1
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Shawky AM, Almalki FA, Alzahrani HA, Abdalla AN, Youssif BGM, Ibrahim NA, Gamal M, El-Sherief HAM, Abdel-Fattah MM, Hefny AA, Abdelazeem AH, Gouda AM. Covalent small-molecule inhibitors of SARS-CoV-2 Mpro: Insights into their design, classification, biological activity, and binding interactions. Eur J Med Chem 2024; 277:116704. [PMID: 39121741 DOI: 10.1016/j.ejmech.2024.116704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 07/10/2024] [Accepted: 07/19/2024] [Indexed: 08/12/2024]
Abstract
Since 2020, many compounds have been investigated for their potential use in the treatment of SARS-CoV-2 infection. Among these agents, a huge number of natural products and FDA-approved drugs have been evaluated as potential therapeutics for SARS-CoV-2 using virtual screening and docking studies. However, the identification of the molecular targets involved in viral replication led to the development of rationally designed anti-SARS-CoV-2 agents. Among these targets, the main protease (Mpro) is one of the key enzymes needed in the replication of the virus. The data gleaned from the crystal structures of SARS-CoV-2 Mpro complexes with small-molecule covalent inhibitors has been used in the design and discovery of many highly potent and broad-spectrum Mpro inhibitors. The current review focuses mainly on the covalent type of SARS-CoV-2 Mpro inhibitors. The design, chemistry, and classification of these inhibitors were also in focus. The biological activity of these inhibitors, including their inhibitory activities against Mpro, their antiviral activities, and the SAR studies, were discussed. The review also describes the potential mechanism of the interaction between these inhibitors and the catalytic Cys145 residue in Mpro. Moreover, the binding modes and key binding interactions of these covalent inhibitors were also illustrated. The covalent inhibitors discussed in this review were of diverse chemical nature and origin. Their antiviral activity was mediated mainly by the inhibition of SARS-CoV-2 Mpro, with IC50 values in the micromolar to the nanomolar range. Many of these inhibitors exhibited broad-spectrum inhibitory activity against the Mpro enzymes of other coronaviruses (SARS-CoV-1 and MERS-CoV). The dual inhibition of the Mpro and PLpro enzymes of SARS-CoV-2 could also provide higher therapeutic benefits than Mpro inhibition. Despite the approval of nirmatrelvir by the FDA, many mutations in the Mpro enzyme of SARS-CoV-2 have been reported. Although some of these mutations did not affect the potency of nirmatrelvir, there is an urgent need to develop a second generation of Mpro inhibitors. We hope that the data summarized in this review could help researchers in the design of a new potent generation of SARS-CoV-2 Mpro inhibitors.
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Affiliation(s)
- Ahmed M Shawky
- Science and Technology Unit (STU), Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | - Faisal A Almalki
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | - Hayat Ali Alzahrani
- Applied Medical Science College, Medical Laboratory Technology Department, Northern Border University, Arar, Saudi Arabia
| | - Ashraf N Abdalla
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Umm Al-Qura University, Makkah, 21955, Saudi Arabia; Department of Pharmacology and Toxicology, Medicinal And Aromatic Plants Research Institute, National Center for Research, Khartoum, 2404, Sudan
| | - Bahaa G M Youssif
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Assiut University, Assiut, 71526, Egypt.
| | - Nashwa A Ibrahim
- Medicinal Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt
| | - Mohammed Gamal
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt
| | - Hany A M El-Sherief
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Deraya University, Minia, Egypt
| | - Maha M Abdel-Fattah
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt
| | - Ahmed A Hefny
- Medicinal Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt; School of Pharmacy, University of Waterloo, Kitchener, Ontario, N2G 1C5, Canada
| | - Ahmed H Abdelazeem
- Medicinal Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt; Pharmacy Department, College of Pharmacy, Nursing and Medical Sciences, Riyadh Elm University, Riyadh, 11681, Saudi Arabia
| | - Ahmed M Gouda
- Medicinal Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt.
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2
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Jhanwar A, Sharma D, Das U. Unraveling the structural and functional dimensions of SARS-CoV2 proteins in the context of COVID-19 pathogenesis and therapeutics. Int J Biol Macromol 2024; 278:134850. [PMID: 39168210 DOI: 10.1016/j.ijbiomac.2024.134850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 08/14/2024] [Accepted: 08/16/2024] [Indexed: 08/23/2024]
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2) has emerged as the causative agent behind the global pandemic of Coronavirus Disease 2019 (COVID-19). As the scientific community strives to comprehend the intricate workings of this virus, a fundamental aspect lies in deciphering the myriad proteins it expresses. This knowledge is pivotal in unraveling the complexities of the viral machinery and devising targeted therapeutic interventions. The proteomic landscape of SARS-CoV2 encompasses structural, non-structural, and open-reading frame proteins, each playing crucial roles in viral replication, host interactions, and the pathogenesis of COVID-19. This comprehensive review aims to provide an updated and detailed examination of the structural and functional attributes of SARS-CoV2 proteins. By exploring the intricate molecular architecture, we have highlighted the significance of these proteins in viral biology. Insights into their roles and interplay contribute to a deeper understanding of the virus's mechanisms, thereby paving the way for the development of effective therapeutic strategies. As the global scientific community strives to combat the ongoing pandemic, this synthesis of knowledge on SARS-CoV2 proteins serves as a valuable resource, fostering informed approaches toward mitigating the impact of COVID-19 and advancing the frontier of antiviral research.
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Affiliation(s)
- Aniruddh Jhanwar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Dipika Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Uddipan Das
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.
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3
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Oneto A, Hamwi GA, Schäkel L, Krüger N, Sylvester K, Petry M, Shamleh RA, Pillaiyar T, Claff T, Schiedel AC, Sträter N, Gütschow M, Müller CE. Nonpeptidic Irreversible Inhibitors of SARS-CoV-2 Main Protease with Potent Antiviral Activity. J Med Chem 2024; 67:14986-15011. [PMID: 39146284 DOI: 10.1021/acs.jmedchem.4c00535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
SARS-CoV-2 infections pose a high risk for vulnerable patients. In this study, we designed benzoic acid halopyridyl esters bearing a variety of substituents as irreversible inhibitors of the main viral protease (Mpro). Altogether, 55 benzoyl chloro/bromo-pyridyl esters were synthesized, with broad variation of the substitution pattern on the benzoyl moiety. A workflow was employed for multiparametric optimization, including Mpro inhibition assays of SARS-CoV-2 and related pathogenic coronaviruses, the duration of enzyme inhibition, the compounds' stability versus glutathione, cytotoxicity, and antiviral activity. Several compounds showed IC50 values in the low nanomolar range, kinact/Ki values of >100,000 M-1 s-1 and high antiviral activity. High-resolution X-ray cocrystal structures indicated an important role of ortho-fluorobenzoyl substitution, forming a water network that stabilizes the inhibitor-bound enzyme. The most potent antiviral compound was the p-ethoxy-o-fluorobenzoyl chloropyridyl ester (PSB-21110, 29b, MW 296 g/mol; EC50 2.68 nM), which may serve as a lead structure for broad-spectrum anticoronaviral therapeutics.
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Affiliation(s)
- Angelo Oneto
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn D-53121, Germany
- PharmaCenter Bonn, University of Bonn, Brühler Straße 7, Bonn D-53121, Germany
| | - Ghazl Al Hamwi
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn D-53121, Germany
- PharmaCenter Bonn, University of Bonn, Brühler Straße 7, Bonn D-53121, Germany
| | - Laura Schäkel
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn D-53121, Germany
- PharmaCenter Bonn, University of Bonn, Brühler Straße 7, Bonn D-53121, Germany
| | - Nadine Krüger
- Platform Infection Models, German Primate Center, Leibniz Institute for Primate Research Göttingen, Kellnerweg 4, Göttingen 37077, Germany
| | - Katharina Sylvester
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn D-53121, Germany
- PharmaCenter Bonn, University of Bonn, Brühler Straße 7, Bonn D-53121, Germany
| | - Marvin Petry
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn D-53121, Germany
- PharmaCenter Bonn, University of Bonn, Brühler Straße 7, Bonn D-53121, Germany
| | - Rasha Abu Shamleh
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn D-53121, Germany
- PharmaCenter Bonn, University of Bonn, Brühler Straße 7, Bonn D-53121, Germany
| | - Thanigaimalai Pillaiyar
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn D-53121, Germany
- PharmaCenter Bonn, University of Bonn, Brühler Straße 7, Bonn D-53121, Germany
| | - Tobias Claff
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn D-53121, Germany
- PharmaCenter Bonn, University of Bonn, Brühler Straße 7, Bonn D-53121, Germany
| | - Anke C Schiedel
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn D-53121, Germany
- PharmaCenter Bonn, University of Bonn, Brühler Straße 7, Bonn D-53121, Germany
| | - Norbert Sträter
- Center for Biotechnology and Biomedicine, Leipzig University, Deutscher Platz 5, Leipzig 04103, Germany
| | - Michael Gütschow
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn D-53121, Germany
- PharmaCenter Bonn, University of Bonn, Brühler Straße 7, Bonn D-53121, Germany
| | - Christa E Müller
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn D-53121, Germany
- PharmaCenter Bonn, University of Bonn, Brühler Straße 7, Bonn D-53121, Germany
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4
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Janin YL. On the origins of SARS-CoV-2 main protease inhibitors. RSC Med Chem 2024; 15:81-118. [PMID: 38283212 PMCID: PMC10809347 DOI: 10.1039/d3md00493g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 10/13/2023] [Indexed: 01/30/2024] Open
Abstract
In order to address the world-wide health challenge caused by the COVID-19 pandemic, the 3CL protease/SARS-CoV-2 main protease (SARS-CoV-2-Mpro) coded by its nsp5 gene became one of the biochemical targets for the design of antiviral drugs. In less than 3 years of research, 4 inhibitors of SARS-CoV-2-Mpro have actually been authorized for COVID-19 treatment (nirmatrelvir, ensitrelvir, leritrelvir and simnotrelvir) and more such as EDP-235, FB-2001 and STI-1558/Olgotrelvir or five undisclosed compounds (CDI-988, ASC11, ALG-097558, QLS1128 and H-10517) are undergoing clinical trials. This review is an attempt to picture this quite unprecedented medicinal chemistry feat and provide insights on how these cysteine protease inhibitors were discovered. Since many series of covalent SARS-CoV-2-Mpro inhibitors owe some of their origins to previous work on other proteases, we first provided a description of various inhibitors of cysteine-bearing human caspase-1 or cathepsin K, as well as inhibitors of serine proteases such as human dipeptidyl peptidase-4 or the hepatitis C protein complex NS3/4A. This is then followed by a description of the results of the approaches adopted (repurposing, structure-based and high throughput screening) to discover coronavirus main protease inhibitors.
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Affiliation(s)
- Yves L Janin
- Structure et Instabilité des Génomes (StrInG), Muséum National d'Histoire Naturelle, INSERM, CNRS, Alliance Sorbonne Université 75005 Paris France
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5
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Hashem HE, Ahmad S, Kumer A, Bakri YE. In silico and in vitro prediction of new synthesized N-heterocyclic compounds as anti-SARS-CoV-2. Sci Rep 2024; 14:1152. [PMID: 38212472 PMCID: PMC10784557 DOI: 10.1038/s41598-024-51443-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 01/04/2024] [Indexed: 01/13/2024] Open
Abstract
Computer-aided drug design has been employed to get the medicinal effects against Corona virus from different pyridine derivatives after synthesizing the new compounds. Additionally, various computational studies are also employed between the newly prepared pyridine derivatives and three controls against three proteins (6Y2E, 6M71 and 6M3M). Different methods were employed to synthesize new pyridine derivatives according to the literature using different reaction mediums. MTT was performed for cytotoxicity study and IC50 for inhibitory concentration. Additionally, in-silico studies including DFT, molecular docking, molecular dynamics, MMPBSA, ADME, pharmacokinetics and Lipinski rules were evaluated. The chemical structures of all new compounds were elucidated based on spectroscopic investigation. A molecular docking study demonstrated that compounds 5, 11, and 12 have the best binders of the SARS-CoV-2 main protease enzyme, with energy scores of - 7.5 kcal/mol, - 7.2 kcal/mol, and - 7.9 kcal/mol, respectively. The net binding energy values of the 11-Mpro, 12-Mpro, and 5-Mpro complexes revealed their highly stable nature in terms of both intermolecular interactions and docked conformation across the simulation time. ADME properties, besides the pharmacokinetics and Lipinski rules, showed that all seven newly synthesized compounds follow Lipinski rules with high GI absorption. The In Vitro antiviral study against SARS-CoV-2 using MTT methods confirms that compound 5 has more potential and is safer than other tested compounds. The study shows that the newly synthesized pyridine derivatives have medicinal properties against SARS-CoV-2 without violating Lipinski rules. Compounds 5, 11, and 12, particularly compound 5, may serve as promising potential candidate for COVID-19.
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Affiliation(s)
- Heba E Hashem
- Department of Chemistry, Faculty of Women, Ain Shams University, HeliopolisCairo, 11757, Egypt.
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, 25000, Pakistan
- Department of Natural Sciences, Lebanese American University, P.O. Box 36, Beirut, Lebanon
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, P.O. Box 36, Beirut, Lebanon
| | - Ajoy Kumer
- Department of Chemistry, College of Arts and Sciences, IUBAT-International University of Business Agriculture and Technology, Dhaka, 1230, Bangladesh
- Center for Global Health Research, Saveetha Institute of Medical and Technical Sciences in Saveetha Medical College and Hospital, Chennai, India
| | - Youness El Bakri
- Department of Theoretical and Applied Chemistry, South Ural State University, Lenin Prospect 76, Chelyabinsk, 454080, Russian Federation
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6
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Li X, Song Y. Structure and function of SARS-CoV and SARS-CoV-2 main proteases and their inhibition: A comprehensive review. Eur J Med Chem 2023; 260:115772. [PMID: 37659195 PMCID: PMC10529944 DOI: 10.1016/j.ejmech.2023.115772] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/24/2023] [Accepted: 08/26/2023] [Indexed: 09/04/2023]
Abstract
Severe acute respiratory syndrome-associated coronavirus (SARS-CoV) identified in 2003 infected ∼8000 people in 26 countries with 800 deaths, which was soon contained and eradicated by syndromic surveillance and enhanced quarantine. A closely related coronavirus SARS-CoV-2, the causative agent of COVID-19 identified in 2019, has been dramatically more contagious and catastrophic. It has infected and caused various flu-like symptoms of billions of people in >200 countries, including >6 million people died of or with the virus. Despite the availability of several vaccines and antiviral drugs against SARS-CoV-2, finding new therapeutics is needed because of viral evolution and a possible emerging coronavirus in the future. The main protease (Mpro) of these coronaviruses plays important roles in their life cycle and is essential for the viral replication. This article represents a comprehensive review of the function, structure and inhibition of SARS-CoV and -CoV-2 Mpro, including structure-activity relationships, protein-inhibitor interactions and clinical trial status.
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Affiliation(s)
- Xin Li
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
| | - Yongcheng Song
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
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7
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Fink EA, Bardine C, Gahbauer S, Singh I, Detomasi TC, White K, Gu S, Wan X, Chen J, Ary B, Glenn I, O'Connell J, O'Donnell H, Fajtová P, Lyu J, Vigneron S, Young NJ, Kondratov IS, Alisoltani A, Simons LM, Lorenzo‐Redondo R, Ozer EA, Hultquist JF, O'Donoghue AJ, Moroz YS, Taunton J, Renslo AR, Irwin JJ, García‐Sastre A, Shoichet BK, Craik CS. Large library docking for novel SARS-CoV-2 main protease non-covalent and covalent inhibitors. Protein Sci 2023; 32:e4712. [PMID: 37354015 PMCID: PMC10364469 DOI: 10.1002/pro.4712] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/29/2023] [Accepted: 06/21/2023] [Indexed: 06/25/2023]
Abstract
Antiviral therapeutics to treat SARS-CoV-2 are needed to diminish the morbidity of the ongoing COVID-19 pandemic. A well-precedented drug target is the main viral protease (MPro ), which is targeted by an approved drug and by several investigational drugs. Emerging viral resistance has made new inhibitor chemotypes more pressing. Adopting a structure-based approach, we docked 1.2 billion non-covalent lead-like molecules and a new library of 6.5 million electrophiles against the enzyme structure. From these, 29 non-covalent and 11 covalent inhibitors were identified in 37 series, the most potent having an IC50 of 29 and 20 μM, respectively. Several series were optimized, resulting in low micromolar inhibitors. Subsequent crystallography confirmed the docking predicted binding modes and may template further optimization. While the new chemotypes may aid further optimization of MPro inhibitors for SARS-CoV-2, the modest success rate also reveals weaknesses in our approach for challenging targets like MPro versus other targets where it has been more successful, and versus other structure-based techniques against MPro itself.
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Affiliation(s)
- Elissa A. Fink
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
- Graduate Program in BiophysicsUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Conner Bardine
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
- Graduate Program in Chemistry and Chemical BiologyUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Stefan Gahbauer
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Isha Singh
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Tyler C. Detomasi
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Kris White
- Department of MicrobiologyIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Global Health and Emerging Pathogens InstituteIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Shuo Gu
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Xiaobo Wan
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Jun Chen
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Beatrice Ary
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Isabella Glenn
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Joseph O'Connell
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Henry O'Donnell
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Pavla Fajtová
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California‐San DiegoSan DiegoCaliforniaUSA
| | - Jiankun Lyu
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Seth Vigneron
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Nicholas J. Young
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Ivan S. Kondratov
- Enamine Ltd.KyïvUkraine
- V.P. Kukhar Institute of Bioorganic Chemistry and PetrochemistryNational Academy of Sciences of UkraineKyïvUkraine
| | - Arghavan Alisoltani
- Division of Infectious Diseases, Center for Pathogen Genomics and Microbial Evolution, Feinberg School of MedicineNorthwestern UniversityChicagoIllinoisUSA
| | - Lacy M. Simons
- Division of Infectious Diseases, Center for Pathogen Genomics and Microbial Evolution, Feinberg School of MedicineNorthwestern UniversityChicagoIllinoisUSA
| | - Ramon Lorenzo‐Redondo
- Division of Infectious Diseases, Center for Pathogen Genomics and Microbial Evolution, Feinberg School of MedicineNorthwestern UniversityChicagoIllinoisUSA
| | - Egon A. Ozer
- Division of Infectious Diseases, Center for Pathogen Genomics and Microbial Evolution, Feinberg School of MedicineNorthwestern UniversityChicagoIllinoisUSA
| | - Judd F. Hultquist
- Division of Infectious Diseases, Center for Pathogen Genomics and Microbial Evolution, Feinberg School of MedicineNorthwestern UniversityChicagoIllinoisUSA
| | - Anthony J. O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California‐San DiegoSan DiegoCaliforniaUSA
| | - Yurii S. Moroz
- National Taras Shevchenko University of KyïvKyïvUkraine
- Chemspace LLCKyïvUkraine
| | - Jack Taunton
- Department of Cellular and Molecular PharmacologyUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Adam R. Renslo
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - John J. Irwin
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Adolfo García‐Sastre
- Department of MicrobiologyIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Global Health and Emerging Pathogens InstituteIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Department of Medicine, Division of Infectious DiseasesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Tisch Cancer Institute, Icahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Department of Pathology, Molecular and Cell‐Based MedicineIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- QBI COVID‐19 Research Group (QCRG)San FranciscoCaliforniaUSA
| | - Brian K. Shoichet
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
- QBI COVID‐19 Research Group (QCRG)San FranciscoCaliforniaUSA
| | - Charles S. Craik
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
- QBI COVID‐19 Research Group (QCRG)San FranciscoCaliforniaUSA
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8
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Chen S, Arutyunova E, Lu J, Khan MB, Rut W, Zmudzinski M, Shahbaz S, Iyyathurai J, Moussa EW, Turner Z, Bai B, Lamer T, Nieman JA, Vederas JC, Julien O, Drag M, Elahi S, Young HS, Lemieux MJ. SARS-CoV-2 M pro Protease Variants of Concern Display Altered Viral Substrate and Cell Host Target Galectin-8 Processing but Retain Sensitivity toward Antivirals. ACS CENTRAL SCIENCE 2023; 9:696-708. [PMID: 37122453 PMCID: PMC10042146 DOI: 10.1021/acscentsci.3c00054] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Indexed: 05/03/2023]
Abstract
The main protease of SARS-CoV-2 (Mpro) is the most promising drug target against coronaviruses due to its essential role in virus replication. With newly emerging variants there is a concern that mutations in Mpro may alter the structural and functional properties of protease and subsequently the potency of existing and potential antivirals. We explored the effect of 31 mutations belonging to 5 variants of concern (VOCs) on catalytic parameters and substrate specificity, which revealed changes in substrate binding and the rate of cleavage of a viral peptide. Crystal structures of 11 Mpro mutants provided structural insight into their altered functionality. Additionally, we show Mpro mutations influence proteolysis of an immunomodulatory host protein Galectin-8 (Gal-8) and a subsequent significant decrease in cytokine secretion, providing evidence for alterations in the escape of host-antiviral mechanisms. Accordingly, mutations associated with the Gamma VOC and highly virulent Delta VOC resulted in a significant increase in Gal-8 cleavage. Importantly, IC50s of nirmatrelvir (Pfizer) and our irreversible inhibitor AVI-8053 demonstrated no changes in potency for both drugs for all mutants, suggesting Mpro will remain a high-priority antiviral drug candidate as SARS-CoV-2 evolves.
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Affiliation(s)
- Sizhu
Amelia Chen
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Elena Arutyunova
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Jimmy Lu
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Muhammad Bashir Khan
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Wioletta Rut
- Department
of Chemical Biology and Bioimaging, Wroclaw
University of Science and Technology, Wroclaw, 50-370, Poland
| | - Mikolaj Zmudzinski
- Department
of Chemical Biology and Bioimaging, Wroclaw
University of Science and Technology, Wroclaw, 50-370, Poland
| | - Shima Shahbaz
- Department
of Dentistry & Dental Hygiene, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Jegan Iyyathurai
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Eman W. Moussa
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Zoe Turner
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Bing Bai
- Li
Ka Shing Applied Virology Institute, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
- Department
of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Tess Lamer
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - James A. Nieman
- Li
Ka Shing Applied Virology Institute, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
- Department
of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - John C. Vederas
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Olivier Julien
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Marcin Drag
- Department
of Chemical Biology and Bioimaging, Wroclaw
University of Science and Technology, Wroclaw, 50-370, Poland
| | - Shokrollah Elahi
- Department
of Dentistry & Dental Hygiene, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Howard S. Young
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - M. Joanne Lemieux
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
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9
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Wan L, Wang X, Wang T, Yuan X, Liu W, Huang Y, Deng C, Cao S. Comparison of Target Pocket Similarity and Progress into Research on Inhibitors of Picornavirus 3C Proteases. Chem Biodivers 2023; 20:e202201100. [PMID: 36808685 DOI: 10.1002/cbdv.202201100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 02/09/2023] [Accepted: 02/09/2023] [Indexed: 02/21/2023]
Abstract
The 3C protease (3C Pro) plays a significant role in the life cycle of picornaviruses from replication to translation, making it an attractive target for structure-based design of drugs against picornaviruses. The structurally related 3C-like protease (3CL Pro) is an important protein involved in the replication of coronaviruses. With the emergence of COVID-19 and consequent intensive research into 3CL Pro, development of 3CL Pro inhibitors has emerged as a popular topic. This article compares the similarities of the target pockets of various 3C and 3CL Pros from numerous pathogenic viruses. This article also reports several types of 3C Pro inhibitors that are currently undergoing extensive studies and introduces various structural modifications of 3C Pro inhibitors to provide a reference for the development of new and more effective inhibitors of 3C Pro and 3CL Pro.
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Affiliation(s)
- Li Wan
- Key Laboratory of Green Chemical Engineering Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, P. R. China
| | - Xiaobo Wang
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, 437100, P. R. China
| | - Tangle Wang
- Key Laboratory of Green Chemical Engineering Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, P. R. China
| | - Xiaolan Yuan
- Key Laboratory of Green Chemical Engineering Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, P. R. China
| | - Wei Liu
- Key Laboratory of Green Chemical Engineering Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, P. R. China
| | - Yan Huang
- Key Laboratory of Green Chemical Engineering Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, P. R. China
| | - Changyong Deng
- Key Laboratory of Green Chemical Engineering Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, P. R. China
| | - Shuang Cao
- Key Laboratory of Green Chemical Engineering Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, P. R. China
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10
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Liu H, Forouhar F, Lin AJ, Wang Q, Polychronidou V, Soni RK, Xia X, Stockwell BR. Small-molecule allosteric inhibitors of GPX4. Cell Chem Biol 2022; 29:1680-1693.e9. [PMID: 36423641 PMCID: PMC9772252 DOI: 10.1016/j.chembiol.2022.11.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 02/27/2022] [Accepted: 11/02/2022] [Indexed: 11/24/2022]
Abstract
Encouraged by the dependence of drug-resistant, metastatic cancers on GPX4, we examined biophysical mechanisms of GPX4 inhibition, which revealed an unexpected allosteric site. We found that this site was involved in native regeneration of GPX4 under low glutathione conditions. Covalent binding of inhibitors to this allosteric site caused a conformational change, inhibition of activity, and subsequent cellular GPX4 protein degradation. To verify this site in an unbiased manner, we screened a library of compounds and identified and validated that an additional compound can covalently bind in this allosteric site, inhibiting and degrading GPX4. We determined co-crystal structures of six different inhibitors bound in this site. We have thus identified an allosteric mechanism for small molecules targeting aggressive cancers dependent on GPX4.
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Affiliation(s)
- Hengrui Liu
- Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - Farhad Forouhar
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
| | - Annie J Lin
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Qian Wang
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | | | - Rajesh Kumar Soni
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
| | - Xin Xia
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Brent R Stockwell
- Department of Chemistry, Columbia University, New York, NY 10027, USA; Department of Biological Sciences, Columbia University, New York, NY 10027, USA; Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA; Irving Institute for Cancer Dynamics, Columbia University, New York, NY 10027, USA.
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11
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Ávila-Gálvez MÁ, Rafael-Pita C, Fernández N, Baixinho J, Anastácio JD, Cankar K, Bosch D, Nunes Dos Santos C. Targeting proteases involved in the viral replication of SARS-CoV-2 by sesquiterpene lactones from chicory ( Cichorium intybus L.). Food Funct 2022; 13:8977-8988. [PMID: 35938740 DOI: 10.1039/d2fo00933a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
SARS-CoV-2 is a highly transmissible and pathogenic coronavirus causing a respiratory disease that emerged in 2019, leading to a public health emergency situation which continues to date. The treatment options are still very limited and vaccines available are less effective against new variants. SARS-CoV-2 enzymes, namely main protease (Mpro) and papain-like protease (PLpro), play a pivotal role in the viral life cycle, making them a putative drug target. Here, we described for the first time the potential inhibitory activity of chicory extract against both proteases. Besides, we have identified that the four most abundant sesquiterpene lactones in chicory inhibited these proteases, showing an effective binding in the active sites of Mpro and PLpro. This paper provides new insight for further drug development or food-based strategies for the prevention of SARS-CoV-2 by targeting viral proteases.
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Affiliation(s)
- María Ángeles Ávila-Gálvez
- Instituto de Biologia Experimental e Tecnológica (iBET), Av. República, Qta. Marquês, 2780-157 Oeiras, Portugal
- NOVA Medical School|Faculdade de Ciências Médicas, NMS|FCM, Universidade Nova de Lisboa, Lisboa, Portugal.
| | - Carlos Rafael-Pita
- Instituto de Biologia Experimental e Tecnológica (iBET), Av. República, Qta. Marquês, 2780-157 Oeiras, Portugal
- NOVA Medical School|Faculdade de Ciências Médicas, NMS|FCM, Universidade Nova de Lisboa, Lisboa, Portugal.
| | - Naiara Fernández
- Instituto de Biologia Experimental e Tecnológica (iBET), Av. República, Qta. Marquês, 2780-157 Oeiras, Portugal
| | - João Baixinho
- Instituto de Biologia Experimental e Tecnológica (iBET), Av. República, Qta. Marquês, 2780-157 Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - José D Anastácio
- Instituto de Biologia Experimental e Tecnológica (iBET), Av. República, Qta. Marquês, 2780-157 Oeiras, Portugal
- NOVA Medical School|Faculdade de Ciências Médicas, NMS|FCM, Universidade Nova de Lisboa, Lisboa, Portugal.
| | - Katarina Cankar
- Wageningen University and Research, Wageningen Plant Research, BU Bioscience, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Dirk Bosch
- Wageningen University and Research, Wageningen Plant Research, BU Bioscience, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Cláudia Nunes Dos Santos
- Instituto de Biologia Experimental e Tecnológica (iBET), Av. República, Qta. Marquês, 2780-157 Oeiras, Portugal
- NOVA Medical School|Faculdade de Ciências Médicas, NMS|FCM, Universidade Nova de Lisboa, Lisboa, Portugal.
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12
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Allaka TR, Katari NK, Jonnalagadda SB. Synthesis of antiviral drugs by using carbon–carbon and carbon–heteroatom bond formation under greener conditions. PHYSICAL SCIENCES REVIEWS 2022. [DOI: 10.1515/psr-2021-0089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Antiviral medications are a branch of medicines notably used to treat that cause many significant diseases in humans and animals. This monograph mainly focuses on recent developments and synthesis of antiviral drugs using carbon-carbon and carbon–hetero bond cross-coupling chemistry. Viral infections exact several severe human diseases, accounting for remarkably high mortality rates. In this sense, academia and the pharmaceutical industry continuously search for novel compounds with better antiviral activity. The researchers face the challenge of developing greener and economical ways to synthesize these compounds and make significant progress.
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Affiliation(s)
- Tejeswara Rao Allaka
- Centre for Chemical Sciences and Technology, Institute of Science and Technology , Jawaharlal Nehru Technological University Hyderabad , Kukatpally , Hyderabad , Telangana 500085 , India
| | - Naresh Kumar Katari
- Department of Chemistry, School of Science , GITAM deemed to be University , Hyderabad , Telangana 502 329 , India
- School of Chemistry & Physics, College of Agriculture, Engineering & Science, Westville Campus , University of KwaZulu-Natal , P Bag X 54001 , Durban 4000 , South Africa
| | - Sreekanth Babu Jonnalagadda
- School of Chemistry & Physics, College of Agriculture, Engineering & Science, Westville Campus , University of KwaZulu-Natal , P Bag X 54001 , Durban 4000 , South Africa
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13
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Liu H, Iketani S, Zask A, Khanizeman N, Bednarova E, Forouhar F, Fowler B, Hong SJ, Mohri H, Nair MS, Huang Y, Tay NES, Lee S, Karan C, Resnick SJ, Quinn C, Li W, Shion H, Xia X, Daniels JD, Bartolo-Cruz M, Farina M, Rajbhandari P, Jurtschenko C, Lauber MA, McDonald T, Stokes ME, Hurst BL, Rovis T, Chavez A, Ho DD, Stockwell BR. Development of optimized drug-like small molecule inhibitors of the SARS-CoV-2 3CL protease for treatment of COVID-19. Nat Commun 2022; 13:1891. [PMID: 35393402 PMCID: PMC8989888 DOI: 10.1038/s41467-022-29413-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 03/14/2022] [Indexed: 11/29/2022] Open
Abstract
The SARS-CoV-2 3CL protease is a critical drug target for small molecule COVID-19 therapy, given its likely druggability and essentiality in the viral maturation and replication cycle. Based on the conservation of 3CL protease substrate binding pockets across coronaviruses and using screening, we identified four structurally distinct lead compounds that inhibit SARS-CoV-2 3CL protease. After evaluation of their binding specificity, cellular antiviral potency, metabolic stability, and water solubility, we prioritized the GC376 scaffold as being optimal for optimization. We identified multiple drug-like compounds with <10 nM potency for inhibiting SARS-CoV-2 3CL and the ability to block SARS-CoV-2 replication in human cells, obtained co-crystal structures of the 3CL protease in complex with these compounds, and determined that they have pan-coronavirus activity. We selected one compound, termed coronastat, as an optimized lead and characterized it in pharmacokinetic and safety studies in vivo. Coronastat represents a new candidate for a small molecule protease inhibitor for the treatment of SARS-CoV-2 infection for eliminating pandemics involving coronaviruses. Small molecule drugs promise to remain a valuable tool in controlling the ongoing COVID-19 pandemic. Here the authors describe optimized drug-like small molecule inhibitors of the SARS-CoV-2 3CL protease for potential treatment of COVID-19.
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Affiliation(s)
- Hengrui Liu
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - Sho Iketani
- Aaron Diamond AIDS Research Center, Columbia University Irving Medical Center, New York, NY, 10032, USA.,Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Arie Zask
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Nisha Khanizeman
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - Eva Bednarova
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - Farhad Forouhar
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Brandon Fowler
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - Seo Jung Hong
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Hiroshi Mohri
- Aaron Diamond AIDS Research Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Manoj S Nair
- Aaron Diamond AIDS Research Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Yaoxing Huang
- Aaron Diamond AIDS Research Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Nicholas E S Tay
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - Sumin Lee
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - Charles Karan
- Sulzberger Columbia Genome Center, Columbia University, New York, NY, 10032, USA
| | - Samuel J Resnick
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA.,Medical Scientist Training Program, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Colette Quinn
- Waters Corporation, 34 Maple Street, Milford, MA, 01757, USA
| | - Wenjing Li
- Waters Corporation, 34 Maple Street, Milford, MA, 01757, USA
| | - Henry Shion
- Waters Corporation, 34 Maple Street, Milford, MA, 01757, USA
| | - Xin Xia
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Jacob D Daniels
- Department of Pharmacology and Molecular Therapeutics, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | | | - Marcelo Farina
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA.,Department of Biochemistry, Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Presha Rajbhandari
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | | | | | - Thomas McDonald
- Waters Corporation, 34 Maple Street, Milford, MA, 01757, USA
| | - Michael E Stokes
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Brett L Hurst
- Institute for Antiviral Research, Utah State University, Logan, UT, 84322, USA
| | - Tomislav Rovis
- Department of Chemistry, Columbia University, New York, NY, 10027, USA.
| | - Alejandro Chavez
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA.
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Irving Medical Center, New York, NY, 10032, USA.
| | - Brent R Stockwell
- Department of Chemistry, Columbia University, New York, NY, 10027, USA. .,Department of Biological Sciences, Columbia University, New York, NY, 10027, USA.
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14
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Gholivand K, Mohammadpanah F, Pooyan M, Roohzadeh R. Evaluating anti-coronavirus activity of some phosphoramides and their influencing inhibitory factors using molecular docking, DFT, QSAR, and NCI-RDG studies. J Mol Struct 2022; 1248:131481. [PMID: 34538931 PMCID: PMC8435241 DOI: 10.1016/j.molstruc.2021.131481] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 12/26/2022]
Abstract
The recent prevalence of coronavirus disease in 2019 (COVID-19) has triggered widespread global health concerns.Antiviral drugs based on phosphoramides have significant inhibitory activity against the main protease (Mpro) of the virus and prevent transcription and viral replication. Hence, in order to design and introduce a group of inhibitors affecting the coronavirus, 35 phosphoramide compounds based on phospho-guanine and phospho-pyrazine derivatives were selected for molecular docking study. The results showed that most phosphoguanides containing the amino benzimidazole have a high interaction tendency with COVID-19. Among them, compound 19 was identified as the strongest inhibitor with the -9.570 kcal/mol binding energy whereas, the binding energy of Remdesivir is -6.75 kcal/mol. The quantitative structure-activity relationship (QSAR) results demonstrated that the number of aromatic rings, amide's nitrogens and their ability in π-staking, and hydrogen interactions with Mpro active sites are major factors contributing to the inhibitory activity of these compounds.Also, the NCI-RDG and DFT results were in good accordance with those of QSAR and molecular docking. The findings of this investigation can be underlying the synthesis of effective and efficient drugs against COVID-19.
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Affiliation(s)
- Khodayar Gholivand
- Department of Chemistry, Faculty of Science, Tarbiat Modares University, Tehran, Iran
| | - Fahimeh Mohammadpanah
- Department of Chemistry, Faculty of Science, Tarbiat Modares University, Tehran, Iran
| | - Mahsa Pooyan
- Department of Chemistry, Faculty of Science, Tarbiat Modares University, Tehran, Iran
| | - Roohollah Roohzadeh
- Department of Chemistry, Faculty of Science, Tarbiat Modares University, Tehran, Iran
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15
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Hasegawa T, Imamura RM, Suzuki T, Hashiguchi T, Nomura T, Otsuguro S, Maenaka K, Sasaki M, Orba Y, Sawa H, Sato A, Okabe T, Nagano T, Kojima H. Application of Acoustic Ejection MS System to High-Throughput Screening for SARS-CoV-2 3CL Protease Inhibitors. Chem Pharm Bull (Tokyo) 2021; 70:199-201. [PMID: 34937844 DOI: 10.1248/cpb.c21-01003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Mass spectrometry is a powerful methodology for chemical screening to directly quantify substrates and products of enzymes, but its low throughput has been an issue. Recently, an acoustic liquid-handling apparatus (Echo®) used for rapid nano-dispensing has been coupled to a high-sensitivity mass spectrometer to create the Echo® MS system, and we applied this system to screening of SARS-CoV-2 3CL protease inhibitors. Primary screening of 32,033 chemical samples was completed in 12 hours. Among the hits showing selective, dose-dependent 3CL-inhibitory activity, 8 compounds showed antiviral activity in cell-based assay.
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Affiliation(s)
| | | | - Tateki Suzuki
- Institute for Frontier Life and Medical Sciences, Kyoto University
| | - Takao Hashiguchi
- Institute for Frontier Life and Medical Sciences, Kyoto University
| | - Takao Nomura
- Faculty of Pharmaceutical Sciences, Hokkaido University
| | | | | | - Michihito Sasaki
- International Institute for Zoonosis Control, Hokkaido University
| | - Yasuko Orba
- International Institute for Zoonosis Control, Hokkaido University
| | - Hirofumi Sawa
- International Institute for Zoonosis Control, Hokkaido University
| | - Akihiko Sato
- International Institute for Zoonosis Control, Hokkaido University.,Drug Discovery and Disease Research Laboratory, Shionogi & Co., Ltd
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16
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Abstract
The main protease (Mpro) plays a crucial role in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication and is highly conserved, rendering it one of the most attractive therapeutic targets for SARS-CoV-2 inhibition. Currently, although two drug candidates targeting SARS-CoV-2 Mpro designed by Pfizer are under clinical trials, no SARS-CoV-2 medication is approved due to the long period of drug development. Here, we collect a comprehensive list of 817 available SARS-CoV-2 and SARS-CoV Mpro inhibitors from the literature or databases and analyze their molecular mechanisms of action. The structure-activity relationships (SARs) among each series of inhibitors are discussed. Additionally, we broadly examine available antiviral activity, ADMET (absorption, distribution, metabolism, excretion, and toxicity), and animal tests of these inhibitors. We comment on their druggability or drawbacks that prevent them from becoming drugs. This Perspective sheds light on the future development of Mpro inhibitors for SARS-CoV-2 and future coronavirus diseases.
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Affiliation(s)
- Kaifu Gao
- Department of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Rui Wang
- Department of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Jiahui Chen
- Department of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Jetze J Tepe
- Department of Chemistry and Pharmacology & Toxicology, Michigan State University, East Lansing, Michigan 48824, United States
| | - Faqing Huang
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, Mississippi 39406, United States
| | - Guo-Wei Wei
- Department of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
- Department of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan 48824, United States
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17
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Yan G, Li D, Lin Y, Fu Z, Qi H, Liu X, Zhang J, Si S, Chen Y. Development of a simple and miniaturized sandwich-like fluorescence polarization assay for rapid screening of SARS-CoV-2 main protease inhibitors. Cell Biosci 2021; 11:199. [PMID: 34865653 PMCID: PMC8645223 DOI: 10.1186/s13578-021-00720-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/19/2021] [Indexed: 12/14/2022] Open
Abstract
Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is highly transmissible and has caused a pandemic named coronavirus disease 2019 (COVID-19), which has quickly spread worldwide. Although several therapeutic agents have been evaluated or approved for the treatment of COVID-19 patients, efficacious antiviral agents are still lacking. An attractive therapeutic target for SARS-CoV-2 is the main protease (Mpro), as this highly conserved enzyme plays a key role in viral polyprotein processing and genomic RNA replication. Therefore, the identification of efficacious antiviral agents against SARS-CoV-2 Mpro using a rapid, miniaturized and economical high-throughput screening (HTS) assay is of the highest importance at the present. Results In this study, we first combined the fluorescence polarization (FP) technique with biotin-avidin system (BAS) to develop a novel and step-by-step sandwich-like FP screening assay to quickly identify SARS-CoV-2 Mpro inhibitors from a natural product library. Using this screening assay, dieckol, a natural phlorotannin component extracted from a Chinese traditional medicine Ecklonia cava, was identified as a novel competitive inhibitor against SARS-CoV-2 Mpro in vitro with an IC50 value of 4.5 ± 0.4 µM. Additionally, dieckol exhibited a high affinity with SARS-CoV-2 Mpro using surface plasmon resonance (SPR) analysis and could bind to the catalytic sites of Mpro through hydrogen-bond interactions in the predicted docking model. Conclusions This innovative sandwich-like FP screening assay enables the rapid discovery of antiviral agents targeting viral proteases, and dieckol will be an excellent lead compound for generating more potent and selective antiviral agents targeting SARS-CoV-2 Mpro.
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Affiliation(s)
- Gangan Yan
- Institute for Drug Screening and Evaluation, Wannan Medical College, 241002, Wuhu, China
| | - Dongsheng Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100050, Beijing, China
| | - Yuan Lin
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, 100050, Beijing, China
| | - Zhenghao Fu
- Institute for Drug Screening and Evaluation, Wannan Medical College, 241002, Wuhu, China
| | - Haiyan Qi
- Institute for Drug Screening and Evaluation, Wannan Medical College, 241002, Wuhu, China
| | - Xiaoping Liu
- Institute for Drug Screening and Evaluation, Wannan Medical College, 241002, Wuhu, China
| | - Jing Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100050, Beijing, China.
| | - Shuyi Si
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100050, Beijing, China.
| | - Yunyu Chen
- Institute for Drug Screening and Evaluation, Wannan Medical College, 241002, Wuhu, China. .,Anhui Provincial Engineering Laboratory for Screening and Reevaluation of Bioactive Compounds of Herbal Medicines in Southern Anhui, Wannan Medical College, 241002, Wuhu, China.
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18
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Franko N, Teixeira AP, Xue S, Charpin-El Hamri G, Fussenegger M. Design of modular autoproteolytic gene switches responsive to anti-coronavirus drug candidates. Nat Commun 2021; 12:6786. [PMID: 34811361 PMCID: PMC8609006 DOI: 10.1038/s41467-021-27072-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 10/20/2021] [Indexed: 11/28/2022] Open
Abstract
The main (Mpro) and papain-like (PLpro) proteases encoded by SARS-CoV-2 are essential to process viral polyproteins into functional units, thus representing key targets for anti-viral drug development. There is a need for an efficient inhibitor screening system that can identify drug candidates in a cellular context. Here we describe modular, tunable autoproteolytic gene switches (TAGS) relying on synthetic transcription factors that self-inactivate, unless in the presence of coronavirus protease inhibitors, consequently activating transgene expression. TAGS rapidly report the impact of drug candidates on Mpro and PLpro activities with a high signal-to-noise response and a sensitivity matching concentration ranges inhibiting viral replication. The modularity of the TAGS enabled the study of other Coronaviridae proteases, characterization of mutations and multiplexing of gene switches in human cells. Mice implanted with Mpro or PLpro TAGS-engineered cells enabled analysis of the activity and bioavailability of protease inhibitors in vivo in a virus-free setting.
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Affiliation(s)
- Nik Franko
- ETH Zurich, Department of Biosystems Science and Engineering, Mattenstrasse 26, CH-4058, Basel, Switzerland
| | - Ana Palma Teixeira
- ETH Zurich, Department of Biosystems Science and Engineering, Mattenstrasse 26, CH-4058, Basel, Switzerland
| | - Shuai Xue
- ETH Zurich, Department of Biosystems Science and Engineering, Mattenstrasse 26, CH-4058, Basel, Switzerland
| | - Ghislaine Charpin-El Hamri
- Département Génie Biologique, Institut Universitaire de Technologie, Université Claude Bernard Lyon 1, F-69622, Villeurbanne, Cedex, France
| | - Martin Fussenegger
- ETH Zurich, Department of Biosystems Science and Engineering, Mattenstrasse 26, CH-4058, Basel, Switzerland.
- University of Basel, Faculty of Life Science, Basel, Switzerland.
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19
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Ghosh AK, Raghavaiah J, Shahabi D, Yadav M, Anson BJ, Lendy EK, Hattori SI, Higashi-Kuwata N, Mitsuya H, Mesecar AD. Indole Chloropyridinyl Ester-Derived SARS-CoV-2 3CLpro Inhibitors: Enzyme Inhibition, Antiviral Efficacy, Structure-Activity Relationship, and X-ray Structural Studies. J Med Chem 2021; 64:14702-14714. [PMID: 34528437 PMCID: PMC8457330 DOI: 10.1021/acs.jmedchem.1c01214] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Indexed: 12/31/2022]
Abstract
Here, we report the synthesis, structure-activity relationship studies, enzyme inhibition, antiviral activity, and X-ray crystallographic studies of 5-chloropyridinyl indole carboxylate derivatives as a potent class of SARS-CoV-2 chymotrypsin-like protease inhibitors. Compound 1 exhibited a SARS-CoV-2 3CLpro inhibitory IC50 value of 250 nM and an antiviral EC50 value of 2.8 μM in VeroE6 cells. Remdesivir, an RNA-dependent RNA polymerase inhibitor, showed an antiviral EC50 value of 1.2 μM in the same assay. Compound 1 showed comparable antiviral activity with remdesivir in immunocytochemistry assays. Compound 7d with an N-allyl derivative showed the most potent enzyme inhibitory IC50 value of 73 nM. To obtain molecular insight into the binding properties of these molecules, X-ray crystal structures of compounds 2, 7b, and 9d-bound to SARS-CoV 3CLpro were determined, and their binding properties were compared.
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Affiliation(s)
- Arun K. Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Jakka Raghavaiah
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Dana Shahabi
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Monika Yadav
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Brandon J. Anson
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Emma K. Lendy
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Shin-ichiro Hattori
- Departments of Hematology and Infectious Diseases, Kumamoto University School of Medicine, Kumamoto 860-8556, Japan
| | - Nobuyo Higashi-Kuwata
- Departments of Hematology and Infectious Diseases, Kumamoto University School of Medicine, Kumamoto 860-8556, Japan
| | - Hiroaki Mitsuya
- Departments of Hematology and Infectious Diseases, Kumamoto University School of Medicine, Kumamoto 860-8556, Japan
- Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, MD 20892
- Department of Refractory Viral Infections, National Center for Global Health and Medicine Research Institute, Shinjuku, Tokyo 162-8655, Japan
| | - Andrew D. Mesecar
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
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20
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Kleandrova VV, Scotti MT, Speck-Planche A. Indirect-Acting Pan-Antivirals vs. Respiratory Viruses: A Fresh Perspective on Computational Multi-Target Drug Discovery. Curr Top Med Chem 2021; 21:2687-2693. [PMID: 34636311 DOI: 10.2174/1568026621666211012110819] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/23/2021] [Accepted: 09/23/2021] [Indexed: 12/22/2022]
Abstract
Respiratory viruses continue to afflict mankind. Among them, pathogens such as coronaviruses [including the current pandemic agent known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)] and the one causing influenza A (IAV) are highly contagious and deadly. These can evade the immune system defenses while causing a hyperinflammatory response that can damage different tissues/organs. Simultaneously targeting immunomodulatory proteins is a plausible antiviral strategy since it could lead to the discovery of indirect-acting pan-antiviral (IAPA) agents for the treatment of diseases caused by respiratory viruses. In this context, computational approaches, which are an essential part of the modern drug discovery campaigns, could accelerate the identification of multi-target immunomodulators. This perspective discusses the usefulness of computational multi-target drug discovery for the virtual screening (drug repurposing) of IAPA agents capable of boosting the immune system through the activation of the toll-like receptor 7 (TLR7) and/or the stimulator of interferon genes (STING) while inhibiting key pro-inflammatory proteins, such as caspase-1 and tumor necrosis factor-alpha (TNF-α).
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Affiliation(s)
- Valeria V Kleandrova
- Laboratory of Fundamental and Applied Research of Quality and Technology of Food Production, Moscow State University of Food Production, Volokolamskoe shosse 11, 125080, Moscow. Russian Federation
| | - Marcus T Scotti
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, 58051-900, João Pessoa. Brazil
| | - Alejandro Speck-Planche
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, 58051-900, João Pessoa. Brazil
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21
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Ghosh AK, Shahabi D, Yadav M, Kovela S, Anson BJ, Lendy EK, Bonham C, Sirohi D, Brito-Sierra CA, Hattori SI, Kuhn R, Mitsuya H, Mesecar AD. Chloropyridinyl Esters of Nonsteroidal Anti-Inflammatory Agents and Related Derivatives as Potent SARS-CoV-2 3CL Protease Inhibitors. Molecules 2021; 26:5782. [PMID: 34641337 PMCID: PMC8510097 DOI: 10.3390/molecules26195782] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/16/2021] [Accepted: 09/20/2021] [Indexed: 12/14/2022] Open
Abstract
We report the design and synthesis of a series of new 5-chloropyridinyl esters of salicylic acid, ibuprofen, indomethacin, and related aromatic carboxylic acids for evaluation against SARS-CoV-2 3CL protease enzyme. These ester derivatives were synthesized using EDC in the presence of DMAP to provide various esters in good to excellent yields. Compounds are stable and purified by silica gel chromatography and characterized using 1H-NMR, 13C-NMR, and mass spectral analysis. These synthetic derivatives were evaluated in our in vitro SARS-CoV-2 3CLpro inhibition assay using authentic SARS-CoV-2 3CLpro enzyme. Compounds were also evaluated in our in vitro antiviral assay using quantitative VeroE6 cell-based assay with RNAqPCR. A number of compounds exhibited potent SARS-CoV-2 3CLpro inhibitory activity and antiviral activity. Compound 9a was the most potent inhibitor, with an enzyme IC50 value of 160 nM. Compound 13b exhibited an enzyme IC50 value of 4.9 µM. However, it exhibited a potent antiviral EC50 value of 24 µM in VeroE6 cells. Remdesivir, an RdRp inhibitor, exhibited an antiviral EC50 value of 2.4 µM in the same assay. We assessed the mode of inhibition using mass spectral analysis which suggested the formation of a covalent bond with the enzyme. To obtain molecular insight, we have created a model of compound 9a bound to SARS-CoV-2 3CLpro in the active site.
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Affiliation(s)
- Arun K. Ghosh
- Department of Chemistry; Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA; (D.S.); (M.Y.); (S.K.)
| | - Dana Shahabi
- Department of Chemistry; Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA; (D.S.); (M.Y.); (S.K.)
| | - Monika Yadav
- Department of Chemistry; Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA; (D.S.); (M.Y.); (S.K.)
| | - Satish Kovela
- Department of Chemistry; Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA; (D.S.); (M.Y.); (S.K.)
| | - Brandon J. Anson
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; (B.J.A.); (D.S.); (C.A.B.-S.); (R.K.); (A.D.M.)
| | - Emma K. Lendy
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA; (E.K.L.)
| | - Connie Bonham
- Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907, USA;
| | - Devika Sirohi
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; (B.J.A.); (D.S.); (C.A.B.-S.); (R.K.); (A.D.M.)
- Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN 47907, USA
| | - Carlos A. Brito-Sierra
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; (B.J.A.); (D.S.); (C.A.B.-S.); (R.K.); (A.D.M.)
- Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN 47907, USA
| | - Shin-ichiro Hattori
- Departments of Hematology and Infectious Diseases, Kumamoto University School of Medicine, Kumamoto 860-8556, Japan; (S.-i.H.); (H.M.)
- Department of Refractory Viral Infections, National Center for Global Health and Medicine Research Institute, Tokyo 162-8655, Japan
| | - Richard Kuhn
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; (B.J.A.); (D.S.); (C.A.B.-S.); (R.K.); (A.D.M.)
- Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN 47907, USA
| | - Hiroaki Mitsuya
- Departments of Hematology and Infectious Diseases, Kumamoto University School of Medicine, Kumamoto 860-8556, Japan; (S.-i.H.); (H.M.)
- Department of Refractory Viral Infections, National Center for Global Health and Medicine Research Institute, Tokyo 162-8655, Japan
- Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | - Andrew D. Mesecar
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; (B.J.A.); (D.S.); (C.A.B.-S.); (R.K.); (A.D.M.)
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA; (E.K.L.)
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22
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Khater I, Nassar A. In silico molecular docking analysis for repurposing approved antiviral drugs against SARS-CoV-2 main protease. Biochem Biophys Rep 2021; 27:101032. [PMID: 34099985 PMCID: PMC8173495 DOI: 10.1016/j.bbrep.2021.101032] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 11/30/2022] Open
Abstract
Developing a safe and effective antiviral treatment takes a decade, however, when it comes to the coronavirus disease (COVID-19), time is a sensitive matter to slow the spread of the pandemic. Screening approved antiviral drugs against COVID-19 would speed the process of finding therapeutic treatment. The current study examines commercially approved drugs to repurpose them against COVID-19 virus main protease using structure-based in-silico screening. The main protease of the coronavirus is essential in the viral replication and is involved in polyprotein cleavage and immune regulation, making it an effective target when developing the treatment. A Number of approved antiviral drugs were tested against COVID-19 virus using molecular docking analysis by calculating the free natural affinity of the binding ligand to the active site pocket and the catalytic residues without forcing the docking of the ligand to active site. COVID-19 virus protease solved structure (PDB ID: 6LU7) is targeted by repurposed drugs. The molecular docking analysis results have shown that the binding of Remdesivir and Mycophenolic acid acyl glucuronide with the protein drug target has optimal binding features supporting that Remdesivir and Mycophenolic acid acyl glucuronide can be used as potential anti-viral treatment against COVID-19 disease.
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Affiliation(s)
- Ibrahim Khater
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Aaya Nassar
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
- Department of Clinical Research and Leadership, School of Medicine and Health Sciences, George Washington University, Washington DC, USA
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23
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Sutanto F, Shaabani S, Oerlemans R, Eris D, Patil P, Hadian M, Wang M, Sharpe ME, Groves MR, Dömling A. Combining High-Throughput Synthesis and High-Throughput Protein Crystallography for Accelerated Hit Identification. Angew Chem Int Ed Engl 2021; 60:18231-18239. [PMID: 34097796 PMCID: PMC8456925 DOI: 10.1002/anie.202105584] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 05/31/2021] [Indexed: 12/24/2022]
Abstract
Protein crystallography (PX) is widely used to drive advanced stages of drug optimization or to discover medicinal chemistry starting points by fragment soaking. However, recent progress in PX could allow for a more integrated role into early drug discovery. Here, we demonstrate for the first time the interplay of high throughput synthesis and high throughput PX. We describe a practical multicomponent reaction approach to acrylamides and -esters from diverse building blocks suitable for mmol scale synthesis on 96-well format and on a high-throughput nanoscale format in a highly automated fashion. High-throughput PX of our libraries efficiently yielded potent covalent inhibitors of the main protease of the COVID-19 causing agent, SARS-CoV-2. Our results demonstrate, that the marriage of in situ HT synthesis of (covalent) libraires and HT PX has the potential to accelerate hit finding and to provide meaningful strategies for medicinal chemistry projects.
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Affiliation(s)
- Fandi Sutanto
- University of GroningenDepartment of Drug DesignA. Deusinglaan 19713AVGroningenThe Netherlands
| | - Shabnam Shaabani
- University of GroningenDepartment of Drug DesignA. Deusinglaan 19713AVGroningenThe Netherlands
| | - Rick Oerlemans
- University of GroningenDepartment of Drug DesignA. Deusinglaan 19713AVGroningenThe Netherlands
| | - Deniz Eris
- Photon Science DivisionPaul Scherrer InstituteSwitzerland
| | - Pravin Patil
- University of GroningenDepartment of Drug DesignA. Deusinglaan 19713AVGroningenThe Netherlands
| | - Mojgan Hadian
- University of GroningenDepartment of Drug DesignA. Deusinglaan 19713AVGroningenThe Netherlands
| | - Meitian Wang
- Photon Science DivisionPaul Scherrer InstituteSwitzerland
| | | | - Matthew R. Groves
- University of GroningenDepartment of Drug DesignA. Deusinglaan 19713AVGroningenThe Netherlands
| | - Alexander Dömling
- University of GroningenDepartment of Drug DesignA. Deusinglaan 19713AVGroningenThe Netherlands
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24
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Sutanto F, Shaabani S, Oerlemans R, Eris D, Patil P, Hadian M, Wang M, Sharpe ME, Groves MR, Dömling A. Combining High‐Throughput Synthesis and High‐Throughput Protein Crystallography for Accelerated Hit Identification. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202105584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Fandi Sutanto
- University of Groningen Department of Drug Design A. Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Shabnam Shaabani
- University of Groningen Department of Drug Design A. Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Rick Oerlemans
- University of Groningen Department of Drug Design A. Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Deniz Eris
- Photon Science Division Paul Scherrer Institute Switzerland
| | - Pravin Patil
- University of Groningen Department of Drug Design A. Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Mojgan Hadian
- University of Groningen Department of Drug Design A. Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Meitian Wang
- Photon Science Division Paul Scherrer Institute Switzerland
| | | | - Matthew R. Groves
- University of Groningen Department of Drug Design A. Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Alexander Dömling
- University of Groningen Department of Drug Design A. Deusinglaan 1 9713 AV Groningen The Netherlands
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25
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Abstract
CoVID-19 is a multi-symptomatic disease which has made a global impact due to its ability to spread rapidly, and its relatively high mortality rate. Beyond the heroic efforts to develop vaccines, which we do not discuss herein, the response of scientists and clinicians to this complex problem has reflected the need to detect CoVID-19 rapidly, to diagnose patients likely to show adverse symptoms, and to treat severe and critical CoVID-19. Here we aim to encapsulate these varied and sometimes conflicting approaches and the resulting data in terms of chemistry and biology. In the process we highlight emerging concepts, and potential future applications that may arise out of this immense effort.
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Affiliation(s)
| | - Yimon Aye
- Swiss Federal Institute of Technology in Lausanne (EPFL)1015LausanneSwitzerland
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26
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Marjomäki V, Kalander K, Hellman M, Permi P. Enteroviruses and coronaviruses: similarities and therapeutic targets. Expert Opin Ther Targets 2021; 25:479-489. [PMID: 34253126 PMCID: PMC8330013 DOI: 10.1080/14728222.2021.1952985] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Introduction: Enteroviruses are common viruses causing a huge number of acute and chronic infections and producing towering economic costs. Similarly, coronaviruses cause seasonal mild infections, epidemics, and even pandemics and can lead to severe respiratory symptoms. It is important to develop broadly acting antiviral molecules to efficiently tackle the infections caused by thes.Areas covered: This review illuminates the differences and similarities between enteroviruses and coronaviruses and examines the most appealing therapeutic targets to combat both virus groups. Publications of both virus groups and deposited structures discovered through PubMed to March 2021 for viral proteases have been evaluated.Expert opinion: The main protease of coronaviruses and enteroviruses share similarities in their structure and function. These proteases process their viral polyproteins and thus drugs that bind to the active site have potential to target both virus groups. It is important to develop drugs that target more evolutionarily conserved processes and proteins. Moreover, it is a wise strategy to concentrate on processes that are similar between several virus families.
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Affiliation(s)
- Varpu Marjomäki
- Department of Biological and Environmental Science/Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Kerttu Kalander
- Department of Biological and Environmental Science/Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Maarit Hellman
- Department of Biological and Environmental Science/Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Perttu Permi
- Department of Biological and Environmental Science/Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
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27
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Synthetic and computational efforts towards the development of peptidomimetics and small-molecule SARS-CoV 3CLpro inhibitors. Bioorg Med Chem 2021; 46:116301. [PMID: 34332853 PMCID: PMC8254399 DOI: 10.1016/j.bmc.2021.116301] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 06/25/2021] [Accepted: 06/27/2021] [Indexed: 12/24/2022]
Abstract
Severe Acute Respiratory Syndrome (SARS) is a severe febrile respiratory disease caused by the beta genus of human coronavirus, known as SARS-CoV. Last year, 2019-n-CoV (COVID-19) was a global threat for everyone caused by the outbreak of SARS-CoV-2. 3CLpro, chymotrypsin-like protease, is a major cysteine protease that substantially contributes throughout the viral life cycle of SARS-CoV and SARS-CoV-2. It is a prospective target for the development of SARS-CoV inhibitors by applying a repurposing strategy. This review focuses on a detailed overview of the chemical synthesis and computational chemistry perspectives of peptidomimetic inhibitors (PIs) and small-molecule inhibitors (SMIs) targeting viral proteinase discovered from 2004 to 2020. The PIs and SMIs are one of the primary therapeutic inventions for SARS-CoV. The journey of different analogues towards the evolution of SARS-CoV 3CLpro inhibitors and complete synthetic preparation of nineteen derivatives of PIs and ten derivatives of SMIs and their computational chemistry perspectives were reviewed. From each class of derivatives, we have identified and highlighted the most compelling PIs and SMIs for SARS-CoV 3CLpro. The protein-ligand interaction of 29 inhibitors were also studied that involved with the 3CLpro inhibition, and the frequent amino acid residues of the protease were also analyzed that are responsible for the interactions with the inhibitors. This work will provide an initiative to encourage further research for the development of effective and drug-like 3CLpro inhibitors against coronaviruses in the near future.
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28
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Cava C, Bertoli G, Castiglioni I. Potential drugs against COVID-19 revealed by gene expression profile, molecular docking and molecular dynamic simulation. Future Virol 2021; 16:10.2217/fvl-2020-0392. [PMID: 34306168 PMCID: PMC8293696 DOI: 10.2217/fvl-2020-0392] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 06/30/2021] [Indexed: 02/07/2023]
Abstract
Aim: SARS-CoV-2, an emerging betacoronavirus, is the causative agent of COVID-19. Currently, there are few specific and selective antiviral drugs for the treatment and vaccines to prevent contagion. However, their long-term effects can be revealed after several years, and new drugs for COVID-19 should continue to be investigated. Materials & methods: In the first step of our study we identified, through a gene expression analysis, several drugs that could act on the biological pathways altered in COVID-19. In the second step, we performed a docking simulation to test the properties of the identified drugs to target SARS-CoV-2. Results: The drugs that showed a higher binding affinity are bardoxolone (-8.78 kcal/mol), irinotecan (-8.40 kcal/mol) and pyrotinib (-8.40 kcal/mol). Conclusion: We suggested some drugs that could be efficient in treating COVID-19.
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Affiliation(s)
- Claudia Cava
- Institute of Molecular Bioimaging & Physiology, National Research Council (IBFM-CNR), Via F. Cervi 93, Segrate-Milan, Milan, 20090, Italy
| | - Gloria Bertoli
- Institute of Molecular Bioimaging & Physiology, National Research Council (IBFM-CNR), Via F. Cervi 93, Segrate-Milan, Milan, 20090, Italy
| | - Isabella Castiglioni
- Department of Physics “Giuseppe Occhialini”, University of Milan-Bicocca Piazza dell'Ateneo Nuovo, Milan, 20126, Italy
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29
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Niesor EJ, Boivin G, Rhéaume E, Shi R, Lavoie V, Goyette N, Picard ME, Perez A, Laghrissi-Thode F, Tardif JC. Inhibition of the 3CL Protease and SARS-CoV-2 Replication by Dalcetrapib. ACS OMEGA 2021; 6:16584-16591. [PMID: 34235330 PMCID: PMC8230949 DOI: 10.1021/acsomega.1c01797] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 06/08/2021] [Indexed: 06/13/2023]
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) 3CL protease is a promising target for inhibition of viral replication by interaction with a cysteine residue (Cys145) at its catalytic site. Dalcetrapib exerts its lipid-modulating effect by binding covalently to cysteine 13 of a cholesteryl ester transfer protein. Because 12 free cysteine residues are present in the 3CL protease, we investigated the potential of dalcetrapib to inhibit 3CL protease activity and SARS-CoV-2 replication. Molecular docking investigations suggested that dalcetrapib-thiol binds to the catalytic site of the 3CL protease with a delta G value of -8.5 kcal/mol. Dalcetrapib inhibited both 3CL protease activity in vitro and viral replication in Vero E6 cells with IC50 values of 14.4 ± 3.3 μM and an EC50 of 17.5 ± 3.5 μM (mean ± SD). Near-complete inhibition of protease activity persisted despite 1000-fold dilution after ultrafiltration with a nominal dalcetrapib-thiol concentration of approximately 100 times below the IC50 of 14.4 μM, suggesting stable protease-drug interaction. The inhibitory effect of dalcetrapib on the SARS-CoV-2 3CL protease and viral replication warrants its clinical evaluation for the treatment of COVID-19.
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Affiliation(s)
| | - Guy Boivin
- Centre
Hospitalier Universitaire de Québec, Université Laval, Québec
City G1V 0A6, Canada
| | - Eric Rhéaume
- Montreal
Heart Institute, Université de Montréal, Montreal H1T 1C8, Canada
| | - Rong Shi
- Department
of Biochemistry, Microbiology and Bioinformatics, Université Laval, Quebec G1V 0A6, Canada
| | - Véronique Lavoie
- Montreal
Heart Institute, Université de Montréal, Montreal H1T 1C8, Canada
| | - Nathalie Goyette
- Centre
Hospitalier Universitaire de Québec, Université Laval, Québec
City G1V 0A6, Canada
| | - Marie-Eve Picard
- Department
of Biochemistry, Microbiology and Bioinformatics, Université Laval, Quebec G1V 0A6, Canada
| | | | | | - Jean-Claude Tardif
- Montreal
Heart Institute, Université de Montréal, Montreal H1T 1C8, Canada
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30
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Guijarro-Real C, Plazas M, Rodríguez-Burruezo A, Prohens J, Fita A. Potential In Vitro Inhibition of Selected Plant Extracts against SARS-CoV-2 Chymotripsin-Like Protease (3CL Pro) Activity. Foods 2021; 10:1503. [PMID: 34209659 PMCID: PMC8304378 DOI: 10.3390/foods10071503] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/15/2021] [Accepted: 06/22/2021] [Indexed: 12/16/2022] Open
Abstract
Antiviral treatments inhibiting Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication may represent a strategy complementary to vaccination to fight the ongoing Coronavirus disease 19 (COVID-19) pandemic. Molecules or extracts inhibiting the SARS-CoV-2 chymotripsin-like protease (3CLPro) could contribute to reducing or suppressing SARS-CoV-2 replication. Using a targeted approach, we identified 17 plant products that are included in current and traditional cuisines as promising inhibitors of SARS-CoV-2 3CLPro activity. Methanolic extracts were evaluated in vitro for inhibition of SARS-CoV-2 3CLPro activity using a quenched fluorescence resonance energy transfer (FRET) assay. Extracts from turmeric (Curcuma longa) rhizomes, mustard (Brassica nigra) seeds, and wall rocket (Diplotaxis erucoides subsp. erucoides) at 500 µg mL-1 displayed significant inhibition of the 3CLPro activity, resulting in residual protease activities of 0.0%, 9.4%, and 14.9%, respectively. Using different extract concentrations, an IC50 value of 15.74 µg mL-1 was calculated for turmeric extract. Commercial curcumin inhibited the 3CLPro activity, but did not fully account for the inhibitory effect of turmeric rhizomes extracts, suggesting that other components of the turmeric extract must also play a main role in inhibiting the 3CLPro activity. Sinigrin, a major glucosinolate present in mustard seeds and wall rocket, did not have relevant 3CLPro inhibitory activity; however, its hydrolysis product allyl isothiocyanate had an IC50 value of 41.43 µg mL-1. The current study identifies plant extracts and molecules that can be of interest in the search for treatments against COVID-19, acting as a basis for future chemical, in vivo, and clinical trials.
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Affiliation(s)
| | - Mariola Plazas
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, 46022 Valencia, Spain; (C.G.-R.); (A.R.-B.); (J.P.); (A.F.)
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Identification of known drugs as potential SARS-CoV-2 Mpro inhibitors using ligand- and structure-based virtual screening. Future Med Chem 2021; 13:1353-1366. [PMID: 34169729 PMCID: PMC8240648 DOI: 10.4155/fmc-2021-0025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Background: The new coronavirus pandemic has had a significant impact worldwide, and therapeutic treatment for this viral infection is being strongly pursued. Efforts have been undertaken by medicinal chemists to discover molecules or known drugs that may be effective in COVID-19 treatment – in particular, targeting the main protease (Mpro) of the virus. Materials & methods: We have employed an innovative strategy – application of ligand- and structure-based virtual screening – using a special compilation of an approved and diverse set of SARS-CoV-2 crystallographic complexes that was recently published. Results and conclusion: We identified seven drugs with different original indications that might act as potential Mpro inhibitors and may be preferable to other drugs that have been repurposed. These drugs will be experimentally tested to confirm their potential Mpro inhibition and thus their effectiveness against COVID-19.
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Inhibitors of Coronavirus 3CL Proteases Protect Cells from Protease-Mediated Cytotoxicity. J Virol 2021; 95:e0237420. [PMID: 33910954 DOI: 10.1128/jvi.02374-20] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
We describe a mammalian cell-based assay to identify coronavirus 3CL protease (3CLpro) inhibitors. This assay is based on rescuing protease-mediated cytotoxicity and does not require live virus. By enabling the facile testing of compounds across a range of 15 distantly related coronavirus 3CLpro enzymes, we identified compounds with broad 3CLpro-inhibitory activity. We also adapted the assay for use in compound screening and in doing so uncovered additional severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) 3CLpro inhibitors. We observed strong concordance between data emerging from this assay and those obtained from live-virus testing. The reported approach democratizes the testing of 3CLpro inhibitors by developing a simplified method for identifying coronavirus 3CLpro inhibitors that can be used by the majority of laboratories, rather than the few with extensive biosafety infrastructure. We identified two lead compounds, GC376 and compound 4, with broad activity against all 3CL proteases tested, including 3CLpro enzymes from understudied zoonotic coronaviruses. IMPORTANCE Multiple coronavirus pandemics have occurred over the last 2 decades. This has highlighted a need to be proactive in the development of therapeutics that can be readily deployed in the case of future coronavirus pandemics. We developed and validated a simplified cell-based assay for the identification of chemical inhibitors of 3CL proteases encoded by a wide range of coronaviruses. This assay is reporter free, does not require specialized biocontainment, and is optimized for performance in high-throughput screening. By testing reported 3CL protease inhibitors against a large collection of 3CL proteases with variable sequence similarity, we identified compounds with broad activity against 3CL proteases and uncovered structural insights into features that contribute to their broad activity. Furthermore, we demonstrated that this assay is suitable for identifying chemical inhibitors of proteases from families other than 3CL proteases.
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Hu Z, Lin J, Chen J, Cai T, Xia L, Liu Y, Song X, He Z. Overview of Viral Pneumonia Associated With Influenza Virus, Respiratory Syncytial Virus, and Coronavirus, and Therapeutics Based on Natural Products of Medicinal Plants. Front Pharmacol 2021; 12:630834. [PMID: 34234668 PMCID: PMC8256264 DOI: 10.3389/fphar.2021.630834] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 05/19/2021] [Indexed: 01/29/2023] Open
Abstract
Viral pneumonia has been a serious threat to global health, especially now we have dramatic challenges such as the COVID-19 pandemic. Approximately six million cases of community-acquired pneumonia occur every year, and over 20% of which need hospital admission. Influenza virus, respiratory virus, and coronavirus are the noteworthy causative agents to be investigated based on recent clinical research. Currently, anaphylactic reaction and inflammation induced by antiviral immunity can be incriminated as causative factors for clinicopathological symptoms of viral pneumonia. In this article, we illustrate the structure and related infection mechanisms of these viruses and the current status of antiviral therapies. Owing to a set of antiviral regiments with unsatisfactory clinical effects resulting from side effects, genetic mutation, and growing incidence of resistance, much attention has been paid on medicinal plants as a natural source of antiviral agents. Previous research mainly referred to herbal medicines and plant extracts with curative effects on viral infection models of influenza virus, respiratory virus, and coronavirus. This review summarizes the results of antiviral activities of various medicinal plants and their isolated substances, exclusively focusing on natural products for the treatment of the three types of pathogens that elicit pneumonia. Furthermore, we have introduced several useful screening tools to develop antiviral lead compounds.
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Affiliation(s)
- Ziwei Hu
- School of Basic Medicine, School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen, China
| | - Jinhong Lin
- School of Basic Medicine, School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen, China
| | - Jintao Chen
- School of Basic Medicine, School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen, China
| | - Tengxi Cai
- School of Basic Medicine, School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen, China
| | - Lixin Xia
- School of Basic Medicine, School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen, China
| | - Ying Liu
- School of Basic Medicine, School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen, China
| | - Xun Song
- School of Basic Medicine, School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen, China
| | - Zhendan He
- School of Basic Medicine, School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen, China.,College of Pharmacy, Shenzhen Technology University, Shenzhen, China
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Dražić T, Kühl N, Leuthold MM, Behnam MA, Klein CD. Efficiency Improvements and Discovery of New Substrates for a SARS-CoV-2 Main Protease FRET Assay. SLAS DISCOVERY 2021; 26:1189-1199. [PMID: 34151620 PMCID: PMC8458682 DOI: 10.1177/24725552211020681] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has a huge impact on the world. Although several vaccines have recently reached the market, the development of specific antiviral drugs against SARS-CoV-2 is an important additional strategy in fighting the pandemic. One of the most promising pharmacological targets is the viral main protease (Mpro). Here, we present an optimized biochemical assay procedure for SARS-CoV-2 Mpro. We have comprehensively investigated the influence of different buffer components and conditions on the assay performance and characterized Förster resonance energy transfer (FRET) substrates with a preference for 2-Abz/Tyr(3-NO2) FRET pairs. The substrates 2-AbzSAVLQSGTyr(3-NO2)R-OH, a truncated version of the established DABCYL/EDANS FRET substrate, and 2-AbzVVTLQSGTyr(3-NO2)R-OH are promising candidates for screening and inhibitor characterization. In the latter substrate, the incorporation of Val at position P5 improved the catalytic efficiency. Based on the obtained results, we present here a reproducible, reliable assay protocol using highly affordable buffer components.
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Affiliation(s)
- Tonko Dražić
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Heidelberg, Germany
| | - Nikos Kühl
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Heidelberg, Germany
| | - Mila M. Leuthold
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Heidelberg, Germany
| | - Mira A.M. Behnam
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Heidelberg, Germany
| | - Christian D. Klein
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Heidelberg, Germany
- Corresponding Author: Christian D. Klein, Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, Heidelberg, 69120, Germany.
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Dos Santos Nascimento IJ, de Aquino TM, da Silva-Júnior EF. Drug Repurposing: A Strategy for Discovering Inhibitors against Emerging Viral Infections. Curr Med Chem 2021; 28:2887-2942. [PMID: 32787752 DOI: 10.2174/0929867327666200812215852] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Viral diseases are responsible for several deaths around the world. Over the past few years, the world has seen several outbreaks caused by viral diseases that, for a long time, seemed to possess no risk. These are diseases that have been forgotten for a long time and, until nowadays, there are no approved drugs or vaccines, leading the pharmaceutical industry and several research groups to run out of time in the search for new pharmacological treatments or prevention methods. In this context, drug repurposing proves to be a fast and economically viable technique, considering the fact that it uses drugs that have a well-established safety profile. Thus, in this review, we present the main advances in drug repurposing and their benefit for searching new treatments against emerging viral diseases. METHODS We conducted a search in the bibliographic databases (Science Direct, Bentham Science, PubMed, Springer, ACS Publisher, Wiley, and NIH's COVID-19 Portfolio) using the keywords "drug repurposing", "emerging viral infections" and each of the diseases reported here (CoV; ZIKV; DENV; CHIKV; EBOV and MARV) as an inclusion/exclusion criterion. A subjective analysis was performed regarding the quality of the works for inclusion in this manuscript. Thus, the selected works were those that presented drugs repositioned against the emerging viral diseases presented here by means of computational, high-throughput screening or phenotype-based strategies, with no time limit and of relevant scientific value. RESULTS 291 papers were selected, 24 of which were CHIKV; 52 for ZIKV; 43 for DENV; 35 for EBOV; 10 for MARV; and 56 for CoV and the rest (72 papers) related to the drugs repurposing and emerging viral diseases. Among CoV-related articles, most were published in 2020 (31 papers), updating the current topic. Besides, between the years 2003 - 2005, 10 articles were created, and from 2011 - 2015, there were 7 articles, portraying the outbreaks that occurred at that time. For ZIKV, similar to CoV, most publications were during the period of outbreaks between the years 2016 - 2017 (23 articles). Similarly, most CHIKV (13 papers) and DENV (14 papers) publications occur at the same time interval. For EBOV (13 papers) and MARV (4 papers), they were between the years 2015 - 2016. Through this review, several drugs were highlighted that can be evolved in vivo and clinical trials as possible used against these pathogens showed that remdesivir represent potential treatments against CoV. Furthermore, ribavirin may also be a potential treatment against CHIKV; sofosbuvir against ZIKV; celgosivir against DENV, and favipiravir against EBOV and MARV, representing new hopes against these pathogens. CONCLUSION The conclusions of this review manuscript show the potential of the drug repurposing strategy in the discovery of new pharmaceutical products, as from this approach, drugs could be used against emerging viral diseases. Thus, this strategy deserves more attention among research groups and is a promising approach to the discovery of new drugs against emerging viral diseases and also other diseases.
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Gurung AB, Al-Anazi KM, Ali MA, Lee J, Farah MA. Identification of novel drug candidates for the inhibition of catalytic cleavage activity of coronavirus 3CL-like protease enzyme. Curr Pharm Biotechnol 2021; 23:959-969. [PMID: 34097590 DOI: 10.2174/1389201022666210604150041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/27/2021] [Accepted: 03/28/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND There has been tremendous pressure on healthcare facilities globally due to the recent emergence of novel coronavirus infections known as COVID-19 and its rapid spread across the continents. The lack of effective therapeutics for the management of the pandemic calls for the discovery of new drugs and vaccines. OBJECTIVE In the present study, a chemical library was screened for molecules against three coronavirus 3CL-like protease enzymes (SARS-CoV-2 3CLpro, SARS-CoV 3CLpro and MERS-CoV 3CLpro), which are a key player in the viral replication cycle. METHODS Extensive computational methods, such as virtual screening and molecular docking, were employed in this study. RESULTS Two lead molecules- ZINC08825480 (4-bromo-N'-{(E)-[1-phenyl-3-(pyridin-3-yl)-1H-pyrazol-4-yl]methylidene}benzene-1-sulfonohydrazide) and ZINC72009942 (N-[[2-[[(3S)-3-methyl-1-piperidyl]methyl]phenyl]methyl]-6-oxo-1-(p-tolyl)-4,5-dihydro-1,2,4-triazine-3-carboxamide) were identified with better affinity with the three target enzymes as compared to the approved antiviral drugs. Both the lead molecules possess favourable drug-like properties, fit well into the active site pocket close to His-Cys dyad and show a good number of hydrogen bonds with the backbone as well as side chains of key amino acid residues. CONCLUSION Thus, the present study offers two novel chemical entities against coronavirus infections, which can be validated through various biological assays.
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Affiliation(s)
- Arun Bahadur Gurung
- Department of Basic Sciences and Social Sciences, North-Eastern Hill University, Shillong 793022, Meghalaya, India
| | - Khalid Mashay Al-Anazi
- Department of Zoology, College of Science, King Saud University, Riyadh-11451, Saudi Arabia
| | - Mohammad Ajmal Ali
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh-11451, Saudi Arabia
| | - Joongku Lee
- Department of Environment and Forest Resources, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134. South Korea
| | - Mohammad Abul Farah
- Department of Zoology, College of Science, King Saud University, Riyadh-11451, Saudi Arabia
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Rocha REO, Chaves EJF, Fischer PHC, Costa LSC, Grillo IB, da Cruz LEG, Guedes FC, da Silveira CH, Scotti MT, Camargo AD, Machado KS, Werhli AV, Ferreira RS, Rocha GB, de Lima LHF. A higher flexibility at the SARS-CoV-2 main protease active site compared to SARS-CoV and its potentialities for new inhibitor virtual screening targeting multi-conformers. J Biomol Struct Dyn 2021; 40:9214-9234. [PMID: 33970798 PMCID: PMC8127201 DOI: 10.1080/07391102.2021.1924271] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 04/26/2021] [Indexed: 12/14/2022]
Abstract
The main-protease (Mpro) catalyzes a crucial step for the SARS-CoV-2 life cycle. The recent SARS-CoV-2 presents the main protease (MCoV2pro) with 12 mutations compared to SARS-CoV (MCoV1pro). Recent studies point out that these subtle differences lead to mobility variances at the active site loops with functional implications. We use metadynamics simulations and a sort of computational analysis to probe the dynamic, pharmacophoric and catalytic environment differences between the monomers of both enzymes. So, we verify how much intrinsic distinctions are preserved in the functional dimer of MCoV2pro, as well as its implications for ligand accessibility and optimized drug screening. We find a significantly higher accessibility to open binding conformers in the MCoV2pro monomer compared to MCoV1pro. A higher hydration propensity for the MCoV2pro S2 loop with the A46S substitution seems to exercise a key role. Quantum calculations suggest that the wider conformations for MCoV2pro are less catalytically active in the monomer. However, the statistics for contacts involving the N-finger suggest higher maintenance of this activity at the dimer. Docking analyses suggest that the ability to vary the active site width can be important to improve the access of the ligand to the active site in different ways. So, we carry out a multiconformational virtual screening with different ligand bases. The results point to the importance of taking into account the protein conformational multiplicity for new promissors anti MCoV2pro ligands. We hope these results will be useful in prospecting, repurposing and/or designing new anti SARS-CoV-2 drugs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rafael E. O. Rocha
- Laboratory of Molecular Modeling and Drug Design, Department of Biochemistry and Imunology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Laboratory of Structural Biology, Department of Molecular Biology, Universität Salzburg, Salzburg, Austria
| | - Elton J. F. Chaves
- Laboratory of Computational and Quantum Chemistry, Department of Chemistry, Universidade Federal da Paraíba, João Pessoa, Brazil
| | - Pedro H. C. Fischer
- Laboratory of Molecular Modeling and Bioinformatics, Department of Exact and Biological Sciences, Universidade Federal de São João Del Rei, Sete Lagoas, Brazil
| | - Leon S. C. Costa
- Comp. Modeling Coordination, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Igor Barden Grillo
- Laboratory of Computational and Quantum Chemistry, Department of Chemistry, Universidade Federal da Paraíba, João Pessoa, Brazil
| | - Luiz E. G. da Cruz
- Laboratory of Computational and Quantum Chemistry, Department of Chemistry, Universidade Federal da Paraíba, João Pessoa, Brazil
| | - Fabiana C. Guedes
- Structural Bioinformatic Laboratory, Institute of Technological Sciences, Universidade Federal de Itajubá, Itabira, Brazil
| | - Carlos H. da Silveira
- Structural Bioinformatic Laboratory, Institute of Technological Sciences, Universidade Federal de Itajubá, Itabira, Brazil
| | - Marcus T. Scotti
- Graduate Program in Natural and Synthetic Bioactive Products; Universidade Federal da Paraíba, João Pessoa, Brazil
| | - Alex D. Camargo
- Computational Biology Laboratory, Center for computational sciences, Universidade Federal do Rio Grande, Rio Grande, Brazil
| | - Karina S. Machado
- Computational Biology Laboratory, Center for computational sciences, Universidade Federal do Rio Grande, Rio Grande, Brazil
| | - Adriano V. Werhli
- Computational Biology Laboratory, Center for computational sciences, Universidade Federal do Rio Grande, Rio Grande, Brazil
| | - Rafaela S. Ferreira
- Laboratory of Molecular Modeling and Drug Design, Department of Biochemistry and Imunology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Gerd B. Rocha
- Laboratory of Computational and Quantum Chemistry, Department of Chemistry, Universidade Federal da Paraíba, João Pessoa, Brazil
| | - Leonardo H. F. de Lima
- Laboratory of Molecular Modeling and Bioinformatics, Department of Exact and Biological Sciences, Universidade Federal de São João Del Rei, Sete Lagoas, Brazil
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Xiong C, Baker D, Pietrantonio PV. A random small molecule library screen identifies novel antagonists of the kinin receptor from the cattle fever tick, Rhipicephalus microplus (Acari: Ixodidae). PEST MANAGEMENT SCIENCE 2021; 77:2238-2251. [PMID: 33415807 DOI: 10.1002/ps.6249] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 12/17/2020] [Accepted: 01/07/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND The southern cattle tick, Rhipicephalus microplus, is a primary vector of the deadly bovine disease babesiosis. Worldwide populations of ticks have developed resistance to acaricides, underscoring the need for novel target discovery for tick control. The arthropod-specific R. microplus kinin receptor is such a target, previously validated by silencing, which resulted in female reproductive fitness costs, including a reduced percentage of eggs hatching. RESULTS In order to identify potent small molecules that bind and activate or inhibit the kinin receptor, a high-throughput screening (HTS) assay was developed using a CHO-K1 cell line expressing the recombinant tick kinin receptor (BMLK3 ). A total of ~20 000 molecules from a random in-house small molecule library were screened in a 'dual-addition' calcium fluorescence assay. This was followed by dose-response validation of the hit molecules identified both from HTS and an in silico screen of ~390 000 molecules. We validated 29 antagonists, 11 of them were full antagonists with IC50 values between 0.67 and 8 μmol L-1 . To explore the structure-activity relationships (SAR) of the small molecules, we tested the activities of seven analogs of the most potent identified antagonist, additionally discovering three full antagonists and four partial antagonists. These three potent antagonists (IC50 < 3.2 μmol L-1 ) were validated in vitro using the recombinant mosquito kinin receptor and showed similar antagonistic activities. In vivo, these three compounds also inhibited the mosquito hindgut contraction rate induced by a myotropic kinin agonist analog 1728. CONCLUSION Antagonists identified in this study could become pesticide leads and are reagents for probing the kinin signaling system. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Caixing Xiong
- Department of Entomology, Texas A&M University, College Station, TX, USA
| | - Dwight Baker
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
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Borkotoky S, Banerjee M, Modi GP, Dubey VK. Identification of high affinity and low molecular alternatives of boceprevir against SARS-CoV-2 main protease: A virtual screening approach. Chem Phys Lett 2021; 770:138446. [PMID: 33623170 PMCID: PMC7892318 DOI: 10.1016/j.cplett.2021.138446] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/06/2021] [Accepted: 02/10/2021] [Indexed: 12/16/2022]
Abstract
SARS-CoV-2 has posed global challenge for healthcare due to COVID-19. The main protease (Mpro) of this virus is considered as a major target for drug development efforts. In this work, we have used virtual screening approach with molecular dynamics simulations to identify high affinity and low molecular weight alternatives of boceprevir, a repurposed drug currently being evaluated against Mpro. Out of 180 compounds screened, two boceprevir analogs (PubChem ID: 57841991 and 58606278) were reported as potential alternatives with comparable predicted protease inhibitor potential and pharmacological properties. Further experimental validation of the reported compounds may contribute to the ongoing investigation of boceprevir.
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Affiliation(s)
- Subhomoi Borkotoky
- School of Biochemical Engineering, Indian Institute of Technology BHU, Varanasi, UP 221005, India
| | - Manidipa Banerjee
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Gyan Prakash Modi
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi, UP 221005, India
| | - Vikash Kumar Dubey
- School of Biochemical Engineering, Indian Institute of Technology BHU, Varanasi, UP 221005, India,Corresponding author
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Seck I, Nguemo F. Triazole, imidazole, and thiazole-based compounds as potential agents against coronavirus. RESULTS IN CHEMISTRY 2021; 3:100132. [PMID: 33907666 PMCID: PMC8061185 DOI: 10.1016/j.rechem.2021.100132] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 04/19/2021] [Indexed: 02/08/2023] Open
Abstract
The expansion of the novel coronavirus known as SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), COVID-19 (coronavirus disease 2019), or 2019-nCoV (2019 novel coronavirus) is a global concern over its pandemic potential. The need for therapeutic alternatives to stop this new pandemic is urgent. Nowadays, no efficacious therapy is available, and vaccines and drugs are underdeveloped to cure or prevent SARS-CoV-2 infections in many countries. Some vaccines candidates have been approved; however, a number of people are still skeptical of this coronavirus vaccines. Probably because of issues related to the quantity of the vaccine and a possible long-term side effects which are still being studied. The previous pandemics of infections caused by coronavirus, such as SARS-CoV in 2003, the Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012, HCoV-229E, and HCoV-OC43 were described in the 1960 s, -HCoV-NL63 isolated in 2004, and HCoV-HKU1identified in 2005 prompted researchers to characterize many compounds against these viruses. Most of them could be potentially active against the currently emerging novel coronavirus. Five membered nitrogen heterocycles with a triazole, imidazole, and thiazole moiety are often found in many bioactive molecules such as coronavirus inhibitors. This present work summarizes to review the biological and structural studies of these compound types as coronavirus inhibitors.
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Affiliation(s)
- Insa Seck
- Department of Chemistry, Faculty of Sciences and Technics, Cheikh Anta Diop University of Dakar, Dakar, Senegal
| | - Filomain Nguemo
- Institute for Neurophysiology, University of Cologne, Cologne, Germany
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Impact of montelukast as add on treatment to the novel coronavirus pneumonia (COVID-19): protocol for an investigator-initiated open labeled randomized controlled pragmatic trial. Porto Biomed J 2021; 6:e134. [PMID: 33869886 PMCID: PMC8049153 DOI: 10.1097/j.pbj.0000000000000134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 11/26/2022] Open
Abstract
Background Montelukast, a safe drug widely use in asthmatic patients, may be an adjuvant in the treatment of Covid-19, either by improving lung injury and inflammation, or by acting as an anti-viral drug. We aim to assess the efficacy and safety of montelukast as add-on treatment in patients with Covid-19. Methods We propose a randomized, controlled, parallel, open-label trial involving 160 hospitalized adult patients with confirmed Covid-19. Patients will be randomly assigned in a 1:1 ratio to receive either montelukast 10 mg, once a day for 14 days, in addition to standard of care (SoC), or SoC alone. SoC will follow the best practice for treating these patients, according to updated recommendations. The primary outcome is time to recovery. Participants will be assessed using diary cards to capture data on treatment-related improvements in an 8-point ordinal scale. Secondary endpoints will include changes in respiratory and inflammatory parameters, and adverse events. This phase IV clinical trial will take place at the University Hospital of São João, Porto. EudraCT number: 2020-001747-21. Results This study intends to generate scientific evidence on efficacy and safety of montelukast as add-on treatment in Covid-19. The results will be essential to improve clinical outcomes which remains to be determined. Conclusion Montelukast has been suggested as a potential drug with 2 main actions on Covid-19. The validation of montelukast as an adjuvant treatment may improve lung injury, inflammation, and symptoms leading to a better prognosis. The use of this drug may fulfil the existing gap on therapeutic options.
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Wen L, Tang K, Chik KKH, Chan CCY, Tsang JOL, Liang R, Cao J, Huang Y, Luo C, Cai JP, Ye ZW, Yin F, Chu H, Jin DY, Yuen KY, Yuan S, Chan JFW. In silico structure-based discovery of a SARS-CoV-2 main protease inhibitor. Int J Biol Sci 2021; 17:1555-1564. [PMID: 33907519 PMCID: PMC8071767 DOI: 10.7150/ijbs.59191] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 03/01/2021] [Indexed: 11/05/2022] Open
Abstract
The Coronavirus Disease 2019 (COVID-19) pandemic caused by the novel lineage B betacoroanvirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in significant mortality, morbidity, and socioeconomic disruptions worldwide. Effective antivirals are urgently needed for COVID-19. The main protease (Mpro) of SARS-CoV-2 is an attractive antiviral target because of its essential role in the cleavage of the viral polypeptide. In this study, we performed an in silico structure-based screening of a large chemical library to identify potential SARS-CoV-2 Mpro inhibitors. Among 8,820 compounds in the library, our screening identified trichostatin A, a histone deacetylase inhibitor and an antifungal compound, as an inhibitor of SARS-CoV-2 Mpro activity and replication. The half maximal effective concentration of trichostatin A against SARS-CoV-2 replication was 1.5 to 2.7µM, which was markedly below its 50% effective cytotoxic concentration (75.7µM) and peak serum concentration (132µM). Further drug compound optimization to develop more stable analogues with longer half-lives should be performed. This structure-based drug discovery platform should facilitate the identification of additional enzyme inhibitors of SARS-CoV-2.
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Affiliation(s)
- Lei Wen
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Kaiming Tang
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Kenn Ka-Heng Chik
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Chris Chun-Yiu Chan
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Jessica Oi-Ling Tsang
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Ronghui Liang
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Jianli Cao
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Yaoqiang Huang
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Cuiting Luo
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Jian-Piao Cai
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Zi-Wei Ye
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Feifei Yin
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, Hainan, China.,Hainan-Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, Hainan, and The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.,Department of Pathogen Biology, Hainan Medical University, Haikou, Hainan, China
| | - Hin Chu
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Dong-Yan Jin
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.,Hainan-Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, Hainan, and The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.,Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China
| | - Shuofeng Yuan
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Jasper Fuk-Woo Chan
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China
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43
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Amin SA, Banerjee S, Gayen S, Jha T. Protease targeted COVID-19 drug discovery: What we have learned from the past SARS-CoV inhibitors? Eur J Med Chem 2021; 215:113294. [PMID: 33618158 PMCID: PMC7880840 DOI: 10.1016/j.ejmech.2021.113294] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 02/06/2021] [Accepted: 02/08/2021] [Indexed: 12/25/2022]
Abstract
The fascinating similarity between the SARS-CoV and SARS-CoV-2, inspires scientific community to investigate deeper into the SARS-CoV proteases such as main protease (Mpro) and papain-like protease (PLpro) and their inhibitors for the discovery of SARS-CoV-2 protease inhibitors. Because of the similarity in the proteases of these two corona viruses, there is a greater chance for the previous SARS-CoV Mpro and PLpro inhibitors to provide effective results against SARS-CoV-2. In this context, the molecular fragments from the SARS-CoV protease inhibitors through the fragment-based drug design and discovery technique can be useful guidance for COVID-19 drug discovery. Here, we have focused on the structure-activity relationship studies of previous SARS-CoV protease inhibitors and discussed about crucial fragments generated from previous SARS-CoV protease inhibitors important for the lead optimization of SARS-CoV-2 protease inhibitors. This study surely offers different strategic options of lead optimization to the medicinal chemists to discover effective anti-viral agent against the devastating disease, COVID-19.
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Affiliation(s)
- Sk Abdul Amin
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, P. O. Box 17020, Jadavpur University, Kolkata, 700032, India
| | - Suvankar Banerjee
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, P. O. Box 17020, Jadavpur University, Kolkata, 700032, India
| | - Shovanlal Gayen
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences, Dr. Harisingh Gour University, Sagar, MP, India.
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, P. O. Box 17020, Jadavpur University, Kolkata, 700032, India.
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44
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Lead compounds for the development of SARS-CoV-2 3CL protease inhibitors. Nat Commun 2021; 12:2016. [PMID: 33795671 PMCID: PMC8016852 DOI: 10.1038/s41467-021-22362-2] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 03/10/2021] [Indexed: 12/26/2022] Open
Abstract
We report the identification of three structurally diverse compounds - compound 4, GC376, and MAC-5576 - as inhibitors of the SARS-CoV-2 3CL protease. Structures of each of these compounds in complex with the protease revealed strategies for further development, as well as general principles for designing SARS-CoV-2 3CL protease inhibitors. These compounds may therefore serve as leads for the basis of building effective SARS-CoV-2 3CL protease inhibitors.
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45
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Peñalver L, Schmid P, Szamosvári D, Schildknecht S, Globisch C, Sawade K, Peter C, Böttcher T. A Ligand Selection Strategy Identifies Chemical Probes Targeting the Proteases of SARS-CoV-2. Angew Chem Int Ed Engl 2021; 60:6799-6806. [PMID: 33350010 PMCID: PMC7986205 DOI: 10.1002/anie.202016113] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Indexed: 01/05/2023]
Abstract
Activity-based probes are valuable tools for chemical biology. However, finding probes that specifically target the active site of an enzyme remains a challenging task. Herein, we present a ligand selection strategy that allows to rapidly tailor electrophilic probes to a target of choice and showcase its application for the two cysteine proteases of SARS-CoV-2 as proof of concept. The resulting probes were specific for the active site labeling of 3CLpro and PLpro with sufficient selectivity in a live cell model as well as in the background of a native human proteome. Exploiting the probes as tools for competitive profiling of a natural product library identified salvianolic acid derivatives as promising 3CLpro inhibitors. We anticipate that our ligand selection strategy will be useful to rapidly develop customized probes and discover inhibitors for a wide range of target proteins also beyond corona virus proteases.
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Affiliation(s)
- Lilian Peñalver
- Department of ChemistryKonstanz Research School Chemical BiologyZukunftskollegUniversity of KonstanzKonstanzGermany
| | - Philipp Schmid
- Department of ChemistryKonstanz Research School Chemical BiologyZukunftskollegUniversity of KonstanzKonstanzGermany
- Faculty of ChemistryDepartment of Biological Chemistry & Centre for Microbiology and Environmental Systems ScienceDivision of Microbial EcologyUniversity of ViennaViennaAustria
| | - Dávid Szamosvári
- Department of ChemistryKonstanz Research School Chemical BiologyZukunftskollegUniversity of KonstanzKonstanzGermany
| | - Stefan Schildknecht
- In Vitro Toxicology and BiomedicineDepartment of BiologyUniversity of KonstanzKonstanzGermany
- Albstadt-Sigmaringen UniversitySigmaringenGermany
| | | | - Kevin Sawade
- Department of ChemistryUniversity of KonstanzKonstanzGermany
| | - Christine Peter
- Department of ChemistryUniversity of KonstanzKonstanzGermany
| | - Thomas Böttcher
- Department of ChemistryKonstanz Research School Chemical BiologyZukunftskollegUniversity of KonstanzKonstanzGermany
- Faculty of ChemistryDepartment of Biological Chemistry & Centre for Microbiology and Environmental Systems ScienceDivision of Microbial EcologyUniversity of ViennaViennaAustria
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46
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Peñalver L, Schmid P, Szamosvári D, Schildknecht S, Globisch C, Sawade K, Peter C, Böttcher T. Eine Strategie zur Ligandenselektion identifiziert chemische Sonden für die Markierung von SARS‐CoV‐2‐Proteasen. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Lilian Peñalver
- Fachbereich Chemie Konstanz Research School Chemical Biology Zukunftskolleg Universität Konstanz Konstanz Deutschland
| | - Philipp Schmid
- Fachbereich Chemie Konstanz Research School Chemical Biology Zukunftskolleg Universität Konstanz Konstanz Deutschland
- Fakultät für Chemie Institut für Biologische Chemie & Centre for Microbiology and Environmental Systems Science Division of Microbial Ecology Universität Wien Wien Österreich
| | - Dávid Szamosvári
- Fachbereich Chemie Konstanz Research School Chemical Biology Zukunftskolleg Universität Konstanz Konstanz Deutschland
| | - Stefan Schildknecht
- In Vitro Toxicology and Biomedicine Fachbereich Biologie Universität Konstanz Konstanz Deutschland
- Hochschule Albstadt-Sigmaringen Sigmaringen Deutschland
| | | | - Kevin Sawade
- Fachbereich Chemie Universität Konstanz Konstanz Deutschland
| | - Christine Peter
- Fachbereich Chemie Universität Konstanz Konstanz Deutschland
| | - Thomas Böttcher
- Fachbereich Chemie Konstanz Research School Chemical Biology Zukunftskolleg Universität Konstanz Konstanz Deutschland
- Fakultät für Chemie Institut für Biologische Chemie & Centre for Microbiology and Environmental Systems Science Division of Microbial Ecology Universität Wien Wien Österreich
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47
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Chen CC, Yu X, Kuo CJ, Min J, Chen S, Ma L, Liu K, Guo RT. Overview of antiviral drug candidates targeting coronaviral 3C-like main proteases. FEBS J 2021; 288:5089-5121. [PMID: 33400393 DOI: 10.1111/febs.15696] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 12/15/2020] [Accepted: 01/04/2021] [Indexed: 01/18/2023]
Abstract
Coronaviruses (CoVs) are positive single-stranded RNA viruses that cause severe respiratory syndromes in humans, including severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS). Coronavirus disease 2019 (COVID-19) caused by a novel severe acute respiratory syndrome CoV (SARS-CoV-2) at the end of 2019 became a global pandemic. The 3C-like cysteine protease (3CLpro) processes viral polyproteins to yield mature non-structural proteins, thus playing an important role in the CoV life cycle, and therefore is considered as a prominent target for antiviral drugs. To date, many 3CLpro inhibitors have been reported, and their molecular mechanisms have been illustrated. Here, we briefly introduce the structural features of 3CLpro of the human-related SARS-CoV, MERS-CoV and SARS-CoV-2, and explore the potency and mechanism of their cognate inhibitors. This information will shed light on the development and optimization of CoV 3CLpro inhibitors, which may benefit the further designation of therapeutic strategies for treating CoV diseases.
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Affiliation(s)
- Chun-Chi Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Xuejing Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Chih-Jung Kuo
- Department of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Jian Min
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Sizhuo Chen
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Ke Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Rey-Ting Guo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
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48
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Selvaraj C, Panwar U, Dinesh DC, Boura E, Singh P, Dubey VK, Singh SK. Microsecond MD Simulation and Multiple-Conformation Virtual Screening to Identify Potential Anti-COVID-19 Inhibitors Against SARS-CoV-2 Main Protease. Front Chem 2021; 8:595273. [PMID: 33585398 PMCID: PMC7873971 DOI: 10.3389/fchem.2020.595273] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 11/19/2020] [Indexed: 12/14/2022] Open
Abstract
The recent pandemic outbreak of COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), raised global health and economic concerns. Phylogenetically, SARS-CoV-2 is closely related to SARS-CoV, and both encode the enzyme main protease (Mpro/3CLpro), which can be a potential target inhibiting viral replication. Through this work, we have compiled the structural aspects of Mpro conformational changes, with molecular modeling and 1-μs MD simulations. Long-scale MD simulation resolves the mechanism role of crucial amino acids involved in protein stability, followed by ensemble docking which provides potential compounds from the Traditional Chinese Medicine (TCM) database. These lead compounds directly interact with active site residues (His41, Gly143, and Cys145) of Mpro, which plays a crucial role in the enzymatic activity. Through the binding mode analysis in the S1, S1′, S2, and S4 binding subsites, screened compounds may be functional for the distortion of the oxyanion hole in the reaction mechanism, and it may lead to the inhibition of Mpro in SARS-CoV-2. The hit compounds are naturally occurring compounds; they provide a sustainable and readily available option for medical treatment in humans infected by SARS-CoV-2. Henceforth, extensive analysis through molecular modeling approaches explained that the proposed molecules might be promising SARS-CoV-2 inhibitors for the inhibition of COVID-19, subjected to experimental validation.
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Affiliation(s)
- Chandrabose Selvaraj
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India
| | - Umesh Panwar
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India
| | - Dhurvas Chandrasekaran Dinesh
- Section of Molecular Biology and Biochemistry, Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Prague, Czechia
| | - Evzen Boura
- Section of Molecular Biology and Biochemistry, Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Prague, Czechia
| | - Poonam Singh
- Corrosion and Materials Protection Division, Council of Scientific and Industrial Research (CSIR)-Central Electrochemical Research Institute, Karaikudi, India
| | - Vikash Kumar Dubey
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, India
| | - Sanjeev Kumar Singh
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India
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49
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Ng CS, Stobart CC, Luo H. Innate immune evasion mediated by picornaviral 3C protease: Possible lessons for coronaviral 3C-like protease? Rev Med Virol 2021; 31:1-22. [PMID: 33624382 PMCID: PMC7883238 DOI: 10.1002/rmv.2206] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/03/2020] [Accepted: 12/04/2020] [Indexed: 01/10/2023]
Abstract
Severe acute respiratory syndrome coronavirus-2 is the etiological agent of the ongoing pandemic of coronavirus disease-2019, a multi-organ disease that has triggered an unprecedented global health and economic crisis. The virally encoded 3C-like protease (3CLpro ), which is named after picornaviral 3C protease (3Cpro ) due to their similarities in substrate recognition and enzymatic activity, is essential for viral replication and has been considered as the primary drug target. However, information regarding the cellular substrates of 3CLpro and its interaction with the host remains scarce, though recent work has begun to shape our understanding more clearly. Here we summarized and compared the mechanisms by which picornaviruses and coronaviruses have evolved to evade innate immune surveillance, with a focus on the established role of 3Cpro in this process. Through this comparison, we hope to highlight the potential action and mechanisms that are conserved and shared between 3Cpro and 3CLpro . In this review, we also briefly discussed current advances in the development of broad-spectrum antivirals targeting both 3Cpro and 3CLpro .
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Affiliation(s)
- Chen Seng Ng
- Centre for Heart Lung Innovation, St Paul's Hospital, University of British Columbia, Vancouver, Canada.,Department of Pathology and Laboratory of Medicine, University of British Columbia, Vancouver, Canada
| | | | - Honglin Luo
- Centre for Heart Lung Innovation, St Paul's Hospital, University of British Columbia, Vancouver, Canada.,Department of Pathology and Laboratory of Medicine, University of British Columbia, Vancouver, Canada
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50
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Konwar M, Sarma D. Advances in developing small molecule SARS 3CL pro inhibitors as potential remedy for corona virus infection. Tetrahedron 2021; 77:131761. [PMID: 33230349 PMCID: PMC7674993 DOI: 10.1016/j.tet.2020.131761] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 10/06/2020] [Accepted: 11/09/2020] [Indexed: 01/08/2023]
Abstract
Originated in China, coronavirus disease 2019 (COVID-19)- the highly contagious and fatal respiratory disease caused by SARS-CoV-2 has already infected more than 29 million people worldwide with a mortality rate of 3.15% (according to World Health Organization's (WHO's) report, September 2020) and the number is exponentially increasing with no remedy whatsoever discovered till date. But it is not the first time this infectious viral disease has appeared, in 2002 SARS-CoV infected more than 8000 individuals of which 9.6% patients died and in 2012 approximately 35% of MERS-CoV infected patients have died. Literature reports indicate that a chymotripsin-like cystein protease (3CLpro) is responsible for the replication of the virus inside the host cell. Therefore, design and synthesis of 3CLpro inhibitor molecules play a great impact in drug development against this COVID-19 pandemic. In this review, we are discussing the anti-SARS effect of some small molecule 3CLpro inhibitors with their various binding modes of interactions to the target protein.
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Affiliation(s)
- Manashjyoti Konwar
- Department of Chemistry, Dibrugarh University, Dibrugarh, 786004, Assam, India
- Department of Chemistry, Dibru College, Dibrugarh, 786003, Assam, India
| | - Diganta Sarma
- Department of Chemistry, Dibrugarh University, Dibrugarh, 786004, Assam, India
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