Open Access

Computer-aided approaches reveal trihydroxychroman and pyrazolone derivatives as potential inhibitors of SARS-CoV-2 virus main protease


Cite

1. R. Lu, X. Zhao, J. Li, P. Niu, B. Yang, H. Wu, W. Wang, H. Song, B. Huang, N. Zhu, Y. Bi, X. Ma, F. Zhan, L Wang, T. Hu, H. Zhou, Z Hu, W. Zhou, L. Zhao, J. Chen, Y. Meng, J.Wang, Y. Lin, J. Yuan, Z. Xie, J. Ma, W. J. Liu, D. Wang, W. Xu, E. C. Holmes, G. F. Gao, G. Wu, W. Chen, W. Shi and W. Tan, Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding, Lancet395 (2020) 565–574; https://doi.org/10.1016/S0140-6736(20)30251-810.1016/S0140-6736(20)30251-8Search in Google Scholar

2. M. Yuan, N. C. Wu, X. Zhu, C. D. Lee, R. T. Y. So, H. Lv, C. K. P. Mok and I. A. Wilson, A highly conserved cryptic epitope in the receptor binding domains of SARS-CoV-2 and SARS-CoV, Science368 (2020) 630–633; https://doi.org/10.1126%2Fscience.abb726910.1126/science.abb7269716439132245784Search in Google Scholar

3. A. Wu, Y. Peng, B. Huang, X. Ding, X. Wang, P. Niu, J. Meng, Z. Zhu, Z. Zhang, J. Wang, J. Sheng, L. Quan, Z. Xia, W. Tan, G. Cheng and T. Jiang, Genome composition and divergence of the novel coronavirus (2019-nCoV) originating in China, Cell Host Microbe27 (2020) 325–328; https://doi.org/10.1016/j.chom.2020.02.00110.1016/j.chom.2020.02.001715451432035028Search in Google Scholar

4. Z. Jin, X. Du, Y. Xu, Y. Deng, M. Liu, Y. Zhao, B. Zhang, X. Li, L. Zhang, C. Peng, Y. Duan, J. Yu, L. Wang, K. Yang, F. Liu, R. Jiang, X. Yang, T. You, X. Liu, X. Yang, F. Bai, H. Liu, X. Liu, L. W. Guddat, W. Xu, G. Xiao, C. Qin, Z. Shi, H. Jiang, Z. Rao and H. Yang, Structure of M(pro) from SARS-CoV-2 and discovery of its inhibitors, Nature582 (2020) 289–293; https://doi.org/10.1038/s41586-020-2223-y10.1038/s41586-020-2223-y32272481Search in Google Scholar

5. A. Shulla, T. Heald-Sargent, G. Subramanya, J. Zhao, S. Perlman and T. Gallagher, A transmembrane serine protease is linked to the severe acute respiratory syndrome coronavirus receptor and activates virus entry, J. Virol. 85 (2011) 873–882; https://doi.org/10.1128/JVI.02062-1010.1128/JVI.02062-10302002321068237Search in Google Scholar

6. S. Lam, A. Lombardi and A. Ouanounou, COVID-19: A review of the proposed pharmacological treatments, Eur. J. Pharmacol.886 (2020) Article ID 173451 (11 pages); https://doi.org/10.1016/j.ejphar.2020.17345110.1016/j.ejphar.2020.173451740647732768505Search in Google Scholar

7. Chemical Computing Group, Manual Version 2018.09, Molecular Operating Environment (MOE), Montreal 2018; http://www.chemcomp.comSearch in Google Scholar

8. G. M. Sastry, M. Adzhigirey, T. Day, R. Annabhimoju and W. Sherman, Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments, J. Comp. Aided Mol. Des. 27 (2013) 221–234; https://doi.org/10.1007/s10822-013-9644-810.1007/s10822-013-9644-823579614Search in Google Scholar

9. R. A. Friesner, J. L. Banks, R. B. Murphy, T. A. Halgren, J. J. Klicic, D. T. Mainz, M. P. Repasky, E. H. Knoll, M. Shelley, J. K. Perry, D. E. Shaw, P. Francis, P. S. Shenkin, Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy, J. Med. Chem. 47 (2004) 1739–1749; https://doi.org/10.1021/jm030643010.1021/jm030643015027865Search in Google Scholar

10. J. Wang, W. Wang, P. A. Kollman and D. A. Case, Automatic atom type and bond type perception in molecular mechanical calculations, J. Mol. Graph. Mod. 25 (2006) 247–260; https://doi.org/10.1016/j.jmgm.2005.12.00510.1016/j.jmgm.2005.12.00516458552Search in Google Scholar

11. A. Jakalian, D. B. Jack and C. I. Bayly, Fast, efficient generation of high-quality atomic charges, AM1-BCC model: II. Parameterization and validation, J. Comp. Chem. 23 (2002) 1623–1641; https://doi.org/10.1002/jcc.1012810.1002/jcc.1012812395429Search in Google Scholar

12. T. S. Lee, B. K. Allen, T. J. Giese, Z. Guo, P. Li, C. Lin, T. D. McGee, D. A. Pearlman, B. K. Radak, Y. Tao, H. Tsai, H. Xu, W. Sherman and D. M. York, Alchemical binding free energy calculations in AMBER20: Advances and best practices for drug discovery, J. Chem. Inf. Model. 2020, in press; https://doi.org/10.1021/acs.jcim.0c0061310.1021/acs.jcim.0c00613768602632936637Search in Google Scholar

13. C. R. Guimarães and M. Cardozo, MM-GB/SA rescoring of docking poses in structure-based lead optimization, J. Chem. Inf. Model.48 (2008) 958–970; https://doi.org/10.1021/ci800004w10.1021/ci800004w18422307Search in Google Scholar

14. J. Shao, S. W. Tanner, N. Thompson and T. E. Cheatham, Clustering molecular dynamics trajectories: 1. Characterizing the performance of different clustering algorithms, J. Chem. Theory Comp. 3 (2007) 2312–2334; https://doi.org/10.1021/ct700119m10.1021/ct700119m26636222Search in Google Scholar

15. W. Dai, B. Zhang, X. M. Jiang, H. Su, J. Li, Y. Zhao, X. Xie, Z. Jin, J. Peng, F. Liu, C. Li, Y. Li, F. Bai, H. Wang, X. Cheng, X. Cen, S. Hu, X. Yang, J. Wang, X. Liu, G. Xiao, H. Jiang, Z. Rao, L. K. Zhang, Y. Xu, H. Yang and H. Liu, Structure-based design of antiviral drug candidates targeting the SARSCoV-2 main protease, Science368 (2020) 1331–1335; https://doi.org/10.1126/science.abb448910.1126/science.abb4489717993732321856Search in Google Scholar

eISSN:
1846-9558
Language:
English
Publication timeframe:
4 times per year
Journal Subjects:
Pharmacy, other