SARS-COV-2 M^pro conformational changes induced by covalently bound ligands

References

• Abel, R., Young, T., Farid, R., Berne, B. J., & Friesner, R. A. (2008). Role of the active-site solvent in the thermodynamics of factor Xa ligand binding. Journal of the American Chemical Society, 130(9), 2817–2831. https://doi.org/10.1021/ja0771033
   PubMed Web of Science ®Google Scholar
• Bello, M. (2020). Prediction of potential inhibitors of the dimeric SARS-CoV2 main proteinase through the MM/GBSA approach. Journal of Molecular Graphics & Modelling, 101, 107762. https://doi.org/10.1016/j.jmgm.2020.107762
   PubMed Web of Science ®Google Scholar
• Böhm, H. J., Flohr, A., & Stahl, M. (2004). Scaffold hopping. Drug Discovery Today Technology, 1(3), 217–224. https://doi.org/10.1016/j.ddtec.2004.10.009
   Google Scholar
• Bowers, K. J., Chow, D. E., Xu, H., Dror, R. O., Eastwood, M. P., Gregersen, B. A., Klepeis, J. L., Kolossvary, I., Moraes, M. A., Sacerdoti, F. D., Salmon, J. K., Shan, Y., & Shaw, D. E. (2007). Scalable algorithms for molecular dynamics simulations on commodity clusters. Proceedings of the ACM/IEEE Conference on Supercomputing (SC06), 2006, Tampa, FL, 43. https://doi.org/10.1109/sc.2006.54
   Google Scholar
• Bowers, K. J., Sacerdoti, F. D., Salmon, J. K., Shan, Y., Shaw, D. E., Chow, E., Xu, H., Dror, R. O., Eastwood, M. P., Gregersen, B. A., Klepeis, J. L., Kolossvary, I., & Moraes, M. A. (2006). Molecular dynamics---Scalable algorithms for molecular dynamics simulations on commodity clusters [Paper presentation]. Proceedings of the 2006 ACM/IEEE Conference on Supercomputing - SC ’06, 84. https://doi.org/10.1145/1188455.1188544
   Google Scholar
• Bzówka, M., Mitusińska, K., Raczyńska, A., Samol, A., Tuszyński, J. A., & Góra, A. (2020). Structural and evolutionary analysis indicate that the sars-COV-2 mpro is a challenging target for small-molecule inhibitor design. International Journal of Molecular Sciences, 21(9), 3099-4016. https://doi.org/10.3390/ijms21093099
   Google Scholar
• Chen, H., Wei, P., Huang, C., Tan, L., Liu, Y., & Lai, L. (2006). Only one protomer is active in the dimer of SARS 3C-like proteinase. The Journal of Biological Chemistry, 281(20), 13894–13898. https://doi.org/10.1074/jbc.M510745200
   PubMed Web of Science ®Google Scholar
• Chen, S., Chen, L., Tan, J., Chen, J., Du, L., Sun, T., Shen, J., Chen, K., Jiang, H., & Shen, X. (2005). Severe acute respiratory syndrome coronavirus 3C-like proteinase N terminus is indispensable for proteolytic activity but not for enzyme dimerization. Biochemical and thermodynamic investigation in conjunction with molecular dynamics simulations. The Journal of Biological Chemistry, 280(1), 164–173. https://doi.org/10.1074/jbc.M408211200
   PubMed Web of Science ®Google Scholar
• Chou, C. Y., Chang, H. C., Hsu, W. C., Lin, T. Z., Lin, C. H., & Chang, G. G. (2004). Quaternary structure of the severe acute respiratory syndrome (SARS) coronavirus main protease. Biochemistry, 43(47), 14958–14970. https://doi.org/10.1021/bi0490237
   PubMed Web of Science ®Google Scholar
• Coronavirus Disease (COVID-19) Situation Reports. ( 2021). Retrieved June 15, from https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports/
   Google Scholar
• Dai, W., Zhang, B., Jiang, X.-M., Su, H., Li, J., Zhao, Y., Xie, X., Jin, Z., Peng, J., Liu, F., Li, C., Li, Y., Bai, F., Wang, H., Cheng, X., Cen, X., Hu, S., Yang, X., Wang, J., … Liu, H. (2020). Structure-based design of antiviral drug candidates targeting the SARS-CoV-2 main protease. Science (New York, NY), 368(6497), 1331–1335. https://doi.org/10.1126/science.abb4489
   Google Scholar
• Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N ⋅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
• Ferreira, G. M., Kronenberger, T., De Almeida, É. C., Sampaio, J., Terra, C. F., Pinto, E., & Trossini, G. H. G. (2019). Inhibition of porcine aminopeptidase M (pAMP) by the pentapeptide microginins. Molecules (Basel, Switzerland), 24(23), 4369-4383. https://doi.org/10.3390/molecules24234369
   Google Scholar
• Ghosh, A. K., Brindisi, M., Shahabi, D., Chapman, M. E., & Mesecar, A. D. (2020). Drug development and medicinal chemistry efforts toward SARS-Coronavirus and Covid-19 therapeutics. ChemMedChem, 15(11), 907–932. https://doi.org/10.1002/cmdc.202000223
   PubMed Web of Science ®Google Scholar
• Harder, E., Damm, W., Maple, J., Wu, C., Reboul, M., Xiang, J. Y., Wang, L., Lupyan, D., Dahlgren, M. K., Knight, J. L., Kaus, J. W., Cerutti, D. S., Krilov, G., Jorgensen, W. L., Abel, R., & Friesner, R. A. (2016). OPLS3: A force field providing broad coverage of drug-like small molecules and proteins. Journal of Chemical Theory and Computation, 12(1), 281–296. https://doi.org/10.1021/acs.jctc.5b00864
   PubMed Web of Science ®Google Scholar
• Henzler-Wildman, K., & Kern, D. (2007). Dynamic personalities of proteins. Nature, 450(7172), 964–972. https://doi.org/10.1038/nature06522
   PubMed Web of Science ®Google Scholar
• Hsu, W. C., Chang, H. C., Chou, C. Y., Tsai, P. J., Lin, P. I., & Chang, G. G. (2005). Critical assessment of important regions in the subunit association and catalytic action of the severe acute respiratory syndrome coronavirus main protease. The Journal of Biological Chemistry, 280(24), 22741–22748. https://doi.org/10.1074/jbc.M502556200
   PubMed Web of Science ®Google Scholar
• Jacobson, M. P., Pincus, D. L., Rapp, C. S., Day, T. J. F., Honig, B., Shaw, D. E., & Friesner, R. A. (2004). A hierarchical approach to all-atom protein loop prediction. Proteins, 55(2), 351–367. https://doi.org/10.1002/prot.10613
   PubMed Web of Science ®Google Scholar
• 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
   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
• Komatsu, T. S., Okimoto, N., Koyama, Y. M., Hirano, Y., Morimoto, G., Ohno, Y., & Taiji, M. (2020). Drug binding dynamics of the dimeric SARS-CoV-2 main protease, determined by molecular dynamics simulation. Scientific Reports, 10(1), 16986. https://doi.org/10.1038/s41598-020-74099-5
   PubMedGoogle Scholar
• Krishnamoorthy, N., & Fakhro, K. (2021). Identification of mutation resistance coldspots for targeting the SARS-CoV2 main protease. IUBMB Life, 73(4), 670–675. https://doi.org/10.1002/iub.2465
   PubMed Web of Science ®Google Scholar
• Krissinel, E., & Henrick, K. (2005). Detection of protein assemblies in crystals. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 3695 LNBI, 163–174. https://doi.org/10.1007/11560500_15
   Google Scholar
• Landau, M., Mayrose, I., Rosenberg, Y., Glaser, F., Martz, E., Pupko, T., & Ben-Tal, N. (2005). ConSurf 2005: The projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res, 33(Web Server issue), W299–W302. https://doi.org/10.1093/nar/gki370
   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
• Mendoza, E. J., Manguiat, K., Wood, H., & Drebot, M. (2020). Two detailed plaque assay protocols for the quantification of infectious SARS‐CoV‐2. Current Protocols in Microbiology, 57(1), 105. https://doi.org/10.1002/cpmc.105
   Google Scholar
• Paasche, A., Zipper, A., Schäfer, S., Ziebuhr, J., Schirmeister, T., & Engels, B. (2014). Evidence for substrate binding-induced zwitterion formation in the catalytic Cys-His Dyad of the SARS-CoV main protease. Biochemistry, 53(37), 5930–5946. https://doi.org/10.1021/bi400604t
   PubMed Web of Science ®Google Scholar
• Pavlova, A., Lynch, D. L., Daidone, I., Zanetti-Polzi, L., Smith, M. D., Chipot, C., Kneller, D. W., Kovalevsky, A., Coates, L., Golosov, A. A., Dickson, C. J., Velez-Vega, C., Duca, J. S., Vermaas, J. V., Pang, Y. T., Acharya, A., Parks, J. M., Smith, J. C., & Gumbart, J. C. (2021). Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease. Chemical Science, 12(4), 1513–1527. https://doi.org/10.1039/D0SC04942E
   PubMed Web of Science ®Google Scholar
• Penman, S. L., Kiy, R. T., Jensen, R. L., Beoku-Betts, C., Alfirevic, A., Back, D., Khoo, S. H., Owen, A., Pirmohamed, M., Park, B. K., Meng, X., Goldring, C. E., & Chadwick, A. E. (2020). Safety perspectives on presently considered drugs for the treatment of COVID-19. In British Journal of Pharmacology (Vol. 177, Issue 19, pp. 4353–4374). John Wiley and Sons Inc. https://doi.org/10.1111/bph.15204
   Google Scholar
• Peterson, L. (2020). COVID-19 and Flavonoids: In silico molecular dynamics docking to the active catalytic site of SARS-CoV and SARS-CoV-2 main protease. SSRN Electronic Journal, https://doi.org/10.2139/ssrn.3599426
   Google Scholar
• Pillaiyar, T., Manickam, M., Namasivayam, V., Hayashi, Y., & Jung, S. H. (2016). An overview of severe acute respiratory syndrome-coronavirus (SARS-CoV) 3CL protease inhibitors: Peptidomimetics and small molecule chemotherapy. In. Journal of Medicinal Chemistry, 59(14), 6595–6628. https://doi.org/10.1021/acs.jmedchem.5b01461
   PubMed Web of Science ®Google Scholar
• Pinacho Crisóstomo, F. R., Carrillo, R., León, L. G., Martín, T., Padrón, J. M., & Martín, V. S. (2006). Molecular simplification in bioactive molecules: Formal synthesis of (+)-muconin. The Journal of Organic Chemistry, 71(6), 2339–2345. https://doi.org/10.1021/jo0524674
   PubMed Web of Science ®Google Scholar
• Raschke, T. M. (2006). Water structure and interactions with protein surfaces. Current Opinion in Structural Biology, 16(2), 152–159. https://doi.org/10.1016/j.sbi.2006.03.002
   PubMed Web of Science ®Google Scholar
• Roos, K., Wu, C., Damm, W., Reboul, M., Stevenson, J. M., Lu, C., Dahlgren, M. K., Mondal, S., Chen, W., Wang, L., Abel, R., Friesner, R. A., & Harder, E. D. (2019). OPLS3e: Extending force field coverage for drug-like small molecules. Journal of Chemical Theory and Computation, 15(3), 1863–1874. https://doi.org/10.1021/acs.jctc.8b01026
   PubMed Web of Science ®Google Scholar
• Rut, W., Groborz, K., Zhang, L., Sun, X., Zmudzinski, M., Pawlik, B., Wang, X., Jochmans, D., Neyts, J., Młynarski, W., Hilgenfeld, R., & Drag, M. (2021). SARS-CoV-2 Mpro inhibitors and activity-based probes for patient-sample imaging. Nature Chemical Biology, 17(2), 222–228. https://doi.org/10.1038/s41589-020-00689-z
   PubMed Web of Science ®Google Scholar
• Silvestrini, L., Belhaj, N., Comez, L., Gerelli, Y., Lauria, A., Libera, V., Mariani, P., Marzullo, P., Ortore, M. G., Palumbo Piccionello, A., Petrillo, C., Savini, L., Paciaroni, A., & Spinozzi, F. (2021). The dimer-monomer equilibrium of SARS-CoV-2 main protease is affected by small molecule inhibitors. Scientific Reports, 11(1), 9283. https://doi.org/10.1038/s41598-021-88630-9
   PubMed Web of Science ®Google Scholar
• Suárez, D., & Díaz, N. (2020). SARS-CoV-2 main protease: A molecular dynamics study. Journal of Chemical Information and Modeling, 60(12), 5815–5831. https://doi.org/10.1021/acs.jcim.0c00575
   PubMed Web of Science ®Google Scholar
• Wang, F., Chen, C., Tan, W., Yang, K., & Yang, H. (2016). Structure of main protease from human coronavirus NL63: Insights for wide spectrum anti-coronavirus drug design. Scientific Reports, 6, 22677. https://doi.org/10.1038/srep22677
   PubMed Web of Science ®Google Scholar
• Wang, Y.-C., Yang, W.-H., Yang, C.-S., Hou, M.-H., Tsai, C.-L., Chou, Y.-Z., Hung, M.-C., & Chen, Y. (2020). Structural basis of SARS-CoV-2 main protease inhibition by a broad-spectrum anti-coronaviral drug. American Journal of Cancer Research, 10(8), 2535–2545. www.ajcr.us/
   PubMed Web of Science ®Google Scholar
• Wu, F., Zhao, S., Yu, B., Chen, Y. M., Wang, W., Song, Z. G., Hu, Y., Tao, Z. W., Tian, J. H., Pei, Y. Y., Yuan, M. L., Zhang, Y. L., Dai, F. H., Liu, Y., Wang, Q. M., Zheng, J. J., Xu, L., Holmes, E. C., & Zhang, Y. Z. (2020). A new coronavirus associated with human respiratory disease in China. Nature, 579(7798), 265–269. https://doi.org/10.1038/s41586-020-2008-3
   PubMed Web of Science ®Google Scholar
• Yang, H., Xie, W., Xue, X., Yang, K., Ma, J., Liang, W., Zhao, Q., Zhou, Z., Pei, D., Ziebuhr, J., Hilgenfeld, R., Kwok, Y. Y., Wong, L., Gao, G., Chen, S., Chen, Z., Ma, D., Bartlam, M., & Rao, Z. (2005). Design of wide-spectrum inhibitors targeting coronavirus main proteases. PLoS Biology, 3(10), e324. https://doi.org/10.1371/journal.pbio.0030324
   PubMed Web of Science ®Google Scholar
• Young, T., Abel, R., Kim, B., Berne, B. J., & Friesner, R. A. (2007). Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding. Proceedings of the National Academy of Sciences of the United States of America, 104(3), 808–813. https://doi.org/10.1073/pnas.0610202104
   PubMed Web of Science ®Google Scholar
• Zhang, C.-H., Stone, E. A., Deshmukh, M., Ippolito, J. A., Ghahremanpour, M. M., Tirado-Rives, J., Spasov, K. A., Zhang, S., Takeo, Y., Kudalkar, S. N., Liang, Z., Isaacs, F., Lindenbach, B., Miller, S. J., Anderson, K. S., & Jorgensen, W. L. (2021). Potent noncovalent inhibitors of the main protease of SARS-CoV-2 from molecular sculpting of the drug perampanel guided by free energy perturbation calculations. ACS Central Science, 7(3), 467–475. acscentsci.1c00039. https://doi.org/10.1021/acscentsci.1c00039
   PubMed Web of Science ®Google Scholar
• Zhang, L., Lin, D., Sun, X., Curth, U., Drosten, C., Sauerhering, L., Becker, S., Rox, K., & Hilgenfeld, R. (2020). Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors. Science (New York, NY), 368(6489), 409–412. https://doi.org/10.1126/science.abb3405
   Google Scholar