Virtual screening assisted identification of small molecule against 2019 novel coronavirus protease enzyme

Versions

PDF

Keywords

Drug Re-purposing
GROMACS
Molecular Dynamics
SARS-CoV-2

How to Cite

(1)
Sarkar, A.; Shilkar, D.; Maity, A.; Sardar, S.; Debnath, S.; Sen, D.; Jayaprakash, V. Virtual Screening Assisted Identification of Small Molecule Against 2019 Novel Coronavirus Protease Enzyme. J Pharm Chem 2020, 7, 7-12. https://doi.org/10.14805/jphchem.2020.art116.

Abstract

The 2019 novel coronavirus infection or COVID-19 can be designated as a global threat. Till date, there is a lack of dedicated therapeutics available against this fatal infection. In the present work, we performed structure-based drug design studies in order to identify clinically used molecules exhibiting crucial binding with 2019-coronavirus main protease enzyme. Based on ligand binding energy and interaction with essential amino acids, two molecules were selected. The stability of the complexed molecules with main protease enzyme was further studied by performing molecular dynamics simulation.

PDF

References

Lai, C.-C.; Shih, T.-P.; Ko, W.-C.; Tang, H.-J.; Hsueh, P.-R. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease-2019 (COVID-19): The epidemic and the challenges. International Journal of Antimicrobial Agents 2020, 55 (3), 105924.

https://doi.org/10.1016/j.ijantimicag.2020.105924

Peeri, N. C.; Shrestha, N.; Rahman, M. S.; Zaki, R.; Tan, Z.; Bibi, S.; Baghbanzadeh, M.; Aghamohammadi, N.; Zhang, W.; Haque, U. The SARS, MERS and novel coronavirus (COVID-19) epidemics, the newest and biggest global health threats: what lessons have we learned? International Journal of Epidemiology 2020, 49 (3), 717-726.

https://doi.org/10.1093/ije/dyaa033

Brian, D. A.; Baric, R. S. Coronavirus Genome Structure and Replication. In Coronavirus Replication and Reverse Genetics, Enjuanes, L., Ed. Springer Berlin Heidelberg: Berlin, Heidelberg, 2005, 10.1007/3-540-26765-4_1pp 1-30.

https://doi.org/10.1007/3-540-26765-4_1

Arya, R.; Das, A.; Prashar, V.; Kumar, M. Potential Inhibitors Against Papain-like Protease of Novel Coronavirus (COVID-19) from FDA Approved Drugs. ChemRxiv: 2020, 10.26434/chemrxiv.11860011.v1.

https://doi.org/10.26434/chemrxiv.11860011.v1

Ton, A.-T.; Gentile, F.; Hsing, M.; Ban, F.; Cherkasov, A. Rapid Identification of Potential Inhibitors of SARS-CoV-2 Main Protease by Deep Docking of 1.3 Billion Compounds. Molecular Informatics 2020, 39 (8), 2000028.

https://doi.org/10.1002/minf.202000028

Chu, C. M.; Cheng, V. C. C.; Hung, I. F. N.; Wong, M. M. L.; Chan, K. H.; Chan, K. S.; Kao, R. Y. T.; Poon, L. L. M.; Wong, C. L. P.; Guan, Y.; Peiris, J. S. M.; Yuen, K. Y. Role of lopinavir/ritonavir in the treatment of SARS: initial virological and clinical findings. Thorax 2004, 59 (3), 252.

https://doi.org/10.1136/thorax.2003.012658

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, X.; Bai, F.; Liu, H.; Liu, X.; Guddat, L. W.; Xu, W.; Xiao, G.; Qin, C.; Shi, Z.; Jiang, H.; Rao, Z.; Yang, H. Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors. Nature 2020, 582 (7811), 289-293.

https://doi.org/10.1038/s41586-020-2223-y

Bacha, U.; Barrila, J.; Velazquez-Campoy, A.; Leavitt, S. A.; Freire, E. Identification of Novel Inhibitors of the SARS Coronavirus Main Protease 3CLpro. Biochemistry 2004, 43 (17), 4906-4912.

https://doi.org/10.1021/bi0361766

Cuker, A.; Arepally, G. M.; Chong, B. H.; Cines, D. B.; Greinacher, A.; Gruel, Y.; Linkins, L. A.; Rodner, S. B.; Selleng, S.; Warkentin, T. E.; Wex, A.; Mustafa, R. A.; Morgan, R. L.; Santesso, N. American Society of Hematology 2018 guidelines for management of venous thromboembolism: heparin-induced thrombocytopenia. Blood Advances 2018, 2 (22), 3360-3392.

https://doi.org/10.1182/bloodadvances.2018024489

Thabit, A. K.; Fatani, D. F.; Bamakhrama, M. S.; Barnawi, O. A.; Basudan, L. O.; Alhejaili, S. F. Antibiotic penetration into bone and joints: An updated review. International Journal of Infectious Diseases 2019, 81, 128-136.

https://doi.org/10.1016/j.ijid.2019.02.005

Laskowski, R. A.; Swindells, M. B. LigPlot+: Multiple Ligand-Protein Interaction Diagrams for Drug Discovery. Journal of Chemical Information and Modeling 2011, 51 (10), 2778-2786.

https://doi.org/10.1021/ci200227u

Severin, P. N.; Awad, S.; Shields, B.; Hoffman, J.; Bonney, W.; Cortez, E.; Ganesan, R.; Patel, A.; Barnes, S.; Barnes, S.; Al-Anani, S.; Gupta, U.; Cheddar, Y. B.; Gonzalez, I. E.; Mallula, K.; Ghawi, H.; Kazmouz, S.; Gendi, S.; Abdulla, R.-i. The Pediatric Cardiology Pharmacopeia: 2013 Update. Pediatric Cardiology 2013, 34 (1), 1-29.

https://doi.org/10.1007/s00246-012-0553-8

Occhipinti, D. J.; Pendland, S. L.; Schoonover, L. L.; Rypins, E. B.; Danziger, L. H.; Rodvold, K. A. Pharmacokinetics and pharmacodynamics of two multiple-dose piperacillin-tazobactam regimens. Antimicrobial Agents and Chemotherapy 1997, 41 (11), 2511-2517.

https://doi.org/10.1128/AAC.41.11.2511

Benaboud, S.; Urien, S.; Thervet, E.; Prié, D.; Legendre, C.; Souberbielle, J.-C.; Hirt, D.; Friedlander, G.; Treluyer, J. M.; Courbebaisse, M. Determination of optimal cholecalciferol treatment in renal transplant recipients using a population pharmacokinetic approach. European Journal of Clinical Pharmacology 2013, 69 (3), 499-506.

https://doi.org/10.1007/s00228-012-1378-3

Robin, A. L.; Faulkner, R.; Curtis, M.; Patil, S.; McCarty, G.; Clifford, W.; Dahlin, D. C. Safety and Pharmacokinetics of Travoprost a Potent Prostaglandin F (FP) Receptor Agonist, in Patients With Renal and Hepatic Impairment. Investigative Ophthalmology & Visual Science 2002, 43 (13), 4106-4106.

Leppik, I. E.; Boucher, B. A.; Wilder, B. J.; Murthy, V. S.; Watridge, C.; Graves, N. M.; Rangel, R. J.; Rask, C. A.; Turlapaty, P. Pharmacokinetics and safety of a phenytoin prodrug given IV or IM in patients. Neurology 1990, 40 (3 Part 1), 456.

https://doi.org/10.1212/WNL.40.3_Part_1.456

Hsu, A.; Granneman, G. R.; Cao, G.; Carothers, L.; Japour, A.; El-Shourbagy, T.; Dennis, S.; Berg, J.; Erdman, K.; Leonard John, M.; Sun, E. Pharmacokinetic Interaction between Ritonavir and Indinavir in Healthy Volunteers. Antimicrobial Agents and Chemotherapy 1998, 42 (11), 2784-2791.

https://doi.org/10.1128/AAC.42.11.2784

Forli, S.; Huey, R.; Pique, M. E.; Sanner, M. F.; Goodsell, D. S.; Olson, A. J. Computational protein-ligand docking and virtual drug screening with the AutoDock suite. Nature Protocols 2016, 11 (5), 905-919.

https://doi.org/10.1038/nprot.2016.051

Samdani, A.; Vetrivel, U. POAP: A GNU parallel based multithreaded pipeline of open babel and AutoDock suite for boosted high throughput virtual screening. Computational Biology and Chemistry 2018, 74, 39-48.

https://doi.org/10.1016/j.compbiolchem.2018.02.012

Schrodinger, LLC. The PyMOL Molecular Graphics System, Version 1.8. 2015.

Creative Commons License

This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.

Copyright (c) 2020 JOURNAL OF PHARMACEUTICAL CHEMISTRY