Identification of potential COVID-19 main protease inhibitors using structure-based pharmacophore approach, molecular docking and repurposing studies

1. N. Zhu, D. Zhang, W. Wang, X. Li, B. Yang, J. Song, X. Zhao, B. Huang, W. Shi, R. Lu and P. Niu, A novel coronavirus from patients with pneumonia in China, 2019, N. Engl. J. Med. 382 (2020) 727–733; https://doi.org/10.1056/NEJMoa200101710.1056/NEJMoa2001017709280331978945Search in Google Scholar

2. A. Zumla, J. F. Chan, E. I. Azhar, D. S. Hui and K. Y Yuen, Coronaviruses—drug discovery and therapeutic options, Nat. Rev. Drug Discov. 15 (2016) 327–347; https://doi.org/10.1038/nrd.2015.3710.1038/nrd.2015.37709718126868298Search in Google Scholar

3. F. He, Y. Deng and W. Li, Coronavirus Disease 2019 (COVID-19): What we know? J. Med. Virol. (2020) (7 pages); https://doi.org/10.1002/jmv.2576610.1002/jmv.25766722834032170865Search in Google Scholar

4. C. C. Lai, T. P. Shih, W. C. Ko, H. J. Tang and P. R. Hsueh, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease-2019 (COVID-19): The epidemic and the challenges, Int. J. Antimicrob. Agents55 (2020) Article ID 105924; https://doi.org/10.1016/j.ijantimicag.2020.10592410.1016/j.ijantimicag.2020.105924712780032081636Search in Google Scholar

5. J. She, J. Jiang, L. Ye, L. Hu, C. Bai and Y. Song, 2019 Novel coronavirus of pneumonia in Wuhan, China: emerging attack and management strategies, Clin.. Transl. Med.9 (2020) Article ID 19; https://doi.org/10.1186/s40169-020-00271-z10.1186/s40169-020-00271-z703326332078069Search in Google Scholar

6. World Health Organization, Novel Coronavirus (Covid-19): Situation Report, 3. 2020, WHO, Geneve 2020; https://www.who.int/emergencies/diseases/novel-coronavirus-2019?gclid=CjwKCAjwq832BRA5EiwACvCWsSQ_-qAh4z8Z5_gvnayDI2PrSx4poydPpu-pvDZX-k34RQDqn8TgEBoChdkQA-vD_BwE; last access date May 31, 2020Search in Google Scholar

7. H. A. Rothan and S. N. Byrareddy, The epidemiology and pathogenesis of coronavirus disease (COVID-19) outbreak, J. Autoimmun.109 (2020) Article ID 102433 (4 pages); https://doi.org/10.1016/j.jaut.2020.10243310.1016/j.jaut.2020.102433712706732113704Search in Google Scholar

8. S. L. Senanayake, Drug repurposing strategies for COVID-19, Future Drug Discov.2 (2020) (3 pages); https://doi.org/10.4155/fdd-2020-001010.4155/fdd-2020-0010Search in Google Scholar

9. S. Pushpakom, F. Iorio, P. A. Eyers, K. J. Escott, S. Hopper, A. Wells, A. Doig, T. Guilliams, J. Latimer, C. McNamee and A. Norris, Drug repurposing: progress, challenges and recommendations, Nat. Rev. Drug Discov. 18 (2019) 41–58; https://doi.org/10.1038/nrd.2018.16810.1038/nrd.2018.16830310233Search in Google Scholar

10. S. G. V. Rosa and W. C. Santos, Clinical trials on drug repositioning for COVID-19 treatment, Rev. Panam. Salud Públ. 44 (2020) e40; https://doi.org/10.26633/RPSP.2020.4010.26633/RPSP.2020.40710528032256547Search in Google Scholar

11. A. Gaurav, V. Gautam, S. Pereira, J. Alvarez-Leite, F. Vetri, M. Choudhury, D. Pelligrino, P. Sundivakkam, K. Radhakrishnan and A. Krieger, Structure-based three-dimensional pharmacophores as an alternative to traditional methodologies, J. Receptor Ligand Channel Res.7 (2014) 27–38; https://doi.org/10.2147/JRLCR.S4684510.2147/JRLCR.S46845Search in Google Scholar

12. M. P. Sanders, R. McGuire, L. Roumen, I. J. de Esch, J. de Vlieg, J. P. Klomp and C. de Graaf, From the protein’s perspective: the benefits and challenges of protein structure-based pharmacophore modeling, MedChemComm.3 (2012) 28–38; https://doi.org/10.1039/C1MD00210D10.1039/C1MD00210DSearch in Google Scholar

13. M. Wieder, U. Perricone, T. Seidel, S. Boresch and T. Langer, Comparing pharmacophore models derived from crystal structures and from molecular dynamics simulations, Monatsh. Chem. 147 (2016) 553–563, https://doi.org/10.1007/s00706-016-1674-110.1007/s00706-016-1674-1Search in Google Scholar

14. M. Arooj, S. Sakkiah, S. Kim, V. Arulalapperumal and K. W. Lee, A combination of receptor-based pharmacophore modeling & QM techniques for identification of human chymase inhibitors. PLoS One8 (2013) e63030; https://doi.org/10.1371/journal.pone.006303010.1371/journal.pone.0063030Search in Google Scholar

15. 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 SARSCoV-2 and discovery of its inhibitors, Nature5 (2020) (20 pages); https://doi.org/10.1038/s41586-020-2223-y10.1038/s41586-020-2223-ySearch in Google Scholar

16. L. A. Dahabiyeh, E. Y. Abu-rish and M. O. Taha, Inhibition of monoglyceride lipase by proton pump inhibitors: investigation using docking and in vitro experiments, Pharmacol. Rep.72 (2019) 435–442; https://doi.org/10.1007/s43440-019-00013-010.1007/s43440-019-00013-0Search in Google Scholar

17. L. A. Dahabiyeh, Y. Bustanji and M. O. Taha, The herbicide quinclorac as potent lipase inhibitor: Discovery via virtual screening and in vitro/in vivo validation, Chem. Biol. Drug Des. 93 (2019) 787–797; https://doi.org/10.1111/cbdd.1346310.1111/cbdd.13463Search in Google Scholar

18. D. J. Diller and K. M. Merz, Jr, High throughput docking for library design and library prioritization, Proteins43 (2001) 113–124; https://doi.org/10.1002/1097-0134(20010501)43:2<113::aidprot1023>3.0.co;2-tSearch in Google Scholar

19. S. N. Rao, M. S. Head, A. Kulkarni and J. M. LaLonde, Validation studies of the site-directed docking program LibDock, J. Chem. Inf. Model.47 (2007) 2159–2171; https://doi.org/10.1021/ci600429910.1021/ci6004299Search in Google Scholar

20. A. N. Jain, Scoring noncovalent protein-ligand interactions: a continuous differentiable function tuned to compute binding affinities, J. Comput. Aided Mol. Des.10 (1996) 427–440; https://doi.org/10.1007/BF0012447410.1007/BF00124474Search in Google Scholar

21. A. Krammer, P. D. Kirchhoff, X. Jiang, C. Venkatachalam and M. Waldman, LigScore: a novel scoring function for predicting binding affinities, J. Mol. Graph. Model. 23 (2005) 395–407; https://doi.org/10.1016/j.jmgm.2004.11.00710.1016/j.jmgm.2004.11.007Search in Google Scholar

22. C. M. Venkatachalam, X. Jiang, T. Oldfield and M. Waldman, LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites, J. Mol. Graph. Model. 21 (2003) 289–307; https://doi.org/10.1016/s1093-3263(02)00164-x10.1016/S1093-3263(02)00164-XSearch in Google Scholar

23. D. K. Gehlhaar, D. Bouzida and P. A. Rejto, Reduced dimensionality in ligand-protein structure prediction: covalent inhibitors of serine proteases and design of site-directed combinatorial libraries, ACS Pub.719 (1999); https://doi.org/10.1021/bk-1999-0719.ch01910.1021/bk-1999-0719.ch019Search in Google Scholar

24. I. Muegge, PMF scoring revisited, J. Med. Chem. 49 (2006) 5895–5902; https://doi.org/10.1021/jm050038s10.1021/jm050038s17004705Search in Google Scholar

25. I. Muegge and Y. C. Martin, A general and fast scoring function for protein-ligand interactions: a simplified potential approach, J. Med. Chem. 42 (1999) 791–804; https://doi.org/10.1021/jm980536j10.1021/jm980536j10072678Search in Google Scholar

26. J. Wang, Fast identification of possible drug treatment of coronavirus disease-19 (COVID-19) through computational drug repurposing study, J. Chem. Inf. Model. (2020) (10 pages); https://doi.org/10.1021/acs.jcim.0c0017910.1021/acs.jcim.0c00179719797232315171Search in Google Scholar

27. A. Farag, P. Wang, M. Ahmed and H. Sadek, Identification of FDA approved drugs targeting COVID-19 virus by structure-based drug repositioning, ChemRxiv. (preprint) (2020); https://doi.org/10.26434/chemrxiv.12049647.v110.26434/chemrxiv.12049647.v1Search in Google Scholar

28. A. D. Mesecar (Center for Structural Genomics of Infectious Diseases, CSGID), A taxonomically-driven approach to development of potent, broad-spectrum inhibitors of coronavirus main pro-tease including SARS-CoV-2 (COVID-19), to be published; PDB ID 6W63, title: Structure of COVID-19 main protease bound to potent broad-spectrum non-covalent inhibitor X77, 2020; https://doi.org/10.2210/pdb6W63/pdb10.2210/pdb6w63/pdbSearch in Google Scholar

29. J. Meslamani and D. Rognan, Protein-ligand pharmacophores: concept, design and applications, CICSJ Bull. 33 (2015) 27–32; https://doi.org/10.11546/cicsj.33.27Search in Google Scholar

30. L. Dong, S. Hu and J. Gao, Discovering drugs to treat coronavirus disease 2019 (COVID-19), Drug Discov. Ther.14 (2020) 58–60; https://doi.org/10.5582/ddt.2020.0101210.5582/ddt.2020.0101232147628Search in Google Scholar

31. E. P. Tchesnokov, J. Y. Feng, D. P. Porter and M. Götte, Mechanism of inhibition of Ebola virus RNA-dependent RNA polymerase by remdesivir, Viruses11 (2019) Article ID 326; https://doi.org/10.3390/v1104032610.3390/v11040326652071930987343Search in Google Scholar

32. J. A. Al-Tawfiq, A. H. Al-Homoud and Z. A. Memish, Remdesivir as a possible therapeutic option for the COVID-19, Travel. Med. Infect. Dis.34 (2020) Article ID 101615; https://doi.org/10.1016/j.tmaid.2020.10161510.1016/j.tmaid.2020.101615712939132145386Search in Google Scholar

33. T. Stanković, J. Dinić, A. Podolski-Renić, L. Musso, S. S. Burić, S. Dallavalle and M. Pešić, Dual inhibitors as a new challenge for cancer multidrug resistance treatment, Curr. Med. Chem.26 (2019) 6074–6106; https://doi.org/10.2174/092986732566618060709485610.2174/092986732566618060709485629874992Search in Google Scholar

34. A. Chandwani and J. Shuter, Lopinavir/ritonavir in the treatment of HIV-1 infection: a review, Ther. Clin. Risk Manag. 4 (2008) 1023–1033; https://doi.org/10.2147/tcrm.s328510.2147/TCRM.S3285Search in Google Scholar

35. J. Dorward and K. Gbinigie, Lopinavir/ritonavir: A rapid review of effectiveness in COVID-19 (on behalf of the Oxford COVID-19 Evidence Service Team Centre for Evidence-Based Medicine-CEBM); https://www.cebm.net/covid-19/lopinavir-ritonavir-a-rapid-review-of-the-evidence-for-effectiveness-in-treating-covid/; last access date April 14, 2020Search in Google Scholar

36. B. Cao, Y. Wang, D. Wen, W. Liu, J. Wang, G. Fan, L. Ruan, B Song, Y. Cai, M. Wei, X. Li, J. Xia, N. Chen, J. Xiang, T. Yu, T. Bai, X. Xie, L. Zhang, C. Li, Y. Yuan, H. Chen, H. Li, H. Huang, S. Tu, F. Gong, Y. Liu, Y. Wei, C. Dong, F. Zhou, X. Gu, J. Xu, Z. Liu, Y. Zhang, H. Li, L. Shang, K. Wang, K. Li, X. Zhou, X. Dong, Z. Qu, S. Lu, X. Hu, S. Ruan, S. Luo, J. Wu, L. Peng, F. Cheng, L. Pan, J. Zou, C. Jia, J. Wang, X. Liu, S. Wang, X. Wu, Q. Ge, J. He, H. Zhan, F. Qiu, L. Guo, C. Huang, T. Jaki, F. G. Hayden, P. W. Horby, D. Zhang and C. Wang, A trial of lopinavir-ritonavir in adults hospitalized with severe Covid-19, N. Engl. J. Med. 382 (2020) 1787–1799; https://doi.org/10.1056/NEJMoa200128210.1056/NEJMoa2001282712149232187464Search in Google Scholar