. (2021). Structure-based virtual screening to identify novel potential compound as an alternative to remdesivir to overcome the RdRp protein mutations in SARS-CoV-2. Frontiers in Molecular Biosciences, 8(April), 645216. https://doi.org/10.3389/fmolb.2021.645216
   PubMedGoogle Scholar
• Li, J., Abel, R., Zhu, K., Cao, Y., Zhao, S., & Friesner, R. A. (2011). The VSGB 2.0 model: A next generation energy model for high resolution protein structure modeling. Proteins, 79(10), 2794–2812. https://doi.org/10.1002/prot.23106
   PubMed Web of Science ®Google Scholar
• Liang, C., Tian, L., Liu, Y., Hui, N., Qiao, G., Li, H., Shi, Z., Tang, Y., Zhang, D., Xie, X., & Zhao, X. (2020). A promising antiviral candidate drug for the COVID-19 pandemic: A mini-review of remdesivir. European Journal of Medicinal Chemistry, 201, 112527. https://doi.org/10.1016/j.ejmech.2020.112527
   PubMed Web of Science ®Google Scholar
• Lu, C., Wu, C., Ghoreishi, D., Chen, W., Wang, L., Damm, W., Ross, G. A., Dahlgren, M. K., Russell, E., Von Bargen, C. D., Abel, R., Friesner, R. A., & Harder, E. D. (2021). OPLS4: Improving force field accuracy on challenging regimes of chemical space. Journal of Chemical Theory and Computation, 17(7), 4291–4300. https://doi.org/10.1021/acs.jctc.1c00302
   PubMed Web of Science ®Google Scholar
• Madhavi Sastry, G., Adzhigirey, M., Day, T., Annabhimoju, R., & Sherman, W. (2013). Protein and ligand preparation: Parameters, protocols, and influence on virtual screening enrichments. Journal of Computer-Aided Molecular Design, 27(3), 221–234. https://doi.org/10.1007/s10822-013-9644-8
   PubMed Web of Science ®Google Scholar
• Majumdar, P., & Niyogi, S. (2021). SARS-CoV-2 mutations: The biological trackway towards viral fitness. Epidemiology and Infection, 149, 0–7. https://doi.org/10.1017/S0950268821001060
   Web of Science ®Google Scholar
• Miyata, T. (2015). Discovery studio modeling environment. Discovery Studio Modeling Environment, 2(17), 98–104.
   Google Scholar
• Mohammad, A., Al-Mulla, F., Wei, D. Q., & Abubaker, J. (2021). Remdesivir md simulations suggest a more favourable binding to SARS-COV-2 RNA dependent RNA polymerase mutant p323l than wild-type. Biomolecules, 11(7), 919. https://doi.org/10.3390/biom11070919
   PubMed Web of Science ®Google Scholar
• Pachetti, M., Marini, B., Benedetti, F., Giudici, F., Mauro, E., Storici, P., Masciovecchio, C., Angeletti, S., Ciccozzi, M., Gallo, R. C., Zella, D., & Ippodrino, R. (2020). Emerging SARS ‑ CoV ‑ 2 mutation hot spots include a novel RNA ‑ dependent ‑ RNA polymerase variant. Journal of Translational Medicine, 18(1), 9. https://doi.org/10.1186/s12967-020-02344-6
   PubMed Web of Science ®Google Scholar
• Pandit, B., Bhattacharjee, S., & Bhattacharjee, B. (2021). Association of clade-G SARS-CoV-2 viruses and age with increased mortality rates across 57 countries and India. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases, 90, 104734. https://doi.org/10.1016/j.meegid.2021.104734
   PubMed Web of Science ®Google Scholar
• Pitts, J., Li, J., Perry, J. K., Du Pont, V., Riola, N., Rodriguez, L., Lu, X., Kurhade, C., Xie, X., Camus, G., Manhas, S., Martin, R., Shi, P.-Y., Cihlar, T., Porter, D. P., Mo, H., Maiorova, E., & Bilello, J. P. (2022). Remdesivir and GS-441524 retain antiviral activity against delta, omicron, and other emergent SARS-CoV-2 variants. Antimicrobial Agents and Chemotherapy, 66(6), e0022222 https://doi.org/10.1128/aac.00222-22
   PubMed Web of Science ®Google Scholar
• Prüβ, B. M. (2022). Variants of SARS CoV-2: Mutations, transmissibility, virulence, drug resistance, and antibody/vaccine sensitivity. Frontiers in Bioscience (Landmark Edition), 27(2), 65. https://doi.org/10.31083/j.fbl2702065
   PubMed Web of Science ®Google Scholar
• Schrödinger, LLC, New York, NY. (2021). Schrödinger Release 2021-3: LigPrep.
   Google Scholar
• Sherman, W., Beard, H. S., & Farid, R. (2006). Use of an induced fit receptor structure in virtual screening. Chemical Biology & Drug Design, 67(1), 83–84. https://doi.org/10.1111/j.1747-0285.2005.00327.x
   PubMed Web of Science ®Google Scholar
• Showers, W. M., Leach, S. M., Kechris, K., & Strong, M. (2022). Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases, 97, 105153. https://doi.org/10.1016/j.meegid.2021.105153
   PubMed Web of Science ®Google Scholar
• Stevens, L. J., Pruijssers, A. J., Lee, H. W., Gordon, C. J., Tchesnokov, E. P., Gribble, J., George, A. S., Hughes, T. M., Lu, X., Li, J., Perry, J. K., Porter, D. P., Cihlar, T., Sheahan, T. P., Baric, R. S., Götte, M., & Denison, M. R. (2022). Mutations in the SARS-CoV-2 RNA-dependent RNA polymerase confer resistance to remdesivir by distinct mechanisms. Science Translational Medicine, 14(656), eabo0718. https://doi.org/10.1126/scitranslmed.abo0718
   PubMed Web of Science ®Google Scholar
• Wang, R., Hozumi, Y., Yin, C., & Wei, G. W. (2020). Decoding SARS-CoV-2 transmission and evolution and ramifications for COVID-19 diagnosis, vaccine, and medicine. Journal of Chemical Information and Modeling, 60(12), 5853–5865. https://doi.org/10.1021/acs.jcim.0c00501
   PubMed 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 [Review-article. Chemical Reviews, 119(16), 9478–9508. https://doi.org/10.1021/acs.chemrev.9b00055
   PubMed Web of Science ®Google Scholar
• Yin, W., Luan, X., Li, Z., Zhou, Z., Wang, Q., Gao, M., Wang, X., Zhou, F., Shi, J., You, E., Liu, M., Wang, Q., Jiang, Y., Jiang, H., Xiao, G., Zhang, L., Yu, X., Zhang, S., & Eric Xu, H. (2021). Structural basis for inhibition of the SARS-CoV-2 RNA polymerase by suramin. Nature Structural & Molecular Biology, 28(3), 319–325. https://doi.org/10.1038/s41594-021-00570-0
   PubMed Web of Science ®Google Scholar
• Zhang, L., & Zhou, R. (2020). Structural Basis of the Potential Binding Mechanism of Remdesivir to SARS-CoV-2 RNA-Dependent RNA Polymerase. The Journal of Physical Chemistry B. 124, 6955–6962. https://doi.org/10.1021/acs.jpcb.0c04198
   Web of Science ®Google Scholar