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Gupta Y, Kumar S, Zak SE, Jones KA, Upadhyay C, Sharma N, Azizi SA, Kathayat RS, Poonam, Herbert AS, Durvasula R, Dickinson BC, Dye JM, Rathi B, Kempaiah P. Antiviral evaluation of hydroxyethylamine analogs: Inhibitors of SARS-CoV-2 main protease (3CLpro), a virtual screening and simulation approach. Bioorg Med Chem 2021; 47:116393. [PMID: 34509862 PMCID: PMC8416325 DOI: 10.1016/j.bmc.2021.116393] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 07/25/2021] [Accepted: 08/30/2021] [Indexed: 12/22/2022]
Abstract
The continued toll of COVID-19 has halted the smooth functioning of civilization on a global scale. With a limited understanding of all the essential components of viral machinery and the lack of structural information of this new virus, initial drug discovery efforts had limited success. The availability of high-resolution crystal structures of functionally essential SARS-CoV-2 proteins, including 3CLpro, supports the development of target-specific therapeutics. 3CLpro, the main protease responsible for the processing of viral polypeptide, plays a vital role in SARS-CoV-2 viral replication and translation and is an important target in other coronaviruses. Additionally, 3CLpro is the target of repurposed drugs, such as lopinavir and ritonavir. In this study, target proteins were retrieved from the protein data bank (PDB IDs: 6 M03, 6LU7, 2GZ7, 6 W63, 6SQS, 6YB7, and 6YVF) representing different open states of the main protease to accommodate macromolecular substrate. A hydroxyethylamine (HEA) library was constructed from harvested chemical structures from all the series being used in our laboratories for screening against malaria and Leishmania parasites. The database consisted of ∼1000 structure entries, of which 70% were new to ChemSpider at the time of screening. This in-house library was subjected to high throughput virtual screening (HTVS), followed by standard precision (SP) and then extra precision (XP) docking (Schrodinger LLC 2021). The ligand strain and complex energy of top hits were calculated by Molecular Mechanics Generalized Born Surface Area (MM/GBSA) method. Promising hit compounds (n = 40) specifically binding to 3CLpro with high energy and average MM/GBSA scores were then subjected to (100-ns) MD simulations. Using this sequential selection followed by an in-silico validation approach, we found a promising HEA-based compound (N,N'-((3S,3'S)-piperazine-1,4-diylbis(3-hydroxy-1-phenylbutane-4,2-diyl))bis(2-(5-methyl-1,3-dioxoisoindolin-2-yl)-3-phenylpropanamide)), which showed high in vitro antiviral activity against SARS-CoV-2. Further to reduce the size of the otherwise larger ligand, a pharmacophore-based predicted library of ∼42 derivatives was constructed, which were added to the previous compound library and rescreened virtually. Out of several hits from the predicted library, two compounds were synthesized, tested against SARS-CoV-2 culture, and found to have markedly improved antiviral activity.
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Affiliation(s)
- Yash Gupta
- Department of Infectious Diseases, Mayo Clinic, Jacksonville, FL, USA
| | - Sumit Kumar
- Department of Chemistry, Miranda House, University of Delhi, Delhi, India
| | - Samantha E Zak
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, USA; The Geneva Foundation, 917 Pacific Avenue, Tacoma, WA, USA
| | - Krysten A Jones
- Department of Chemistry, The University of Chicago, 5801 South Ellis Avenue, Chicago, IL, USA
| | - Charu Upadhyay
- Department of Chemistry, Miranda House, University of Delhi, Delhi, India
| | - Neha Sharma
- Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College, University of Delhi, India
| | - Saara-Anne Azizi
- Department of Chemistry, The University of Chicago, 5801 South Ellis Avenue, Chicago, IL, USA
| | - Rahul S Kathayat
- Department of Chemistry, The University of Chicago, 5801 South Ellis Avenue, Chicago, IL, USA
| | - Poonam
- Department of Chemistry, Miranda House, University of Delhi, Delhi, India
| | - Andrew S Herbert
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, USA
| | - Ravi Durvasula
- Department of Infectious Diseases, Mayo Clinic, Jacksonville, FL, USA
| | - Bryan C Dickinson
- Department of Chemistry, The University of Chicago, 5801 South Ellis Avenue, Chicago, IL, USA
| | - John M Dye
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, USA; The Geneva Foundation, 917 Pacific Avenue, Tacoma, WA, USA.
| | - Brijesh Rathi
- Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College, University of Delhi, India.
| | - Prakasha Kempaiah
- Department of Infectious Diseases, Mayo Clinic, Jacksonville, FL, USA.
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