901
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Gupta S, Singh V, Varadwaj PK, Chakravartty N, Katta AVSKM, Lekkala SP, Thomas G, Narasimhan S, Reddy AR, Reddy Lachagari VB. Secondary metabolites from spice and herbs as potential multitarget inhibitors of SARS-CoV-2 proteins. J Biomol Struct Dyn 2020; 40:2264-2283. [PMID: 33107812 PMCID: PMC7605658 DOI: 10.1080/07391102.2020.1837679] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been responsible for the current global pandemic that has caused a death toll of >1.12 million worldwide and number continues to climb in several countries. Currently, there are neither specific antiviral drugs nor vaccines for the treatment and prevention of COVID-19. We screened in silico, a group of natural spice and herbal secondary metabolites (SMs) for their inhibition efficacy against multiple target proteins of SARS-CoV-2 as well as the human angiotensin-converting enzyme 2 protein. Docking and simulation results indicated that epicatechin, embelin, hesperidin, cafestol, murrayanine and murrayaquinone-A have higher inhibition efficacy over at least one of the known antiviral drugs such as Hydroxychloroquine, Remdesivir and Ribavirin. Combination of these potentially effective SMs from their respective plant sources was analysed, and its absorption and acute oral toxicity were examined in Wistar rats and classified as category 5 as per the Globally Harmonized System. The identified SMs may be useful in the development of preventive nutraceuticals, food supplements and antiviral drugs. Communicated by Ramaswamy H. Sarma
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Affiliation(s)
| | - Vishal Singh
- Department of Applied Sciences, Indian Institute of Information Technology, Allahabad, India
| | - Pritish Kumar Varadwaj
- Department of Applied Sciences, Indian Institute of Information Technology, Allahabad, India
| | | | | | | | | | | | - Arjula R Reddy
- Department of Plant Sciences, University of Hyderabad, Hyderabad, India
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902
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Development of a Fluorescence-Based, High-Throughput SARS-CoV-2 3CL pro Reporter Assay. J Virol 2020; 94:JVI.01265-20. [PMID: 32843534 PMCID: PMC7592234 DOI: 10.1128/jvi.01265-20] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 08/20/2020] [Indexed: 12/27/2022] Open
Abstract
The COVID-19 pandemic has already led to more than 700,000 deaths and innumerable changes to daily life worldwide. Along with development of a vaccine, identification of effective antivirals to treat infected patients is of the highest importance. However, rapid drug discovery requires efficient methods to identify novel compounds that can inhibit the virus. In this work, we present a method for identifying inhibitors of the SARS-CoV-2 main protease, 3CLpro. This reporter-based assay allows for antiviral drug screening in human cell culture at biosafety level 2 (BSL2) with high-throughput compatible sample processing and analysis. This assay may help identify novel antivirals to control the COVID-19 pandemic. In late 2019, a human coronavirus, now known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged, likely from a zoonotic reservoir. This virus causes COVID-19, has infected millions of people, and has led to hundreds of thousands of deaths across the globe. While the best interventions to control and ultimately stop the pandemic are prophylactic vaccines, antiviral therapeutics are important to limit morbidity and mortality in those already infected. At this time, only one FDA-approved anti-SARS-CoV-2 antiviral drug, remdesivir, is available, and unfortunately, its efficacy appears to be limited. Thus, the identification of new and efficacious antivirals is of the highest importance. In order to facilitate rapid drug discovery, flexible, sensitive, and high-throughput screening methods are required. With respect to drug targets, most attention is focused on either the viral RNA-dependent RNA polymerase or the main viral protease, 3CLpro. 3CLpro is an attractive target for antiviral therapeutics, as it is essential for processing newly translated viral proteins and the viral life cycle cannot be completed without protease activity. In this work, we report a new assay to identify inhibitors of 3CLpro. Our reporter is based on a green fluorescent protein (GFP)-derived protein that fluoresces only after cleavage by 3CLpro. This experimentally optimized reporter assay allows for antiviral drug screening in human cell culture at biosafety level 2 (BSL2) with high-throughput compatible protocols. Using this screening approach in combination with existing drug libraries may lead to the rapid identification of novel antivirals to suppress SARS-CoV-2 replication and spread. IMPORTANCE The COVID-19 pandemic has already led to more than 700,000 deaths and innumerable changes to daily life worldwide. Along with development of a vaccine, identification of effective antivirals to treat infected patients is of the highest importance. However, rapid drug discovery requires efficient methods to identify novel compounds that can inhibit the virus. In this work, we present a method for identifying inhibitors of the SARS-CoV-2 main protease, 3CLpro. This reporter-based assay allows for antiviral drug screening in human cell culture at biosafety level 2 (BSL2) with high-throughput compatible sample processing and analysis. This assay may help identify novel antivirals to control the COVID-19 pandemic.
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903
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Ivanov J, Polshakov D, Kato-Weinstein J, Zhou Q, Li Y, Granet R, Garner L, Deng Y, Liu C, Albaiu D, Wilson J, Aultman C. Quantitative Structure-Activity Relationship Machine Learning Models and their Applications for Identifying Viral 3CLpro- and RdRp-Targeting Compounds as Potential Therapeutics for COVID-19 and Related Viral Infections. ACS OMEGA 2020; 5:27344-27358. [PMID: 33134697 PMCID: PMC7571315 DOI: 10.1021/acsomega.0c03682] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 09/29/2020] [Indexed: 05/20/2023]
Abstract
In response to the ongoing COVID-19 pandemic, there is a worldwide effort being made to identify potential anti-SARS-CoV-2 therapeutics. Here, we contribute to these efforts by building machine-learning predictive models to identify novel drug candidates for the viral targets 3 chymotrypsin-like protease (3CLpro) and RNA-dependent RNA polymerase (RdRp). Chemist-curated training sets of substances were assembled from CAS data collections and integrated with curated bioassay data. The best-performing classification models were applied to screen a set of FDA-approved drugs and CAS REGISTRY substances that are similar to, or associated with, antiviral agents. Numerous substances with potential activity against 3CLpro or RdRp were found, and some were validated by published bioassay studies and/or by their inclusion in upcoming or ongoing COVID-19 clinical trials. This study further supports that machine learning-based predictive models may be used to assist the drug discovery process for COVID-19 and other diseases.
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904
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Amamuddy OS, Verkhivker GM, Bishop ÖT. Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M pro. J Chem Inf Model 2020; 60:5080-5102. [PMID: 32853525 PMCID: PMC7496595 DOI: 10.1021/acs.jcim.0c00634] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Indexed: 12/15/2022]
Abstract
A new coronavirus (SARS-CoV-2) is a global threat to world health and economy. Its dimeric main protease (Mpro), which is required for the proteolytic cleavage of viral precursor proteins, is a good candidate for drug development owing to its conservation and the absence of a human homolog. Improving our understanding of Mpro behavior can accelerate the discovery of effective therapies to reduce mortality. All-atom molecular dynamics (MD) simulations (100 ns) of 50 mutant Mpro dimers obtained from filtered sequences from the GISAID database were analyzed using root-mean-square deviation, root-mean-square fluctuation, Rg, averaged betweenness centrality, and geometry calculations. The results showed that SARS-CoV-2 Mpro essentially behaves in a similar manner to its SAR-CoV homolog. However, we report the following new findings from the variants: (1) Residues GLY15, VAL157, and PRO184 have mutated more than once in SARS CoV-2; (2) the D48E variant has lead to a novel "TSEEMLN"" loop at the binding pocket; (3) inactive apo Mpro does not show signs of dissociation in 100 ns MD; (4) a non-canonical pose for PHE140 widens the substrate binding surface; (5) dual allosteric pockets coinciding with various stabilizing and functional components of the substrate binding pocket were found to display correlated compaction dynamics; (6) high betweenness centrality values for residues 17 and 128 in all Mpro samples suggest their high importance in dimer stability-one such consequence has been observed for the M17I mutation whereby one of the N-fingers was highly unstable. (7) Independent coarse-grained Monte Carlo simulations suggest a relationship between the rigidity/mutability and enzymatic function. Our entire approach combining database preparation, variant retrieval, homology modeling, dynamic residue network (DRN), relevant conformation retrieval from 1-D kernel density estimates from reaction coordinates to other existing approaches of structural analysis, and data visualization within the coronaviral Mpro is also novel and is applicable to other coronaviral proteins.
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Affiliation(s)
- Olivier Sheik Amamuddy
- Research Unit in Bioinformatics, Department of Microbiology and Biochemistry, Rhodes University, Grahamstown 6140, South Africa
| | - Gennady M. Verkhivker
- Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA
- Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics, Department of Microbiology and Biochemistry, Rhodes University, Grahamstown 6140, South Africa
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905
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Dong X, Tian Z, Shen C, Zhao C. An overview of potential therapeutic agents to treat COVID-19. Biosci Trends 2020; 14:318-327. [PMID: 33100290 DOI: 10.5582/bst.2020.03345] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The emerging novel coronavirus disease (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has swept across the world and become a global threat to public health. More than 200 countries and territories worldwide are suffering from this COVID-19 pandemic. Worryingly, no specific vaccines or drugs have been approved for the prevention or treatment of COVID-19. Under the pressure of a sustained rise in the incidence and mortality of COVID-19, an unprecedented global effort is being implemented to identify effective drugs to combat the current coronavirus. As the understanding of SARS-CoV-2 virology, the underlying mechanism by which it attacks host cells, and the host response to the infection rapidly evolves, drugs are being repurposed and novel drugs are being identified and designed to target the SARS-CoV-2 pathogenesis. Presented here is a brief overview of both virus-based and host-based potential therapeutic drugs that are currently being investigated.
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Affiliation(s)
- Xueqin Dong
- Community Health Service Center of the Qianfo Mountain Office, the People's Hospital of Lixia District of Jinan, Ji'nan, Shandong, China
| | - Zhenxue Tian
- Department of Pharmacy, Qingdao Municipal Hospital, Qingdao, Shandong, China
| | - Chengwu Shen
- Department of Pharmacy, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Ji'nan, Shandong, China
| | - Cuirong Zhao
- Department of Pharmacy, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Ji'nan, Shandong, China
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906
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Ahamad S, Kanipakam H, Birla S, Ali MS, Gupta D. Screening Malaria-box compounds to identify potential inhibitors against SARS-CoV-2 M pro, using molecular docking and dynamics simulation studies. Eur J Pharmacol 2020; 890:173664. [PMID: 33131721 PMCID: PMC7584923 DOI: 10.1016/j.ejphar.2020.173664] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 10/14/2020] [Accepted: 10/21/2020] [Indexed: 12/11/2022]
Abstract
Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) Main protease (Mpro) is one of the vital drug targets amongst all the coronaviruses, as the protein is indispensable for virus replication. The study aimed to identify promising lead molecules against Mpro enzyme through virtual screening of Malaria Venture (MMV) Malaria Box (MB) comprising of 400 experimentally proven compounds. The binding affinities were studied using virtual screening based molecular docking, which revealed five molecules having the highest affinity scores compared to the reference molecules. Utilizing the established 3D structure of Mpro the binding affinity conformations of the docked complexes were studied by Molecular Dynamics (MD) simulations. The MD simulation trajectories were analysed to monitor protein deviation, relative fluctuation, atomic gyration, compactness covariance, residue-residue map and free energy landscapes. Based on the present study outcome, we propose three Malaria_box (MB) compounds, namely, MB_241, MB_250 and MB_266 to be the best lead compounds against Mpro activity. The compounds may be evaluated for their inhibitory activities using experimental techniques.
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Affiliation(s)
- Shahzaib Ahamad
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067, India
| | - Hema Kanipakam
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067, India
| | - Shweta Birla
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067, India
| | - Md Shaukat Ali
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067, India
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067, India.
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907
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Ghosh R, Chakraborty A, Biswas A, Chowdhuri S. Potential therapeutic use of corticosteroids as SARS CoV-2 main protease inhibitors: a computational study. J Biomol Struct Dyn 2020; 40:2053-2066. [PMID: 33094701 PMCID: PMC7596904 DOI: 10.1080/07391102.2020.1835728] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The outbreak of COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS CoV-2), represents a pandemic threat to global public health. To date, ∼530,000 people died of this disease worldwide. Presently, researchers/clinicians are adopting the drug repurposing strategy to combat this disease. It has also been observed that some repurposed anti-viral drugs may serve as potent inhibitors of SARS CoV-2 Mpro, a key component of viral replication. Apart from these anti-viral drugs, recently dexamethasone (an important corticosteroid) is effectively used to treat COVID-19 patients. However, the mechanism behind the mode of its action is not so clear. Additionally, the effect of other well-known corticosteroids to control this disease by inhibiting the proteolytic activity of Mpro is ambiguous. In this study, we have adopted computational approaches to understand these aspects. Six well-known corticosteroids (cortisone, hydrocortisone, prednisolone, methylprednisolone, betamethasone and dexamethasone) and two repurposed drugs (darunavir and lopinavir) against COVID-19 were subjected for molecular docking studies. Two of them (betamethasone and dexamethasone) were selected by comparing their binding affinities with selected repurposed drugs toward Mpro. Betamethasone and dexamethasone interacted with both the catalytic residues of Mpro (His41 and Cys145). Molecular dynamics studies further revealed that these two Mpro-corticosteroid complexes are more stable, experience less conformational fluctuations and more compact than Mpro-darunavir/lopinavir complexes. These findings were additionally validated by MM-GBSA analysis. This study provides corroboration for execution of anti-COVID-19 activity of dexamethasone. Our study also emphasizes on the use of another important corticosteroid (betamethasone) as potential therapeutic agent for COVID-19 treatment.
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Affiliation(s)
- Rajesh Ghosh
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Ayon Chakraborty
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Ashis Biswas
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Snehasis Chowdhuri
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
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908
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Maurya VK, Kumar S, Bhatt MLB, Saxena SK. Antiviral activity of traditional medicinal plants from Ayurveda against SARS-CoV-2 infection. J Biomol Struct Dyn 2020; 40:1719-1735. [PMID: 33073699 PMCID: PMC7597308 DOI: 10.1080/07391102.2020.1832577] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
SARS-CoV-2 is the etiological agent of COVID-19 and responsible for more than 6 million cases globally, for which no vaccine or antiviral is available. Therefore, this study was planned to investigate the antiviral role of the active constituents against spike glycoprotein of SARS-CoV-2 as well as its host ACE2 receptor. Structure-based drug design approach has been used to elucidate the antiviral activity of active constituents present in traditional medicinal plants from Ayurveda. Further, parameters like drug-likeness, pharmacokinetics, and toxicity were determined to ensure the safety and efficacy of active constituents. Gene network analysis was performed to investigate the pathways altered during COVID-19. The prediction of drug–target interactions was performed to discover novel targets for active constituents. The results suggested that amarogentin, eufoliatorin, α-amyrin, caesalpinins, kutkin, β-sitosterol, and belladonnine are the top-ranked molecules have the highest affinity towards both the spike glycoprotein and ACE2. Most active constituents have passed the criteria of drug-likeness and demonstrated good pharmacokinetic profile with minimum predicted toxicity level. Gene network analysis confirmed that G-protein coupled receptor, protein kinase B signaling, protein secretion, peptidyl-serine phosphorylation, nuclear transport, apoptotic pathway, tumor necrosis factor, regulation of angiotensin level, positive regulation of ion transport, and membrane protein proteolysis were altered during COVID-19. The target prediction analysis revealed that most active constituents target the same pathways which are found to be altered during COVID-19. Collectively, our data encourages the use of active constituents as a potential therapy for COVID-19. However, further studies are ongoing to confirm its efficacy against disease.
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Affiliation(s)
- Vimal K Maurya
- Department of Centre for Advanced Research (CFAR), Faculty of Medicine, King George's Medical University (KGMU), Lucknow, India
| | - Swatantra Kumar
- Department of Centre for Advanced Research (CFAR), Faculty of Medicine, King George's Medical University (KGMU), Lucknow, India
| | - Madan L B Bhatt
- Department of Centre for Advanced Research (CFAR), Faculty of Medicine, King George's Medical University (KGMU), Lucknow, India
| | - Shailendra K Saxena
- Department of Centre for Advanced Research (CFAR), Faculty of Medicine, King George's Medical University (KGMU), Lucknow, India
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909
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Mohammad T, Shamsi A, Anwar S, Umair M, Hussain A, Rehman MT, AlAjmi MF, Islam A, Hassan MI. Identification of high-affinity inhibitors of SARS-CoV-2 main protease: Towards the development of effective COVID-19 therapy. Virus Res 2020; 288:198102. [PMID: 32717346 PMCID: PMC7380256 DOI: 10.1016/j.virusres.2020.198102] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/17/2020] [Accepted: 07/19/2020] [Indexed: 01/08/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is an infectious disease, caused by a newly emerged highly pathogenic virus called novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Targeting the main protease (Mpro, 3CLpro) of SARS-CoV-2 is an appealing approach for drug development because this enzyme plays a significant role in the viral replication and transcription. The available crystal structures of SARS-CoV-2 Mpro determined in the presence of different ligands and inhibitor-like compounds provide a platform for the quick development of selective inhibitors of SARS-CoV-2 Mpro. In this study, we utilized the structural information of co-crystallized SARS-CoV-2 Mpro for the structure-guided drug discovery of high-affinity inhibitors from the PubChem database. The screened compounds were selected on the basis of their physicochemical properties, drug-likeliness, and strength of affinity to the SARS-CoV-2 Mpro. Finally, we have identified 6-Deaminosinefungin (PubChem ID: 10428963) and UNII-O9H5KY11SV (PubChem ID: 71481120) as potential inhibitors of SARS-CoV-2 Mpro which may be further exploited in drug development to address SARS-CoV-2 pathogenesis. Both compounds are structural analogs of known antivirals, having considerable protease inhibitory potential with improved pharmacological properties. All-atom molecular dynamics simulations suggested SARS-CoV-2 Mpro in complex with these compounds is stable during the simulation period with minimal structural changes. This work provides enough evidence for further implementation of the identified compounds in the development of effective therapeutics of COVID-19.
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Affiliation(s)
- Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Anas Shamsi
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Saleha Anwar
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Mohd Umair
- Department of Computer Science, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Afzal Hussain
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Md Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Mohamed F AlAjmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India.
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910
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Caruso F, Rossi M, Pedersen JZ, Incerpi S. Computational studies reveal mechanism by which quinone derivatives can inhibit SARS-CoV-2. Study of embelin and two therapeutic compounds of interest, methyl prednisolone and dexamethasone. J Infect Public Health 2020; 13:1868-1877. [PMID: 33109497 PMCID: PMC7556809 DOI: 10.1016/j.jiph.2020.09.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 09/14/2020] [Accepted: 09/27/2020] [Indexed: 12/15/2022] Open
Abstract
Background Quinones are reactive to proteins containing cysteine residues and the main protease in Covid-19 contains an active site that includes Cys145. Embelin, a quinone natural product, is known to have antiviral activity against influenza and hepatitis B. Preliminary studies by our group also indicate its ability to inhibit HSV-1 in cultured cells. Methods Docking and DFT methods applied to the protease target. Results a mechanism for this inhibition of the SARS-CoV-2 Mpro protease is described, specifically due to formation of a covalent bond between S(Cys145) and an embelin C(carbonyl). This is assisted by two protein amino acids (1) N(imidazole-His41) which is able to capture H[S(Cys145)] and (2) HN(His163), which donates a proton to embelin O(carbonyl) forming an OH moiety that results in inhibition of the viral protease. A similar process is also seen with the anti-inflammatory drugs methyl prednisolone and dexamethasone, used for Covid-19 patients. Methyl prednisolone and dexamethasone are methide quinones, and possess only one carbonyl moiety, instead of two for embelin. Additional consideration was given to another natural product, emodin, recently patented against Covid-19, as well as some therapeutic quinones, vitamin K, suspected to be involved in Covid-19 action, and coenzyme Q10. All show structural similarities with embelin, dexamethasone and methyl prednisolone results. Conclusions Our data on embelin and related quinones indicate that these natural compounds may represent a feasible, strategic tool against Covid-19.
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Affiliation(s)
- Francesco Caruso
- Vassar College, Department of Chemistry, Poughkeepsie NY 12604, USA.
| | - Miriam Rossi
- Vassar College, Department of Chemistry, Poughkeepsie NY 12604, USA
| | - Jens Z Pedersen
- Department of Biology, University Tor Vergata, 00133 Rome, Italy
| | - Sandra Incerpi
- Department of Sciences, University Roma Tre, 00146 Rome, Italy
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911
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Dong Y, Dai T, Wei Y, Zhang L, Zheng M, Zhou F. A systematic review of SARS-CoV-2 vaccine candidates. Signal Transduct Target Ther 2020; 5:237. [PMID: 33051445 PMCID: PMC7551521 DOI: 10.1038/s41392-020-00352-y] [Citation(s) in RCA: 355] [Impact Index Per Article: 88.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/06/2020] [Accepted: 09/27/2020] [Indexed: 01/18/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging virus that is highly pathogenic and has caused the recent worldwide pandemic officially named coronavirus disease (COVID-19). Currently, considerable efforts have been put into developing effective and safe drugs and vaccines against SARS-CoV-2. Vaccines, such as inactivated vaccines, nucleic acid-based vaccines, and vector vaccines, have already entered clinical trials. In this review, we provide an overview of the experimental and clinical data obtained from recent SARS-CoV-2 vaccines trials, and highlight certain potential safety issues that require consideration when developing vaccines. Furthermore, we summarize several strategies utilized in the development of vaccines against other infectious viruses, such as severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV), with the aim of aiding in the design of effective therapeutic approaches against SARS-CoV-2.
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MESH Headings
- Angiotensin-Converting Enzyme 2
- Antibodies, Viral/biosynthesis
- Betacoronavirus/drug effects
- Betacoronavirus/immunology
- Betacoronavirus/pathogenicity
- COVID-19
- COVID-19 Vaccines
- Clinical Trials as Topic
- Coronavirus Infections/immunology
- Coronavirus Infections/prevention & control
- Coronavirus Infections/virology
- Gene Expression Regulation/drug effects
- Humans
- Immunity, Innate/drug effects
- Immunization Schedule
- Immunogenicity, Vaccine
- Middle East Respiratory Syndrome Coronavirus/drug effects
- Middle East Respiratory Syndrome Coronavirus/immunology
- Middle East Respiratory Syndrome Coronavirus/pathogenicity
- Pandemics/prevention & control
- Patient Safety
- Peptidyl-Dipeptidase A/genetics
- Peptidyl-Dipeptidase A/metabolism
- Pneumonia, Viral/immunology
- Pneumonia, Viral/prevention & control
- Pneumonia, Viral/virology
- Protein Binding
- Receptors, Virus/antagonists & inhibitors
- Receptors, Virus/genetics
- Receptors, Virus/metabolism
- Severe acute respiratory syndrome-related coronavirus/drug effects
- Severe acute respiratory syndrome-related coronavirus/immunology
- Severe acute respiratory syndrome-related coronavirus/pathogenicity
- SARS-CoV-2
- Severe Acute Respiratory Syndrome/immunology
- Severe Acute Respiratory Syndrome/prevention & control
- Severe Acute Respiratory Syndrome/virology
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/metabolism
- Vaccines, Attenuated
- Vaccines, DNA
- Vaccines, Subunit
- Vaccines, Virus-Like Particle
- Viral Vaccines/administration & dosage
- Viral Vaccines/biosynthesis
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Affiliation(s)
- Yetian Dong
- The State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310058, China
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Hangzhou, 310058, China
| | - Tong Dai
- Institutes of Biology and Medical Science, Soochow University, Suzhou, 215123, China
| | - Yujun Wei
- Anhui Anlong Gene Technology Co., Ltd, Hefei, 230041, China
| | - Long Zhang
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Hangzhou, 310058, China
| | - Min Zheng
- The State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310058, China.
| | - Fangfang Zhou
- Institutes of Biology and Medical Science, Soochow University, Suzhou, 215123, China.
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912
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Komatsu TS, Okimoto N, Koyama YM, Hirano Y, Morimoto G, Ohno Y, Taiji M. Drug binding dynamics of the dimeric SARS-CoV-2 main protease, determined by molecular dynamics simulation. Sci Rep 2020; 10:16986. [PMID: 33046764 PMCID: PMC7550358 DOI: 10.1038/s41598-020-74099-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 09/24/2020] [Indexed: 11/14/2022] Open
Abstract
We performed molecular dynamics simulation of the dimeric SARS-CoV-2 (severe acute respiratory syndrome corona virus 2) main protease (Mpro) to examine the binding dynamics of small molecular ligands. Seven HIV inhibitors, darunavir, indinavir, lopinavir, nelfinavir, ritonavir, saquinavir, and tipranavir, were used as the potential lead drugs to investigate access to the drug binding sites in Mpro. The frequently accessed sites on Mpro were classified based on contacts between the ligands and the protein, and the differences in site distributions of the encounter complex were observed among the ligands. All seven ligands showed binding to the active site at least twice in 28 simulations of 200 ns each. We further investigated the variations in the complex structure of the active site with the ligands, using microsecond order simulations. Results revealed a wide variation in the shapes of the binding sites and binding poses of the ligands. Additionally, the C-terminal region of the other chain often interacted with the ligands and the active site. Collectively, these findings indicate the importance of dynamic sampling of protein-ligand complexes and suggest the possibilities of further drug optimisations.
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Affiliation(s)
- Teruhisa S Komatsu
- Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan.
| | - Noriaki Okimoto
- Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
- Drug Discovery Molecular Simulation Platform Unit, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
| | - Yohei M Koyama
- Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
| | - Yoshinori Hirano
- Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
- Drug Discovery Molecular Simulation Platform Unit, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
| | - Gentaro Morimoto
- Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
- Drug Discovery Molecular Simulation Platform Unit, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
| | - Yousuke Ohno
- Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
| | - Makoto Taiji
- Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan.
- Drug Discovery Molecular Simulation Platform Unit, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan.
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913
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Stasi C, Fallani S, Voller F, Silvestri C. Treatment for COVID-19: An overview. Eur J Pharmacol 2020; 889:173644. [PMID: 33053381 PMCID: PMC7548059 DOI: 10.1016/j.ejphar.2020.173644] [Citation(s) in RCA: 173] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/03/2020] [Accepted: 10/08/2020] [Indexed: 02/06/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is an infectious disease caused by coronavirus-2 (SARS-CoV-2) that causes a severe acute respiratory syndrome, a characteristic hyperinflammatory response, vascular damage, microangiopathy, angiogenesis and widespread thrombosis. Four stages of COVID-19 have been identified: the first stage is characterised by upper respiratory tract infection; the second by the onset of dyspnoea and pneumonia; the third by a worsening clinical scenario dominated by a cytokine storm and the consequent hyperinflammatory state; and the fourth by death or recovery. Currently, no treatment can act specifically against the SARS-CoV-2 infection. Based on the pathological features and different clinical phases of COVID-19, particularly in patients with moderate to severe COVID-19, the classes of drugs used are antiviral agents, inflammation inhibitors/antirheumatic drugs, low molecular weight heparins, plasma, and hyperimmune immunoglobulins. During this emergency period of the COVID-19 outbreak, clinical researchers are using and testing a variety of possible treatments. Based on these premises, this review aims to discuss the most updated pharmacological treatments to effectively act against the SARS-CoV-2 infection and support researchers and clinicians in relation to any current and future developments in curing COVID-19 patients.
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Affiliation(s)
- Cristina Stasi
- Epidemiology Unit, Tuscany Regional Health Agency, Florence, Italy; Department of Experimental and Clinical Medicine, Careggi University Hospital, Florence, Italy.
| | - Silvia Fallani
- Epidemiology Unit, Tuscany Regional Health Agency, Florence, Italy
| | - Fabio Voller
- Epidemiology Unit, Tuscany Regional Health Agency, Florence, Italy
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914
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Zhu W, Xu M, Chen CZ, Guo H, Shen M, Hu X, Shinn P, Klumpp-Thomas C, Michael SG, Zheng W. Identification of SARS-CoV-2 3CL Protease Inhibitors by a Quantitative High-Throughput Screening. ACS Pharmacol Transl Sci 2020; 3:1008-1016. [PMID: 33062953 PMCID: PMC7507806 DOI: 10.1021/acsptsci.0c00108] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Indexed: 12/13/2022]
Abstract
The outbreak of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has emphasized the urgency to develop effective therapeutics. Drug repurposing screening is regarded as one of the most practical and rapid approaches for the discovery of such therapeutics. The 3C-like protease (3CLpro), or main protease (Mpro) of SARS-CoV-2 is a valid drug target as it is a specific viral enzyme and plays an essential role in viral replication. We performed a quantitative high-throughput screening (qHTS) of 10 755 compounds consisting of approved and investigational drugs, and bioactive compounds using a SARS-CoV-2 3CLpro assay. Twenty-three small molecule inhibitors of SARS-CoV-2 3CLpro have been identified with IC50s ranging from 0.26 to 28.85 μM. Walrycin B (IC50 = 0.26 μM), hydroxocobalamin (IC50 = 3.29 μM), suramin sodium (IC50 = 6.5 μM), Z-DEVD-FMK (IC50 = 6.81 μM), LLL-12 (IC50 = 9.84 μM), and Z-FA-FMK (IC50 = 11.39 μM) are the most potent 3CLpro inhibitors. The activity of the anti-SARS-CoV-2 viral infection was confirmed in 7 of 23 compounds using a SARS-CoV-2 cytopathic effect assay. The results demonstrated a set of SARS-CoV-2 3CLpro inhibitors that may have potential for further clinical evaluation as part of drug combination therapies to treating COVID-19 patients and as starting points for chemistry optimization for new drug development.
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Affiliation(s)
- Wei Zhu
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Miao Xu
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Catherine Z Chen
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Hui Guo
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Min Shen
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Xin Hu
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Paul Shinn
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Carleen Klumpp-Thomas
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Samuel G Michael
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Wei Zheng
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
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915
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Zhou QA, Kato-Weinstein J, Li Y, Deng Y, Granet R, Garner L, Liu C, Polshakov D, Gessner C, Watkins S. Potential Therapeutic Agents and Associated Bioassay Data for COVID-19 and Related Human Coronavirus Infections. ACS Pharmacol Transl Sci 2020; 3:813-834. [PMID: 33062950 PMCID: PMC7447080 DOI: 10.1021/acsptsci.0c00074] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Indexed: 02/07/2023]
Abstract
The COVID-19 pandemic, caused by the novel coronavirus SARS-CoV-2, has led to several million confirmed cases and hundreds of thousands of deaths worldwide. To support the ongoing research and development of COVID-19 therapeutics, this report provides an overview of protein targets and corresponding potential drug candidates with bioassay and structure-activity relationship data found in the scientific literature and patents for COVID-19 or related virus infections. Highlighted are several sets of small molecules and biologics that act on specific targets, including 3CLpro, PLpro, RdRp, S-protein-ACE2 interaction, helicase/NTPase, TMPRSS2, and furin, which are involved in the viral life cycle or in other aspects of the disease pathophysiology. We hope this report will be valuable to the ongoing drug repurposing efforts and the discovery of new therapeutics with the potential for treating COVID-19.
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Affiliation(s)
- Qiongqiong Angela Zhou
- CAS, a division
of the American Chemical Society, 2540 Olentangy River Road, Columbus, Ohio 43210-3012, United States
| | | | - Yingzhu Li
- CAS, a division
of the American Chemical Society, 2540 Olentangy River Road, Columbus, Ohio 43210-3012, United States
| | - Yi Deng
- CAS, a division
of the American Chemical Society, 2540 Olentangy River Road, Columbus, Ohio 43210-3012, United States
| | - Roger Granet
- CAS, a division
of the American Chemical Society, 2540 Olentangy River Road, Columbus, Ohio 43210-3012, United States
| | - Linda Garner
- CAS, a division
of the American Chemical Society, 2540 Olentangy River Road, Columbus, Ohio 43210-3012, United States
| | - Cynthia Liu
- CAS, a division
of the American Chemical Society, 2540 Olentangy River Road, Columbus, Ohio 43210-3012, United States
| | - Dmitrii Polshakov
- CAS, a division
of the American Chemical Society, 2540 Olentangy River Road, Columbus, Ohio 43210-3012, United States
| | - Chris Gessner
- CAS, a division
of the American Chemical Society, 2540 Olentangy River Road, Columbus, Ohio 43210-3012, United States
| | - Steven Watkins
- CAS, a division
of the American Chemical Society, 2540 Olentangy River Road, Columbus, Ohio 43210-3012, United States
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916
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Ma C, Hu Y, Townsend JA, Lagarias PI, Marty MT, Kolocouris A, Wang J. Ebselen, Disulfiram, Carmofur, PX-12, Tideglusib, and Shikonin Are Nonspecific Promiscuous SARS-CoV-2 Main Protease Inhibitors. ACS Pharmacol Transl Sci 2020; 3:1265-1277. [PMID: 33330841 PMCID: PMC7571300 DOI: 10.1021/acsptsci.0c00130] [Citation(s) in RCA: 155] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Indexed: 12/19/2022]
Abstract
![]()
Among the drug targets being investigated
for SARS-CoV-2, the viral
main protease (Mpro) is one of the most extensively studied.
Mpro is a cysteine protease that hydrolyzes the viral polyprotein
at more than 11 sites. It is highly conserved and has a unique substrate
preference for glutamine in the P1 position. Therefore, Mpro inhibitors are expected to have broad-spectrum antiviral activity
and a high selectivity index. Structurally diverse compounds have
been reported as Mpro inhibitors. In this study, we investigated
the mechanism of action of six previously reported Mpro inhibitors, ebselen, disulfiram, tideglusib, carmofur, shikonin,
and PX-12, using a consortium of techniques including FRET-based enzymatic
assay, thermal shift assay, native mass spectrometry, cellular antiviral
assays, and molecular dynamics simulations. Collectively, the results
showed that the inhibition of Mpro by these six compounds
is nonspecific and that the inhibition is abolished or greatly reduced
with the addition of reducing reagent 1,4-dithiothreitol (DTT). Without
DTT, these six compounds inhibit not only Mpro but also
a panel of viral cysteine proteases including SARS-CoV-2 papain-like
protease and 2Apro and 3Cpro from enterovirus
A71 (EV-A71) and EV-D68. However, none of the compounds inhibits the
viral replication of EV-A71 or EV-D68, suggesting that the enzymatic
inhibition potency IC50 values obtained in the absence
of DTT cannot be used to faithfully predict their cellular antiviral
activity. Overall, we provide compelling evidence suggesting that
these six compounds are nonspecific SARS-CoV-2 Mpro inhibitors
and urge the scientific community to be stringent with hit validation.
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Affiliation(s)
- Chunlong Ma
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, Arizona 85721, United States
| | - Yanmei Hu
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, Arizona 85721, United States
| | - Julia Alma Townsend
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
| | - Panagiotis I Lagarias
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Athens 15771, Greece
| | - Michael Thomas Marty
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
| | - Antonios Kolocouris
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Athens 15771, Greece
| | - Jun Wang
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, Arizona 85721, United States
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917
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Abstract
A large-scale screening campaign has yielded dozens of crystal structures of small molecule fragments that bind to the main protease of SARS-CoV-2. The global research community is encouraged to pursue these as drug discovery starting points for COVID-19.
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Affiliation(s)
- Daniel A Erlanson
- Frontier Medicines Corporation, 151 Oyster Point Blvd., 2nd Floor, South San Francisco, CA, 94080, USA.
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918
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Coelho C, Gallo G, Campos CB, Hardy L, Würtele M. Biochemical screening for SARS-CoV-2 main protease inhibitors. PLoS One 2020; 15:e0240079. [PMID: 33022015 PMCID: PMC7537881 DOI: 10.1371/journal.pone.0240079] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 09/18/2020] [Indexed: 01/22/2023] Open
Abstract
The Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) pandemic represents a global challenge. SARS-CoV-2's ability to replicate in host cells relies on the action of its non-structural proteins, like its main protease (Mpro). This cysteine protease acts by processing the viruses' precursor polyproteins. As proteases, together with polymerases, are main targets of antiviral drug design, we here have performed biochemical high throughput screening (HTS) with recombinantly expressed SARS-CoV-2 Mpro. A fluorescent assay was used to identify inhibitors in a compound library containing known drugs, bioactive molecules and natural products. These screens led to the identification of 13 inhibitors with IC50 values ranging from 0.2 μM to 23 μM. The screens confirmed several known SARS-CoV Mpro inhibitors as inhibitors of SARS-CoV-2 Mpro, such as the organo-mercuric compounds thimerosal and phenylmercuric acetate. Benzophenone derivatives could also be identified among the most potent screening hits. Additionally, Evans blue, a sulfonic acid-containing dye, could be identified as an Mpro inhibitor. The obtained compounds could be of interest as lead compounds for the development of future SARS-CoV-2 drugs.
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Affiliation(s)
- Camila Coelho
- Department of Science and Technology, Federal University of São Paulo, São José dos Campos, Brazil
| | - Gloria Gallo
- Department of Science and Technology, Federal University of São Paulo, São José dos Campos, Brazil
| | - Claudia B Campos
- Department of Science and Technology, Federal University of São Paulo, São José dos Campos, Brazil
| | - Leon Hardy
- Department of Physics, University of South Florida, Tampa, FL, United States of America
| | - Martin Würtele
- Department of Science and Technology, Federal University of São Paulo, São José dos Campos, Brazil
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919
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Xu Y, Jiang H. Potential treatment of COVID-19 by inhibitors of human dihydroorotate dehydrogenase. Protein Cell 2020; 11:699-702. [PMID: 32761523 PMCID: PMC7406694 DOI: 10.1007/s13238-020-00769-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Affiliation(s)
- Yechun Xu
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hualiang Jiang
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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920
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Charre C, Ginevra C, Sabatier M, Regue H, Destras G, Brun S, Burfin G, Scholtes C, Morfin F, Valette M, Lina B, Bal A, Josset L. Evaluation of NGS-based approaches for SARS-CoV-2 whole genome characterisation. Virus Evol 2020; 6:veaa075. [PMID: 33318859 PMCID: PMC7665770 DOI: 10.1093/ve/veaa075] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Since the beginning of the COVID-19 outbreak, SARS-CoV-2 whole-genome sequencing (WGS) has been performed at unprecedented rate worldwide with the use of very diverse Next-Generation Sequencing (NGS) methods. Herein, we compare the performance of four NGS-based approaches for SARS-CoV-2 WGS. Twenty-four clinical respiratory samples with a large scale of Ct values (from 10.7 to 33.9) were sequenced with four methods. Three used Illumina sequencing: an in-house metagenomic NGS (mNGS) protocol and two newly commercialised kits including a hybridisation capture method developed by Illumina (DNA Prep with Enrichment kit and Respiratory Virus Oligo Panel, RVOP), and an amplicon sequencing method developed by Paragon Genomics (CleanPlex SARS-CoV-2 kit). We also evaluated the widely used amplicon sequencing protocol developed by ARTIC Network and combined with Oxford Nanopore Technologies (ONT) sequencing. All four methods yielded near-complete genomes (>99%) for high viral loads samples (n = 8), with mNGS and RVOP producing the most complete genomes. For mid viral loads (Ct 20–25), amplicon-based enrichment methods led to genome coverage >99 per cent for all samples while 1/8 sample sequenced with RVOP and 2/8 samples sequenced with mNGS had a genome coverage below 99 per cent. For low viral loads (Ct ≥25), amplicon-based enrichment methods were the most sensitive techniques. All methods were highly concordant in terms of identity in complete consensus sequence. Just one mismatch in three samples was observed in CleanPlex vs the other methods, due to the dedicated bioinformatics pipeline setting a high threshold to call SNP compared to reference sequence. Importantly, all methods correctly identified a newly observed 34nt-deletion in ORF6 but required specific bioinformatic validation for RVOP. Finally, as a major warning for targeted techniques, a loss of coverage in any given region of the genome should alert to a potential rearrangement or a SNP in primer-annealing or probe-hybridizing regions and would require further validation using unbiased metagenomic sequencing.
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Affiliation(s)
- Caroline Charre
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France.,Université de Lyon, Université Claude Bernard Lyon 1 (UCBL1), Lyon, France.,Centre de recherche en cancérologie (CRCL), INSERM U1052- 69008, Lyon, France
| | - Christophe Ginevra
- CIRI, Centre International de Recherche en Infectiologie, (Team pathogenesis of Legionella), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon 69007, France.,Hospices Civils de Lyon, Centre National de Référence des Légionelles, Lyon, France
| | - Marina Sabatier
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France.,Université de Lyon, Université Claude Bernard Lyon 1 (UCBL1), Lyon, France.,Université de Lyon, Virpath, CIRI, INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Hadrien Regue
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France.,Université de Lyon, Université Claude Bernard Lyon 1 (UCBL1), Lyon, France
| | - Grégory Destras
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France.,Université de Lyon, Université Claude Bernard Lyon 1 (UCBL1), Lyon, France.,Université de Lyon, Virpath, CIRI, INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France.,Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France
| | - Solenne Brun
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France.,Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France
| | - Gwendolyne Burfin
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France.,Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France
| | - Caroline Scholtes
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France.,Université de Lyon, Université Claude Bernard Lyon 1 (UCBL1), Lyon, France.,Centre de recherche en cancérologie (CRCL), INSERM U1052- 69008, Lyon, France
| | - Florence Morfin
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France.,Université de Lyon, Université Claude Bernard Lyon 1 (UCBL1), Lyon, France.,Université de Lyon, Virpath, CIRI, INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France.,Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France
| | - Martine Valette
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France.,Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France
| | - Bruno Lina
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France.,Université de Lyon, Université Claude Bernard Lyon 1 (UCBL1), Lyon, France.,Université de Lyon, Virpath, CIRI, INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France.,Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France
| | - Antonin Bal
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France.,Université de Lyon, Université Claude Bernard Lyon 1 (UCBL1), Lyon, France.,Université de Lyon, Virpath, CIRI, INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France.,Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France
| | - Laurence Josset
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France.,Université de Lyon, Université Claude Bernard Lyon 1 (UCBL1), Lyon, France.,Université de Lyon, Virpath, CIRI, INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France.,Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France
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921
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Dong Y, Dai T, Liu J, Zhang L, Zhou F. Coronavirus in Continuous Flux: From SARS-CoV to SARS-CoV-2. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2001474. [PMID: 32837848 PMCID: PMC7361144 DOI: 10.1002/advs.202001474] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/25/2020] [Indexed: 05/07/2023]
Abstract
The world is currently experiencing a global pandemic caused by a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes severe respiratory disease similar to SARS. Previous studies have suggested that SARS-CoV-2 shares 79% and 96% sequence identity to SARS-CoV and to bat coronavirus RaTG13, respectively, at the whole-genome level. Furthermore, a series of studies have shown that SARS-CoV-2 induces clusters of severe respiratory illnesses (i.e., pneumonia, acute lung injury, acute respiratory distress syndrome) resembling SARS-CoV. Moreover, the pathological syndrome may, in part, be caused by cytokine storms and dysregulated immune responses. Thus, in this work the recent literature surrounding the biology, clinical manifestations, and immunology of SARS-CoV-2 is summarized, with the aim of aiding prevention, diagnosis, and treatment for SARS-CoV-2 infection.
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Affiliation(s)
- Yetian Dong
- Institutes of Biology and Medical SciencesSoochow UniversitySuzhou215123P. R. China
- Life Sciences Institute and Innovation Center for Cell Signaling NetworkHangzhouZhejiang310058P. R. China
| | - Tong Dai
- Institutes of Biology and Medical SciencesSoochow UniversitySuzhou215123P. R. China
| | - Jun Liu
- Pinghu Food and Drug Inspection CenterPinghuZhejiang314200P. R. China
| | - Long Zhang
- Life Sciences Institute and Innovation Center for Cell Signaling NetworkHangzhouZhejiang310058P. R. China
| | - Fangfang Zhou
- Institutes of Biology and Medical SciencesSoochow UniversitySuzhou215123P. R. China
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922
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Mahalapbutr P, Kongtaworn N, Rungrotmongkol T. Structural insight into the recognition of S-adenosyl-L-homocysteine and sinefungin in SARS-CoV-2 Nsp16/Nsp10 RNA cap 2'-O-Methyltransferase. Comput Struct Biotechnol J 2020; 18:2757-2765. [PMID: 33020707 PMCID: PMC7527316 DOI: 10.1016/j.csbj.2020.09.032] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 09/21/2020] [Accepted: 09/23/2020] [Indexed: 01/07/2023] Open
Abstract
The binding affinity towards SARS-CoV-2 nsp16 of SFG is higher than that of SAH. Asp99 is a key binding residue for SAH and SFG via charge-charge attraction. SFG could electrostatically interact with the 2′-OH and N3 groups of adenosine moiety of RNA substrate. The distance between 2′-OH of RNA and –NH3+ (at 6′ position) of SFG mimics the methyl transfer reaction.
The recent ongoing coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to rapidly spread across the world. To date, neither a specific antiviral drug nor a clinically effective vaccine is available. Among the 15 viral non-structural proteins (nsps), nsp16 methyltransferase has been considered as a potential target due to its crucial role in RNA cap 2′-O-methylation process, preventing the virus detection by cell innate immunity mechanisms. In the present study, molecular recognition between the two natural nucleoside analogs (S-adenosyl-l-homocysteine (SAH) and sinefungin (SFG)) and the SARS-CoV-2 nsp16/nsp10/m7GpppAC5 was studied using all-atom molecular dynamics simulations and free energy calculations based on MM/GBSA and WaterSwap approaches. The binding affinity and the number of hot-spot residues, atomic contacts, and H-bond formations of SFG/nsp16 complex were distinctly higher than those of SAH/nsp16 system, consistent with the lower water accessibility at the enzyme active site. Notably, only SFG could electrostatically interact with the 2′-OH and N3 of RNA’s adenosine moiety, mimicking the methyl transfer reaction of S-adenosyl-l-methionine substrate. The atomistic binding mechanism obtained from this work paves the way for further optimizations and designs of more specific SARS-CoV-2 nsp16 inhibitors in the fight against COVID-19.
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Affiliation(s)
- Panupong Mahalapbutr
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Napat Kongtaworn
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
| | - Thanyada Rungrotmongkol
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
- Biocatalyst and Environmental Biotechnology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Corresponding author at: Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand.
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923
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Ferraz WR, Gomes RA, S Novaes AL, Goulart Trossini GH. Ligand and structure-based virtual screening applied to the SARS-CoV-2 main protease: an in silico repurposing study. Future Med Chem 2020; 12:1815-1828. [PMID: 32787684 PMCID: PMC7453759 DOI: 10.4155/fmc-2020-0165] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 07/02/2020] [Indexed: 12/17/2022] Open
Abstract
Aim: The identification of drugs for the coronavirus disease-19 pandemic remains urgent. In this manner, drug repurposing is a suitable strategy, saving resources and time normally spent during regular drug discovery frameworks. Essential for viral replication, the main protease has been explored as a promising target for the drug discovery process. Materials & methods: Our virtual screening pipeline relies on the known 3D properties of noncovalent ligands and features of crystalized complexes, applying consensus analyses in each step. Results: Two oral (bedaquiline and glibenclamide) and one buccal drug (miconazole) presented 3D similarity to known ligands, reasonable predicted binding modes and micromolar predicted binding affinity values. Conclusion: We identified three approved drugs as promising inhibitors of the main viral protease and suggested design insights for future studies for development of novel selective inhibitors.
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Affiliation(s)
- Witor Ribeiro Ferraz
- Faculdade de Ciências Farmacêuticas, Universidade de São Paulo; Av. Prof. Lineu Prestes, 580, São Paulo, SP, 05508-000, Brasil
| | - Renan Augusto Gomes
- Faculdade de Ciências Farmacêuticas, Universidade de São Paulo; Av. Prof. Lineu Prestes, 580, São Paulo, SP, 05508-000, Brasil
| | - Andre Luis S Novaes
- Faculdade de Ciências Farmacêuticas, Universidade de São Paulo; Av. Prof. Lineu Prestes, 580, São Paulo, SP, 05508-000, Brasil
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924
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Nguyen DD, Gao K, Chen J, Wang R, Wei GW. Unveiling the molecular mechanism of SARS-CoV-2 main protease inhibition from 137 crystal structures using algebraic topology and deep learning. Chem Sci 2020; 11:12036-12046. [PMID: 34123218 PMCID: PMC8162568 DOI: 10.1039/d0sc04641h] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 09/30/2020] [Indexed: 12/27/2022] Open
Abstract
Currently, there is neither effective antiviral drugs nor vaccine for coronavirus disease 2019 (COVID-19) caused by acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Due to its high conservativeness and low similarity with human genes, SARS-CoV-2 main protease (Mpro) is one of the most favorable drug targets. However, the current understanding of the molecular mechanism of Mpro inhibition is limited by the lack of reliable binding affinity ranking and prediction of existing structures of Mpro-inhibitor complexes. This work integrates mathematics (i.e., algebraic topology) and deep learning (MathDL) to provide a reliable ranking of the binding affinities of 137 SARS-CoV-2 Mpro inhibitor structures. We reveal that Gly143 residue in Mpro is the most attractive site to form hydrogen bonds, followed by Glu166, Cys145, and His163. We also identify 71 targeted covalent bonding inhibitors. MathDL was validated on the PDBbind v2016 core set benchmark and a carefully curated SARS-CoV-2 inhibitor dataset to ensure the reliability of the present binding affinity prediction. The present binding affinity ranking, interaction analysis, and fragment decomposition offer a foundation for future drug discovery efforts.
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Affiliation(s)
- Duc Duy Nguyen
- Department of Mathematics, University of Kentucky KY 40506 USA
| | - Kaifu Gao
- Department of Mathematics, Michigan State University MI 48824 USA
| | - Jiahui Chen
- Department of Mathematics, Michigan State University MI 48824 USA
| | - Rui Wang
- Department of Mathematics, Michigan State University MI 48824 USA
| | - Guo-Wei Wei
- Department of Mathematics, Michigan State University MI 48824 USA
- Department of Biochemistry and Molecular Biology, Michigan State University MI 48824 USA
- Department of Electrical and Computer Engineering, Michigan State University MI 48824 USA
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925
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Ramos-Guzmán CA, Ruiz-Pernía JJ, Tuñón I. Unraveling the SARS-CoV-2 Main Protease Mechanism Using Multiscale Methods. ACS Catal 2020; 10:12544-12554. [PMID: 34192089 PMCID: PMC7556163 DOI: 10.1021/acscatal.0c03420] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/26/2020] [Indexed: 12/25/2022]
Abstract
We present a detailed theoretical analysis of the reaction mechanism of proteolysis catalyzed by the main protease of SARS-CoV-2. Using multiscale simulation methods, we have characterized the interactions established by a peptidic substrate in the active site, and then we have explored the free energy landscape associated with the acylation and deacylation steps of the proteolysis reaction, characterizing the transition states of the process. Our mechanistic proposals can explain most of the experimental observations made on the highly similar ortholog protease of SARS-CoV. We point to some key interactions that may facilitate the acylation process and thus can be crucial in the design of more specific and efficient inhibitors of the main protease activity. In particular, from our results, the P1' residue can be a key factor to improve the thermodynamics and kinetics of the inhibition process.
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Affiliation(s)
| | | | - Iñaki Tuñón
- Departamento de Química
Física, Universidad de Valencia,
46100 Burjassot, Spain
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926
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Kumar BK, Faheem, Sekhar KVGC, Ojha R, Prajapati VK, Pai A, Murugesan S. Pharmacophore based virtual screening, molecular docking, molecular dynamics and MM-GBSA approach for identification of prospective SARS-CoV-2 inhibitor from natural product databases. J Biomol Struct Dyn 2020; 40:1363-1386. [PMID: 32981461 PMCID: PMC7544939 DOI: 10.1080/07391102.2020.1824814] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) primarily
appeared in Wuhan, China, in December 2019. At present, no proper therapy and vaccinations
are available for the disease, and it is increasing day by day with a high mortality rate.
Pharmacophore based virtual screening of the selected natural product databases followed
by Glide molecular docking and dynamics studies against SARS-CoV-2 main protease was
investigated to identify potential ligands that may act as inhibitors. The molecules
SN00293542 and SN00382835 revealed the highest docking score
of −14.57 and −12.42 kcal/mol, respectively, when compared with
the co-crystal ligands of PDB-6Y2F (O6K) and 6W63 (X77) of the SARS-CoV-2 Mpro.
To further validate the interactions of top scored molecules SN00293542 and
SN00382835, molecular dynamics study of 100 ns was carried out. This
indicated that the protein-ligand complex was stable throughout the simulation period, and
minimal backbone fluctuations have ensued in the system. Post-MM-GBSA analysis of
molecular dynamics data showed free binding energy-71.7004 +/− 7.98, −56.81+/−
7.54 kcal/mol, respectively. The computational study identified several ligands
that may act as potential inhibitors of SARS-CoV-2 Mpro. The top-ranked
molecules SN00293542, and SN00382835 occupied the active site of
the target, the main protease like that of the co-crystal ligand. These molecules may
emerge as a promising ligands against SARS-CoV-2 and thus needs further detailed
investigations. Communicated by Ramaswamy H. Sarma
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Affiliation(s)
- Banoth Karan Kumar
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Pilani, India
| | - Faheem
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Pilani, India
| | | | - Rupal Ojha
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Kishangarh, India
| | - Vijay Kumar Prajapati
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Kishangarh, India
| | - Aravinda Pai
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences (MCOPS); MAHE, Manipal, India
| | - Sankaranarayanan Murugesan
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Pilani, India
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927
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Abstract
The magnitude of the morbidity and mortality inflicted upon the global population in less than 1 year has driven the inescapable conclusion that the discovery and development of effective antiviral drugs for COVID-19 are urgent and should be prioritized. The antiviral drug discovery programs that emerged for HIV and hepatitis C virus have enabled technology and expertise to accelerate this process for SARS-CoV-2. The description of candidate lead inhibitors for the viral main protease (Mpro) exemplifies this accelerated approach and reminds us of the needs and opportunities for addressing this pandemic. The magnitude of the morbidity and mortality inflicted upon the global population in less than 1 year has driven the inescapable conclusion that the discovery and development of effective antiviral drugs for COVID-19 are urgent and should be prioritized. The antiviral drug discovery programs that emerged for HIV and hepatitis C virus have enabled technology and expertise to accelerate this process for SARS-CoV-2. The description of candidate lead inhibitors for the viral main protease (Mpro) exemplifies this accelerated approach and reminds us of the needs and opportunities for addressing this pandemic.
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928
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Borquaye LS, Gasu EN, Ampomah GB, Kyei LK, Amarh MA, Mensah CN, Nartey D, Commodore M, Adomako AK, Acheampong P, Mensah JO, Mormor DB, Aboagye CI. Alkaloids from Cryptolepis sanguinolenta as Potential Inhibitors of SARS-CoV-2 Viral Proteins: An In Silico Study. BIOMED RESEARCH INTERNATIONAL 2020; 2020:5324560. [PMID: 33029513 PMCID: PMC7512045 DOI: 10.1155/2020/5324560] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 08/31/2020] [Accepted: 09/10/2020] [Indexed: 01/18/2023]
Abstract
The ongoing global pandemic caused by the human coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has infected millions of people and claimed hundreds of thousands of lives. The absence of approved therapeutics to combat this disease threatens the health of all persons on earth and could cause catastrophic damage to society. New drugs are therefore urgently required to bring relief to people everywhere. In addition to repurposing existing drugs, natural products provide an interesting alternative due to their widespread use in all cultures of the world. In this study, alkaloids from Cryptolepis sanguinolenta have been investigated for their ability to inhibit two of the main proteins in SARS-CoV-2, the main protease and the RNA-dependent RNA polymerase, using in silico methods. Molecular docking was used to assess binding potential of the alkaloids to the viral proteins whereas molecular dynamics was used to evaluate stability of the binding event. The results of the study indicate that all 13 alkaloids bind strongly to the main protease and RNA-dependent RNA polymerase with binding energies ranging from -6.7 to -10.6 kcal/mol. In particular, cryptomisrine, cryptospirolepine, cryptoquindoline, and biscryptolepine exhibited very strong inhibitory potential towards both proteins. Results from the molecular dynamics study revealed that a stable protein-ligand complex is formed upon binding. Alkaloids from Cryptolepis sanguinolenta therefore represent a promising class of compounds that could serve as lead compounds in the search for a cure for the corona virus disease.
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Affiliation(s)
- Lawrence Sheringham Borquaye
- Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Central Laboratory, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Edward Ntim Gasu
- Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Central Laboratory, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Gilbert Boadu Ampomah
- Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Lois Kwane Kyei
- Central Laboratory, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Margaret Amerley Amarh
- Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Caleb Nketia Mensah
- Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Daniel Nartey
- Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Michael Commodore
- Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Philipina Acheampong
- Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - David Batsa Mormor
- Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Caleb Impraim Aboagye
- Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
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929
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Kneller DW, Phillips G, O’Neill HM, Tan K, Joachimiak A, Coates L, Kovalevsky A. Room-temperature X-ray crystallography reveals the oxidation and reactivity of cysteine residues in SARS-CoV-2 3CL M pro: insights into enzyme mechanism and drug design. IUCRJ 2020; 7:S2052252520012634. [PMID: 33063790 PMCID: PMC7553146 DOI: 10.1107/s2052252520012634] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 09/16/2020] [Indexed: 05/12/2023]
Abstract
The emergence of the novel coronavirus SARS-CoV-2 has resulted in a worldwide pandemic not seen in generations. Creating treatments and vaccines to battle COVID-19, the disease caused by the virus, is of paramount importance in order to stop its spread and save lives. The viral main protease, 3CL Mpro, is indispensable for the replication of SARS-CoV-2 and is therefore an important target for the design of specific protease inhibitors. Detailed knowledge of the structure and function of 3CL Mpro is crucial to guide structure-aided and computational drug-design efforts. Here, the oxidation and reactivity of the cysteine residues of the protease are reported using room-temperature X-ray crystallography, revealing that the catalytic Cys145 can be trapped in the peroxysulfenic acid oxidation state at physiological pH, while the other surface cysteines remain reduced. Only Cys145 and Cys156 react with the alkylating agent N-ethylmaleimide. It is suggested that the zwitterionic Cys145-His45 catalytic dyad is the reactive species that initiates catalysis, rather than Cys145-to-His41 proton transfer via the general acid-base mechanism upon substrate binding. The structures also provide insight into the design of improved 3CL Mpro inhibitors.
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Affiliation(s)
- Daniel W. Kneller
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Gwyndalyn Phillips
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Hugh M. O’Neill
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Kemin Tan
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60667, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60667, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60367, USA
| | - Leighton Coates
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
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930
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Ma C, Hu Y, Townsend JA, Lagarias PI, Marty MT, Kolocouris A, Wang J. Ebselen, disulfiram, carmofur, PX-12, tideglusib, and shikonin are non-specific promiscuous SARS-CoV-2 main protease inhibitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.09.15.299164. [PMID: 32995786 PMCID: PMC7523112 DOI: 10.1101/2020.09.15.299164] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
There is an urgent need for vaccines and antiviral drugs to combat the COVID-19 pandemic. Encouraging progress has been made in developing antivirals targeting SARS-CoV-2, the etiological agent of COVID-19. Among the drug targets being investigated, the viral main protease (M pro ) is one of the most extensively studied drug targets. M pro is a cysteine protease that hydrolyzes the viral polyprotein at more than 11 sites and it is highly conserved among coronaviruses. In addition, M pro has a unique substrate preference for glutamine in the P1 position. Taken together, it appears that M pro inhibitors can achieve both broad-spectrum antiviral activity and a high selectivity index. Structurally diverse compounds have been reported as M pro inhibitors, with several of which also showed antiviral activity in cell culture. In this study, we investigated the mechanism of action of six previously reported M pro inhibitors, ebselen, disulfiram, tideglusib, carmofur, shikonin, and PX-12 using a consortium of techniques including FRET-based enzymatic assay, thermal shift assay, native mass spectrometry, cellular antiviral assays, and molecular dynamics simulations. Collectively, the results showed that the inhibition of M pro by these six compounds is non-specific and the inhibition is abolished or greatly reduced with the addition of reducing reagent DTT. In the absence of DTT, these six compounds not only inhibit M pro , but also a panel of viral cysteine proteases including SARS-CoV-2 papain-like protease, the 2A pro and 3C pro from enterovirus A71 (EV-A71) and EV-D68. However, none of the compounds inhibits the viral replication of EV-A71 or EV-D68, suggesting that the enzymatic inhibition potency IC 50 values obtained in the absence of DTT cannot be used to faithfully predict their cellular antiviral activity. Overall, we provide compelling evidence suggesting that ebselen, disulfiram, tideglusib, carmofur, shikonin, and PX-12 are non-specific SARS-CoV-2 M pro inhibitors, and urge the scientific community to be stringent with hit validation.
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Affiliation(s)
- Chunlong Ma
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, Arizona 85721, United States
| | - Yanmei Hu
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, Arizona 85721, United States
| | - Julia Alma Townsend
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
| | - Panagiotis I. Lagarias
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Greece
| | - Michael Thomas Marty
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
| | - Antonios Kolocouris
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Greece
| | - Jun Wang
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, Arizona 85721, United States
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931
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Khrenova MG, Tsirelson VG, Nemukhin AV. Dynamical properties of enzyme-substrate complexes disclose substrate specificity of the SARS-CoV-2 main protease as characterized by the electron density descriptors. Phys Chem Chem Phys 2020; 22:19069-19079. [PMID: 32812956 DOI: 10.1039/d0cp03560b] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A dynamical approach is proposed to discriminate between reactive (rES) and nonreactive (nES) enzyme-substrate complexes taking the SARS-CoV-2 main protease (Mpro) as an important example. Molecular dynamics simulations with the quantum mechanics/molecular mechanics potentials (QM(DFT)/MM-MD) followed by the electron density analysis are employed to evaluate geometry and electronic properties of the enzyme with different substrates along MD trajectories. We demonstrate that mapping the Laplacian of the electron density and the electron localization function provides easily visible images of the substrate activation that allow one to distinguish rES and nES. The computed fractions of reactive enzyme-substrate complexes along MD trajectories well correlate with the findings of recent experimental studies on the substrate specificity of Mpro. The results of our simulations demonstrate the role of the theory level used in QM subsystems for a proper description of the nucleophilic attack of the catalytic cysteine residue in Mpro. The activation of the carbonyl group of a substrate is correctly characterized with the hybrid DFT functional PBE0, whereas the use of a GGA-type PBE functional, that lacks the admixture of the Hartree-Fock exchange fails to describe activation.
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Affiliation(s)
- Maria G Khrenova
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Leninsky Prospect, 33, bld. 2, Moscow, 119071, Russia and Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | - Vladimir G Tsirelson
- Mendeleev University of Chemical Technology, Miusskaya Square, 9, Moscow, 125047, Russia
| | - Alexander V Nemukhin
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia. and Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia
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932
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Li S, Li S, Disoma C, Zheng R, Zhou M, Razzaq A, Liu P, Zhou Y, Dong Z, Du A, Peng J, Hu L, Huang J, Feng P, Jiang T, Xia Z. SARS‐CoV‐2: Mechanism of infection and emerging technologies for future prospects. Rev Med Virol 2020; 31:e2168. [DOI: 10.1002/rmv.2168] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 08/23/2020] [Accepted: 08/30/2020] [Indexed: 01/08/2023]
Affiliation(s)
- Shiqin Li
- Department of Cell Biology School of Life Sciences Central South University Changsha China
| | - Sijia Li
- Department of Cell Biology School of Life Sciences Central South University Changsha China
| | - Cyrollah Disoma
- Department of Cell Biology School of Life Sciences Central South University Changsha China
| | - Rong Zheng
- Department of Cell Biology School of Life Sciences Central South University Changsha China
| | - Mei Zhou
- Department of Cell Biology School of Life Sciences Central South University Changsha China
| | - Aroona Razzaq
- Department of Cell Biology School of Life Sciences Central South University Changsha China
| | - Pinjia Liu
- Department of Cell Biology School of Life Sciences Central South University Changsha China
| | - Yuzheng Zhou
- Department of Cell Biology School of Life Sciences Central South University Changsha China
- Section of Infection and Immunity Herman Ostrow School of Dentistry University of Southern California Los Angeles California USA
| | - Zijun Dong
- Department of Cell Biology School of Life Sciences Central South University Changsha China
| | - Ashuai Du
- Department of Cell Biology School of Life Sciences Central South University Changsha China
| | - Jian Peng
- Department of General Surgery Xiangya Hospital Central South University Changsha China
| | - Liqiang Hu
- The First Hospital of Changsha University of South China Changsha China
| | - Jufang Huang
- Department of Anatomy and Neurobiology School of Basic Medical Sciences Central South University Changsha China
- School of Life Sciences Central South University Changsha China
| | - Pinghui Feng
- Section of Infection and Immunity Herman Ostrow School of Dentistry University of Southern California Los Angeles California USA
| | - Taijiao Jiang
- Center for Systems Medicine Institute of Basic Medical Sciences Chinese Academy of Medical Sciences & Peking Union Medical College Beijing China
- Suzhou Institute of Systems Medicine Suzhou Jiangsu China
| | - Zanxian Xia
- Department of Cell Biology School of Life Sciences Central South University Changsha China
- Hunan Key Laboratory of Medical Genetics & Center for Medical Genetics School of Life Sciences Hunan Key Laboratory of Animal Models for Human Diseases Central South University Changsha China
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933
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Pavlova A, Lynch DL, Daidone I, Zanetti-Polzi L, Smith MD, Chipot C, Kneller DW, Kovalevsky A, Coates L, Golosov AA, Dickson CJ, Velez-Vega C, Duca JS, Vermaas JV, Pang YT, Acharya A, Parks JM, Smith JC, Gumbart JC. Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 32935106 DOI: 10.1101/2020.09.07.286344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The main protease (M pro ) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an attractive target for antiviral therapeutics. Recently, many high-resolution apo and inhibitor-bound structures of M pro , a cysteine protease, have been determined, facilitating structure-based drug design. M pro plays a central role in the viral life cycle by catalyzing the cleavage of SARS-CoV-2 polyproteins. In addition to the catalytic dyad His41-Cys145, M pro contains multiple histidines including His163, His164, and His172. The protonation states of these histidines and the catalytic nu-cleophile Cys145 have been debated in previous studies of SARS-CoV M pro , but have yet to be investigated for SARS-CoV-2. In this work we have used molecular dynamics simulations to determine the structural stability of SARS-CoV-2 M pro as a function of the protonation assignments for these residues. We simulated both the apo and inhibitor-bound enzyme and found that the conformational stability of the binding site, bound inhibitors, and the hydrogen bond networks of M pro are highly sensitive to these assignments. Additionally, the two inhibitors studied, the peptidomimetic N3 and an α -ketoamide, display distinct His41/His164 protonation-state-dependent stabilities. While the apo and the N3-bound systems favored N δ (HD) and N ϵ (HE) protonation of His41 and His164, respectively, the α -ketoamide was not stably bound in this state. Our results illustrate the importance of using appropriate histidine protonation states to accurately model the structure and dynamics of SARS-CoV-2 M pro in both the apo and inhibitor-bound states, a necessary prerequisite for drug-design efforts.
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934
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Bonatto V, Batista PHJ, Cianni L, De Vita D, Silva DG, Cedron R, Tezuka DY, de Albuquerque S, Moraes CB, Franco CH, Lameira J, Leitão A, Montanari CA. On the intrinsic reactivity of highly potent trypanocidal cruzain inhibitors. RSC Med Chem 2020; 11:1275-1284. [PMID: 34095840 DOI: 10.1039/d0md00097c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 08/03/2020] [Indexed: 11/21/2022] Open
Abstract
The cysteine protease cruzipain is considered to be a validated target for therapeutic intervention in the treatment of Chagas disease. Hence, peptidomimetic cruzipain inhibitors having a reactive group (known as warhead) are subject to continuous studies to discover novel antichagasic compounds. Here, we evaluated how different warheads for a set of structurally similar related compounds could inhibit the activity of cruzipain and, ultimately, their trypanocidal effect. We first investigated in silico the intrinsic reactivity of these compounds by applying the Fukui index to correlate it with the enzymatic affinity. Then, we evaluated their potency against T. cruzi (Y and Tulahuen strains), which revealed the reversible cruzain inhibitor Neq0656 as a better trypanocidal agent (ECY.strain 50 = 0.1 μM; SI = 58.4) than the current drug benznidazole (ECY.strain 50 = 5.1 μM; SI > 19.6). We also measured the half-life time by HPLC analysis of three lead compounds in the presence of glutathione and cysteine to experimentally assess their intrinsic reactivity. Results clearly illustrated the reactivity trend for the warheads (azanitrile > aldehyde > nitrile), where the aldehyde displayed an intermediate intrinsic reactivity. Therefore, the aldehyde bearing peptidomimetic compounds should be subject for in-depth evaluation in the drug discovery process.
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Affiliation(s)
- Vinicius Bonatto
- Medicinal Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo Avenue Trabalhador Sancarlense, 400 23566-590 São Carlos/SP Brazil
| | - Pedro Henrique Jatai Batista
- Medicinal Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo Avenue Trabalhador Sancarlense, 400 23566-590 São Carlos/SP Brazil
| | - Lorenzo Cianni
- Medicinal Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo Avenue Trabalhador Sancarlense, 400 23566-590 São Carlos/SP Brazil
| | - Daniela De Vita
- Medicinal Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo Avenue Trabalhador Sancarlense, 400 23566-590 São Carlos/SP Brazil
| | - Daniel G Silva
- Medicinal Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo Avenue Trabalhador Sancarlense, 400 23566-590 São Carlos/SP Brazil
| | - Rodrigo Cedron
- Medicinal Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo Avenue Trabalhador Sancarlense, 400 23566-590 São Carlos/SP Brazil
| | - Daiane Y Tezuka
- Medicinal Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo Avenue Trabalhador Sancarlense, 400 23566-590 São Carlos/SP Brazil .,Ribeirão Preto School of Pharmaceutical Sciences, University of São Paulo Ribeirão Preto São Paulo Brazil
| | - Sérgio de Albuquerque
- Ribeirão Preto School of Pharmaceutical Sciences, University of São Paulo Ribeirão Preto São Paulo Brazil
| | - Carolina Borsoi Moraes
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM) Campinas São Paulo Brazil
| | - Caio Haddad Franco
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM) Campinas São Paulo Brazil
| | - Jerônimo Lameira
- Medicinal Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo Avenue Trabalhador Sancarlense, 400 23566-590 São Carlos/SP Brazil .,Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará Rua Augusto Corrêa 01 CP 66075-110 Belém-PA Brazil
| | - Andrei Leitão
- Medicinal Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo Avenue Trabalhador Sancarlense, 400 23566-590 São Carlos/SP Brazil
| | - Carlos A Montanari
- Medicinal Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo Avenue Trabalhador Sancarlense, 400 23566-590 São Carlos/SP Brazil
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935
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Evaluation of SARS-CoV-2 3C-like protease inhibitors using self-assembled monolayer desorption ionization mass spectrometry. Antiviral Res 2020; 182:104924. [PMID: 32896566 PMCID: PMC7834858 DOI: 10.1016/j.antiviral.2020.104924] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/21/2020] [Accepted: 08/22/2020] [Indexed: 01/25/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the COVID-19 pandemic that began in 2019. The coronavirus 3-chymotrypsin-like cysteine protease (3CLpro) controls replication and is therefore considered a major target for antiviral discovery. This study describes the evaluation of SARS-CoV-2 3CLpro inhibitors in a novel self-assembled monolayer desorption ionization mass spectrometry (SAMDI-MS) enzymatic assay. Compared with a traditional FRET readout, the label-free SAMDI-MS assay offers greater sensitivity and eliminates false positive inhibition from compound interference with the optical signal. The SAMDI-MS assay was optimized and validated with known inhibitors of coronavirus 3CLpro such as GC376 (IC50 = 0.060 μM), calpain inhibitors II and XII (IC50 ~20–25 μM). The FDA-approved drugs shikonin, disulfiram, and ebselen did not inhibit SARS-CoV-2 3CLpro activity in the SAMDI-MS assay under physiologically relevant reducing conditions. The three drugs did not directly inhibit human β-coronavirus OC-43 or SARS-CoV-2 in vitro, but instead induced cell death. In conclusion, the SAMDI-MS 3CLpro assay, combined with antiviral and cytotoxic assessment, provides a robust platform to evaluate antiviral agents directed against SARS-CoV-2. A novel label-free SARS-CoV-2 3CLpro enzymatic assay was developed using mass spectrometry (SAMDI-MS). Protease inhibitors active in the SAMDI-MS assay under reducing conditions also have antiviral effects in cells. Shikonin, disulfiram, and ebselen do not inhibit SARS-CoV-2 3CLpro in the SAMDI-MS assay. Shikonin, disulfiram, and ebselen do not directly inhibit SARS-CoV-2 but instead are toxic to cells.
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936
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Liang J, Karagiannis C, Pitsillou E, Darmawan KK, Ng K, Hung A, Karagiannis TC. Site mapping and small molecule blind docking reveal a possible target site on the SARS-CoV-2 main protease dimer interface. Comput Biol Chem 2020; 89:107372. [PMID: 32911432 PMCID: PMC7833639 DOI: 10.1016/j.compbiolchem.2020.107372] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/28/2020] [Accepted: 09/02/2020] [Indexed: 02/06/2023]
Abstract
The SARS-CoV-2 main protease (Mpro) has an important role in the viral life cycle. Inhibition of the active site or dimerization site of Mpro can mitigate activity. Mapping reveals a reactive pocket in the dimerization pocket at the apex of Mpro. Blind docking shows that ligands may preferentially bind at the apex of Mpro. Stable ligand interactions are formed at the active and apex sites of Mpro.
The SARS-CoV-2 virus is causing COVID-19 resulting in an ongoing pandemic with serious health, social, and economic implications. Much research is focused in repurposing or identifying new small molecules which may interact with viral or host-cell molecular targets. An important SARS-CoV-2 target is the main protease (Mpro), and the peptidomimetic α-ketoamides represent prototypical experimental inhibitors. The protease is characterised by the dimerization of two monomers each which contains the catalytic dyad defined by Cys145 and His41 residues (active site). Dimerization yields the functional homodimer. Here, our aim was to investigate small molecules, including lopinavir and ritonavir, α-ketoamide 13b, and ebselen, for their ability to interact with the Mpro. The sirtuin 1 agonist SRT1720 was also used in our analyses. Blind docking to each monomer individually indicated preferential binding of the ligands in the active site. Site-mapping of the dimeric protease indicated a highly reactive pocket in the dimerization region at the domain III apex. Blind docking consistently indicated a strong preference of ligand binding in domain III, away from the active site. Molecular dynamics simulations indicated that ligands docked both to the active site and in the dimerization region at the apex, formed relatively stable interactions. Overall, our findings do not obviate the superior potency with respect to inhibition of protease activity of covalently-linked inhibitors such as α-ketoamide 13b in the Mpro active site. Nevertheless, along with those from others, our findings highlight the importance of further characterisation of the Mpro active site and any potential allosteric sites.
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Affiliation(s)
- Julia Liang
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia; School of Science, College of Science, Engineering & Health, RMIT University, VIC 3001, Australia
| | - Chris Karagiannis
- School of Science, College of Science, Engineering & Health, RMIT University, VIC 3001, Australia; School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC 3052, Australia
| | - Eleni Pitsillou
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia; School of Science, College of Science, Engineering & Health, RMIT University, VIC 3001, Australia
| | - Kevion K Darmawan
- School of Science, College of Science, Engineering & Health, RMIT University, VIC 3001, Australia
| | - Ken Ng
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC 3052, Australia
| | - Andrew Hung
- School of Science, College of Science, Engineering & Health, RMIT University, VIC 3001, Australia
| | - Tom C Karagiannis
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia; Department of Clinical Pathology, The University of Melbourne, Parkville, VIC 3052, Australia.
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937
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Fu L, Ye F, Feng Y, Yu F, Wang Q, Wu Y, Zhao C, Sun H, Huang B, Niu P, Song H, Shi Y, Li X, Tan W, Qi J, Gao GF. Both Boceprevir and GC376 efficaciously inhibit SARS-CoV-2 by targeting its main protease. Nat Commun 2020; 11:4417. [PMID: 32887884 PMCID: PMC7474075 DOI: 10.1038/s41467-020-18233-x] [Citation(s) in RCA: 346] [Impact Index Per Article: 86.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 07/22/2020] [Indexed: 01/08/2023] Open
Abstract
COVID-19 was declared a pandemic on March 11 by WHO, due to its great threat to global public health. The coronavirus main protease (Mpro, also called 3CLpro) is essential for processing and maturation of the viral polyprotein, therefore recognized as an attractive drug target. Here we show that a clinically approved anti-HCV drug, Boceprevir, and a pre-clinical inhibitor against feline infectious peritonitis (corona) virus (FIPV), GC376, both efficaciously inhibit SARS-CoV-2 in Vero cells by targeting Mpro. Moreover, combined application of GC376 with Remdesivir, a nucleotide analogue that inhibits viral RNA dependent RNA polymerase (RdRp), results in sterilizing additive effect. Further structural analysis reveals binding of both inhibitors to the catalytically active side of SARS-CoV-2 protease Mpro as main mechanism of inhibition. Our findings may provide critical information for the optimization and design of more potent inhibitors against the emerging SARS-CoV-2 virus.
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Affiliation(s)
- Lifeng Fu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
- Center for Influenza Research and Early Warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Disease (CEEID), Chinese Academy of Sciences, 100101, Beijing, China
| | - Fei Ye
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control & Prevention, Chinese Center for Disease Control and Prevention, China CDC, 102206, Beijing, China
| | - Yong Feng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Feng Yu
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, 201204, Shanghai, China
| | - Qisheng Wang
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, 201204, Shanghai, China
| | - Yan Wu
- Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, 100101, Beijing, China
- Department of Pathogen Microbiology, School of Basic Medical Sciences, Capital Medical University, 100069, Beijing, China
| | - Cheng Zhao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Huan Sun
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Baoying Huang
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control & Prevention, Chinese Center for Disease Control and Prevention, China CDC, 102206, Beijing, China
| | - Peihua Niu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control & Prevention, Chinese Center for Disease Control and Prevention, China CDC, 102206, Beijing, China
| | - Hao Song
- Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, 100101, Beijing, China
| | - Yi Shi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
- Center for Influenza Research and Early Warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Disease (CEEID), Chinese Academy of Sciences, 100101, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Xuebing Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
| | - Wenjie Tan
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control & Prevention, Chinese Center for Disease Control and Prevention, China CDC, 102206, Beijing, China.
| | - Jianxun Qi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China.
- Savaid Medical School, University of Chinese Academy of Sciences, 100049, Beijing, China.
| | - George Fu Gao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China.
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938
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Rao P, Shukla A, Parmar P, Rawal RM, Patel BV, Saraf M, Goswami D. Proposing a fungal metabolite-flaviolin as a potential inhibitor of 3CLpro of novel coronavirus SARS-CoV-2 identified using docking and molecular dynamics. J Biomol Struct Dyn 2020; 40:348-360. [DOI: 10.1080/07391102.2020.1813202] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Priyashi Rao
- Department of Biochemistry & Forensic Science, University School of Sciences, Gujarat University, Ahmedabad, India
| | - Arpit Shukla
- Department of Microbiology & Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, India
| | - Paritosh Parmar
- Department of Microbiology & Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, India
| | - Rakesh M. Rawal
- Department of Biochemistry & Forensic Science, University School of Sciences, Gujarat University, Ahmedabad, India
| | - Baldev V. Patel
- Department of Microbiology & Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, India
| | - Meenu Saraf
- Department of Microbiology & Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, India
| | - Dweipayan Goswami
- Department of Microbiology & Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, India
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939
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Drayman N, Jones KA, Azizi SA, Froggatt HM, Tan K, Maltseva NI, Chen S, Nicolaescu V, Dvorkin S, Furlong K, Kathayat RS, Firpo MR, Mastrodomenico V, Bruce EA, Schmidt MM, Jedrzejczak R, Muñoz-Alía MÁ, Schuster B, Nair V, Botten JW, Brooke CB, Baker SC, Mounce BC, Heaton NS, Dickinson BC, Jaochimiak A, Randall G, Tay S. Drug repurposing screen identifies masitinib as a 3CLpro inhibitor that blocks replication of SARS-CoV-2 in vitro. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 32908976 DOI: 10.1101/2020.08.31.274639] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
There is an urgent need for anti-viral agents that treat SARS-CoV-2 infection. The shortest path to clinical use is repurposing of drugs that have an established safety profile in humans. Here, we first screened a library of 1,900 clinically safe drugs for inhibiting replication of OC43, a human beta-coronavirus that causes the common-cold and is a relative of SARS-CoV-2, and identified 108 effective drugs. We further evaluated the top 26 hits and determined their ability to inhibit SARS-CoV-2, as well as other pathogenic RNA viruses. 20 of the 26 drugs significantly inhibited SARS-CoV-2 replication in human lung cells (A549 epithelial cell line), with EC50 values ranging from 0.1 to 8 micromolar. We investigated the mechanism of action for these and found that masitinib, a drug originally developed as a tyrosine-kinase inhibitor for cancer treatment, strongly inhibited the activity of the SARS-CoV-2 main protease 3CLpro. X-ray crystallography revealed that masitinib directly binds to the active site of 3CLpro, thereby blocking its enzymatic activity. Mastinib also inhibited the related viral protease of picornaviruses and blocked picornaviruses replication. Thus, our results show that masitinib has broad anti-viral activity against two distinct beta-coronaviruses and multiple picornaviruses that cause human disease and is a strong candidate for clinical trials to treat SARS-CoV-2 infection.
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940
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Russo M, Moccia S, Spagnuolo C, Tedesco I, Russo GL. Roles of flavonoids against coronavirus infection. Chem Biol Interact 2020; 328:109211. [PMID: 32735799 PMCID: PMC7385538 DOI: 10.1016/j.cbi.2020.109211] [Citation(s) in RCA: 189] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/13/2020] [Accepted: 07/23/2020] [Indexed: 01/18/2023]
Abstract
In terms of public health, the 21st century has been characterized by coronavirus pandemics: in 2002-03 the virus SARS-CoV caused SARS; in 2012 MERS-CoV emerged and in 2019 a new human betacoronavirus strain, called SARS-CoV-2, caused the unprecedented COVID-19 outbreak. During the course of the current epidemic, medical challenges to save lives and scientific research aimed to reveal the genetic evolution and the biochemistry of the vital cycle of the new pathogen could lead to new preventive and therapeutic strategies against SARS-CoV-2. Up to now, there is no cure for COVID-19 and waiting for an efficacious vaccine, the development of "savage" protocols, based on "old" anti-inflammatory and anti-viral drugs represents a valid and alternative therapeutic approach. As an alternative or additional therapeutic/preventive option, different in silico and in vitro studies demonstrated that small natural molecules, belonging to polyphenol family, can interfere with various stages of coronavirus entry and replication cycle. Here, we reviewed the capacity of well-known (e.g. quercetin, baicalin, luteolin, hesperetin, gallocatechin gallate, epigallocatechin gallate) and uncommon (e.g. scutellarein, amentoflavone, papyriflavonol A) flavonoids, secondary metabolites widely present in plant tissues with antioxidant and anti-microbial functions, to inhibit key proteins involved in coronavirus infective cycle, such as PLpro, 3CLpro, NTPase/helicase. Due to their pleiotropic activities and lack of systemic toxicity, flavonoids and their derivative may represent target compounds to be tested in future clinical trials to enrich the drug arsenal against coronavirus infections.
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Affiliation(s)
| | | | | | | | - Gian Luigi Russo
- National Research Council, Institute of Food Sciences, 83100, Avellino, Italy.
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941
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Li C, Wang L, Ren L. Antiviral mechanisms of candidate chemical medicines and traditional Chinese medicines for SARS-CoV-2 infection. Virus Res 2020; 286:198073. [PMID: 32592817 PMCID: PMC7313518 DOI: 10.1016/j.virusres.2020.198073] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 06/22/2020] [Accepted: 06/22/2020] [Indexed: 01/08/2023]
Abstract
The Coronavirus Disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly become a global pandemic. Up to now, numerous medicines have been applied or approved for the prevention and control of the virus infection. However, the efficiency of each medicine or combination is completely different or still unknown. In this review, we discuss the types, characteristics, antiviral mechanisms, and shortcomings of recommended candidate medicines for SARS-CoV-2 infection, as well as perspectives of the drugs for the disease treatment, which may provide a theoretical basis for drug screening and application.
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Affiliation(s)
- Chang Li
- Research Unit of Key Technologies for Prevention and Control of Virus Zoonoses, Chinese Academy of Medical Sciences, Military Veterinary Institute, Academy of Military Medical Sciences, Changchun, 130122, China
| | - Lin Wang
- Key Lab for Zoonoses Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Linzhu Ren
- Key Lab for Zoonoses Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun 130062, China.
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942
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Fan S, Xiao D, Wang Y, Liu L, Zhou X, Zhong W. Research progress on repositioning drugs and specific therapeutic drugs for SARS-CoV-2. Future Med Chem 2020; 12:1565-1578. [PMID: 32638628 PMCID: PMC7341957 DOI: 10.4155/fmc-2020-0158] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 06/22/2020] [Indexed: 12/12/2022] Open
Abstract
SARS-CoV-2 has been widely spread around the world and COVID-19 was declared a global pandemic by the WHO. Limited clinically effective antiviral drugs are available now. The development of anti-SARS-CoV-2 drugs has become an urgent work worldwide. At present, potential therapeutic targets and drugs for SARS-CoV-2 are continuously reported, and many repositioning drugs are undergoing extensive clinical research, including remdesivir and chloroquine. On the other hand, structures of many important viral target proteins and host target proteins, including that of RdRp and Mpro were constantly reported, which greatly promoted structure-based drug design. This paper summarizes the current research progress and challenges in the development of anti-SARS-CoV-2 drugs, and proposes novel short-term and long-term drug research strategies.
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Affiliation(s)
- Shiyong Fan
- National Engineering Research Center For The Emergency Drug, Beijing Institute of Pharmacology & Toxicology, Beijing, 100850, China
| | - Dian Xiao
- National Engineering Research Center For The Emergency Drug, Beijing Institute of Pharmacology & Toxicology, Beijing, 100850, China
| | - Yanming Wang
- National Engineering Research Center For The Emergency Drug, Beijing Institute of Pharmacology & Toxicology, Beijing, 100850, China
| | - Lianqi Liu
- National Engineering Research Center For The Emergency Drug, Beijing Institute of Pharmacology & Toxicology, Beijing, 100850, China
| | - Xinbo Zhou
- National Engineering Research Center For The Emergency Drug, Beijing Institute of Pharmacology & Toxicology, Beijing, 100850, China
| | - Wu Zhong
- National Engineering Research Center For The Emergency Drug, Beijing Institute of Pharmacology & Toxicology, Beijing, 100850, China
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943
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Anti-SARS-CoV-2 activities in vitro of Shuanghuanglian preparations and bioactive ingredients. Acta Pharmacol Sin 2020; 41:1167-1177. [PMID: 32737471 PMCID: PMC7393338 DOI: 10.1038/s41401-020-0483-6] [Citation(s) in RCA: 285] [Impact Index Per Article: 71.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 07/14/2020] [Indexed: 12/24/2022] Open
Abstract
Human infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19) and there is no cure currently. The 3CL protease (3CLpro) is a highly conserved protease which is indispensable for CoVs replication, and is a promising target for development of broad-spectrum antiviral drugs. In this study we investigated the anti-SARS-CoV-2 potential of Shuanghuanglian preparation, a Chinese traditional patent medicine with a long history for treating respiratory tract infection in China. We showed that either the oral liquid of Shuanghuanglian, the lyophilized powder of Shuanghuanglian for injection or their bioactive components dose-dependently inhibited SARS-CoV-2 3CLpro as well as the replication of SARS-CoV-2 in Vero E6 cells. Baicalin and baicalein, two ingredients of Shuanghuanglian, were characterized as the first noncovalent, nonpeptidomimetic inhibitors of SARS-CoV-2 3CLpro and exhibited potent antiviral activities in a cell-based system. Remarkably, the binding mode of baicalein with SARS-CoV-2 3CLpro determined by X-ray protein crystallography was distinctly different from those of known 3CLpro inhibitors. Baicalein was productively ensconced in the core of the substrate-binding pocket by interacting with two catalytic residues, the crucial S1/S2 subsites and the oxyanion loop, acting as a “shield” in front of the catalytic dyad to effectively prevent substrate access to the catalytic dyad within the active site. Overall, this study provides an example for exploring the in vitro potency of Chinese traditional patent medicines and effectively identifying bioactive ingredients toward a specific target, and gains evidence supporting the in vivo studies of Shuanghuanglian oral liquid as well as two natural products for COVID-19 treatment.
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944
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Ullrich S, Nitsche C. The SARS-CoV-2 main protease as drug target. Bioorg Med Chem Lett 2020; 30:127377. [PMID: 32738988 PMCID: PMC7331567 DOI: 10.1016/j.bmcl.2020.127377] [Citation(s) in RCA: 443] [Impact Index Per Article: 110.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/27/2020] [Accepted: 06/29/2020] [Indexed: 01/08/2023]
Abstract
The unprecedented pandemic of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is threatening global health. The virus emerged in late 2019 and can cause a severe disease associated with significant mortality. Several vaccine development and drug discovery campaigns are underway. The SARS-CoV-2 main protease is considered a promising drug target, as it is dissimilar to human proteases. Sequence and structure of the main protease are closely related to those from other betacoronaviruses, facilitating drug discovery attempts based on previous lead compounds. Covalently binding peptidomimetics and small molecules are investigated. Various compounds show antiviral activity in infected human cells.
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Affiliation(s)
- Sven Ullrich
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
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945
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Zhou X, Zhong F, Lin C, Hu X, Zhang Y, Xiong B, Yin X, Fu J, He W, Duan J, Fu Y, Zhou H, McCormick PJ, Wang Q, Li J, Zhang J. Structure of SARS-CoV-2 main protease in the apo state. SCIENCE CHINA-LIFE SCIENCES 2020; 64:656-659. [PMID: 32880863 PMCID: PMC7471536 DOI: 10.1007/s11427-020-1791-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 08/01/2020] [Indexed: 12/29/2022]
Affiliation(s)
- Xuelan Zhou
- School of Basic Medical Sciences, Nanchang University, Nanchang, 330031, China
| | - Fanglin Zhong
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou, 341000, China
- Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou, 341000, China
| | - Cheng Lin
- Shenzhen Crystalo Biopharmaceutical Co., Ltd, Shenzhen, 518118, China
- Jiangxi Jmerry Biopharmaceutical Co., Ltd, Ganzhou, 341000, China
| | - Xiaohui Hu
- School of Basic Medical Sciences, Nanchang University, Nanchang, 330031, China
| | - Yan Zhang
- The Second Affiliated Hospital of Nanchang University, Nanchang, 330031, China
| | - Bing Xiong
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Xiushan Yin
- Applied Biology Laboratory, Shenyang University of Chemical Technology, Shenyang, 110142, China
- Biotech & Biomedicine Science (Jiangxi) Co. Ltd, Ganzhou, 341000, China
| | - Jinheng Fu
- Jiangxi-OAI Joint Research Institution, Nanchang University, Nanchang, 330047, China
| | - Wei He
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou, 341000, China
| | - Jingjing Duan
- Human Aging Research Institute (HARI), School of Life Sciences, Nanchang University, Nanchang, 330031, China
| | - Yang Fu
- School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Huan Zhou
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China
| | - Peter J McCormick
- Centre for Endocrinology, William Harvey Research Institute, Bart's and the London School of Medicine and Dentistry, Queen Mary, University of London, London, EC1M 6BQ, UK
| | - Qisheng Wang
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China.
| | - Jian Li
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou, 341000, China.
- Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou, 341000, China.
| | - Jin Zhang
- School of Basic Medical Sciences, Nanchang University, Nanchang, 330031, China.
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946
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Mast FD, Navare AT, van der Sloot AM, Coulombe-Huntington J, Rout MP, Baliga NS, Kaushansky A, Chait BT, Aderem A, Rice CM, Sali A, Tyers M, Aitchison JD. Crippling life support for SARS-CoV-2 and other viruses through synthetic lethality. J Cell Biol 2020; 219:152015. [PMID: 32785687 PMCID: PMC7659715 DOI: 10.1083/jcb.202006159] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/28/2020] [Accepted: 07/28/2020] [Indexed: 02/07/2023] Open
Abstract
With the rapid global spread of SARS-CoV-2, we have become acutely aware of the inadequacies of our ability to respond to viral epidemics. Although disrupting the viral life cycle is critical for limiting viral spread and disease, it has proven challenging to develop targeted and selective therapeutics. Synthetic lethality offers a promising but largely unexploited strategy against infectious viral disease; as viruses infect cells, they abnormally alter the cell state, unwittingly exposing new vulnerabilities in the infected cell. Therefore, we propose that effective therapies can be developed to selectively target the virally reconfigured host cell networks that accompany altered cellular states to cripple the host cell that has been converted into a virus factory, thus disrupting the viral life cycle.
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Affiliation(s)
- Fred D Mast
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA
| | - Arti T Navare
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA
| | - Almer M van der Sloot
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Canada
| | | | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY
| | | | - Alexis Kaushansky
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA.,Department of Pediatrics, University of Washington, Seattle, WA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY
| | - Alan Aderem
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA.,Department of Pediatrics, University of Washington, Seattle, WA
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA
| | - Mike Tyers
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Canada
| | - John D Aitchison
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA.,Department of Pediatrics, University of Washington, Seattle, WA.,Department of Biochemistry, University of Washington, Seattle, WA
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947
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Resnick SJ, Iketani S, Hong SJ, Zask A, Liu H, Kim S, Melore S, Nair MS, Huang Y, Tay NE, Rovis T, Yang HW, Stockwell BR, Ho DD, Chavez A. A simplified cell-based assay to identify coronavirus 3CL protease inhibitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.08.29.272864. [PMID: 32869020 PMCID: PMC7457602 DOI: 10.1101/2020.08.29.272864] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We describe a mammalian cell-based assay capable of identifying coronavirus 3CL protease (3CLpro) inhibitors without requiring the use of live virus. By enabling the facile testing of compounds across a range of coronavirus 3CLpro enzymes, including the one from SARS-CoV-2, we are able to quickly identify compounds with broad or narrow spectra of activity. We further demonstrate the utility of our approach by performing a curated compound screen along with structure-activity profiling of a series of small molecules to identify compounds with antiviral activity. Throughout these studies, we observed concordance between data emerging from this assay and from live virus assays. By democratizing the testing of 3CL inhibitors to enable screening in the majority of laboratories rather than the few with extensive biosafety infrastructure, we hope to expedite the search for coronavirus 3CL protease inhibitors, to address the current epidemic and future ones that will inevitably arise.
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Affiliation(s)
- 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
| | - 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
| | - Seo Jung Hong
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Arie Zask
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Hengrui Liu
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - Sungsoo Kim
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Schuyler Melore
- Department of Pathology and Cell Biology, 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
| | - Tomislav Rovis
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - Hee Won Yang
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Brent R. Stockwell
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - David D. Ho
- Aaron Diamond AIDS Research Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Alejandro Chavez
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
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948
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Ghahremanpour MM, Tirado-Rives J, Deshmukh M, Ippolito JA, Zhang CH, de Vaca IC, Liosi ME, Anderson KS, Jorgensen WL. Identification of 14 Known Drugs as Inhibitors of the Main Protease of SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 32869018 DOI: 10.1101/2020.08.28.271957] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
A consensus virtual screening protocol has been applied to ca. 2000 approved drugs to seek inhibitors of the main protease (M pro ) of SARS-CoV-2, the virus responsible for COVID-19. 42 drugs emerged as top candidates, and after visual analyses of the predicted structures of their complexes with M pro , 17 were chosen for evaluation in a kinetic assay for M pro inhibition. Remarkably 14 of the compounds at 100-μM concentration were found to reduce the enzymatic activity and 5 provided IC 50 values below 40 μM: manidipine (4.8 μM), boceprevir (5.4 μM), lercanidipine (16.2 μM), bedaquiline (18.7 μM), and efonidipine (38.5 μM). Structural analyses reveal a common cloverleaf pattern for the binding of the active compounds to the P1, P1', and P2 pockets of M pro . Further study of the most active compounds in the context of COVID-19 therapy is warranted, while all of the active compounds may provide a foundation for lead optimization to deliver valuable chemotherapeutics to combat the pandemic.
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949
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Chen Y, Wang G, Ouyang L. Promising inhibitors targeting M pro: an ideal strategy for anti-SARS-CoV-2 drug discovery. Signal Transduct Target Ther 2020; 5:173. [PMID: 32855394 PMCID: PMC7450161 DOI: 10.1038/s41392-020-00291-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 07/29/2020] [Accepted: 08/05/2020] [Indexed: 02/05/2023] Open
Affiliation(s)
- Yi Chen
- State Key Laboratory of Biotherapy and Cancer Center & Department of Gastrointestinal Surgery, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, 610041, Chengdu, China
| | - Guan Wang
- State Key Laboratory of Biotherapy and Cancer Center & Department of Gastrointestinal Surgery, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, 610041, Chengdu, China
| | - Liang Ouyang
- State Key Laboratory of Biotherapy and Cancer Center & Department of Gastrointestinal Surgery, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, 610041, Chengdu, China.
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950
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Pillaiyar T, Wendt LL, Manickam M, Easwaran M. The recent outbreaks of human coronaviruses: A medicinal chemistry perspective. Med Res Rev 2020; 41:72-135. [PMID: 32852058 PMCID: PMC7461420 DOI: 10.1002/med.21724] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/22/2020] [Accepted: 08/08/2020] [Indexed: 01/18/2023]
Abstract
Coronaviruses (CoVs) infect both humans and animals. In humans, CoVs can cause respiratory, kidney, heart, brain, and intestinal infections that can range from mild to lethal. Since the start of the 21st century, three β‐coronaviruses have crossed the species barrier to infect humans: severe‐acute respiratory syndrome (SARS)‐CoV‐1, Middle East respiratory syndrome (MERS)‐CoV, and SARS‐CoV‐2 (2019‐nCoV). These viruses are dangerous and can easily be transmitted from human to human. Therefore, the development of anticoronaviral therapies is urgently needed. However, to date, no approved vaccines or drugs against CoV infections are available. In this review, we focus on the medicinal chemistry efforts toward the development of antiviral agents against SARS‐CoV‐1, MERS‐CoV, SARS‐CoV‐2, targeting biochemical events important for viral replication and its life cycle. These targets include the spike glycoprotein and its host‐receptors for viral entry, proteases that are essential for cleaving polyproteins to produce functional proteins, and RNA‐dependent RNA polymerase for viral RNA replication.
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Affiliation(s)
- Thanigaimalai Pillaiyar
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, Bonn, Germany
| | - Lukas L Wendt
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, Bonn, Germany
| | - Manoj Manickam
- Department of Chemistry, PSG Institute of Technology and Applied Research, Coimbatore, Tamil Nadu, India
| | - Maheswaran Easwaran
- Department of Biomedical Engineering, Sethu Institute of Technology, Virudhunagar, Tamilnadu, India
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