On the search for COVID-19 therapeutics: identification of potential SARS-CoV-2 main protease inhibitors by virtual screening, pharmacophore modeling and molecular dynamics

References

• Adem, S., Eyupoglu, V., Sarfraz, I., Rasul, A., & Ali, M. (2020). Identification of potent COVID-19 main protease (Mpro) inhibitors from natural polyphenols: An in silico strategy unveils a hope against CORONA. https://doi.org/10.20944/preprints202003.0333.v1
   Google Scholar
• Avdeef, A. (2001). Physicochemical profiling (solubility, permeability and charge state). Current Topics in Medicinal Chemistry, 1(4), 277–351. https://doi.org/10.2174/1568026013395100
   PubMedGoogle Scholar
• Brenk, R., Schipani, A., James, D., Krasowski, A., Gilbert, I. H., Frearson, J., & Wyatt, P. G. (2008). Lessons learnt from assembling screening libraries for drug discovery for neglected diseases. ChemMedChem, 3(3), 435–444. https://doi.org/10.1002/cmdc.200700139
   PubMed Web of Science ®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. https://doi.org/10.3390/ijms21093099
   PubMed Web of Science ®Google Scholar
• Daina, A., Michielin, O., & Zoete, V. (2017). Swiss ADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules, Scientific Reports, 7, 42717. https://doi.org/10.1038/srep42717
   Google Scholar
• Dahlin, J. L., Nissink, J. W. M., Strasser, J. M., Francis, S., Higgins, L., Zhou, H., Zhang, Z., & Walters, M. A. (2015). PAINS in the assay: Chemical mechanisms of assay interference and promiscuous enzymatic inhibition observed during a sulfhydryl-scavenging HTS. Journal of Medicinal Chemistry, 58(5), 2091–2113. https://doi.org/10.1021/jm5019093
   PubMed Web of Science ®Google Scholar
• Durdagi, S., Aksoydan, B., Dogan, B., Sahin, K., Shahraki, A., & Birgul-Iyison, N. (2020). Screening of clinically approved and investigation drugs as potential inhibitors of SARS-CoV-2 main protease and spike receptor binding domain bound with ACE2 COVID19 target proteins: A virtual drug repurposing study. (Version 2). ChemRxiv. https://doi.org/10.26434/chemrxiv.12032712.v2
   Google Scholar
• Ertl, P., & Schuffenhauer, A. (2009). Estimation of synthetic accessibility score of drug-like molecules based on molecular complexity and fragment contributions. Journal of Cheminformatics, 1(1), 8. https://doi.org/10.1186/1758-2946-1-8
   PubMed Web of Science ®Google Scholar
• Fan, J., & de Lannoy, I. A. M. (2014). Pharmacokinetics. Biochemical Pharmacology, 87(1), 93–120. https://doi.org/10.1016/j.bcp.2013.09.007
   PubMed Web of Science ®Google Scholar
• Ge, X.-Y., Li, J.-L., Yang, X.-L., Chmura, A. A., Zhu, G., Epstein, J. H., Mazet, J. K., Hu, B., Zhang, W., Peng, C., Zhang, Y.-J., Luo, C.-M., Tan, B., Wang, N., Zhu, Y., Crameri, G., Zhang, S.-Y., Wang, L.-F., Daszak, P., & Shi, Z.-L. (2013). Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor. Nature, 503(7477), 535–538. https://doi.org/10.1038/nature12711
   PubMed Web of Science ®Google Scholar
• Ghose, A. K., Viswanadhan, V. N., & Wendoloski, J. J. (1999). A knowledge-based approach in designing combinatorial or medicinal chemistry libraries for drug discovery. 1. A qualitative and quantitative characterization of known drug databases. Journal of Combinatorial Chemistry, 1(1), 55–68. https://doi.org/10.1021/cc9800071
   PubMedGoogle Scholar
• Golo, V. L., & Shaĭtan, K. V. (2002). Dynamic attractor for the Berendsen thermostat and the slow dynamics of biomacromolecules. Biofizika, 47(4), 611–617.
   PubMed Web of Science ®Google Scholar
• Hann, M. M., & Oprea, T. I. (2004). Pursuing the lead likeness concept in pharmaceutical research. Current Opinion in Chemical Biology, 8(3), 255–263. https://doi.org/10.1016/j.cbpa.2004.04.003
   PubMed Web of Science ®Google Scholar
• Hebert, A., Bishop, M., Bhattacharyya, D., Gleason, K., & Torosian, S. (2015). Assessment by Ames test and comet assay of toxicity potential of polymer used to develop field-capable rapid-detection device to analyze environmental samples. Applied Nanoscience, 5(6), 763–769. https://doi.org/10.1007/s13204-014-0373-7
   PubMed Web of Science ®Google Scholar
• Hedley, P. L., Jørgensen, P., Schlamowitz, S., Wangari, R., Moolman-Smook, J., Brink, P. A., Kanters, J. K., Corfield, V. A., & Christiansen, M. (2009). The genetic basis of long QT and short QT syndromes: A mutation update. Human Mutation, 30(11), 1486–1511. https://doi.org/10.1002/humu.21106
   PubMed Web of Science ®Google Scholar
• Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14 (1), 33–38. https://doi.org/10.1016/0263-7855(96)00018-5
   PubMedGoogle Scholar
• Irwin, J. J., & Shoichet, B. K. (2005). ZINC-a free database of commercially available compounds for virtual screening. Journal of Chemical Information and Modeling, 45(1), 177–182. https://doi.org/10.1021/ci049714+
   PubMed Web of Science ®Google Scholar
• Kandeel, M., & Al-Nazawi, M. (2020). Virtual screening and repurposing of FDA approved drugs against COVID-19 main protease. Life Sciences, 251, 117627.
   PubMed Web of Science ®Google Scholar
• Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (1997). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews, 23(1-3), 3–25. https://doi.org/10.1016/S0169-409X(96)00423-1
   Web of Science ®Google Scholar
• McKee, D. L., Sternberg, A., Stange, U., Laufer, S., & Naujokat, C. (2020). Candidate drugs against SARS-CoV-2 and COVID-19. Pharmacological Research, 157, 104859.
   PubMed Web of Science ®Google Scholar
• Morse, J. S., Lalonde, T., Xu, S., & Liu, W. R. (2020). Learning from the past: Possible urgent prevention and treatment options for severe acute respiratory infections caused by 2019-nCoV. Chembiochem : a European Journal of Chemical Biology, 21(5), 730–738. https://doi.org/10.1002/cbic.202000047
   PubMed Web of Science ®Google Scholar
• Mothay, D., & Ramesh, K. V. (2020). Binding site analysis of potential protease inhibitors of COVID-19 using AutoDock. VirusDisease, 31, 1–6.
   PubMedGoogle Scholar
• Munikumar, M., Krishna, V. S., Reddy, V. S., Rajeswari, B., Sriram, D., & Rao, M. V. (2018). In silico design of small peptides antagonist against leptin receptor for the treatment of obesity and its associated immune-mediated diseases. Journal of Molecular Graphics & Modelling, 82, 20–36. https://doi.org/10.1016/j.jmgm.2018.04.002
   PubMed Web of Science ®Google Scholar
• Naik, V. R., Munikumar, M., Ramakrishna, U., Srujana, M., Goudar, G., Naresh, P., Kumar, P. N., & Hemalatha, R. (2020). Remdesivir (GS-5734) as a therapeutic option of 2019-nCOV main protease–in silico approach. Journal of Biomolecular Structure and Dynamics, 1–14. https://doi.org/10.1080/07391102.2020.1781694
   Google Scholar
• Natarajan, P., Priyadarshini, V., Pradhan, D., Manne, M., Swargam, S., Kanipakam, H., Bhuma, V., & Amineni, U. (2016). E-pharmacophore-based virtual screening to identify GSK-3β inhibitors. Journal of Receptor and Signal Transduction Research, 36(5), 445–458. https://doi.org/10.3109/10799893.2015.1122043
   PubMed Web of Science ®Google Scholar
• Pires, D. E., Blundell, T. L., & Ascher, D. B. (2015). pkCSM: Predicting small-molecule pharmacokinetic and toxicity properties using graph-based signatures. Journal of Medicinal Chemistry, 58(9), 4066–4072. https://doi.org/10.1021/acs.jmedchem.5b00104
   PubMed Web of Science ®Google Scholar
• Rothan, H. A., & Byrareddy, S. N. (2020). The epidemiology and pathogenesis of coronavirus disease (COVID-19) outbreak. Journal of Autoimmunity, 109, 102433. https://doi.org/10.1016/j.jaut.2020.102433
   PubMed Web of Science ®Google Scholar
• Sadek, H., Ahmed, M., Wang, P., & Farag, A. (2020). Identification of FDA approved drugs targeting COVID-19 virus by structure-based drug repositioning. ChemRxiv. https://doi.org/10.26434/chemrxiv.12003930.v1
   Google Scholar
• Schneider, G. (2002). Trends in virtual combinatorial library design. Current Medicinal Chemistry, 9(23), 2095–2101. https://doi.org/10.2174/0929867023368755
   PubMed Web of Science ®Google Scholar
• Singh, P., Sharma, A., & Nandi, S. P. (2020). Identification of potent inhibitors of COVID-19 main protease enzyme by molecular docking study. ChemRxiv. https://doi.org/10.26434/chemrxiv.12179202.v1
   Google Scholar
• Sohrabi, C., Alsafi, Z., O'Neill, N., Khan, M., Kerwan, A., Al-Jabir, A., Iosifidis, C., & Agha, R. (2020). World Health Organization declares global emergency: A review of the 2019 novel coronavirus (COVID-19). International Journal of Surgery (London, England), 76, 71–76. https://doi.org/10.1016/j.ijsu.2020.02.034
   PubMed Web of Science ®Google Scholar
• Teague, S. J., Davis, A. M., Leeson, P. D., & Oprea, T. (1999). The design of leadlike combinatorial libraries. Angewandte Chemie International Edition, 38(24), 3743–3748. https://doi.org/10.1002/(SICI)1521-3773(19991216)38:24<3743::AID-ANIE3743>3.0.CO;2-U
   PubMed Web of Science ®Google Scholar
• Tuble, S. C., Anwar, J., & Gale, J. D. (2004). An approach to developing a force field for molecular simulation of martensitic phase transitions between phases with subtle differences in energy and structure. Journal of the American Chemical Society, 126(1), 396–405. https://doi.org/10.1021/ja0356131
   PubMed Web of Science ®Google Scholar
• Ullrich, S., & Nitsche, C. (2020). The SARS-CoV-2 main protease as drug target. Bioorganic & Medicinal Chemistry Letters, 30, 127377.
   PubMed Web of Science ®Google Scholar
• Veber, D. F., Johnson, S. R., Cheng, H. Y., Smith, B. R., Ward, K. W., & Kopple, K. D. (2002). Molecular properties that influence the oral bioavailability of drug candidates. Journal of Medicinal Chemistry, 45(12), 2615–2623. https://doi.org/10.1021/jm020017n
   PubMed Web of Science ®Google Scholar
• Wang, C., Horby, P. W., Hayden, F. G., & Gao, G. F. (2020). A novel coronavirus outbreak of global health concern. The Lancet, 395(10223), 470–473. https://doi.org/10.1016/S0140-6736(20)30185-9
   PubMed Web of Science ®Google Scholar
• Xu, X., Chen, P., Wang, J., Feng, J., Zhou, H., Li, X., Zhong, W., & Hao, P. (2020). Evolution of the novel coronavirus from the ongoing Wuhan outbreak and modeling of its spike protein for risk of human transmission. Science China. Life Sciences, 63(3), 457–460. https://doi.org/10.1007/s11427-020-1637-5
   PubMed Web of Science ®Google Scholar
• Yang, Y., Peng, F., Wang, R., Yange, M., Guan, K., Jiang, T., Xu, G., Sun, J., & Chang, C. (2020). The deadly coronaviruses: The 2003 SARS pandemic and the 2020 novel coronavirus epidemic in China. Journal of Autoimmunity, 109, 102434. https://doi.org/10.1016/j.jaut.2020.102434
   PubMed Web of Science ®Google Scholar
• Yoshino, R., Yasuo, N., & Sekijima, M. (2020). Identification of key interactions between SARS-CoV-2 Main Protease and inhibitor drug candidates. Scientific Reports, 10, 12493. https://doi.org/10.1038/s41598-020-69337-9
   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, 368(6489), 409–412. https://doi.org/10.1126/science.abb3405
   PubMed Web of Science ®Google Scholar