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Nguyen TH, Tam NM, Tuan MV, Zhan P, Vu VV, Quang DT, Ngo ST. Searching for potential inhibitors of SARS-COV-2 main protease using supervised learning and perturbation calculations. Chem Phys 2023; 564:111709. [PMID: 36188488 PMCID: PMC9511900 DOI: 10.1016/j.chemphys.2022.111709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 08/11/2022] [Accepted: 09/21/2022] [Indexed: 11/28/2022]
Abstract
Inhibiting the biological activity of SARS-CoV-2 Mpro can prevent viral replication. In this context, a hybrid approach using knowledge- and physics-based methods was proposed to characterize potential inhibitors for SARS-CoV-2 Mpro. Initially, supervised machine learning (ML) models were trained to predict a ligand-binding affinity of ca. 2 million compounds with the correlation on a test set of R = 0.748 ± 0.044 . Atomistic simulations were then used to refine the outcome of the ML model. Using LIE/FEP calculations, nine compounds from the top 100 ML inhibitors were suggested to bind well to the protease with the domination of van der Waals interactions. Furthermore, the binding affinity of these compounds is also higher than that of nirmatrelvir, which was recently approved by the US FDA to treat COVID-19. In addition, the ligands altered the catalytic triad Cys145 - His41 - Asp187, possibly disturbing the biological activity of SARS-CoV-2.
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Affiliation(s)
- Trung Hai Nguyen
- Laboratory of Theoretical and Computational Biophysics, Advanced Institute of Materials Science, Ton Duc Thang University, Ho Chi Minh City, Viet Nam
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Viet Nam
| | - Nguyen Minh Tam
- Laboratory of Theoretical and Computational Biophysics, Advanced Institute of Materials Science, Ton Duc Thang University, Ho Chi Minh City, Viet Nam
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Viet Nam
| | - Mai Van Tuan
- Department of Microbiology, Hue Central Hospital, Hue City, Viet Nam
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Van V Vu
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Viet Nam
| | - Duong Tuan Quang
- Department of Chemistry, Hue University, Thua Thien Hue Province, Hue City, Viet Nam
| | - Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics, Advanced Institute of Materials Science, Ton Duc Thang University, Ho Chi Minh City, Viet Nam
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Viet Nam
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Shih PC, Mao YW, Hu JW, Hsieh HY, Shih TM, Lu LP, Chang WH, Huang CH, Lin CH, Lin CH, Tan P, Yang YC, Chien MH, Su CC, Yeh CH, Chuang PY, Hsieh TL, Wang CC, Hsieh PS, Chou TY, Tsai GE. Development of Ultrapure and Potent Tannic Acids as a Pan-coronal Antiviral Therapeutic. ACS Pharmacol Transl Sci 2022; 5:400-412. [PMID: 37582235 PMCID: PMC9128009 DOI: 10.1021/acsptsci.1c00264] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The rampageous transmission of SARS-CoV-2 has been devastatingly impacting human life and public health since late 2019. The waves of pandemic events caused by distinct coronaviruses at present and over the past decades have prompted the need to develop broad-spectrum antiviral drugs against them. In this study, our Pentarlandir ultrapure and potent tannic acids (UPPTA) showed activities against two coronaviral strains, SARS-CoV-2 and HCoV-OC43, the earliest-known coronaviruses. The mode of inhibition of Pentarlandir UPPTA is likely to act on 3-chymotrypsin-like protease (3CLpro) to prevent viral replication, as supported by results of biochemical analysis, a 3CLpro assay, and a "gain-of-function" 3CLpro overexpressed cell-based method. Even in the 3CLpro overexpressed environment, Pentarlandir UPPTA remained its antiviral characteristic. Utilizing cell-based virucidal and cytotoxicity assays, the 50% effective concentrations (EC50) and 50% cytotoxicity concentration (CC50) of Pentarlandir UPPTA were determined to be ∼0.5 and 52.5 μM against SARS-CoV-2, while they were 1.3 and 205.9 μM against HCoV-OC43, respectively. In the pharmacokinetic studies, Pentarlandir UPPTA was distributable at a high level to the lung tissue with no accumulation in the body, although the distribution was affected by the food effect. With further investigation in toxicology, Pentarlandir UPPTA demonstrated an overall safe toxicology profile. Taking these findings together, Pentarlandir UPPTA is considered to be a safe and efficacious pancoronal antiviral drug candidate that has been advanced to clinical development.
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Affiliation(s)
- Po-Chang Shih
- Department
of Research and Development, SyneuRx International
(Taiwan) Corp., New Taipei City 22175, Taiwan
| | - Yi-Wen Mao
- Department
of Research and Development, SyneuRx International
(Taiwan) Corp., New Taipei City 22175, Taiwan
| | - Jhe-Wei Hu
- Department
of Research and Development, SyneuRx International
(Taiwan) Corp., New Taipei City 22175, Taiwan
| | - Han-Yi Hsieh
- Department
of Research and Development, SyneuRx International
(Taiwan) Corp., New Taipei City 22175, Taiwan
| | - Tsai-Miao Shih
- Department
of Research and Development, SyneuRx International
(Taiwan) Corp., New Taipei City 22175, Taiwan
| | - Lu-Ping Lu
- Department
of Research and Development, SyneuRx International
(Taiwan) Corp., New Taipei City 22175, Taiwan
| | - Wei-Hua Chang
- Department
of Research and Development, SyneuRx International
(Taiwan) Corp., New Taipei City 22175, Taiwan
| | - Chan-Hui Huang
- Department
of Research and Development, SyneuRx International
(Taiwan) Corp., New Taipei City 22175, Taiwan
| | - Chia-Hung Lin
- Department
of Research and Development, SyneuRx International
(Taiwan) Corp., New Taipei City 22175, Taiwan
| | - Chih-Hung Lin
- Department
of Research and Development, SyneuRx International
(Taiwan) Corp., New Taipei City 22175, Taiwan
| | - Peng Tan
- Department
of Research and Development, SyneuRx International
(Taiwan) Corp., New Taipei City 22175, Taiwan
| | - Ya-Ching Yang
- Department
of Research and Development, SyneuRx International
(Taiwan) Corp., New Taipei City 22175, Taiwan
| | - Ming-Hong Chien
- Department
of Research and Development, SyneuRx International
(Taiwan) Corp., New Taipei City 22175, Taiwan
| | - Chen-Che Su
- Department
of Research and Development, SyneuRx International
(Taiwan) Corp., New Taipei City 22175, Taiwan
| | - Cheng-Hsin Yeh
- Department
of Research and Development, SyneuRx International
(Taiwan) Corp., New Taipei City 22175, Taiwan
| | - Pei-Yun Chuang
- Department
of Research and Development, SyneuRx International
(Taiwan) Corp., New Taipei City 22175, Taiwan
| | - Tien-Lan Hsieh
- Department
of Research and Development, SyneuRx International
(Taiwan) Corp., New Taipei City 22175, Taiwan
| | - Ching-Cheng Wang
- Department
of Research and Development, SyneuRx International
(Taiwan) Corp., New Taipei City 22175, Taiwan
| | - Po-Shiuan Hsieh
- Institute
of Physiology, National Defense Medical
Center, Taipei
City 11490, Taiwan
- Department
of Medical Research, Tri-Service General
Hospital, Taipei City 114, Taiwan
| | - Teh-Ying Chou
- Department
of Pathology and Laboratory Medicine, Taipei
Veterans General Hospital, Taipei City 112, Taiwan
- Institute
of Clinical Medicine, National Yang-Ming
Chiao Tung University, Taipei City 112304, Taiwan
| | - Guochuan Emil Tsai
- Department
of Research and Development, SyneuRx International
(Taiwan) Corp., New Taipei City 22175, Taiwan
- UCLA School
of Medicine, Los Angeles, California 90095, United States
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Greasley SE, Noell S, Plotnikova O, Ferre R, Liu W, Bolanos B, Fennell K, Nicki J, Craig T, Zhu Y, Stewart AE, Steppan CM. Structural basis for the in vitro efficacy of nirmatrelvir against SARS-CoV-2 variants. J Biol Chem 2022. [PMID: 35461811 DOI: 10.1101/2022.01.17.476556] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023] Open
Abstract
The COVID-19 pandemic continues to be a public health threat with emerging variants of SARS-CoV-2. Nirmatrelvir (PF-07321332) is a reversible, covalent inhibitor targeting the main protease (Mpro) of SARS-CoV-2 and the active protease inhibitor in PAXLOVID (nirmatrelvir tablets and ritonavir tablets). However, the efficacy of nirmatrelvir is underdetermined against evolving SARS-CoV-2 variants. Here, we evaluated the in vitro catalytic activity and potency of nirmatrelvir against the Mpro of prevalent variants of concern (VOCs) or variants of interest (VOIs): Alpha (α, B.1.1.7), Beta (β, B.1.351), Delta (δ, B1.617.2), Gamma (γ, P.1), Lambda (λ, B.1.1.1.37/C37), Omicron (ο, B.1.1.529), as well as the original Washington or wildtype strain. These VOCs/VOIs carry prevalent mutations at varying frequencies in the Mpro specifically for α, β, γ (K90R), λ (G15S), and ο (P132H). In vitro biochemical enzymatic assay characterization of the enzyme kinetics of the mutant Mpros demonstrates that they are catalytically comparable to wildtype. We found that nirmatrelvir has similar potency against each mutant Mpro including P132H that is observed in the Omicron variant with a Ki of 0.635 nM as compared to a Ki of 0.933 nM for wildtype. The molecular basis for these observations were provided by solution-phase structural dynamics and structural determination of nirmatrelvir bound to the ο, λ, and β Mpro at 1.63 to 2.09 Å resolution. These in vitro data suggest that PAXLOVID has the potential to maintain plasma concentrations of nirmatrelvir many-fold times higher than the amount required to stop the SARS-CoV-2 VOC/VOI, including Omicron, from replicating in cells.
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Affiliation(s)
- Samantha E Greasley
- Medicine Design, Pfizer Worldwide Research, Development & Medical, La Jolla, California, USA
| | - Stephen Noell
- Medicine Design, Pfizer Worldwide Research, Development & Medical, Groton, Connecticut, USA
| | - Olga Plotnikova
- Medicine Design, Pfizer Worldwide Research, Development & Medical, Groton, Connecticut, USA
| | - RoseAnn Ferre
- Medicine Design, Pfizer Worldwide Research, Development & Medical, La Jolla, California, USA
| | - Wei Liu
- Medicine Design, Pfizer Worldwide Research, Development & Medical, La Jolla, California, USA
| | - Ben Bolanos
- Medicine Design, Pfizer Worldwide Research, Development & Medical, La Jolla, California, USA
| | - Kimberly Fennell
- Medicine Design, Pfizer Worldwide Research, Development & Medical, Groton, Connecticut, USA
| | - Jennifer Nicki
- Medicine Design, Pfizer Worldwide Research, Development & Medical, Groton, Connecticut, USA
| | - Tim Craig
- Medicine Design, Pfizer Worldwide Research, Development & Medical, Groton, Connecticut, USA
| | - Yuao Zhu
- VRD Bacterial Vaccines, Pfizer Worldwide Research, Development & Medical, Pearl River, New York, USA
| | - Al E Stewart
- Medicine Design, Pfizer Worldwide Research, Development & Medical, La Jolla, California, USA
| | - Claire M Steppan
- Medicine Design, Pfizer Worldwide Research, Development & Medical, Groton, Connecticut, USA.
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