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Ma C, Tan H, Choza J, Wang Y, Wang J. Validation and invalidation of SARS-CoV-2 main protease inhibitors using the Flip-GFP and Protease-Glo luciferase assays. Acta Pharm Sin B 2022; 12:1636-1651. [PMID: 34745850 PMCID: PMC8558150 DOI: 10.1016/j.apsb.2021.10.026] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/24/2021] [Accepted: 10/14/2021] [Indexed: 12/14/2022] Open
Abstract
SARS-CoV-2 main protease (Mpro) is one of the most extensively exploited drug targets for COVID-19. Structurally disparate compounds have been reported as Mpro inhibitors, raising the question of their target specificity. To elucidate the target specificity and the cellular target engagement of the claimed Mpro inhibitors, we systematically characterize their mechanism of action using the cell-free FRET assay, the thermal shift-binding assay, the cell lysate Protease-Glo luciferase assay, and the cell-based FlipGFP assay. Collectively, our results have shown that majority of the Mpro inhibitors identified from drug repurposing including ebselen, carmofur, disulfiram, and shikonin are promiscuous cysteine inhibitors that are not specific to Mpro, while chloroquine, oxytetracycline, montelukast, candesartan, and dipyridamole do not inhibit Mpro in any of the assays tested. Overall, our study highlights the need of stringent hit validation at the early stage of drug discovery.
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Vijayakumar M, Janani B, Kannappan P, Renganathan S, Al-Ghamdi S, Alsaidan M, Abdelaziz MA, Peer Mohideen A, Shahid M, Ramesh T. In silico identification of potential inhibitors against main protease of SARS-CoV-2 6LU7 from Andrographis panniculata via molecular docking, binding energy calculations and molecular dynamics simulation studies. Saudi J Biol Sci 2021; 29:18-29. [PMID: 34729030 PMCID: PMC8555113 DOI: 10.1016/j.sjbs.2021.10.060] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/12/2021] [Accepted: 10/21/2021] [Indexed: 12/23/2022] Open
Abstract
Background The ongoing global outbreak of new corona virus (SARS-CoV-2) has been recognized as global public health concern since it causes high morbidity and mortality every day. Due to the rapid spreading and re-emerging, we need to find a potent drug against SARS-CoV-2. Synthetic drugs, such as hydroxychloroquine, remdisivir have paid more attention and the effects of these drugs are still under investigation, due to their severe side effects. Therefore, the aim of the present study was performed to identify the potential inhibitor against main protease SARS-CoV-2 6LU7. Objective In this study, RO5, ADME properties, molecular dynamic simulations and free binding energy prediction were mainly investigated. Results The molecular docking study findings revealed that andrographolide had higher binding affinity among the selected natural diterpenoids compared to co-crystal native ligand inhibitor N3. The persistent inhibition of Ki for diterpenoids was analogous. Furthermore, the simulations of molecular dynamics and free binding energy findings have shown that andrographolide possesses a large amount of dynamic properties such as stability, flexibility and binding energy. Conclusion In conclusion, findings of the current study suggest that selected diterpenoids were predicted to be the significant phytonutrient-based inhibitor against SARS-CoV-2 6LU7 (Mpro). However, preclinical and clinical trials are needed for the further scientific validation before use.
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Affiliation(s)
- Mayakrishnan Vijayakumar
- Laboratory of Cell and Molecular Biology, Grassland and Forage Science Division, National Institute of Animal Science, Rural Development Administration, Cheonan-si, Chungcheongnam-do 31000, Republic of Korea
| | - Balakarthikeyan Janani
- Department of Biochemistry, PSG College of Arts and Science (Autonomous), Affiliated to Bharathiar University, Coimbatore 641014, Tamil Nadu, India
| | - Priya Kannappan
- Department of Biochemistry, PSG College of Arts and Science (Autonomous), Affiliated to Bharathiar University, Coimbatore 641014, Tamil Nadu, India
| | - Senthil Renganathan
- Department of Bioinformatics, Marudupandiyar College, Thanjavur 613 403, Tamil Nadu, India.,Lysine Biotech Private Limited, Periyar Technology Incubator, DST Business Incubator, Periyar Maniammai Institute of Science and Technology (PMIST), Vallam, Thanjavur 613403, Tamil Nadu, India
| | - Sameer Al-Ghamdi
- Family and Community Medicine Department, College of Medicine, Prince Sattam Bin Abdulaziz University, Al-Kharj-11942, Kingdom of Saudi Arabia
| | - Mohammed Alsaidan
- Internal Medicine Department, College of Medicine, Prince Sattam Bin Abdulaziz University, Al-Kharj-11942, Kingdom of Saudi Arabia
| | - Mohamed A Abdelaziz
- Department of Basic Medical Sciences, College of Medicine, Prince Sattam Bin Abdulaziz University, Al-Kharj-11942, Kingdom of Saudi Arabia.,Department of Medical Physiology, College of Medicine, Al-Azhar University, Cairo, Egypt
| | - Abubucker Peer Mohideen
- Department of Basic Medical Sciences, College of Medicine, Prince Sattam Bin Abdulaziz University, Al-Kharj-11942, Kingdom of Saudi Arabia
| | - Mohammad Shahid
- Department of Basic Medical Sciences, College of Medicine, Prince Sattam Bin Abdulaziz University, Al-Kharj-11942, Kingdom of Saudi Arabia
| | - Thiyagarajan Ramesh
- Department of Basic Medical Sciences, College of Medicine, Prince Sattam Bin Abdulaziz University, Al-Kharj-11942, Kingdom of Saudi Arabia
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Gajjar ND, Dhameliya TM, Shah GB. In search of RdRp and Mpro inhibitors against SARS CoV-2: Molecular docking, molecular dynamic simulations and ADMET analysis. J Mol Struct 2021; 1239:130488. [PMID: 33903778 PMCID: PMC8059878 DOI: 10.1016/j.molstruc.2021.130488] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/08/2021] [Accepted: 04/10/2021] [Indexed: 12/16/2022]
Abstract
Corona Virus Disease 2019 (COVID-19) caused by Severe Acute Respiratory Syndrome coronavirus (SARS CoV-2) has been declared a worldwide pandemic by WHO recently. The complete understanding of the complex genomic structure of SARS CoV-2 has enabled the use of computational tools in search of SARS CoV-2 inhibitors against the multiple proteins responsible for its entry and multiplication in human cells. With this endeavor, 177 natural, anti-viral chemical entities and their derivatives, selected through the critical analysis of the literatures, were studied using pharmacophore screening followed by molecular docking against RNA dependent RNA polymerase and main protease. The identified hits have been subjected to molecular dynamic simulations to study the stability of ligand-protein complexes followed by ADMET analysis and Lipinski filters to confirm their drug likeliness. It has led to an important start point in the drug discovery and development of therapeutic agents against SARS CoV-2.
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Key Words
- 3CLpro, 3-chymotrypsin-like protease
- ACE, Angiotensin converting enzyme
- ADMET, Absorption, distribution, metabolism, excretion, and toxicity
- ASL, Atom specification language
- COVID-19, Corona virus disease-2019
- Dscore, Druggability score
- EM, Electron microscopy
- HB, Hydrogen bond
- MD simulation
- MD simulation, Molecular dynamic simulation
- Molecular docking
- Mpro
- Mpro, Main protease
- Natural products
- PLpro, Papain-like protease
- RMSD, Root mean square deviation
- RMSF, Root mean square fluctuation
- RdRP, RNA-dependent RNA polymerase
- RdRp
- RoG, Radius of gyration
- SARS CoV-2
- SARS CoV-2, Severe acute respiratory syndrome coronavirus 2
- SASA, Solvent accessible surface area
- SP, Standard precision
- WHO, World health organization
- nsp, Non-structural protein
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Zhu G, Zhu C, Zhu Y, Sun F. Minireview of progress in the structural study of SARS-CoV-2 proteins. Curr Res Microb Sci 2020; 1:53-61. [PMID: 33236001 PMCID: PMC7323663 DOI: 10.1016/j.crmicr.2020.06.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 06/24/2020] [Accepted: 06/25/2020] [Indexed: 01/18/2023] Open
Abstract
Major progress has been achieved with regard to the understanding of the phylogeny and genomic organization of SARS-CoV-2. This review summarized crucial developments in the elucidation of the structure and function of key SARS-CoV-2 proteins. The molecular details of SARS-CoV-2 infection and replication could improve the effective clinical treatment.
A severe form of pneumonia, named coronavirus disease 2019 (COVID-19) by the World Health Organization, broke out in China and rapidly developed into a global pandemic, with millions of cases and hundreds of thousands of deaths reported globally. The novel coronavirus, which was designated as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was identified as the etiological agent of COVID-19. On the basis of experience accumulated following previous SARS-CoV and MERS-CoV outbreaks and research, a series of studies have been conducted rapidly, and major progress has been achieved with regard to the understanding of the phylogeny and genomic organization of SARS-CoV-2 in addition its molecular mechanisms of infection and replication. In the present review, we summarized crucial developments in the elucidation of the structure and function of key SARS-CoV-2 proteins, especially the main protease, RNA-dependent RNA polymerase, spike glycoprotein, and nucleocapsid protein. Results of studies on their associated inhibitors and drugs have also been highlighted.
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Key Words
- 3CLpro, 3C-like protease
- 6-HB, six-helix bundle
- ACE2, angiotensin-converting enzyme 2
- COVID-19
- COVID-19, coronavirus disease 2019
- CatB/L, cysteine proteases-cathepsin B and L
- Drug-screening
- E protein, Envelope protein
- Genome-encoded proteins
- HR1, heptad repeat 1
- HR2, heptad repeat 2
- M protein, Membrane protein
- MERS-CoV, the Middle Eastern respiratory syndrome coronavirus
- Mpro, Main protease
- N protein, Nucleocapsid protein
- NSP, non-structural protein
- ORF, Open reading frame
- PD, peptidase domain
- RBD, receptor-binding domain
- RBM, receptor-binding motif
- RMP, The remdesivir monophosphate
- RdRp, RNA-dependent RNA polymerase
- S protein, Spike glycoprotein
- SARS-CoV, severe acute respiratory syndrome coronavirus
- SARS-CoV-2
- SARS-CoV-2, severe acute respiratory syndrome coronavirus 2
- Structure-based screening
- gRNA, genomic RNA
- sgRNA, subgenomic RNA
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Affiliation(s)
- Guoliang Zhu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chunmei Zhu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yun Zhu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Corresponding authors.
| | - Fei Sun
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Corresponding authors.
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