Targeting two potential sites of SARS-CoV-2 main protease through computational drug repurposing

References

• Acharya, A., Agarwal, R., Baker, M. B., Baudry, J., Bhowmik, D., Boehm, S., Byler, K. G., Chen, S. Y., Coates, L., Cooper, C. J., Demerdash, O., Daidone, I., Eblen, J. D., Ellingson, S., Forli, S., Glaser, J., Gumbart, J. C., Gunnels, J., Hernandez, O., … Zanetti-Polzi, L. (2020). Supercomputer-based ensemble docking drug discovery pipeline with application to covid-19. Journal of Chemical Information and Modeling, 60(12), 5832–5852. https://doi.org/10.1021/acs.jcim.0c01010
   PubMed Web of Science ®Google Scholar
• Borkotoky, S., Banerjee, M., Modi, G. P., & Dubey, V. K. (2021). Identification of high affinity and low molecular alternatives of boceprevir against SARS-CoV-2 main protease: A virtual screening approach. Chemical Physics Letters, 770, 138446. https://doi.org/10.1016/j.cplett.2021.138446
   PubMed Web of Science ®Google Scholar
• Borkotoky, S., & Murali, A. (2017). A computational assessment of pH-dependent differential interaction of T7 lysozyme with T7 RNA polymerase. BMC Structure Biology, 17(1), 7. https://doi.org/10.1186/s12900-017-0077-9
   PubMedGoogle Scholar
• Bundgaard, C., Eneberg, E., & Sanchez, C. (2016). P-glycoprotein differentially affects escitalopram, levomilnacipran, vilazodone and vortioxetine transport at the mouse blood-brain barrier in vivo. Neuropharmacology, 103, 104–111. https://doi.org/10.1016/j.neuropharm.2015.12.009
   PubMed Web of Science ®Google Scholar
• Chen, P. L., Lee, N. Y., Cia, C. T., Ko, W. C., & Hsueh, P. R. (2020). A review of treatment of coronavirus disease 2019 (COVID-19): Therapeutic repurposing and unmet clinical needs. Frontiers in Pharmacology, 11, 584956. https://doi.org/10.3389/fphar.2020.584956
   PubMed Web of Science ®Google Scholar
• Cheng, S. C., Chang, G. G., & Chou, C. Y. (2010). Mutation of Glu-166 blocks the substrate-induced dimerization of SARS coronavirus main protease. Biophysical Journal, 98(7), 1327–1336. https://doi.org/10.1016/j.bpj.2009.12.4272
   PubMed Web of Science ®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 [Research Support, Non-U.S. Science (New York, NY), 368(6497), 1331–1335. https://doi.org/10.1126/science.abb4489
   Google Scholar
• Ferreira, J. C., Fadl, S., Villanueva, A. J., & Rabeh, W. M. (2021). Catalytic dyad residues His41 and Cys145 impact the catalytic activity and overall conformational fold of the main SARS-CoV-2 protease 3-chymotrypsin-like protease. Frontiers in Chemistry, 9, 692168. https://doi.org/10.3389/fchem.2021.692168
   PubMed Web of Science ®Google Scholar
• Ghofrani, H. A., Osterloh, I. H., & Grimminger, F. (2006). Sildenafil: from angina to erectile dysfunction to pulmonary hypertension and beyond. Nature Reviews Drug Discovery, 5(8), 689–702. https://doi.org/10.1038/nrd2030
   PubMed Web of Science ®Google Scholar
• Grover, A., Katiyar, S. P., Singh, S. K., Dubey, V. K., & Sundar, D. (2012a). A leishmaniasis study: structure-based screening and molecular dynamics mechanistic analysis for discovering potent inhibitors of spermidine synthase. Biochimica et Biophysica Acta, 1824 (12), 1476–1483. https://doi.org/10.1016/j.bbapap.2012.05.016
   PubMed Web of Science ®Google Scholar
• Grover, A., Katiyar, S. P., Jeyakanthan, J., Dubey, V. K., & Sundar, D. (2012b). Blocking Protein kinase C signaling pathway: Mechanistic insights into the anti-leishmanial activity of prospective herbal drugs from Withania somnifera. BMC Genomics, 13(S7), 20. Shttps://doi.org/10.1186/1471-2164-13-S7-S20
   PubMedGoogle Scholar
• Goyal, B., & Goyal, D. (2020). Targeting the dimerization of the main protease of coronaviruses: A potential broad-spectrum therapeutic strategy. ACS Combinatorial Science, 22(6), 297–305. https://doi.org/10.1021/acscombsci.0c00058
   PubMed Web of Science ®Google Scholar
• Gupta, S., Singh, A. K., Kushwaha, P. P., Prajapati, K. S., Shuaib, M., Senapati, S., & Kumar, S. (2021). Identification of potential natural inhibitors of SARS-CoV2 main protease by molecular docking and simulation studies. Journal of Biomolecular Structure and Dynamics, 39(12), 4334–4345. https://doi.org/10.1080/07391102.2020.1776157
   Google Scholar
• Hess, B., Bekker, H., Berendsen, H. J. C., & Fraaije, J. G. E. M. (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<1463::AID-JCC4>3.0.CO;2-H
   Web of Science ®Google Scholar
• Huang, W., Lin, Z., & van Gunsteren, W. F. (2011). Validation of the GROMOS 54A7 force field with respect to β-peptide folding. Journal of Chemical Theory and Computation, 7(5), 1237–1243. https://doi.org/10.1021/ct100747y
   PubMed Web of Science ®Google Scholar
• Ibrahim, M. A., & Preuss, C. V. (2021). Antiemetic neurokinin-1 receptor blockers (StatPearls). https://www.ncbi.nlm.nih.gov/pubmed/29262116
   Google Scholar
• Jacobson, J. M. (2000). Thalidomide: A remarkable comeback. Expert Opinion on Pharmacotherapy, 1(4), 849–863. https://doi.org/10.1517/14656566.1.4.849
   PubMedGoogle 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
• Wenzel, J., Lampe, J., Müller-Fielitz, H., Schuster, R., Zille, M., Müller, K., Krohn, M., Körbelin, J., Zhang, L., Özorhan, Ü., Neve, V., Wagner, J. U. G., Bojkova, D., Shumliakivska, M., Jiang, Y., Fähnrich, A., Ott, F., Sencio, V., Robil, C., ... & Schwaninger, M. (2021). The SARS-CoV-2 main protease Mpro causes microvascular brain pathology by cleaving NEMO in brain endothelial cells. Nature Neuroscience, 24(11), 1522-1533. https://doi.org/10.1038/s41593-021-00926-1
   Google Scholar
• Joshi, R. S., Jagdale, S. S., Bansode, S. B., Shankar, S. S., Tellis, M. B., Pandya, V. K., Chugh, A., Giri, A. P., & Kulkarni, M. J. (2021). Discovery of potential multi-target-directed ligands by targeting host-specific SARS-CoV-2 structurally conserved main protease. Journal of Biomolecular Structure & Dynamics, 39(9), 3099–3114. https://doi.org/10.1080/07391102.2020.1760137
   PubMed Web of Science ®Google Scholar
• Kanhed, A. M., Patel, D. V., Teli, D. M., Patel, N. R., Chhabria, M. T., & Yadav, M. R. (2020). Identification of potential Mpro inhibitors for the treatment of COVID-19 by using systematic virtual screening approach. Molecular Diversity, 25(1), 383-401. https://doi.org/10.1007/s11030-020-10130-1
   Google Scholar
• Kneller, D. W., Phillips, G., O'Neill, H. M., Jedrzejczak, R., Stols, L., Langan, P., Joachimiak, A., Coates, L., & Kovalevsky, A. (2020). Structural plasticity of SARS-CoV-2 3CL Mpro active site cavity revealed by room temperature X-ray crystallography. Nature Communications, 11(1), 3202. https://doi.org/10.1038/s41467-020-16954-7
   PubMed Web of Science ®Google Scholar
• Konreddy, A. K., Rani, G. U., Lee, K., & Choi, Y. (2019). Recent drug-repurposing-driven advances in the discovery of novel antibiotics. Current Medicinal Chemistry, 26(28), 5363–5388. https://doi.org/10.2174/0929867325666180706101404
   PubMed Web of Science ®Google Scholar
• Kumar, Y., Singh, H., & Patel, C. N. (2020). In silico prediction of potential inhibitors for the main protease of SARS-CoV-2 using molecular docking and dynamics simulation based drug-repurposing. Journal of Infection and Public Health, 13(9), 1210–1223. https://doi.org/10.1016/j.jiph.2020.06.016
   PubMed Web of Science ®Google Scholar
• Kumari, R., Kumar, R., Open Source Drug Discovery, C., & Lynn, A, Open Source Drug Discovery Consortium. (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
   PubMed Web of Science ®Google Scholar
• Lagorce, D., Bouslama, L., Becot, J., Miteva, M. A., & Villoutreix, B. O. (2017). FAF-Drugs4: Free ADME-tox filtering computations for chemical biology and early stages drug discovery. Bioinformatics (Oxford, England), 33(22), 3658–3660. https://doi.org/10.1093/bioinformatics/btx491
   PubMed Web of Science ®Google Scholar
• Lazim, R., Suh, D., & Choi, S. (2020). Advances in molecular dynamics simulations and enhanced sampling methods for the study of protein systems. International Journal of Molecular Sciences, 21(17), 6339. https://doi.org/10.3390/ijms21176339
   PubMed Web of Science ®Google Scholar
• Lee, H. M., & Kim, Y. (2016). Drug repurposing is a new opportunity for developing drugs against neuropsychiatric disorders. Schizophrenia Research and Treatment, 2016, 6378137. https://doi.org/10.1155/2016/6378137
   PubMedGoogle Scholar
• Liang, J., Karagiannis, C., Pitsillou, E., Darmawan, K. K., Ng, K., Hung, A., & Karagiannis, T. C. (2020). Site mapping and small molecule blind docking reveal a possible target site on the SARS-CoV-2 main protease dimer interface. Computational Biology and Chemistry, 89, 107372. https://doi.org/10.1016/j.compbiolchem.2020.107372
   PubMed Web of Science ®Google Scholar
• Loryan, I., Melander, E., Svensson, M., Payan, M., Konig, F., Jansson, B., & Hammarlund-Udenaes, M. (2016). In-depth neuropharmacokinetic analysis of antipsychotics based on a novel approach to estimate unbound target-site concentration in CNS regions: link to spatial receptor occupancy. Molecular Psychiatry, 21(11), 1527–1536. https://doi.org/10.1038/mp.2015.229
   PubMed Web of Science ®Google Scholar
• Majumder, R., & Mandal, M. (2020). Screening of plant-based natural compounds as a potential COVID-19 main protease inhibitor: an in silico docking and molecular dynamics simulation approach. Journal of Biomolecular Structure and Dynamics, 40(2), 696-711. https://doi.org/10.1080/07391102.2020.1817787
   Google Scholar
• Malde, A. K., Zuo, L., Breeze, M., Stroet, M., Poger, D., Nair, P. C., Oostenbrink, C., & Mark, A. E. (2011). An automated force field topology builder (ATB) and repository: Version 1.0. Journal of Chemical Theory and Computation, 7(12), 4026–4037. https://doi.org/10.1021/ct200196m
   PubMed Web of Science ®Google Scholar
• Martonak, R., Laio, A., & Parrinello, M. (2003). Predicting crystal structures: The Parrinello-Rahman method revisited. Physical Review Letters, 90(7), 075503. https://doi.org/10.1103/PhysRevLett.90.075503
   PubMed Web of Science ®Google Scholar
• Mehboob, R., Ahmad, F. J., Qayyum, A., Rana, M. A., Gilani, S. A., Tariq, M. A., Ali, G., Akram, S. J., & Akram, J. (2020). Aprepitant as a combinant with dexamethasone reduces the inflammation via neurokinin 1 receptor antagonism in severe to critical covid-19 patients and potentiates respiratory recovery: A novel therapeutic approach. medRxiv. https://doi.org/10.1101/2020.08.01.20166678]
   Google Scholar
• Mengist, H. M., Fan, X., & Jin, T. (2020). Designing of improved drugs for COVID-19: Crystal structure of SARS-CoV-2 main protease M(pro). Signal Transduction and Targeted Therapy, 5(1), 67. https://doi.org/10.1038/s41392-020-0178-y
   PubMed Web of Science ®Google Scholar
• Menon, S., & Sengupta, N. (2015). Perturbations in inter-domain associations may trigger the onset of pathogenic transformations in PrP(C): Insights from atomistic simulations. Molecular bioSystems, 11(5), 1443–1453. https://doi.org/10.1039/c4mb00689e
   PubMedGoogle Scholar
• Nussbaum, A. M., & Stroup, T. S. (2008). Paliperidone for treatment of schizophrenia. Schizophrenia Bulletin, 34(3), 419–422. https://doi.org/10.1093/schbul/sbn015
   PubMed Web of Science ®Google Scholar
• Paasche, A., Zipper, A., Schafer, 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
• Pedretti, A., Villa, L., & Vistoli, G. (2002). VEGA: a versatile program to convert, handle and visualize molecular structure on Windows-based PCs. Journal of Molecular Graphics & Modelling, 21(1), 47–49. https://doi.org/10.1016/S1093-3263(02)00123-7
   PubMed Web of Science ®Google Scholar
• Peterson, S. E., Selvaggi, K. J., Scullion, B. F., & Blinderman, C. D. (2018). Chapter 91 - Pain management and antiemetic therapy in hematologic disorders. In R. Hoffman, E. J. Benz, L. E. Silberstein, H. E. Heslop, J. I. Weitz, J. Anastasi, M. E. Salama, & S. A. Abutalib (Eds.), Hematology (7th ed. pp. 1473–1487). Elsevier. https://doi.org/10.1016/B978-0-323-35762-3.00091-3
   Google Scholar
• Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera-a visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. https://doi.org/10.1002/jcc.20084
   PubMed Web of Science ®Google Scholar
• Pushpakom, S., Iorio, F., Eyers, P. A., Escott, K. J., Hopper, S., Wells, A., Doig, A., Guilliams, T., Latimer, J., McNamee, C., Norris, A., Sanseau, P., Cavalla, D., & Pirmohamed, M. (2019). Drug repurposing: progress, challenges and recommendations. Nature Reviews. Drug Discovery, 18(1), 41–58. https://doi.org/10.1038/nrd.2018.168
   PubMed Web of Science ®Google Scholar
• Rout, J., Swain, B. C., & Tripathy, U. (2020). In silico investigation of spice molecules as potent inhibitor of SARS-CoV-2. Journal of Biomolecular Structure and Dynamics, 40(2), 860-874. https://doi.org/10.1080/07391102.2020.1819879
   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
• Stahl, S. M. (2014). Mechanism of action of the SPARI vilazodone: Serotonin 1A partial agonist and reuptake inhibitor. CNS Spectrums, 19(2), 105–109. https://doi.org/10.1017/S1092852914000169
   PubMed Web of Science ®Google Scholar
• Sterling, T., & Irwin, J. J. (2015). ZINC 15-ligand discovery for everyone. Journal of Chemical Information and Modeling, 55(11), 2324–2337. https://doi.org/10.1021/acs.jcim.5b00559
   PubMed Web of Science ®Google Scholar
• Tam, N. M., Pham, D.-H., Hiep, D. M., Tran, P.-T., Quang, D. T., & Ngo, S. T. (2021). Searching and designing potential inhibitors for SARS-CoV-2 Mpro from natural sources using atomistic and deep-learning calculations. RSC Advances, 11(61), 38495–38504. https://doi.org/10.1039/D1RA06534C
   PubMed Web of Science ®Google Scholar
• Tetko, I. V., & Tanchuk, V. Y. (2002). Application of associative neural networks for prediction of lipophilicity in ALOGPS 2.1 program. Journal of Chemical Information and Computer Sciences, 42(5), 1136–1145. https://doi.org/10.1021/ci025515j
   PubMedGoogle Scholar
• 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), e2000028. https://doi.org/10.1002/minf.202000028
   PubMed Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Wei, P., Fan, K., Chen, H., Ma, L., Huang, C., Tan, L., Xi, D., Li, C., Liu, Y., Cao, A., & Lai, L. (2006). The N-terminal octapeptide acts as a dimerization inhibitor of SARS coronavirus 3C-like proteinase. Biochemical and Biophysical Research Communications, 339(3), 865–872. https://doi.org/10.1016/j.bbrc.2005.11.102
   PubMed Web of Science ®Google Scholar
• Zhong, N., Zhang, S., Zou, P., Chen, J., Kang, X., Li, Z., Liang, C., Jin, C., & Xia, B. (2008). Without its N-finger, the main protease of severe acute respiratory syndrome coronavirus can form a novel dimer through its C-terminal domain. Journal of Virology, 82(9), 4227–4234. https://doi.org/10.1128/JVI.02612-07
   PubMed Web of Science ®Google Scholar