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Ali MA, Sheikh H, Yaseen M, Faruqe MO, Ullah I, Kumar N, Bhat MA, Mollah MNH. Exploring the Therapeutic Potential of Petiveria alliacea L. Phytochemicals: A Computational Study on Inhibiting SARS-CoV-2's Main Protease (Mpro). Molecules 2024; 29:2524. [PMID: 38893400 PMCID: PMC11173994 DOI: 10.3390/molecules29112524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 04/29/2024] [Accepted: 04/30/2024] [Indexed: 06/21/2024] Open
Abstract
The outbreak of SARS-CoV-2, also known as the COVID-19 pandemic, is still a critical risk factor for both human life and the global economy. Although, several promising therapies have been introduced in the literature to inhibit SARS-CoV-2, most of them are synthetic drugs that may have some adverse effects on the human body. Therefore, the main objective of this study was to carry out an in-silico investigation into the medicinal properties of Petiveria alliacea L. (P. alliacea L.)-mediated phytocompounds for the treatment of SARS-CoV-2 infections since phytochemicals have fewer adverse effects compared to synthetic drugs. To explore potential phytocompounds from P. alliacea L. as candidate drug molecules, we selected the infection-causing main protease (Mpro) of SARS-CoV-2 as the receptor protein. The molecular docking analysis of these receptor proteins with the different phytocompounds of P. alliacea L. was performed using AutoDock Vina. Then, we selected the three top-ranked phytocompounds (myricitrin, engeletin, and astilbin) as the candidate drug molecules based on their highest binding affinity scores of -8.9, -8.7 and -8.3 (Kcal/mol), respectively. Then, a 100 ns molecular dynamics (MD) simulation study was performed for their complexes with Mpro using YASARA software, computed RMSD, RMSF, PCA, DCCM, MM/PBSA, and free energy landscape (FEL), and found their almost stable binding performance. In addition, biological activity, ADME/T, DFT, and drug-likeness analyses exhibited the suitable pharmacokinetics properties of the selected phytocompounds. Therefore, the results of this study might be a useful resource for formulating a safe treatment plan for SARS-CoV-2 infections after experimental validation in wet-lab and clinical trials.
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Affiliation(s)
- Md. Ahad Ali
- Bioinformatics Laboratory, Department of Statistics, Faculty of Science, University of Rajshahi, Rajshahi 6205, Bangladesh;
- Department of Chemistry, Faculty of Science, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Humaira Sheikh
- Department of Chemistry, Faculty of Science, Bangabandhu Sheikh Mujibur Rahman Science & Technology University, Gopalganj 8100, Bangladesh;
| | - Muhammad Yaseen
- Institute of Chemical Sciences, University of Swat, Main Campus, Charbagh 19130, Pakistan;
| | - Md Omar Faruqe
- Department of Computer Science and Engineering, Faculty of Engineering, University of Rajshahi, Rajshahi 6205, Bangladesh;
| | - Ihsan Ullah
- Institute of Chemical Sciences, University of Swat, Main Campus, Charbagh 19130, Pakistan;
| | - Neeraj Kumar
- Department of Pharmaceutical Chemistry, Bhupal Nobles’ College of Pharmacy, Udaipur 313001, Rajasthan, India;
| | - Mashooq Ahmad Bhat
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Md. Nurul Haque Mollah
- Bioinformatics Laboratory, Department of Statistics, Faculty of Science, University of Rajshahi, Rajshahi 6205, Bangladesh;
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He Z, Yuan J, Zhang Y, Li R, Mo M, Wang Y, Ti H. Recent advances towards natural plants as potential inhibitors of SARS-Cov-2 targets. PHARMACEUTICAL BIOLOGY 2023; 61:1186-1210. [PMID: 37605622 PMCID: PMC10446791 DOI: 10.1080/13880209.2023.2241518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 05/29/2023] [Accepted: 07/23/2023] [Indexed: 08/23/2023]
Abstract
CONTEXT Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is still ongoing and currently the most striking epidemic disease. With the rapid global spread of SARS-CoV-2 variants, new antivirals are urgently needed to avert a more serious crisis. Inhibitors from traditional medicines or natural plants have shown promising results to fight COVID-19 with different mechanisms of action. OBJECTIVES To provide comprehensive and promising approaches to the medical community in the fight against this epidemic by reviewing potential plant-derived anti-SARS-CoV-2 inhibitors. METHODS Structural databases such as TCMSP (http://lsp.nwu.edu.cn/tcmsp.php), TCM Database @ Taiwan (http://tcm.cmu.edu.tw/), BATMAN-TCM (http://bionet.ncpsb.org/batman-tcm/) and TCMID (http://www.megabionet.org/tcmid/), as well as PubMed, Sci Finder, Research Gate, Science Direct, CNKI, Web of Science and Google Scholar were searched for relevant articles on TCMs and natural products against SARS-CoV-2. RESULTS Seven traditional Chinese medicines formulas have unique advantages in regulating the immune system for treating COVID-19. The plant-derived natural compounds as anti-SARS-CoV-2 inhibitors were identified based on 5 SARS-CoV-2 key proteins, namely, angiotensin-converting enzyme 2 (ACE2), 3 C-like protease (3CLpro), papain-like protease (PLpro), spike (S) protein, and nucleocapsid (N) protein. CONCLUSIONS A variety of natural products, such as flavonoids, terpenoids, phenols, and alkaloids, were identified, which could be used as potential SASR-Cov-2 inhibitors. These shed new light on the efficient discovery of SASR-Cov-2 inhibitors from natural products.
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Affiliation(s)
- Zhouman He
- School of Chinese Medicinal Resource, Guangdong Pharmaceutical University, Guangzhou, P. R. China
| | - Jia Yuan
- School of Chinese Medicinal Resource, Guangdong Pharmaceutical University, Guangzhou, P. R. China
| | - Yuanwen Zhang
- School of Chinese Medicinal Resource, Guangdong Pharmaceutical University, Guangzhou, P. R. China
| | - Runfeng Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, P. R. China
| | - Meilan Mo
- School of Chinese Medicinal Resource, Guangdong Pharmaceutical University, Guangzhou, P. R. China
| | - Yutao Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, P. R. China
| | - Huihui Ti
- School of Chinese Medicinal Resource, Guangdong Pharmaceutical University, Guangzhou, P. R. China
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Alghushairy O, Ali F, Alghamdi W, Khalid M, Alsini R, Asiry O. Machine learning-based model for accurate identification of druggable proteins using light extreme gradient boosting. J Biomol Struct Dyn 2023:1-12. [PMID: 37850427 DOI: 10.1080/07391102.2023.2269280] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 10/04/2023] [Indexed: 10/19/2023]
Abstract
The identification of druggable proteins (DPs) is significant for the development of new drugs, personalized medicine, understanding of disease mechanisms, drug repurposing, and economic benefits. By identifying new druggable targets, researchers can develop new therapies for a range of diseases, leading to better patient outcomes. Identification of DPs by machine learning strategies is more efficient and cost-effective than conventional methods. In this study, a computational predictor, namely Drug-LXGB, is introduced to enhance the identification of DPs. Features are discovered by composition, transition, and distribution (CTD), composition of K-spaced amino acid pair (CKSAAP), pseudo-position-specific scoring matrix (PsePSSM), and a novel descriptor, called multi-block pseudo amino acid composition (MB-PseAAC). The dimensions of CTD, CKSAAP, PsePSSM, and MB-PseAAC are integrated and utilized the sequential forward selection as feature selection algorithm. The best characteristics are provided by random forest, extreme gradient boosting, and light eXtreme gradient boosting (LXGB). The predictive analysis of these learning methods is measured via 10-fold cross-validation. The LXGB-based model secures the highest results than other existing predictors. Our novel protocol will perform an active role in designing novel drugs and would be fruitful to explore the potential target. This study will help better to capture a more universal view of a potential target.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Omar Alghushairy
- Department of Information Systems and Technology, College of Computer Science and Engineering, University of Jeddah, Jeddah, Saudi Arabia
| | - Farman Ali
- Department of Software Engineering, Sarhad University of Science and Information Technology Peshawar Mardan Campus, Peshawar, Pakistan
| | - Wajdi Alghamdi
- Department of Information Technology, Faculty of Computing and Information Technology, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Majdi Khalid
- Department of Computer Science, College of Computers and Information Systems, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Raed Alsini
- Department of Information Systems, Faculty of Computing and Information Technology, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Othman Asiry
- Department of Information Technology, College of Computing and Information Technology at Khulais, University of Jeddah, Jeddah, Saudi Arabia
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Dey P. Gut microbial considerations and feasibility of phytochemicals as anti-COVID prophylaxis: Critical role of bioavailability. Phytother Res 2023; 37:4301-4303. [PMID: 36597204 DOI: 10.1002/ptr.7722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/19/2022] [Accepted: 12/27/2022] [Indexed: 01/05/2023]
Affiliation(s)
- Priyankar Dey
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, India
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Swain SP, Ahamad S, Samarth N, Singh S, Gupta D, Kumar S. In silico studies of alkaloids and their derivatives against N-acetyltransferase EIS protein from Mycobacterium tuberculosis. J Biomol Struct Dyn 2023:1-15. [PMID: 37728544 DOI: 10.1080/07391102.2023.2259487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 09/09/2023] [Indexed: 09/21/2023]
Abstract
Antibiotic resistance against Mycobacterium tuberculosis (M.tb.) has been a significant cause of death worldwide. The Enhanced intracellular survival (EIS) protein of the bacteria is an acetyltransferase that multiacetylates aminoglycoside antibiotics, preventing them from binding to the bacterial ribosome. To overcome the EIS-mediated antibiotics resistance of M.tb., we compiled 888 alkaloids and derivatives from five different databases and virtually screened them against the EIS receptor. The compound library was filtered down to 87 compounds, which underwent additional analysis and filtration. Moreover, the top 15 most prominent phytocompounds were obtained after the drug-likeness prediction and ADMET screening. Out of 15, nine compounds confirmed the maximum number of hydrogen bond interactions and reliable binding energies during molecular docking. Additionally, the Molecular dynamics (MD) simulation of nine compounds showed the three most stable complexes, further verified by re-docking with mutated protein. The density functional theory (DFT) calculation was performed to identify the HOMO-LUMO energy gaps of the selected three potential compounds. Finally, our selected top lead compounds i.e., Alkaloid AQC2 (PubChem85634496), Nobilisitine A (ChEbi68116), and N-methylcheilanthifoline (ChEbi140673) demonstrated more favourable outcomes when compared with reference compounds (i.e., 39b and 2i) in all parameters used in this study. Therefore, we anticipate that our findings will help to explore and develop natural compound therapy against multi and extensively drug-resistant strains of M.tb.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Supriya P Swain
- Bioinformatics Lab, National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Shahzaib Ahamad
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Nikhil Samarth
- National Centre for Cell Science, NCCS Complex, Pune, India
| | - Shailza Singh
- National Centre for Cell Science, NCCS Complex, Pune, India
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Shailesh Kumar
- Bioinformatics Lab, National Institute of Plant Genome Research (NIPGR), New Delhi, India
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Giordano D, Facchiano A, Carbone V. Food Plant Secondary Metabolites Antiviral Activity and Their Possible Roles in SARS-CoV-2 Treatment: An Overview. Molecules 2023; 28:molecules28062470. [PMID: 36985442 PMCID: PMC10058909 DOI: 10.3390/molecules28062470] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 02/28/2023] [Accepted: 03/06/2023] [Indexed: 03/30/2023] Open
Abstract
Natural products and plant extracts exhibit many biological activities, including that related to the defense mechanisms against parasites. Many studies have investigated the biological functions of secondary metabolites and reported evidence of antiviral activities. The pandemic emergencies have further increased the interest in finding antiviral agents, and efforts are oriented to investigate possible activities of secondary plant metabolites against human viruses and their potential application in treating or preventing SARS-CoV-2 infection. In this review, we performed a comprehensive analysis of studies through in silico and in vitro investigations, also including in vivo applications and clinical trials, to evaluate the state of knowledge on the antiviral activities of secondary metabolites against human viruses and their potential application in treating or preventing SARS-CoV-2 infection, with a particular focus on natural compounds present in food plants. Although some of the food plant secondary metabolites seem to be useful in the prevention and as a possible therapeutic management against SARS-CoV-2, up to now, no molecules can be used as a potential treatment for COVID-19; however, more research is needed.
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Affiliation(s)
- Deborah Giordano
- Institute of Food Sciences, National Research Council, via Roma 64, 83100 Avellino, Italy
| | - Angelo Facchiano
- Institute of Food Sciences, National Research Council, via Roma 64, 83100 Avellino, Italy
| | - Virginia Carbone
- Institute of Food Sciences, National Research Council, via Roma 64, 83100 Avellino, Italy
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Pavlik P, Jost P, Rehulka P, Vozandychova V, Link M, Spidlova P. Epigallocatechin gallate inhibits Francisella tularensis growth and suppresses the function of DNA-binding protein HU. Microb Pathog 2023; 176:105999. [PMID: 36702369 DOI: 10.1016/j.micpath.2023.105999] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 01/11/2023] [Accepted: 01/18/2023] [Indexed: 01/25/2023]
Abstract
Francisella tularensis is a highly infectious intracellular bacterium causing tularemia disease and is regarded as a potential biological weapon. The development of a vaccine, effective treatment, or prophylactic substances targeted against tularemia is in the forefront of interest and could help to prevent or mitigate possible malevolent acts by bioterrorism utilizing F. tularensis. The viability of F. tularensis, and thus of a tularemia disease outbreak, might potentially be suppressed by simple commonly available natural substances. Epigallocatechin gallate (EGCG) is contained in green tea and its antimicrobial effect has been described. Here, we show that EGCG can suppress F. tularensis growth and is able to reduce the bacterium's ability to replicate inside mouse bone marrow-derived macrophages (BMMs) without side effects on BMMs' own viability. We suggest one (but not the only) mechanism of EGCG action. We demonstrate that EGCG can block the main functions of HU protein, the important regulator of F. tularensis virulence, leading to overall attenuation of F. tularensis viability. EGCG can delay death of mice infected by F. tularensis and can be used as a prophylactic agent against tularemia disease. Postponing death by up to 2 days can provide sufficient opportunity to administer another treatment agent.
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Affiliation(s)
- Pavla Pavlik
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500 01, Hradec Kralove, Czech Republic.
| | - Petr Jost
- Department of Toxicology and Military Pharmacy, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500 01, Hradec Kralove, Czech Republic.
| | - Pavel Rehulka
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500 01, Hradec Kralove, Czech Republic.
| | - Vera Vozandychova
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500 01, Hradec Kralove, Czech Republic.
| | - Marek Link
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500 01, Hradec Kralove, Czech Republic.
| | - Petra Spidlova
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500 01, Hradec Kralove, Czech Republic.
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Kapoor S, Singh A, Gupta V. In silico evaluation of potential intervention against SARS-CoV-2 RNA-dependent RNA polymerase. PHYSICS AND CHEMISTRY OF THE EARTH (2002) 2023; 129:103350. [PMID: 36536697 PMCID: PMC9750507 DOI: 10.1016/j.pce.2022.103350] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 09/17/2022] [Accepted: 12/10/2022] [Indexed: 06/17/2023]
Abstract
Background With few available effective interventions, emergence of novel mutants responding poorly to existing vaccines and ever swelling newer waves of infection, SARS-CoV-2 is posing difficult challenges to mankind. This mandates development of newer and effective therapeutics to prevent loss of life and contain the spread of this deadly virus. Nsp12 or RNA-dependent RNA polymerase (RdRp) is a suitable druggable target as it plays a central role in viral replication. Methodology Catalytically important conserved amino acid residues of RdRp were delineated through a comprehensive literature search and multiple sequence alignments. PDB ID 7BV2 was used to create binding pockets using SeeSAR and to generate docked poses of the FDA approved drugs on the receptor and estimating their binding affinity and other properties. Result In silico approach used in this study assisted in prediction of several potential RdRp inhibitors; and re-validation of the already reported ones. Five molecules namely Inosine, Ribavirin, 2-Deoxy-2-Fluoro-D-glucose, Guaifenesin, and Lamivudine were shortlisted which exhibited reasonable binding affinities, with neither torsional nor intermolecular or intramolecular clashes. Conclusion This study aimed to widen the prospect of interventions against the SARS-CoV-2 RdRp. Our results also re-validate already reported molecules like 2-Deoxy-D-glucose as a similar molecule 2-deoxy-2-fluoro-D-glucose is picked up in this study. Additionally, ribavirin and lamivudine, already known antivirals with polymerase inhibition activity are also picked up as the top leads. Selected potent inhibitors of RdRp hold promise to cater for any future coronavirus-outbreak subject to in vitro and in vivo validations.
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Affiliation(s)
- Shreya Kapoor
- Department of Microbiology, Ram Lal Anand College, University of Delhi, Benito Juarez Road, New Delhi, 110021, India
- Delhi Technological University, New Delhi, India
| | - Anurag Singh
- Department of Microbiology, Ram Lal Anand College, University of Delhi, Benito Juarez Road, New Delhi, 110021, India
- ICMR-National Institute of Virology, Pune, Maharashtra, 411021, India
| | - Vandana Gupta
- Department of Microbiology, Ram Lal Anand College, University of Delhi, Benito Juarez Road, New Delhi, 110021, India
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Vazquez-Rodriguez S, Ramírez-Contreras D, Noriega L, García-García A, Sánchez-Gaytán BL, Melendez FJ, Castro ME, de Azevedo WF, González-Vergara E. Interaction of copper potential metallodrugs with TMPRSS2: A comparative study of docking tools and its implications on COVID-19. Front Chem 2023; 11:1128859. [PMID: 36778030 PMCID: PMC9909424 DOI: 10.3389/fchem.2023.1128859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 01/17/2023] [Indexed: 01/28/2023] Open
Abstract
SARS-CoV-2 is the virus responsible for the COVID-19 pandemic. For the virus to enter the host cell, its spike (S) protein binds to the ACE2 receptor, and the transmembrane protease serine 2 (TMPRSS2) cleaves the binding for the fusion. As part of the research on COVID-19 treatments, several Casiopeina-analogs presented here were looked at as TMPRSS2 inhibitors. Using the DFT and conceptual-DFT methods, it was found that the global reactivity indices of the optimized molecular structures of the inhibitors could be used to predict their pharmacological activity. In addition, molecular docking programs (AutoDock4, Molegro Virtual Docker, and GOLD) were used to find the best potential inhibitors by looking at how they interact with key amino acid residues (His296, Asp 345, and Ser441) in the catalytic triad. The results show that in many cases, at least one of the amino acids in the triad is involved in the interaction. In the best cases, Asp435 interacts with the terminal nitrogen atoms of the side chains in a similar way to inhibitors such as nafamostat, camostat, and gabexate. Since the copper compounds localize just above the catalytic triad, they could stop substrates from getting into it. The binding energies are in the range of other synthetic drugs already on the market. Because serine protease could be an excellent target to stop the virus from getting inside the cell, the analyzed complexes are an excellent place to start looking for new drugs to treat COVID-19.
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Affiliation(s)
- Sergio Vazquez-Rodriguez
- Centro de Química del Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Diego Ramírez-Contreras
- Centro de Química del Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Lisset Noriega
- Laboratorio de Química Teórica, Depto. de Fisicoquímica, Facultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico,Departamento de Física Aplicada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Mexico
| | - Amalia García-García
- Centro de Química del Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico,Departamento de Química Inorgánica, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Brenda L. Sánchez-Gaytán
- Centro de Química del Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Francisco J. Melendez
- Laboratorio de Química Teórica, Depto. de Fisicoquímica, Facultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - María Eugenia Castro
- Centro de Química del Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico,*Correspondence: María Eugenia Castro, ; Enrique González-Vergara,
| | - Walter Filgueira de Azevedo
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Enrique González-Vergara
- Centro de Química del Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico,*Correspondence: María Eugenia Castro, ; Enrique González-Vergara,
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Wang Y, Ma J, Jiang Y. Transcription factor Nrf2 as a potential therapeutic target for COVID-19. Cell Stress Chaperones 2023; 28:11-20. [PMID: 36417098 PMCID: PMC9685020 DOI: 10.1007/s12192-022-01296-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 08/08/2022] [Accepted: 09/09/2022] [Indexed: 11/24/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) is caused by a novel severe acute respiratory syndrome (SARS)-like coronavirus (SARS-CoV-2). Critically ill patients with SARS-COV-2 infection frequently exhibit signs of high oxidative stress and systemic inflammation, which accounts for most of the mortality. Antiviral strategies to inhibit the pathogenic consequences of COVID-19 are urgently required. The nuclear factor erythroid 2-related transcription factor (Nrf2) is a transcription factor that is involved in antioxidant and anti-inflammatory defense in several tissues and cells. This review tries to present an overview of the role of Nrf2 in the treatment of COVID-19.
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Affiliation(s)
- Yifan Wang
- Department of Infectious Diseases, The Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Jing Ma
- Department of Infectious Diseases, The Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Yongfang Jiang
- Department of Infectious Diseases, The Second Xiangya Hospital, Central South University, Changsha, 410011, China.
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Каzachinskaia ЕI, Romanova VD, Ivanоva AV, Chepurnov АА, Murtazalieva ZA, Коnonova YV, Shaulo DN, Romanyuk VV, Shestopalov АМ. Inhibitory activity of dry ethanol extracts of <i>Artemisia</i> spp. on SARS‐CoV‐2 replication <i>in vitro</i>. SOUTH OF RUSSIA: ECOLOGY, DEVELOPMENT 2022. [DOI: 10.18470/1992-1098-2022-4-111-129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Aim. In vitro analysis of the inhibitory activity of dry ethanol extracts of some Artemisia spp. growing in the Novosibirsk region for SARS‐CoV‐2 replication.Materials and Methods. The laboratory strain SARS‐CoV‐2/human/RUS/Nsk‐FRCFTM‐1/2020 was passed on Vero cell culture. Dry ethanol extracts of plant parts (stems, flowers, leaves) of six types of Artemisia were prepared. The types used were: A. vulgaris L.; A. glauca (Pall. Ex Willd.); A. dracunculus L. (from three growth locations); A. absinthium L.; A. frigida Willd.; and A. sieversiana Ehrh. ex Willd. Dry extracts were dissolved in DMSO. In vitro analysis of the inhibitory activity of extracts against SARS‐CoV‐2 (an infectious titer of 103 TCID50/ml) replication was performed in a Vero E6 cell culture. To do this, the method of direct inactivation (neutralization) of virions, as well as schemes of “preventive” and “therapeutic” of cells, were used. Comparison samples were dry ethanol extracts of Inonotus obliquus, Syzygium aromaticum L. and Camellia sinensis L.Results. Extracts of leaves of Artemisia spp. proved to be most effective in direct inactivation of virions. By equal and decreasing activity these are the species: A. vulgaris; A. dracunculus*; A. absinthium; A. dracunculus***; A. dracunculus**; A. frigidа; A. glauca; and A. sieversiana with a 50% effective concentration of range 1.10±0.24 – 11.72±2.89 μg/ml. Extracts of flowers of A. vulgaris, A.glauca, A. dracunculus*, A. dracunculus**, A. dracunculus***, A. frigida and A. sieversiana also contain biologically active substances which act both destructively on virions and after the virus has entered cells. For extracts of stems consistently high values of EC50 were found for A. glauca (6.84±1.35; 7.81±2.00 and 14.06±3.06 μg/ml) according to the results of three experimental schemes.Conclusion. The results obtained can become the basis for the development of inexpensive domestic drugs for the treatment and/or prevention of COVID‐19.
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Affiliation(s)
- Е. I. Каzachinskaia
- Research Institute of Virology, Federal Research Centre of Fundamental and Translational Medicine, Siberian Branch, Russian Academy of Sciences; “Vector” State Research Centre of Virology and Biotechnology, Federal Service for Surveillance in the Sphere of Consumers Rights Protection and Human Welfare
| | - V. D. Romanova
- Research Institute of Virology, Federal Research Centre of Fundamental and Translational Medicine, Siberian Branch, Russian Academy of Sciences
| | - A. V. Ivanоva
- “Vector” State Research Centre of Virology and Biotechnology, Federal Service for Surveillance in the Sphere of Consumers Rights Protection and Human Welfare
| | - А. А. Chepurnov
- Research Institute of Virology, Federal Research Centre of Fundamental and Translational Medicine, Siberian Branch, Russian Academy of Sciences
| | | | - Yu. V. Коnonova
- Research Institute of Virology, Federal Research Centre of Fundamental and Translational Medicine, Siberian Branch, Russian Academy of Sciences
| | - D. N. Shaulo
- Central Siberian Botanical Garden, Siberian Branch, Russian Academy of Sciences
| | | | - А. М. Shestopalov
- Research Institute of Virology, Federal Research Centre of Fundamental and Translational Medicine, Siberian Branch, Russian Academy of Sciences
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12
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Computational investigation of natural compounds as potential main protease (M pro) inhibitors for SARS-CoV-2 virus. Comput Biol Med 2022; 151:106318. [PMID: 36423529 PMCID: PMC9673090 DOI: 10.1016/j.compbiomed.2022.106318] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 11/05/2022] [Accepted: 11/13/2022] [Indexed: 11/19/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is significantly impacting human lives, overburdening the healthcare system and weakening global economies. Plant-derived natural compounds are being largely tested for their efficacy against COVID-19 targets to combat SARS-CoV-2 infection. The SARS-CoV-2 Main protease (Mpro) is considered an appealing target because of its role in replication in host cells. We curated a set of 7809 natural compounds by combining the collections of five databases viz Dr Duke's Phytochemical and Ethnobotanical database, IMPPAT, PhytoHub, AromaDb and Zinc. We applied a rigorous computational approach to identify lead molecules from our curated compound set using docking, dynamic simulations, the free energy of binding and DFT calculations. Theaflavin and ginkgetin have emerged as better molecules with a similar inhibition profile in both SARS-CoV-2 and Omicron variants.
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13
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Pu Y, He X, Chen L, Wang H, Ma Y, Jiang W. Apple polyphenols attenuate the binding ability of angiotensin converting enzyme 2 to viral proteins: Computer simulation and in vitro experiments. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2022.102090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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14
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Tirado-Kulieva VA, Hernández-Martínez E, Choque-Rivera TJ. Phenolic compounds versus SARS-CoV-2: An update on the main findings against COVID-19. Heliyon 2022; 8:e10702. [PMID: 36157310 PMCID: PMC9484857 DOI: 10.1016/j.heliyon.2022.e10702] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/04/2022] [Accepted: 09/14/2022] [Indexed: 11/25/2022] Open
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 remains an international concern. Although there are drugs to fight it, new natural alternatives such as polyphenols are essential due to their antioxidant activity and high antiviral potential. In this context, this review reports the main findings on the effect of phenolic compounds (PCs) against SARS-CoV-2 virus. First, the proven activity of PCs against different human viruses is briefly detailed, which serves as a starting point to study their anti-COVID-19 potential. SARS-CoV-2 targets (its proteins) are defined. Findings from in silico, in vitro and in vivo studies of a wide variety of phenolic compounds are shown, emphasizing their mechanism of action, which is fundamental for drug design. Furthermore, clinical trials have demonstrated the effectiveness of PCs in the prevention and as a possible therapeutic management against COVID-19. The results were complemented with information on the influence of polyphenols in strengthening/modulating the immune system. It is recommended to investigate compounds such as vitamins, minerals, alkaloids, triterpenes and fatty acids, and their synergistic use with PCs, many of which have been successful against SARS-CoV-2. Based on findings on other viruses, synergistic evaluation of PCs with accepted drugs against COVID-19 is also suggested. Other recommendations and limitations are also shown, which is useful for professionals involved in the development of efficient, safe and low-cost therapeutic strategies based on plant matrices rich in PCs. To the authors' knowledge, this manuscript is the first to evaluate the relationship between the antiviral and immunomodulatory (including anti-inflammatory and antioxidant effects) activity of PCs and their underlying mechanisms in relation to the fight against COVID-19. It is also of interest for the general population to be informed about the importance of consuming foods rich in bioactive compounds for their health benefits. Phenolic compounds are known for their high potential against various human viruses. Phenolic compounds also have anti-inflammatory and immunomodulatory activity. Medicinal plants used against COVID-19 are rich in phenolic compounds. Phenolic compounds interfere with the activity of SARS-CoV-2 proteins. A wide variety of food products with high polyphenolic content are presented.
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15
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Rieder AS, Deniz BF, Netto CA, Wyse ATS. A Review of In Silico Research, SARS-CoV-2, and Neurodegeneration: Focus on Papain-Like Protease. Neurotox Res 2022; 40:1553-1569. [PMID: 35917086 PMCID: PMC9343570 DOI: 10.1007/s12640-022-00542-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/17/2022] [Accepted: 06/30/2022] [Indexed: 01/18/2023]
Abstract
Since the appearance of SARS-CoV-2 and the COVID-19 pandemic, the search for new approaches to treat this disease took place in the scientific community. The in silico approach has gained importance at this moment, once the methodologies used in this kind of study allow for the identification of specific protein–ligand interactions, which may serve as a filter step for molecules that can act as specific inhibitors. In addition, it is a low-cost and high-speed technology. Molecular docking has been widely used to find potential viral protein inhibitors for structural and non-structural proteins of the SARS-CoV-2, aiming to block the infection and the virus multiplication. The papain-like protease (PLpro) participates in the proteolytic processing of SARS-CoV-2 and composes one of the main targets studied for pharmacological intervention by in silico methodologies. Based on that, we performed a systematic review about PLpro inhibitors from the perspective of in silico research, including possible therapeutic molecules in relation to this viral protein. The neurological problems triggered by COVID-19 were also briefly discussed, especially relative to the similarities of neuroinflammation present in Alzheimer’s disease. In this context, we focused on two molecules, curcumin and glycyrrhizinic acid, given their PLpro inhibitory actions and neuroprotective properties and potential therapeutic effects on COVID-19.
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Affiliation(s)
- Alessandra S Rieder
- Laboratory of Neuroprotection and Neurometabolic Diseases, Wyse's Lab, Department of Biochemistry, ICBS, Universidade Federal Do Rio Grande Do Sul (UFRGS), Rua Ramiro Barcelos, 2600-Anexo, Porto Alegre, RS, 90035-003, Brazil
| | - Bruna F Deniz
- Laboratory of Neuroprotection and Neurometabolic Diseases, Wyse's Lab, Department of Biochemistry, ICBS, Universidade Federal Do Rio Grande Do Sul (UFRGS), Rua Ramiro Barcelos, 2600-Anexo, Porto Alegre, RS, 90035-003, Brazil
| | - Carlos Alexandre Netto
- Laboratory of Neuroprotection and Neurometabolic Diseases, Wyse's Lab, Department of Biochemistry, ICBS, Universidade Federal Do Rio Grande Do Sul (UFRGS), Rua Ramiro Barcelos, 2600-Anexo, Porto Alegre, RS, 90035-003, Brazil
| | - Angela T S Wyse
- Laboratory of Neuroprotection and Neurometabolic Diseases, Wyse's Lab, Department of Biochemistry, ICBS, Universidade Federal Do Rio Grande Do Sul (UFRGS), Rua Ramiro Barcelos, 2600-Anexo, Porto Alegre, RS, 90035-003, Brazil.
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16
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Gao K, Wang R, Chen J, Cheng L, Frishcosy J, Huzumi Y, Qiu Y, Schluckbier T, Wei X, Wei GW. Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2. Chem Rev 2022; 122:11287-11368. [PMID: 35594413 PMCID: PMC9159519 DOI: 10.1021/acs.chemrev.1c00965] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite tremendous efforts in the past two years, our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), virus-host interactions, immune response, virulence, transmission, and evolution is still very limited. This limitation calls for further in-depth investigation. Computational studies have become an indispensable component in combating coronavirus disease 2019 (COVID-19) due to their low cost, their efficiency, and the fact that they are free from safety and ethical constraints. Additionally, the mechanism that governs the global evolution and transmission of SARS-CoV-2 cannot be revealed from individual experiments and was discovered by integrating genotyping of massive viral sequences, biophysical modeling of protein-protein interactions, deep mutational data, deep learning, and advanced mathematics. There exists a tsunami of literature on the molecular modeling, simulations, and predictions of SARS-CoV-2 and related developments of drugs, vaccines, antibodies, and diagnostics. To provide readers with a quick update about this literature, we present a comprehensive and systematic methodology-centered review. Aspects such as molecular biophysics, bioinformatics, cheminformatics, machine learning, and mathematics are discussed. This review will be beneficial to researchers who are looking for ways to contribute to SARS-CoV-2 studies and those who are interested in the status of the field.
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Affiliation(s)
- Kaifu Gao
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Rui Wang
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Jiahui Chen
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Limei Cheng
- Clinical
Pharmacology and Pharmacometrics, Bristol
Myers Squibb, Princeton, New Jersey 08536, United States
| | - Jaclyn Frishcosy
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuta Huzumi
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuchi Qiu
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Tom Schluckbier
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Xiaoqi Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Guo-Wei Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
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17
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Ohishi T, Hishiki T, Baig MS, Rajpoot S, Saqib U, Takasaki T, Hara Y. Epigallocatechin gallate (EGCG) attenuates severe acute respiratory coronavirus disease 2 (SARS-CoV-2) infection by blocking the interaction of SARS-CoV-2 spike protein receptor-binding domain to human angiotensin-converting enzyme 2. PLoS One 2022; 17:e0271112. [PMID: 35830431 PMCID: PMC9278780 DOI: 10.1371/journal.pone.0271112] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 06/23/2022] [Indexed: 11/18/2022] Open
Abstract
The outbreak of the coronavirus disease 2019 caused by the severe acute respiratory syndrome coronavirus 2 triggered a global pandemic where control is needed through therapeutic and preventive interventions. This study aims to identify natural compounds that could affect the fusion between the viral membrane (receptor-binding domain of the severe acute respiratory syndrome coronavirus 2 spike protein) and the human cell receptor angiotensin-converting enzyme 2. Accordingly, we performed the enzyme-linked immunosorbent assay-based screening of 10 phytochemicals that already showed numerous positive effects on human health in several epidemiological studies and clinical trials. Among these phytochemicals, epigallocatechin gallate, a polyphenol and a major component of green tea, could effectively inhibit the interaction between the receptor-binding domain of the severe acute respiratory syndrome coronavirus 2 spike protein and the human cell receptor angiotensin-converting enzyme 2. Alternately, in silico molecular docking studies of epigallocatechin gallate and angiotensin-converting enzyme 2 indicated a binding score of −7.8 kcal/mol and identified a hydrogen bond between R393 and angiotensin-converting enzyme 2, which is considered as a key interacting residue involved in binding with the severe acute respiratory syndrome coronavirus 2 spike protein receptor-binding domain, suggesting the possible blocking of interaction between receptor-binding domain and angiotensin-converting enzyme 2. Furthermore, epigallocatechin gallate could attenuate severe acute respiratory syndrome coronavirus 2 infection and replication in Caco-2 cells. These results shed insight into identification and validation of severe acute respiratory syndrome coronavirus 2 entry inhibitors.
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Affiliation(s)
- Tomokazu Ohishi
- Institute of Microbial Chemistry (BIKAKEN), Numazu, Microbial Chemistry Research Foundation, Numazu-shi, Shizuoka, Japan
- * E-mail:
| | - Takayuki Hishiki
- Kanagawa Prefectural Institute of Public Health, Chigasaki, Kanagawa, Japan
| | - Mirza S. Baig
- Department of Biosciences and Biomedical Engineering (BSBE), Indian Institute of Technology (IIT), Simrol, Indore, India
| | - Sajjan Rajpoot
- Department of Biosciences and Biomedical Engineering (BSBE), Indian Institute of Technology (IIT), Simrol, Indore, India
| | - Uzma Saqib
- Department of Chemistry, Indian Institute of Technology (IIT), Simrol, Indore, India
| | - Tomohiko Takasaki
- Kanagawa Prefectural Institute of Public Health, Chigasaki, Kanagawa, Japan
| | - Yukihiko Hara
- Tea Solutions, Hara Office Inc., Sumida-ku, Tokyo, Japan
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18
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BREAK LM, GOBOURI AA, Al-HSRTHI WS, HAGAR M, Al-KAFF NS, SAID MA. Design, synthesis, and greener pasture biological assessment of a novel nucleoside: 1-(α-D-ribofuranosyl)-6,7-difluoro-2-methyl-4-quinazolinone as an inhibitor of COVID-19 and Alzheimer's disease. Turk J Chem 2022; 46:1827-1840. [PMID: 37621349 PMCID: PMC10446935 DOI: 10.55730/1300-0527.3483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 12/19/2022] [Accepted: 06/16/2022] [Indexed: 12/24/2022] Open
Abstract
Synthesis of a new fluorinated nucleoside of 6,7-difluoro-2-methyl-4-quinazolinone was described. 2-Amino-4,5-difluorobenzoic acid 1 reacts with (CH3CO)2O followed by ammonia to form (1H)-6,7-difluoro-2-methyl-4-quinazolinone 3a. Ribosylation of a silylated 4 with l-O-acety1-2,3-5-tri-O-benzoyl-α-D-ribofuranose 5 forms a protected nucleoside 6 then unprotected from 6 to give a free nucleoside 7. Greener pasture biological docking of the cystine protease of COVID-19 [Mpro, code 7BQY, PDB] by novel nucleoside and fluoroquinazoline compounds is presented. LIGPLOT (2D) representations calculated for the same ligands are shown. A superposition of remdesivir approved medicine, N3 inhibitor, and our ligands docked together into the binding protein of 7BQY is also given for a fair comparison. The binding affinities of remdesivir, N3 inhibitor, the nucleoside 7, and fluoroquinazoline 3a, 3b compounds with 7BQY calculated under the same conditions are -7.7, -7.4, -7.6, -6.1, and -6.1 kcal mol-1, respectively. The high values were due to the existence of many hydrophobic interactions and hydrogen bonds between the ligands and the active amino acid residues of the receptor, indicating a promising candidate as a COVID-19 inhibitor. Pro Tox -II server showed that compound 7 has a similar feature to the approved antiviral drug remdesivir for COVID-19. Additionally, a fascinating molecular modeling investigation showed that our nucleoside demonstrated good binding inhibition of AChE enzyme towards advancing an efficient medication against Alzheimer's disease. Finally, DFT has been conducted to illustrate the MD results in terms of the molecular descriptor-based structural activity relationship calculated from FMOs.
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Affiliation(s)
- Laila M. BREAK
- Department of Chemistry, College of Science, Taif University, Taif,
Saudi Arabia
| | - Adil A. GOBOURI
- Department of Chemistry, College of Science, Taif University, Taif,
Saudi Arabia
| | - Wafa S. Al-HSRTHI
- Department of Chemistry, College of Science, Taif University, Taif,
Saudi Arabia
| | - Mohamed HAGAR
- Department of Chemistry, Faculty of Science, Alexandria University, Alexandria,
Egypt
| | - Nadia S. Al-KAFF
- Biology Department, College of Science, Taibah University, Al-Madinah Al-Munawara,
Saudi Arabia
| | - Musa A. SAID
- Chemistry Department, College of Science, Taibah University, Al-Madinah Al-Munawara,
Saudi Arabia
- Institute of Inorganic Chemistry, University of Stuttgart Pfaffenwaldring, Stuttgart,
Germany
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19
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Wang L, Tao Q, Wang Z, Shi J, Yan W, Zhang L, Sun Y, Yao X. Tea Ingredients Have Anti-coronavirus Disease 2019 (COVID-19) Targets Based on Bioinformatics Analyses and Pharmacological Effects on LPS-Stimulated Macrophages. Front Nutr 2022; 9:875765. [PMID: 35669076 PMCID: PMC9163550 DOI: 10.3389/fnut.2022.875765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is a contagious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that caused millions of deaths and lacks treatment. Although several studies have focused on the major component of green tea, epigallocatechin 3-gallate (EGCG), which is efficient in preventing COVID-19, systemic analyses of the anti-COVID-19 potential of green tea remain insufficient. Here, we co-analyzed the target genes of tea ingredients and COVID-19 signature genes and found that epigallocatechin 3-acetalbehyde was capable of reversing the major molecular processes of COVID-19 (MAPK and NF-κB activation). These findings were further supported by Western blotting (WB), immunofluorescence, and quantitative polymerase chain reaction (qPCR) in LPS-stimulated macrophages. Moreover, using molecular docking analysis, we identified three tea ingredients ((-)-catechin gallate, D-(+)-cellobiose, and EGCG) that may interact with the vital SARS-CoV-2 protein, 5R84, compared with the qualified 5R84 ligand WGS. Thus, our results indicated that tea ingredients have the potential to treat COVID-19 by suppressing the COVID-19 signature genes and interacting with the vital SARS-CoV-2 protein.
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Affiliation(s)
- Lei Wang
- Department of Clinical Laboratory, Jiangsu Province Hospital on Integration of Chinese and Western Medicine, Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, China
| | - Qing Tao
- Center for Translational Medicine and Jiangsu Key Laboratory of Molecular Medicine, Department of Basic Medicine, Medical School of Nanjing University, Nanjing, China
| | - Zhiguo Wang
- Department of Clinical Laboratory, Jiangsu Province Hospital on Integration of Chinese and Western Medicine, Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, China
| | - Jianfeng Shi
- Department of Clinical Laboratory, Jiangsu Province Hospital on Integration of Chinese and Western Medicine, Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, China
| | - Wei Yan
- Department of Clinical Laboratory, Jiangsu Province Hospital on Integration of Chinese and Western Medicine, Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, China
| | - Li Zhang
- Department of Clinical Laboratory, Jiangsu Province Hospital on Integration of Chinese and Western Medicine, Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, China
| | - Yaoxiang Sun
- Department of Clinical Laboratory, The Affiliated Yixing Hospital of Jiangsu University, Yixing, China
| | - Xiaoming Yao
- Department of Clinical Laboratory, Jiangsu Province Hospital on Integration of Chinese and Western Medicine, Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, China
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20
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Sahadevan R, Singh S, Binoy A, Sadhukhan S. Chemico-biological aspects of (-)-epigallocatechin- 3-gallate (EGCG) to improve its stability, bioavailability and membrane permeability: Current status and future prospects. Crit Rev Food Sci Nutr 2022; 63:10382-10411. [PMID: 35491671 DOI: 10.1080/10408398.2022.2068500] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Natural products have been a bedrock for drug discovery for decades. (-)-Epigallocatechin-3-gallate (EGCG) is one of the widely studied natural polyphenolic compounds derived from green tea. It is the key component believed to be responsible for the medicinal value of green tea. Significant studies implemented in in vitro, in cellulo, and in vivo models have suggested its anti-oxidant, anti-cancer, anti-diabetic, anti-inflammatory, anti-microbial, neuroprotective activities etc. Despite having such a wide array of therapeutic potential and promising results in preclinical studies, its applicability to humans has encountered with rather limited success largely due to the poor bioavailability, poor membrane permeability, rapid metabolic clearance and lack of stability of EGCG. Therefore, novel techniques are warranted to address those limitations so that EGCG or its modified analogs can be used in the clinical setup. This review comprehensively covers different strategies such as structural modifications, nano-carriers as efficient drug delivery systems, synergistic studies with other bioactivities to improve the chemico-biological aspects (e.g., stability, bioavailability, permeability, etc.) of EGCG for its enhanced pharmacokinetics and pharmacological properties, eventually enhancing its therapeutic potentials. We think this review article will serve as a strong platform with comprehensive literature on the development of novel techniques to improve the bioavailability of EGCG so that it can be translated to the clinical applications.
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Affiliation(s)
- Revathy Sahadevan
- Department of Chemistry, Indian Institute of Technology Palakkad, Kerala, India
| | - Satyam Singh
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Madhya Pradesh, India
| | - Anupama Binoy
- Department of Chemistry, Indian Institute of Technology Palakkad, Kerala, India
| | - Sushabhan Sadhukhan
- Department of Chemistry, Indian Institute of Technology Palakkad, Kerala, India
- Department of Biological Sciences and Engineering, Indian Institute of Technology Palakkad, Kerala, India
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21
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Anjomshoa M, Amirheidari B. Nuclease-like metalloscissors: Biomimetic candidates for cancer and bacterial and viral infections therapy. Coord Chem Rev 2022; 458:214417. [PMID: 35153301 PMCID: PMC8816526 DOI: 10.1016/j.ccr.2022.214417] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 01/09/2022] [Indexed: 12/25/2022]
Abstract
Despite the extensive and rapid discovery of modern drugs for treatment of cancer, microbial infections, and viral illnesses; these diseases are still among major global health concerns. To take inspiration from natural nucleases and also the therapeutic potential of metallopeptide antibiotics such as the bleomycin family, artificial metallonucleases with the ability of promoting DNA/RNA cleavage and eventually affecting cellular biological processes can be introduced as a new class of therapeutic candidates. Metal complexes can be considered as one of the main categories of artificial metalloscissors, which can prompt nucleic acid strand scission. Accordingly, biologists, inorganic chemists, and medicinal inorganic chemists worldwide have been designing, synthesizing and evaluating the biological properties of metal complexes as artificial metalloscissors. In this review, we try to highlight the recent studies conducted on the nuclease-like metalloscissors and their potential therapeutic applications. Under the light of the concurrent Covid-19 pandemic, the human need for new therapeutics was highlighted much more than ever before. The nuclease-like metalloscissors with the potential of RNA cleavage of invading viral pathogens hence deserve prime attention.
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22
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Maiti S, Banerjee A, Kanwar M. Effects of theaflavin-gallate in-silico binding with different proteins of SARS-CoV-2 and host inflammation and vasoregulations referring an experimental rat-lung injury. PHYTOMEDICINE PLUS : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2022; 2:100237. [PMID: 35403090 PMCID: PMC8820952 DOI: 10.1016/j.phyplu.2022.100237] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Background SARS-CoV-2 claimed 5,209,104 lives, infected 260,997,910 individuals, globally. Infection is caused due to exposure or susceptibility; deaths occur due to age,comorbidity,higher-viral-load, immuno-suppression, inflammation, and multi-organ failure. Theaflavin-gallate, the major black tea component, showed previous evidence to inhibit HIV-1. Purpose As theaflavin-gallate prevents experimental rat-lung injury, the study of inhibitory effects of theaflavin-gallate was done, on SARS-CoV-2proteins and various host proteins related to some adverse effects in COVID-19 patients. Study Design Currently, some prospective phytochemical, black-tea (Camellia-sinensis) extract (BTE) was initially tested in vivo in strong oxidant-mutagen arsenic-induced model rat lung injury similar to that of COVID-19 manifestations like severe inflammation, oxidative stress, lung tissue degenerations, and apoptotic death. In silico, extensive bioinformatics and molecular docking experiments were performed on all catechin or theaflavin derivatives of C. sinensis, and finally theaflavin-3'-O-gallate (TFMG) were screened for blocking or inactivation of several proteins of SARS CoV-2 and host adversely-acting proteins or factors. Methods In vivo experiments in DNA stability (ladder, comet assay), free radicals attack (malondialdehyde; MDA, superoxide dismutase SOD, catalase gel-zymogram assay), extra cellular matrix damage (matrix metalloprotease; MMP2and9 zymogram assay) and inflammation (TNF-α, ELISA). In silico experiments- molecular docking by AutoDock-Patchdock analysis, Surface Topology Calculation by CASTp, Grid-value calculation, and Ramachandran Plot study. Results The BTE showed strong protection of lung DNA and cell-matrix by decreasing MMPs, TNF-α, and free radicals, the same factors affecting COVID-19 patients. In silico data suggest that TFMG significantly blocked the entry, exit, and amino acids at catalytic active-site of more than thirty proteins including viral (nsp1,nsp2,Mainpro,∼-9.0 kcal/mol) and host inflammatory, oxidants, apoptotic, vaso-destabilizer molecules (FAS, CD40R, BCL2, TLR2, ∼ -10 and ACE1or2 ∼ -9.0 and AT1or2∼ -7.5 kcal/mol and more). When the binding energy of TFMG ranged from -7 to -11.7 kcal/mol(average -9.0) the same for hydroxy‑Chloroquine ranged (-2.5 to -7 average -4.5) and dexamethasone (-3.0 to -6.0, average -4.0 kcal/mol). Conclusions TFMG has some novel physicochemical or structural properties like (ACE values of binding to all tested proteins, -300 to -625), (for TFMG H-bond acceptor or donor: 15/10, for TFDG 20/13). Their topological-polar-surface-area (264Ų and 351Ų) and travel depth/height; 17.0/9.6 Å and 15.4/11.3 Å, respectively) were more potent than other compounds. Conclusively, the efficacy of TFMG may be further verified.
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Affiliation(s)
- Smarajit Maiti
- Departmentof Biochemistry and Biotechnology, Cell and Molecular Therapeutics Laboratory Oriental Institute of Science and Technology, Midnapore, India
- Agricure Biotech Research Society, Epidemiology and Human Health Division, Midnapore 721101, India
| | - Amrita Banerjee
- Departmentof Biochemistry and Biotechnology, Cell and Molecular Therapeutics Laboratory Oriental Institute of Science and Technology, Midnapore, India
| | - Mehak Kanwar
- Departmentof Biochemistry and Biotechnology, Cell and Molecular Therapeutics Laboratory Oriental Institute of Science and Technology, Midnapore, India
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23
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Kicker E, Tittel G, Schaller T, Pferschy-Wenzig EM, Zatloukal K, Bauer R. SARS-CoV-2 neutralizing activity of polyphenols in a special green tea extract preparation. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2022; 98:153970. [PMID: 35144138 PMCID: PMC8801126 DOI: 10.1016/j.phymed.2022.153970] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 01/20/2022] [Accepted: 01/27/2022] [Indexed: 05/05/2023]
Abstract
BACKGROUND The COVID-19 pandemic will continue to threaten our health care systems in the next years. In addition to vaccination there is a need for effective tools for prevention and treatment. Products from natural sources, like standardized plant extracts offer a wide range of antiviral effects and possible applications. PURPOSE The aim of this study was to investigate, whether a sorbitol/lecithin-based throat spray containing concentrated green tea extract (sGTE) interacts with SARS-CoV-2 viral particles and additionally is capable to block the virus replication. STUDY DESIGN AND METHODS The antiviral effect was studied in a VeroE6 cell culture model, including concentration/effect correlations and the biological mechanism of virus blockade, using the Wuhan type of SARS CoV-2 as well as its beta- and delta-mutations. In addition, the qualitative and quantitative tannin profile present on the oral mucosa after spray application has been investigated by LC-MS/MS and HPLC-DAD analyses of (-)-epigallocatechin-3-O-gallate (EGCG) and related catechin derivatives. RESULTS The findings of this study demonstrate, that sGTE has strong neutralizing activity on SARS-CoV-2 resulting in an up to 6,3E+04-fold reduction of infectivity independent from the strain. The type of interaction of sGTE with surface proteins seems to be direct and non-specific concerning the viral surface protein structures and resembles the general non-specific activity of polyphenols. By HPLC-DAD analysis, eight catechins were identified in sGTE, with EGCG and (-)-epicatechin-3-O-gallate as the most abundant ones. The total content of catechin derivatives, calculated as catechin, was 76 g/100 g. LC-MS/MS and HPLC-DAD analyses of throat swabs after application of a sGTE spray have shown that the concentrations of green tea tannins in the pharyngeal mucosa are higher than the effective dose found in the in vitro studies with SARS-CoV-2, even 1 h after the last application. CONCLUSION The findings of this study suggest that sGTE has strong neutralizing activity on SARS-CoV-2 independent from the strain (Wuhan strain, beta- or delta-variants). sGTE might be relevant for reduction of corresponding viral infections when periodically applied to mouth and throat.
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Affiliation(s)
- Eva Kicker
- Diagnostic and Research Center for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; BioTechMed, Mozartgasse 12/II, 8010 Graz, Austria
| | - Gerolf Tittel
- Phytovisions GmbH & Co. KG, Karwendelstrasse 29, 82467 Garmisch-Partenkirchen, Germany
| | - Tanja Schaller
- Dronania pharmaceuticals GmbH, Karl- Benz- Strasse 3, 86825 Bad Woerishofen, Germany
| | - Eva-Maria Pferschy-Wenzig
- Institute of Pharmaceutical Sciences, University of Graz, Beethovenstraße 8, 8010 Graz, Austria; BioTechMed, Mozartgasse 12/II, 8010 Graz, Austria
| | - Kurt Zatloukal
- Diagnostic and Research Center for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; BioTechMed, Mozartgasse 12/II, 8010 Graz, Austria
| | - Rudolf Bauer
- Institute of Pharmaceutical Sciences, University of Graz, Beethovenstraße 8, 8010 Graz, Austria; BioTechMed, Mozartgasse 12/II, 8010 Graz, Austria.
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Wang B, Ding Y, Zhao P, Li W, Li M, Zhu J, Ye S. Systems pharmacology-based drug discovery and active mechanism of natural products for coronavirus pneumonia (COVID-19): An example using flavonoids. Comput Biol Med 2022; 143:105241. [PMID: 35114443 PMCID: PMC8789666 DOI: 10.1016/j.compbiomed.2022.105241] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 01/16/2022] [Accepted: 01/17/2022] [Indexed: 02/06/2023]
Abstract
BACKGROUND Recently, the value of natural products has been extensively considered because these resources can potentially be applied to prevent and treat coronavirus pneumonia 2019 (COVID-19). However, the discovery of nature drugs is problematic because of their complex composition and active mechanisms. METHODS This comprehensive study was performed on flavonoids, which are compounds with anti-inflammatory and antiviral effects, to show drug discovery and active mechanism from natural products in the treatment of COVID-19 via a systems pharmacological model. First, a chemical library of 255 potential flavonoids was constructed. Second, the pharmacodynamic basis and mechanism of action between flavonoids and COVID-19 were explored by constructing a compound-target and target-disease network, targets protein-protein interaction (PPI), MCODE analysis, gene ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment. RESULTS In total, 105 active flavonoid components were identified, of which 6 were major candidate compounds (quercetin, epigallocatechin-3-gallate (EGCG), luteolin, fisetin, wogonin, and licochalcone A). 152 associated targets were yielded based on network construction, and 7 family proteins (PTGS, GSK3β, ABC, NOS, EGFR, and IL) were included as central hub targets. Moreover, 528 GO items and 178 KEGG pathways were selected through enrichment of target functions. Lastly, molecular docking demonstrated good stability of the combination of selected flavonoids with 3CL Pro and ACEⅡ. CONCLUSION Natural flavonoids could enable resistance against COVID-19 by regulating inflammatory, antiviral, and immune responses, and repairing tissue injury. This study has scientific significance for the selective utilization of natural products, medicinal value enhancement of flavonoids, and drug screening for the treatment of COVID-19 induced by SARS-COV-2.
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Affiliation(s)
- Bin Wang
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, Liaoning, 116034, China
| | - Yan Ding
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, Liaoning, 116034, China.
| | - Penghui Zhao
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, Liaoning, 116034, China
| | - Wei Li
- Korean Medicine (KM) Application Center, Korea Institute of Oriental Medicine, Daegu, 41062, South Korea
| | - Ming Li
- College of Basic Medical Science, Dalian Medical University, Dalian, Liaoning, 116044, China
| | - Jingbo Zhu
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, Liaoning, 116034, China; Institute of Chemistry and Applications of Plant Resources, Dalian Polytechnic University, Dalian, Liaoning, 116034, China
| | - Shuhong Ye
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, Liaoning, 116034, China.
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25
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Pan SY, Nie Q, Tai HC, Song XL, Tong YF, Zhang LJF, Wu XW, Lin ZH, Zhang YY, Ye DY, Zhang Y, Wang XY, Zhu PL, Chu ZS, Yu ZL, Liang C. Tea and tea drinking: China's outstanding contributions to the mankind. Chin Med 2022; 17:27. [PMID: 35193642 PMCID: PMC8861626 DOI: 10.1186/s13020-022-00571-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 01/07/2022] [Indexed: 02/06/2023] Open
Abstract
Background Tea trees originated in southwest China 60 million or 70 million years ago. Written records show that Chinese ancestors had begun drinking tea over 3000 years ago. Nowadays, with the aging of populations worldwide and more people suffering from non-communicable diseases or poor health, tea beverages have become an inexpensive and fine complementary and alternative medicine (CAM) therapy. At present, there are 3 billion people who like to drink tea in the world, but few of them actually understand tea, especially on its development process and the spiritual and cultural connotations. Methods We searched PubMed, Google Scholar, Web of Science, CNKI, and other relevant platforms with the key word “tea”, and reviewed and analyzed tea-related literatures and pictures in the past 40 years about tea’s history, culture, customs, experimental studies, and markets. Results China is the hometown of tea, tea trees, tea drinking, and tea culture. China has the oldest wild and planted tea trees in the world, fossil of a tea leaf from 35,400,000 years ago, and abundant tea-related literatures and art works. Moreover, tea may be the first Chinese herbal medicine (CHM) used by Chinese people in ancient times. Tea drinking has many benefits to our physical health via its antioxidant, anti-inflammatory, immuno-regulatory, anticancer, cardiovascular-protective, anti-diabetic, and anti-obesity activities. At the moment, COVID-19 is wreaking havoc across the globe and causing severe damages to people’s health and lives. Tea has anti-COVID-19 functions via the enhancement of the innate immune response and inhibition of viral growth. Besides, drinking tea can allow people to acquire a peaceful, relaxed, refreshed and cheerful enjoyment, and even longevity. According to the meridian theory of traditional Chinese medicine, different kinds of tea can activate different meridian systems in the human body. At present, black tea (fermented tea) and green tea (non-fermented tea) are the most popular in the world. Black tea accounts for over 90% of all teas sold in western countries. The world’s top-grade black teas include Qi Men black in China, Darjeeling and Assam black tea in India, and Uva black tea in Sri Lanka. However, all top ten famous green teas in the world are produced in China, and Xi Hu Long Jing tea is the most famous among all green teas. More than 700 different kinds of components and 27 mineral elements can be found in tea. Tea polyphenols and theaflavin/thearubigins are considered to be the major bioactive components of black tea and green tea, respectively. Overly strong or overheated tea liquid should be avoided when drinking tea. Conclusions Today, CAM provides an array of treatment modalities for the health promotion in both developed and developing countries all over the world. Tea drinking, a simple herb-based CAM therapy, has become a popular man-made non-alcoholic beverage widely consumed worldwide, and it can improve the growth of economy as well. Tea can improve our physical and mental health and promote the harmonious development of society through its chemical and cultural elements.
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Affiliation(s)
- Si-Yuan Pan
- School of Traditional Dai-Thai Medicine, West Yunnan University of Applied Sciences, Jinghong, Yunnan, China. .,School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China.
| | - Qu Nie
- School of Traditional Dai-Thai Medicine, West Yunnan University of Applied Sciences, Jinghong, Yunnan, China
| | - Hai-Chuan Tai
- School of Traditional Dai-Thai Medicine, West Yunnan University of Applied Sciences, Jinghong, Yunnan, China
| | - Xue-Lan Song
- School of Traditional Dai-Thai Medicine, West Yunnan University of Applied Sciences, Jinghong, Yunnan, China
| | - Yu-Fan Tong
- School of Traditional Dai-Thai Medicine, West Yunnan University of Applied Sciences, Jinghong, Yunnan, China
| | - Long-Jian-Feng Zhang
- School of Traditional Dai-Thai Medicine, West Yunnan University of Applied Sciences, Jinghong, Yunnan, China
| | - Xue-Wei Wu
- School of Traditional Dai-Thai Medicine, West Yunnan University of Applied Sciences, Jinghong, Yunnan, China
| | - Zhao-Heng Lin
- School of Traditional Dai-Thai Medicine, West Yunnan University of Applied Sciences, Jinghong, Yunnan, China
| | - Yong-Yu Zhang
- School of Traditional Dai-Thai Medicine, West Yunnan University of Applied Sciences, Jinghong, Yunnan, China
| | - Du-Yun Ye
- School of Traditional Dai-Thai Medicine, West Yunnan University of Applied Sciences, Jinghong, Yunnan, China
| | - Yi Zhang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Xiao-Yan Wang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Pei-Li Zhu
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Zhu-Sheng Chu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Zhi-Ling Yu
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Chun Liang
- Division of Life Science, Center for Cancer Research, and State Key Lab of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China. .,EnKang Pharmaceuticals (Guangzhou) Ltd, Guangzhou, China.
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Souid I, Korchef A, Souid S. In silico evaluation of Vitis amurensis Rupr. polyphenol compounds for their inhibition potency against CoVID-19 main enzymes Mpro and RdRp. Saudi Pharm J 2022; 30:570-584. [PMID: 35250347 PMCID: PMC8883852 DOI: 10.1016/j.jsps.2022.02.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 02/21/2022] [Indexed: 02/07/2023] Open
Abstract
The rapid transmission of the pneumonia (COVID-19) emerged as an entire worldwide health concern and it was declared as pandemic by the World Health Organization (WHO) as a consequence of the increasing reported infections number. COVID-19 disease is caused by the novel SARS-CoV-2 virus, and unfortunatly no drugs are currently approved against this desease. Accordingly, it is of outmost importance to review the possible therapeutic effects of naturally-occuring compounds that showed approved antiviral activities. The molecular docking approach offers a rapid prediction of a possible inhibition of the main enzymes Mpro and RdRp that play crucial role in the SARS-CoV-2 replication and transcription. In the present work, we review the anti-viral activities of polyphenol compounds (phenolic acids, flavonoids and stilbene) derived from the traditional Chinese medicinal Vitis amurensis. Recent molecular docking studies reported the possible binding of these polyphenols on SARS-CoV-2 enzymes Mpro and RdRp active sites and showed interesting inhibitory effects. This antiviral activity was explained by the structure-activity relationships of the studied compounds. Also, pharmacokinetic analysis of the studied molecules is simulated in the present work. Among the studied polyphenol compounds, only five, namely caffeic acid, ferulic acid, quercetin, naringenin and catechin have drug-likeness characteristics. These five polyphenols derived from Vitis amurensis are promising drug candidates for the COVID-19 treatment.
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Hong M, Cheng L, Liu Y, Wu Z, Zhang P, Zhang X. A Natural Plant Source-Tea Polyphenols, a Potential Drug for Improving Immunity and Combating Virus. Nutrients 2022; 14:nu14030550. [PMID: 35276917 PMCID: PMC8839699 DOI: 10.3390/nu14030550] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 02/06/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) is still in a global epidemic, which has profoundly affected people’s lives. Tea polyphenols (TP) has been reported to enhance the immunity of the body to COVID-19 and other viral infectious diseases. The inhibitory effect of TP on COVID-19 may be achieved through a series of mechanisms, including the inhibition of multiple viral targets, the blocking of cellular receptors, and the activation of transcription factors. Emerging evidence shows gastrointestinal tract is closely related to respiratory tract, therefore, the relationship between the state of the gut–lung axis microflora and immune homeostasis of the host needs further research. This article summarized that TP can improve the disorder of flora, reduce the occurrence of cytokine storm, improve immunity, and prevent COVID-19 infection. TP may be regarded as a potential and valuable source for the design of new antiviral drugs with high efficiency and low toxicity.
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Affiliation(s)
- Mengyu Hong
- Department of Food Science and Engineering, Ningbo University, Ningbo 315211, China; (M.H.); (Y.L.); (Z.W.)
| | - Lu Cheng
- Department of Food Science, Rutgers University, New Brunswick, NJ 08901, USA;
| | - Yanan Liu
- Department of Food Science and Engineering, Ningbo University, Ningbo 315211, China; (M.H.); (Y.L.); (Z.W.)
| | - Zufang Wu
- Department of Food Science and Engineering, Ningbo University, Ningbo 315211, China; (M.H.); (Y.L.); (Z.W.)
| | - Peng Zhang
- Department of Student Affairs, Xinyang Normal University, Xinyang 464000, China
- Correspondence: (P.Z.); (X.Z.)
| | - Xin Zhang
- Department of Food Science and Engineering, Ningbo University, Ningbo 315211, China; (M.H.); (Y.L.); (Z.W.)
- Correspondence: (P.Z.); (X.Z.)
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28
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Luo Y, Jian Y, Liu Y, Jiang S, Muhammad D, Wang W. Flavanols from Nature: A Phytochemistry and Biological Activity Review. Molecules 2022; 27:719. [PMID: 35163984 PMCID: PMC8838462 DOI: 10.3390/molecules27030719] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 01/12/2022] [Accepted: 01/17/2022] [Indexed: 12/19/2022] Open
Abstract
Flavanols, a common class of secondary plant metabolites, exhibit several beneficial health properties by acting as antioxidant, anticarcinogen, cardioprotective, anti-microbial, anti-viral, and neuroprotective agents. Furthermore, some flavanols are considered functional ingredients in dairy products. Based on their structural features and health-promoting functions, flavanols have gained the attention of pharmacologists and botanists worldwide. This review collects and summarizes 121 flavanols comprising four categories: flavan-3-ols, flavan-4-ols, isoflavan-4-ols, and flavan-3,4-ols. The research of the various structural features and pharmacological activities of flavanols and their derivatives aims to lay the groundwork for subsequent research and expect to provide mentality and inspiration for the research. The current study provides a starting point for further research and development.
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Affiliation(s)
| | - Yuqing Jian
- Correspondence: (Y.J.); (W.W.); Tel.: +86-150-8486-8970 (Y.J.); +86-136-5743-8606 (W.W.)
| | | | | | | | - Wei Wang
- TCM and Ethnomedicine Innovation & Development International Laboratory, Innovative Materia Medica Research Institute, School of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China; (Y.L.); (Y.L.); (S.J.); (D.M.)
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29
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Nguyen QV, Chong LC, Hor YY, Lew LC, Rather IA, Choi SB. Role of Probiotics in the Management of COVID-19: A Computational Perspective. Nutrients 2022; 14:nu14020274. [PMID: 35057455 PMCID: PMC8781206 DOI: 10.3390/nu14020274] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 02/01/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) was declared a pandemic at the beginning of 2020, causing millions of deaths worldwide. Millions of vaccine doses have been administered worldwide; however, outbreaks continue. Probiotics are known to restore a stable gut microbiota by regulating innate and adaptive immunity within the gut, demonstrating the possibility that they may be used to combat COVID-19 because of several pieces of evidence suggesting that COVID-19 has an adverse impact on gut microbiota dysbiosis. Thus, probiotics and their metabolites with known antiviral properties may be used as an adjunctive treatment to combat COVID-19. Several clinical trials have revealed the efficacy of probiotics and their metabolites in treating patients with SARS-CoV-2. However, its molecular mechanism has not been unraveled. The availability of abundant data resources and computational methods has significantly changed research finding molecular insights between probiotics and COVID-19. This review highlights computational approaches involving microbiome-based approaches and ensemble-driven docking approaches, as well as a case study proving the effects of probiotic metabolites on SARS-CoV-2.
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Affiliation(s)
- Quang Vo Nguyen
- Centre for Bioinformatics, School of Data Sciences, Perdana University, Suite 9.2, 9th Floor, Wisma Chase Perdana, Changkat Semantan, Wilayah Persekutuan, Kuala Lumpur 50490, Malaysia;
| | - Li Chuin Chong
- Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, Beykoz, Istanbul 34820, Turkey;
| | - Yan-Yan Hor
- Department of Biotechnology, Yeungnam University, 280 Daehak-Ro, Gyeongsan 38541, Gyeongbuk, Korea;
| | - Lee-Ching Lew
- Probionic Corporation, Jeonbuk Institute for Food-Bioindustry, Jeonju 54810, Korea;
| | - Irfan A. Rather
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
- Center of Excellence in Bionanoscience Research, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
- Correspondence: (I.A.R.); (S.-B.C.)
| | - Sy-Bing Choi
- Centre for Bioinformatics, School of Data Sciences, Perdana University, Suite 9.2, 9th Floor, Wisma Chase Perdana, Changkat Semantan, Wilayah Persekutuan, Kuala Lumpur 50490, Malaysia;
- Correspondence: (I.A.R.); (S.-B.C.)
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30
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Yang CY, Chen YH, Liu PJ, Hu WC, Lu KC, Tsai KW. The emerging role of miRNAs in the pathogenesis of COVID-19: Protective effects of nutraceutical polyphenolic compounds against SARS-CoV-2 infection. Int J Med Sci 2022; 19:1340-1356. [PMID: 35928726 PMCID: PMC9346380 DOI: 10.7150/ijms.76168] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 07/08/2022] [Indexed: 11/05/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection can cause immunosuppression and cytokine storm, leading to lung damage and death. The clinical efficacy of anti-SARS-CoV-2 drugs in preventing viral entry into host cells and suppressing viral replication remains inadequate. MicroRNAs (miRNAs) are crucial to the immune response to and pathogenesis of coronaviruses, such as SARS-CoV-2. However, the specific roles of miRNAs in the life cycle of SARS-CoV-2 remain unclear. miRNAs can participate in SARS-CoV-2 infection and pathogenesis through at least four possible mechanisms: 1. host cell miRNA expression interfering with SARS-CoV-2 cell entry, 2. SARS-CoV-2-derived RNA transcripts acting as competitive endogenous RNAs (ceRNAs) that may attenuate host cell miRNA expression, 3. host cell miRNA expression modulating SARS-CoV-2 replication, and 4. SARS-CoV-2-encoded miRNAs silencing the expression of host protein-coding genes. SARS-CoV-2-related miRNAs may be used as diagnostic or prognostic biomarkers for predicting outcomes among patients with SARS-CoV-2 infection. Furthermore, accumulating evidence suggests that dietary polyphenolic compounds may protect against SARS-CoV-2 infection by modulating host cell miRNA expression. These findings have major implications for the future diagnosis and treatment of COVID-19.
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Affiliation(s)
- Chih-Yun Yang
- Division of Chest Medicine, Kaohsiung Municipal Min-Sheng Hospital, Kaohsiung, Taiwan, ROC
| | - Yu-Hsuan Chen
- Division of Chest Medicine, Department of Internal Medicine, CHENG HSIN General Hospital, Taipei, Taiwan, ROC
| | - Pei-Jung Liu
- Division of Chest Medicine, Department of Internal Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan, ROC
| | - Wan-Chung Hu
- Department of Clinical Pathology and Medical Research, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei City, Taiwan, ROC
| | - Kuo-Cheng Lu
- Division of Nephrology, Department of Medicine, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei City, Taiwan, ROC.,Division of Nephrology, Department of Medicine, Fu-Jen Catholic University Hospital, School of Medicine, Fu-Jen Catholic University, New Taipei City, Taiwan, ROC
| | - Kuo-Wang Tsai
- Department of Research, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei City, Taiwan, ROC
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Lashgari NA, Momeni Roudsari N, Momtaz S, Abdolghaffari AH. Transmembrane serine protease 2 and angiotensin-converting enzyme 2 anti-inflammatory receptors for COVID-19/inflammatory bowel diseases treatment. World J Gastroenterol 2021; 27:7943-7955. [PMID: 35046622 PMCID: PMC8678820 DOI: 10.3748/wjg.v27.i46.7943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/12/2021] [Accepted: 11/28/2021] [Indexed: 02/06/2023] Open
Abstract
Inflammatory bowel diseases (IBD) refer to a subgroup of chronic, progressive, long-term, and relapsing inflammatory disorders. IBD may spontaneously grow in the colon, and in severe cases may result in tumor lesions such as invasive carcinoma in inflamed regions of the intestine. Recent epidemiological reports indicate that old age and underlying diseases such as IBD contribute to severity and mortality in patients with coronavirus disease 2019 (COVID-19). Currently, the ongoing COVID-19 pandemic caused serious morbidity and mortality worldwide. It has also been shown that the transmembrane serine protease 2 is an essential factor for viral activation and viral engulfment. Generally, viral entry causes a 'cytokine storm' that induces excessive generation of proinflammatory cytokines/chemokines including interleukin (IL)-6, IL-2, IL-7, tumor necrosis factor-α, and interferon-γ. Future research could concentrate on developing inflammatory immunological responses that are efficient to encounter COVID-19. Current analysis elucidates the role of inflammation and immune responses during IBD infection with COVID-19 and provides a list of possible targets for IBD-regulated therapies in particular. Data from clinical, in vitro, and in vivo studies were collected in English from PubMed, Google Scholar, Scopus, and the Cochrane library until May 2021.
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Affiliation(s)
- Naser-Aldin Lashgari
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Tehran Medical Sciences, Islamic Azad University, Tehran 1941933111, Iran
| | - Nazanin Momeni Roudsari
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Tehran Medical Sciences, Islamic Azad University, Tehran 1941933111, Iran
| | - Saeideh Momtaz
- Medicinal Plants Research Center, Institute of Medicinal Plants, ACECR, Karaj 141554364, Iran
- Toxicology and Diseases Group (TDG), Pharmaceutical Sciences Research Center (PSRC), The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran 1941933111, Iran
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran 1941933111, Iran
- Gastrointestinal Pharmacology Interest Group (GPIG), Universal Scientific Education and Research Network (USERN), Tehran 1941933111, Iran
| | - Amir Hossein Abdolghaffari
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Tehran Medical Sciences, Islamic Azad University, Tehran 1941933111, Iran
- Medicinal Plants Research Center, Institute of Medicinal Plants, ACECR, Karaj 141554364, Iran
- Toxicology and Diseases Group (TDG), Pharmaceutical Sciences Research Center (PSRC), The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran 1941933111, Iran
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran 1941933111, Iran
- Gastrointestinal Pharmacology Interest Group (GPIG), Universal Scientific Education and Research Network (USERN), Tehran 1941933111, Iran
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Bimonte S, Forte CA, Cuomo M, Esposito G, Cascella M, Cuomo A. An Overview on the Potential Roles of EGCG in the Treatment of COVID-19 Infection. Drug Des Devel Ther 2021; 15:4447-4454. [PMID: 34737551 PMCID: PMC8560077 DOI: 10.2147/dddt.s314666] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 08/05/2021] [Indexed: 01/18/2023] Open
Abstract
Coronavirus disease-19 (COVID-19) pandemic is currently ongoing worldwide and causes a lot of deaths in many countries. Although different vaccines for the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection have been developed and are now available, there are no effective antiviral drugs to treat the disease, except for Remdesivir authorized by the US FDA to counteract the emergency. Thus, it can be useful to find alternative therapies based on the employment of natural compounds, with antiviral features, to circumvent SARS-CoV-2 infection. Pre-clinical studies highlighted the antiviral activities of epigallocatechin-3-gallate (EGCG), a catechin primarily found in green tea, against various viruses, including SARS-CoV-2. In this review, we summarize this experimental evidence and highlight the potential use of EGCG as an alternative therapeutic choice for the treatment of SARS-CoV-2 infection.
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Affiliation(s)
- Sabrina Bimonte
- Division of Anesthesia and Pain Medicine, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Naples, Italy
| | - Cira Antonietta Forte
- Division of Anesthesia and Pain Medicine, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Naples, Italy
| | - Massimiliano Cuomo
- S.C. Project Management e Formazione, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Naples, Italy
| | - Gennaro Esposito
- Division of Anesthesia and Pain Medicine, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Naples, Italy
| | - Marco Cascella
- Division of Anesthesia and Pain Medicine, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Naples, Italy
| | - Arturo Cuomo
- Division of Anesthesia and Pain Medicine, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Naples, Italy
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Predicting novel drug candidates against Covid-19 using generative deep neural networks. J Mol Graph Model 2021; 110:108045. [PMID: 34688160 PMCID: PMC8510991 DOI: 10.1016/j.jmgm.2021.108045] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/17/2021] [Accepted: 10/04/2021] [Indexed: 12/21/2022]
Abstract
The novel Coronavirus outbreak has created a massive economic crisis, and many succumb to death, disturbing the lives of mankind all over the world. Currently, there are no viable treatment for this condition, drug development approaches are being pursued with vigor. The major treatment options are to repurpose existing drugs or to find new ones. Traditional methods for drug discovery take a longer time, so there is an urgent need to develop some alternative techniques that reduces search space for drug candidates. Towards this endeavor, we propose a novel drug discovery method that leverages on long short term memory (LSTM) model to generate novel molecules that are adept at binding with novel Coronavirus protease. Our study demonstrates that the proposed method is able to recreate novel molecules that correlate very much with the properties of trained molecules. Further, we fine-tune the model to generate novel drug-like molecules that are active towards a specific target. We consider 3CLPro, the main protease of novel Coronavirus, as a therapeutic target and demonstrated in silico screening to assess target structural binding affinities with docking simulations. We observed that 80% of generated molecules show docking free energy of less than −5.8 kcal/mol. The top generated drug candidate has the highest binding affinity with a docking score of −8.5 kcal/mol, which is very much lower when compared to approved existing commercial drugs including, Remdesivir. The low binding energy indicates that the generated molecules could be explored as potential drug candidates for Covid-19.
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Zhao Z, Feng M, Wan J, Zheng X, Teng C, Xie X, Pan W, Hu B, Huang J, Liu Z, Wu J, Cai S. Research progress of epigallocatechin-3-gallate (EGCG) on anti-pathogenic microbes and immune regulation activities. Food Funct 2021; 12:9607-9619. [PMID: 34549212 DOI: 10.1039/d1fo01352a] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
At the end of 2019, the COVID-19 virus spread worldwide, infecting millions of people. Infectious diseases induced by pathogenic microorganisms such as the influenza virus, hepatitis virus, and Mycobacterium tuberculosis are also a major threat to public health. The high mortality caused by infectious pathogenic microorganisms is due to their strong virulence, which leads to the excessive counterattack by the host immune system and severe inflammatory damage of the immune system. This paper reviews the efficacy, mechanism and related immune regulation of epigallocatechin-3-gallate (EGCG) as an anti-pathogenic microorganism drug. EGCG mainly shows both direct and indirect anti-infection effects. EGCG directly inhibits early infection by interfering with the adsorption on host cells, inhibiting virus replication and reducing bacterial biofilm formation and toxin release; EGCG indirectly inhibits infection by regulating immune inflammation and antioxidation. At the same time, we reviewed the bioavailability and safety of EGCG in vivo. At present, the bioavailability of EGCG can be improved to some extent using nanostructured drug delivery systems and molecular modification technology in combination with other drugs. This study provides a theoretical basis for the development of EGCG as an adjuvant drug for anti-pathogenic microorganisms.
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Affiliation(s)
- Zijuan Zhao
- National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China. .,Key Laboratory of Ministry of Education for Tea Science, Hunan Agricultural University, Changsha 410128, China
| | - Meiyan Feng
- National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China. .,Key Laboratory of Ministry of Education for Tea Science, Hunan Agricultural University, Changsha 410128, China
| | - Juan Wan
- National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China. .,Key Laboratory of Ministry of Education for Tea Science, Hunan Agricultural University, Changsha 410128, China
| | - Xin Zheng
- National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China. .,Key Laboratory of Ministry of Education for Tea Science, Hunan Agricultural University, Changsha 410128, China
| | - Cuiqin Teng
- Wuzhou Institute of Agricultural, Wuzhou 543003, China
| | - Xinya Xie
- National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China. .,Key Laboratory of Ministry of Education for Tea Science, Hunan Agricultural University, Changsha 410128, China
| | - Wenjing Pan
- National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China. .,Key Laboratory of Ministry of Education for Tea Science, Hunan Agricultural University, Changsha 410128, China
| | - Baozhu Hu
- National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China. .,Key Laboratory of Ministry of Education for Tea Science, Hunan Agricultural University, Changsha 410128, China
| | - Jianan Huang
- National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China. .,Key Laboratory of Ministry of Education for Tea Science, Hunan Agricultural University, Changsha 410128, China.,Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China
| | - Zhonghua Liu
- National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China. .,Key Laboratory of Ministry of Education for Tea Science, Hunan Agricultural University, Changsha 410128, China.,Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China
| | - Jianhua Wu
- Wuzhou Institute of Agricultural, Wuzhou 543003, China
| | - Shuxian Cai
- National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China. .,Key Laboratory of Ministry of Education for Tea Science, Hunan Agricultural University, Changsha 410128, China.,Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China
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Targeting autophagy with natural products to prevent SARS-CoV-2 infection. J Tradit Complement Med 2021; 12:55-68. [PMID: 34664025 PMCID: PMC8516241 DOI: 10.1016/j.jtcme.2021.10.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/27/2021] [Accepted: 10/12/2021] [Indexed: 01/18/2023] Open
Abstract
Autophagy is a catabolic process that maintains internal homeostasis and energy balance through the lysosomal degradation of redundant or damaged cellular components. During virus infection, autophagy is triggered both in parenchymal and in immune cells with different finalistic objectives: in parenchymal cells, the goal is to destroy the virion particle while in macrophages and dendritic cells the goal is to expose virion-derived fragments for priming the lymphocytes and initiate the immune response. However, some viruses have developed a strategy to subvert the autophagy machinery to escape the destructive destiny and instead exploit it for virion assembly and exocytosis. Coronaviruses (like SARS-CoV-2) possess such ability. The autophagy process requires a set of proteins that constitute the core machinery and is controlled by several signaling pathways. Here, we report on natural products capable of interfering with SARS-CoV-2 cellular infection and replication through their action on autophagy. The present study provides support to the use of such natural products as adjuvant therapeutics for the management of COVID-19 pandemic to prevent the virus infection and replication, and so mitigating the progression of the disease.
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Nath V, Rohini A, Kumar V. Identification of M pro inhibitors of SARS-CoV-2 using structure based computational drug repurposing. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021; 37:102178. [PMID: 34611467 PMCID: PMC8483991 DOI: 10.1016/j.bcab.2021.102178] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 05/03/2021] [Accepted: 09/28/2021] [Indexed: 12/20/2022]
Abstract
The recent outbreak of COVID-19, caused by the novel pathogen SARS-coronavirus 2 (SARS-CoV-2) is a severe health emergency. In this pandemic, drug repurposing seems to be the most promising alternative to identify effective therapeutic agents for immediate treatment of infected patients. The present study aimed to evaluate all the drugs present in drug bank as potential novel SARS-CoV-2 inhibitors, using computational drug repurposing studies. Docking-based virtual screening and binding energy prediction were performed, followed by Absorption Distribution Metabolism Excretion calculation. Hydroxychloroquine and Nelfinavir have been identified as the best potential inhibitor against the SARS-CoV-2, therefore, they were used as reference compounds in computational DR studies. The docking study revealed 13 best compounds based on their highest binding affinity, binding energy, and dock score concerning the other screened compounds. Out of 13, only 4 compounds were further shortlisted based on their binding energy and best ADME properties. The hierarchical virtual screening yielded the best 04 drugs, DB07042 (compound 2), DB13035 (compound 3), DB13604 (compound 5) and DB08253 (compound 6), with commendable binding energies in kcal/mol, i.e. −65.45, −62.01, −52.09 and −51.70 respectively. Further, Molecular dynamics simulation with 04 best-retrieved hits has confirmed stable trajectories in protein in terms of root mean square deviation and root mean square fluctuation. During 30 ns simulation, the interactions were also found similar to the docking-based studies. However, clinical studies are necessary to investigate their therapeutic use against this outbreak.
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Key Words
- ACE, Angiotensin-Converting Enzyme
- ADME, Absorption Distribution Metabolism Excretion
- Binding energy
- CDR, Computational Drug Repurposing
- COVID
- CoV, Corona Virus
- Docking
- Drug repurposing
- HTVS, High-throughput virtual screening
- MMGBSA, Molecular mechanics generalized born surface area
- OPLS, Optimized Potentials for Liquid Simulations
- PDB, Protein data bank
- SARS, Severe Acute Respiratory Syndrome
- SP, Standard Precision
- Virtual screening
- XP, Extra precision
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Affiliation(s)
- Virendra Nath
- Department of Pharmacy, School of Chemical Sciences and Pharmacy, Central University of Rajasthan, Ajmer, India
| | - A Rohini
- College of Pharmacy, JSS Academy of Technical Sciences, Noida, Uttar Pradesh, India
| | - Vipin Kumar
- Department of Pharmacy, School of Chemical Sciences and Pharmacy, Central University of Rajasthan, Ajmer, India
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Diniz LRL, Elshabrawy HA, Souza MTDS, Duarte ABS, Datta S, de Sousa DP. Catechins: Therapeutic Perspectives in COVID-19-Associated Acute Kidney Injury. Molecules 2021; 26:5951. [PMID: 34641495 PMCID: PMC8512361 DOI: 10.3390/molecules26195951] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 12/14/2022] Open
Abstract
Data obtained from several intensive care units around the world have provided substantial evidence of the strong association between impairment of the renal function and in-hospital deaths of critically ill COVID-19 patients, especially those with comorbidities and requiring renal replacement therapy (RRT). Acute kidney injury (AKI) is a common renal disorder of various etiologies characterized by a sudden and sustained decrease of renal function. Studies have shown that 5-46% of COVID-19 patients develop AKI during hospital stay, and the mortality of those patients may reach up to 100% depending on various factors, such as organ failures and RRT requirement. Catechins are natural products that have multiple pharmacological activities, including anti-coronavirus and reno-protective activities against kidney injury induced by nephrotoxic agents, obstructive nephropathies and AKI accompanying metabolic and cardiovascular disorders. Therefore, in this review, we discuss the anti-SARS-CoV-2 and reno-protective effects of catechins from a mechanistic perspective. We believe that catechins may serve as promising therapeutics in COVID-19-associated AKI due to their well-recognized anti-SARS-CoV-2, and antioxidant and anti-inflammatory properties that mediate their reno-protective activities.
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Affiliation(s)
| | - Hatem A. Elshabrawy
- Department of Molecular and Cellular Biology, College of Osteopathic Medicine, Sam Houston State University, Conroe, TX 77304, USA;
| | | | | | - Sabarno Datta
- College of Osteopathic Medicine, Sam Houston State University, Conroe, TX 77304, USA;
| | - Damião Pergentino de Sousa
- Department of Pharmaceutical Sciences, Federal University of Paraíba, João Pessoa 58051-970, PB, Brazil;
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Mousavi SS, Karami A, Haghighi TM, Tumilaar SG, Fatimawali, Idroes R, Mahmud S, Celik I, Ağagündüz D, Tallei TE, Emran TB, Capasso R. In Silico Evaluation of Iranian Medicinal Plant Phytoconstituents as Inhibitors against Main Protease and the Receptor-Binding Domain of SARS-CoV-2. Molecules 2021; 26:5724. [PMID: 34577194 PMCID: PMC8470205 DOI: 10.3390/molecules26185724] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 08/22/2021] [Accepted: 09/01/2021] [Indexed: 12/22/2022] Open
Abstract
The novel coronavirus disease 2019 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which initially appeared in Wuhan, China, in December 2019. Elderly individuals and those with comorbid conditions may be more vulnerable to this disease. Consequently, several research laboratories continue to focus on developing drugs to treat this infection because this disease has developed into a global pandemic with an extremely limited number of specific treatments available. Natural herbal remedies have long been used to treat illnesses in a variety of cultures. Modern medicine has achieved success due to the effectiveness of traditional medicines, which are derived from medicinal plants. The objective of this study was to determine whether components of natural origin from Iranian medicinal plants have an antiviral effect that can prevent humans from this coronavirus infection using the most reliable molecular docking method; in our case, we focused on the main protease (Mpro) and a receptor-binding domain (RBD). The results of molecular docking showed that among 169 molecules of natural origin from common Iranian medicinal plants, 20 molecules (chelidimerine, rutin, fumariline, catechin gallate, adlumidine, astragalin, somniferine, etc.) can be proposed as inhibitors against this coronavirus based on the binding free energy and type of interactions between these molecules and the studied proteins. Moreover, a molecular dynamics simulation study revealed that the chelidimerine-Mpro and somniferine-RBD complexes were stable for up to 50 ns below 0.5 nm. Our results provide valuable insights into this mechanism, which sheds light on future structure-based designs of high-potency inhibitors for SARS-CoV-2.
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Affiliation(s)
- Seyyed Sasan Mousavi
- Department of Horticultural Science, School of Agriculture, Shiraz University, Shiraz 71441, Iran; (S.S.M.); (A.K.); (T.M.H.)
| | - Akbar Karami
- Department of Horticultural Science, School of Agriculture, Shiraz University, Shiraz 71441, Iran; (S.S.M.); (A.K.); (T.M.H.)
| | - Tahereh Movahhed Haghighi
- Department of Horticultural Science, School of Agriculture, Shiraz University, Shiraz 71441, Iran; (S.S.M.); (A.K.); (T.M.H.)
| | - Sefren Geiner Tumilaar
- Pharmacy Study Program, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, Indonesia; (S.G.T.); (F.)
| | - Fatimawali
- Pharmacy Study Program, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, Indonesia; (S.G.T.); (F.)
- The University Center of Excellence for Biotechnology and Conservation of Wallacea, Sam Ratulangi University, Manado 95115, Indonesia
| | - Rinaldi Idroes
- Department of Pharmacy, Faculty of Mathematics and Natural Sciences, Universitas Syiah Kuala, Kopelma Darussalam, Banda Aceh 23111, Indonesia;
| | - Shafi Mahmud
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh;
| | - Ismail Celik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri 38039, Turkey;
| | - Duygu Ağagündüz
- Department of Nutrition and Dietetics, Faculty of Health Sciences, Gazi University, Emek, Ankara 06490, Turkey;
| | - Trina Ekawati Tallei
- The University Center of Excellence for Biotechnology and Conservation of Wallacea, Sam Ratulangi University, Manado 95115, Indonesia
- Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, Indonesia
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh
| | - Raffaele Capasso
- Department of Agricultural Sciences, University of Naples Federico II, Portici, 80055 Naples, Italy
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Flores-Félix JD, Gonçalves AC, Alves G, Silva LR. Consumption of Phenolic-Rich Food and Dietary Supplements as a Key Tool in SARS-CoV-19 Infection. Foods 2021; 10:2084. [PMID: 34574194 PMCID: PMC8469666 DOI: 10.3390/foods10092084] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/29/2021] [Accepted: 09/02/2021] [Indexed: 12/23/2022] Open
Abstract
The first cases of COVID-19, which is caused by the SARS-CoV-2, were reported in December 2019. The vertiginous worldwide expansion of SARS-CoV-2 caused the collapse of health systems in several countries due to the high severity of the COVID-19. In addition to the vaccines, the search for active compounds capable of preventing and/or fighting the infection has been the main direction of research. Since the beginning of this pandemic, some evidence has highlighted the importance of a phenolic-rich diet as a strategy to reduce the progression of this disease, including the severity of the symptoms. Some of these compounds (e.g., curcumin, gallic acid or quercetin) already showed capacity to limit the infection of viruses by inhibiting entry into the cell through its binding to protein Spike, regulating the expression of angiotensin-converting enzyme 2, disrupting the replication in cells by inhibition of viral proteases, and/or suppressing and modulating the host's immune response. Therefore, this review intends to discuss the most recent findings on the potential of phenolics to prevent SARS-CoV-2.
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Affiliation(s)
- José David Flores-Félix
- CICS-UBI–Health Sciences Research Centre, Faculty of Health Science, University of Beira Interior, 6200-506 Covilhã, Portugal; (J.D.F.-F.); (A.C.G.); (G.A.)
| | - Ana C. Gonçalves
- CICS-UBI–Health Sciences Research Centre, Faculty of Health Science, University of Beira Interior, 6200-506 Covilhã, Portugal; (J.D.F.-F.); (A.C.G.); (G.A.)
| | - Gilberto Alves
- CICS-UBI–Health Sciences Research Centre, Faculty of Health Science, University of Beira Interior, 6200-506 Covilhã, Portugal; (J.D.F.-F.); (A.C.G.); (G.A.)
| | - Luís R. Silva
- CICS-UBI–Health Sciences Research Centre, Faculty of Health Science, University of Beira Interior, 6200-506 Covilhã, Portugal; (J.D.F.-F.); (A.C.G.); (G.A.)
- Unidade de Investigação para o Desenvolvimento do Interior (UDI/IPG), Instituto Politécnico da Guarda, 6300-559 Guarda, Portugal
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Jakhmola S, Jonniya NA, Sk MF, Rani A, Kar P, Jha HC. Identification of Potential Inhibitors against Epstein-Barr Virus Nuclear Antigen 1 (EBNA1): An Insight from Docking and Molecular Dynamic Simulations. ACS Chem Neurosci 2021; 12:3060-3072. [PMID: 34340305 DOI: 10.1021/acschemneuro.1c00350] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Epstein-Barr virus (EBV), a known tumorigenic virus, is associated with various neuropathies, including multiple sclerosis (MS). However, there is no anti-EBV FDA-approved drug available in the market. Our study targeted EBV protein EBV nuclear antigen 1 (EBNA1), crucial in virus replication and expressed in all the stages of viral latencies. This dimeric protein binds to an 18 bp palindromic DNA sequence and initiates the process of viral replication. We chose phytochemicals and FDA-approved MS drugs based on literature survey followed by their evaluation efficacies as anti-EBNA1 molecules. Molecular docking revealed FDA drugs ozanimod, siponimod, teriflunomide, and phytochemicals; emodin; protoapigenone; and EGCG bound to EBNA1 with high affinities. ADMET and Lipinski's rule analysis of the phytochemicals predicted favorable druggability. We supported our assessments of pocket druggability with molecular dynamics simulations and binding affinity predictions by the molecular mechanics generalized Born surface area (MM/GBSA) method. Our results establish a stable binding for siponimod and ozanimod with EBNA1 mainly via van der Waals interactions. We identified hot spot residues like I481', K477', L582', and K586' in the binding of ligands. In particular, K477' at the amino terminal of EBNA1 is known to establish interaction with two bases at the major groove of the DNA. Siponimod bound to EBNA1 engaging K477', thus plausibly making it unavailable for DNA interaction. Computational alanine scanning further supported the significant roles of K477', I481', and K586' in the binding of ligands with EBNA1. Conclusively, the compounds showed promising results to be used against EBNA1.
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Affiliation(s)
- Shweta Jakhmola
- Infection Bioengineering Group, Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh 453552, India
| | - Nisha Amarnath Jonniya
- Computational Biophysics Group, Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh 453552, India
| | - Md Fulbabu Sk
- Computational Biophysics Group, Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh 453552, India
| | - Annu Rani
- Infection Bioengineering Group, Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh 453552, India
| | - Parimal Kar
- Computational Biophysics Group, Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh 453552, India
| | - Hem Chandra Jha
- Infection Bioengineering Group, Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh 453552, India
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Joseph J, Karthika T, Das VRA, Raj VS. The use of pseudotyped coronaviruses for the screening of entry inhibitors: Green tea extract inhibits the entry of SARS-CoV-1, MERS-CoV, and SARS-CoV-2 by blocking receptor-spike interaction. Curr Pharm Biotechnol 2021; 23:1118-1129. [PMID: 34375189 DOI: 10.2174/1389201022666210810111716] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/11/2021] [Accepted: 06/11/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Coronaviruses (CoVs) infect a wide range of animals and birds. Their tropism is primarily determined by the ability of the spike protein to bind to a host cell surface receptor. The ongoing outbreak of SARS-CoV-2 inculcates the need for the development of effective intervention strategies. OBJECTIVES In this study, we aim to produce pseudotyped coronaviruses of SARS-CoV-1, MERS-CoV, and SARS-CoV-2 and show its applications, including virus entry, neutralization, and screening of entry inhibitors from natural products. METHODS Here, we generated VSV-based pseudotyped coronaviruses (CoV-PVs) for SARS-CoV-1, MERS-CoV, and SARS-CoV-2. Recombinant spike proteins of SARS-CoV-1, MERS-CoV, and SARS-CoV-2 were transiently expressed in HEK293T cells followed by infection with recombinant VSV. High titer pseudoviruses were harvested and subjected to distinct validation assays, which confirms the proper spike pseudotyping. Further, specific receptor-mediated entry was confirmed by antibody neutralization and soluble form of receptor inhibition assay on Vero E6 cells. Next, these CoV-PVs were used for screening of antiviral activity of natural compounds such as green tea and Spirulina extract. RESULTS Medicinal plants and natural compounds have been traditionally used as antiviral agents. In the first series of experiments, we demonstrated that pseudotyped viruses specifically bind to their receptors for cellular entry. SARS-CoV-1 and MERS-CoV anti-sera neutralize SARS-CoV-1-PV and SARS-CoV-2-PV, and MERS-CoV-PV, respectively. Incubation of soluble ACE2 with CoV-PVs inhibited entry of SARS-CoV-1 and SARS-CoV-2 PVs but not MERS-CoV-PV. Also, transient expression of ACE2 and DPP4 in non-permissive BHK21 cells enabled infection by SARS-CoV-1-PV, SARS-CoV-2-PV, and MERS-CoV-PV, respectively. Next, we showed the antiviral properties of known entry inhibitors of enveloped viruses, Spirulina, and green tea extracts against CoV-PVs. SARS-CoV-1-PV, MERS-CoV-PV, and SARS-CoV-2-PV entry was blocked with higher efficiency when preincubated with either green tea or Spirulina extracts. Green tea provided a better inhibitory effect by binding to the S1 domain of the spike and blocking the spike interaction with its receptor. CONCLUSION In summary, we demonstrated that pseudotyped viruses are an ideal tool for studying viral entry, quantification of neutralizing antibodies, and screening of entry inhibitors in a BSL-2 facility. Moreover, green tea might be a promising natural remedy against emerging coronaviruses.
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Affiliation(s)
- Jeswin Joseph
- Virology Scientific Research (VSR) Laboratory, School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, India
| | - Thankamani Karthika
- Virology Scientific Research (VSR) Laboratory, School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, India
| | - V R Akshay Das
- Virology Scientific Research (VSR) Laboratory, School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, India
| | - V Stalin Raj
- Virology Scientific Research (VSR) Laboratory, School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, India
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Tsvetkov V, Varizhuk A, Kozlovskaya L, Shtro A, Lebedeva O, Komissarov A, Vedekhina T, Manuvera V, Zubkova O, Eremeev A, Shustova E, Pozmogova G, Lioznov D, Ismukhametov A, Lazarev V, Lagarkova M. EGCG as an anti-SARS-CoV-2 agent: Preventive versus therapeutic potential against original and mutant virus. Biochimie 2021; 191:27-32. [PMID: 34389380 PMCID: PMC8353982 DOI: 10.1016/j.biochi.2021.08.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 08/06/2021] [Accepted: 08/07/2021] [Indexed: 01/30/2023]
Abstract
In the search for anti-SARS-CoV-2 drugs, much attention is given to safe and widely available native compounds. The green tea component epigallocatechin 3 gallate (EGCG) is particularly promising because it reportedly inhibits viral replication and viral entry in vitro. However, conclusive evidence for its predominant activity is needed. We tested EGCG effects on the native virus isolated from COVID-19 patients in two independent series of experiments using VERO cells and two different treatment schemes in each series. The results confirmed modest cytotoxicity of EGCG and its substantial antiviral activity. The preincubation scheme aimed at infection prevention has proven particularly beneficial. We complemented that finding with a detailed investigation of EGCG interactions with viral S-protein subunits, including S2, RBD, and the RBD mutant harboring the N501Y mutation. Molecular modeling experiments revealed N501Y-specific stacking interactions in the RBD-ACE2 complex and provided insight into EGCG interference with the complex formation. Together, these findings provide a molecular basis for the observed EGCG effects and reinforce its prospects in COVID-19 prevention therapy.
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Affiliation(s)
- Vladimir Tsvetkov
- Federal Research and Clinical Center of Physical Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, 119435, Moscow, Russia; World-Class Research Center "Digital Biodesign and Personalized Healthcare", I.M. Sechenov First Moscow State Medical University, Trubetskaya Str. 8-2, 119991, Moscow, Russia; A.V. Topchiev Institute of Petrochemical Synthesis RAS, Moscow, 119071, Russia
| | - Anna Varizhuk
- Federal Research and Clinical Center of Physical Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, 119435, Moscow, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435, Moscow, Russia; Moscow Institute of Physics and Technology, Institutskiy Pereulok 9, Dolgoprudny, 141701, Russia
| | - Liubov Kozlovskaya
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Poselok Instituta Poliomiyelita 8, 108819, Moscow, Russia; Institute of Translational Medicine and Biotechnology, Sechenov Moscow State Medical University, Nakhimovsky av. 45, 117418, Moscow, Russia
| | - Anna Shtro
- Smorodintsev Research Institute of Influenza, Professora Popova str., 15/17, 197376, Sankt-Peterburg, Russia
| | - Olga Lebedeva
- Federal Research and Clinical Center of Physical Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, 119435, Moscow, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435, Moscow, Russia
| | - Andrey Komissarov
- Smorodintsev Research Institute of Influenza, Professora Popova str., 15/17, 197376, Sankt-Peterburg, Russia
| | - Tatjana Vedekhina
- Federal Research and Clinical Center of Physical Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, 119435, Moscow, Russia
| | - Valentin Manuvera
- Federal Research and Clinical Center of Physical Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, 119435, Moscow, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435, Moscow, Russia; Moscow Institute of Physics and Technology, Institutskiy Pereulok 9, Dolgoprudny, 141701, Russia
| | - Olga Zubkova
- Federal Research and Clinical Center of Physical Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, 119435, Moscow, Russia
| | - Artem Eremeev
- Federal Research and Clinical Center of Physical Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, 119435, Moscow, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435, Moscow, Russia
| | - Elena Shustova
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Poselok Instituta Poliomiyelita 8, 108819, Moscow, Russia
| | - Galina Pozmogova
- Federal Research and Clinical Center of Physical Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, 119435, Moscow, Russia
| | - Dmitry Lioznov
- Smorodintsev Research Institute of Influenza, Professora Popova str., 15/17, 197376, Sankt-Peterburg, Russia
| | - Aydar Ismukhametov
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Poselok Instituta Poliomiyelita 8, 108819, Moscow, Russia; Institute of Translational Medicine and Biotechnology, Sechenov Moscow State Medical University, Nakhimovsky av. 45, 117418, Moscow, Russia
| | - Vassili Lazarev
- Federal Research and Clinical Center of Physical Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, 119435, Moscow, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435, Moscow, Russia; Moscow Institute of Physics and Technology, Institutskiy Pereulok 9, Dolgoprudny, 141701, Russia.
| | - Maria Lagarkova
- Federal Research and Clinical Center of Physical Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, 119435, Moscow, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435, Moscow, Russia.
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Mhatre S, Gurav N, Shah M, Patravale V. Entry-inhibitory role of catechins against SARS-CoV-2 and its UK variant. Comput Biol Med 2021; 135:104560. [PMID: 34147855 PMCID: PMC8189743 DOI: 10.1016/j.compbiomed.2021.104560] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/06/2021] [Accepted: 06/06/2021] [Indexed: 01/22/2023]
Abstract
BACKGROUND The global pandemic caused by a RNA virus capable of infecting humans and animals, has resulted in millions of deaths worldwide. Severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) infects the lungs, and the gastrointestinal tract to some extent. Rapid structural mutations have increased the virulence and infectivity of the virus drastically. One such mutated strain known as the UK variant has caused many deaths in the United Kingdom. HYPOTHESIS Among several indigenous natural ingredients used for prevention and cure of many diseases, the catechins have been reported for their antiviral activity, even against SARS-CoV-2. Characteristic mutations present on the spike protein have presented the newer strain its enhanced infectivity. The spike protein helps the virus bind to ACE2 receptor of the host cell and hence is a drug target. Catechins have been reported for their entry-inhibitory activity against several viruses. METHOD In this study, we performed molecular docking of different catechins with the wild and mutant variants of the spike protein of SARS-CoV-2. The stability of the best docked complexes was validated using molecular dynamics simulation. RESULTS The in-silico studies show that the catechins form favourable interactions with the spike protein and can potentially impair its function. Epigallocatechin gallate (EGCG) showed the best binding among the catechins against both the strains. Both the protein-ligand complexes were stable throughout the simulation time frame. CONCLUSION The outcomes should encourage further exploration of the antiviral activity of EGCG against SARS-CoV-2 and its variants.
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Affiliation(s)
- Susmit Mhatre
- Department of Pharmaceutical Science and Technology, Institute of Chemical Technology, Mumbai, Nathalal Parekh Marg, Matunga (E), Mumbai-19, Maharashtra, India.
| | - Nitisha Gurav
- School of Biosciences, University of Nottingham, Sutton Bonington, Loughborough, LE12 5RD, United Kingdom.
| | - Mansi Shah
- Department of Pharmaceutical Science and Technology, Institute of Chemical Technology, Mumbai, Nathalal Parekh Marg, Matunga (E), Mumbai-19, Maharashtra, India.
| | - Vandana Patravale
- Department of Pharmaceutical Science and Technology, Institute of Chemical Technology, Mumbai, Nathalal Parekh Marg, Matunga (E), Mumbai-19, Maharashtra, India.
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Cárdenas-Rodríguez N, Bandala C, Vanoye-Carlo A, Ignacio-Mejía I, Gómez-Manzo S, Hernández-Cruz EY, Pedraza-Chaverri J, Carmona-Aparicio L, Hernández-Ochoa B. Use of Antioxidants for the Neuro-Therapeutic Management of COVID-19. Antioxidants (Basel) 2021; 10:971. [PMID: 34204362 PMCID: PMC8235474 DOI: 10.3390/antiox10060971] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 06/07/2021] [Accepted: 06/15/2021] [Indexed: 02/07/2023] Open
Abstract
Coronavirus Disease 2019 (COVID-19), caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), is an emergent infectious disease that has caused millions of deaths throughout the world. COVID-19 infection's main symptoms are fever, cough, fatigue, and neurological manifestations such as headache, myalgias, anosmia, ageusia, impaired consciousness, seizures, and even neuromuscular junctions' disorders. In addition, it is known that this disease causes a series of systemic complications such as adverse respiratory distress syndrome, cardiac injury, acute kidney injury, and liver dysfunction. Due to the neurological symptoms associated with COVID-19, damage in the central nervous system has been suggested as well as the neuroinvasive potential of SARS-CoV-2. It is known that CoV infections are associated with an inflammation process related to the imbalance of the antioxidant system; cellular changes caused by oxidative stress contribute to brain tissue damage. Although anti-COVID-19 vaccines are under development, there is no specific treatment for COVID-19 and its clinical manifestations and complications; only supportive treatments with immunomodulators, anti-vascular endothelial growth factors, modulating drugs, statins, or nutritional supplements have been used. In the present work, we analyzed the potential of antioxidants as adjuvants for the treatment of COVID-19 and specifically their possible role in preventing or decreasing the neurological manifestations and neurological complications present in the disease.
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Affiliation(s)
- Noemí Cárdenas-Rodríguez
- Laboratorio de Neurociencias, Instituto Nacional de Pediatría, Secreatría de Salud, Ciudad de México 04530, Mexico; (A.V.-C.); (L.C.-A.)
| | - Cindy Bandala
- Division de Neurociencias, Instituto Nacional de Rehabilitación, Secretaría de Salud, Ciudad de México 14389, Mexico;
- Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico
| | - América Vanoye-Carlo
- Laboratorio de Neurociencias, Instituto Nacional de Pediatría, Secreatría de Salud, Ciudad de México 04530, Mexico; (A.V.-C.); (L.C.-A.)
| | - Iván Ignacio-Mejía
- Laboratorio de Medicina Traslacional, Escuela Militar de Graduados de Sanidad, SEDENA, Ciudad de México 11200, Mexico;
| | - Saúl Gómez-Manzo
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Ciudad de México 04530, Mexico;
| | | | - José Pedraza-Chaverri
- Departamento de Biología, Facultad de Química, UNAM, Ciudad de México 04150, Mexico; (E.Y.H.-C.); (J.P.-C.)
| | - Liliana Carmona-Aparicio
- Laboratorio de Neurociencias, Instituto Nacional de Pediatría, Secreatría de Salud, Ciudad de México 04530, Mexico; (A.V.-C.); (L.C.-A.)
| | - Beatriz Hernández-Ochoa
- Laboratorio de Inmunoquímica, Hospital Infantil de México Federico Gómez, Secretaría de Salud, Ciudad de México 06720, Mexico;
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Hong S, Seo SH, Woo SJ, Kwon Y, Song M, Ha NC. Epigallocatechin Gallate Inhibits the Uridylate-Specific Endoribonuclease Nsp15 and Efficiently Neutralizes the SARS-CoV-2 Strain. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:5948-5954. [PMID: 34015930 PMCID: PMC8146138 DOI: 10.1021/acs.jafc.1c02050] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/10/2021] [Accepted: 05/11/2021] [Indexed: 05/05/2023]
Abstract
SARS-CoV-2, the coronavirus strain that initiated the COVID-19 pandemic, and its subsequent variants present challenges to vaccine development and treatment. As the coronavirus evades the host innate immune response at the initial stage of infection, the disease can have a long nonsymptomatic period. The uridylate-specific endoribonuclease Nsp15 processes the viral genome for replication and cleaves the polyU sequence in the viral RNA to interfere with the host immune system. This study screened natural compounds in vitro to identify inhibitors against Nsp15 from SARS-CoV-2. Three natural compounds, epigallocatechin gallate (EGCG), baicalin, and quercetin, were identified as potential inhibitors. Potent antiviral activity of EGCG was confirmed in plaque reduction neutralization tests with a SARS-CoV-2 strain (PRNT50 = 0.20 μM). Because the compound has been used as a functional food ingredient due to its beneficial health effects, we theorize that this natural compound may help inhibit viral replication while minimizing safety issues.
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Affiliation(s)
- Seokho Hong
- Department
of Agricultural Biotechnology, Center for Food and Bioconvergence,
and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic
of Korea
| | - Sang Hwan Seo
- Science
Unit, International Vaccine Institute, Seoul 08826, Republic of Korea
| | - Sun-Je Woo
- Science
Unit, International Vaccine Institute, Seoul 08826, Republic of Korea
| | - Yonghoon Kwon
- Department
of Applied Biology and Chemistry, Seoul
National University, Seoul 08826, Republic of Korea
| | - Manki Song
- Science
Unit, International Vaccine Institute, Seoul 08826, Republic of Korea
| | - Nam-Chul Ha
- Department
of Agricultural Biotechnology, Center for Food and Bioconvergence,
and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic
of Korea
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Selvaraj J, Sundar P S, Rajan L, Selvaraj D, Palanisamy D, Namboori Pk K, Mohankumar SK. Identification of (2 R,3 R)-2-(3,4-dihydroxyphenyl)chroman-3-yl-3,4,5-trihydroxy benzoate as multiple inhibitors of SARS-CoV-2 targets; a systematic molecular modelling approach. RSC Adv 2021; 11:13051-13060. [PMID: 35423848 PMCID: PMC8697517 DOI: 10.1039/d1ra01603b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 03/25/2021] [Indexed: 11/21/2022] Open
Abstract
Coronavirus disease of 2019 (COVID-19) is a zoonotic disease caused by a new severe acute respiratory syndrome (SARS-CoV-2) which has quickly resulted in a pandemic. Recent anti-COVID-19 drug discoveries are leaning towards repurposing phytochemicals which have been previously reported for SARS and MERS-CoV outbreaks. However, they have been either virtually screened or tested so far against mono targets and the potent derivatives of virtually sorted lead molecules remain elusive. We aimed to identify the phytochemicals having potentials to inhibit SARS CoV-2 infection via multiple targets. The selected 132 phytochemicals were virtually screened using a structure based in silico technique against main protease (Mpro) which is a potential target of SARS CoV-2. Six compounds were selected based on the LibDock scores and further subjected to induced fit docking using the CDOCKER module of DS. Two compounds namely cinnamtannin-B and gallocatechin gallate were identified as top HITS against main protease (Mpro). Based on the Lipinski rule of five (L-ROF) and synthetic feasibility, gallocatechin gallate was taken for our further studies. Six analogues of gallocatechin gallate were screened against the next important targets such as RNA-dependent RNA polymerase (RdRp), angiotensin converting enzyme-2 (ACE2), transmembrane protease serine -2 (TMPRSS2) and interleukin-6 (IL-6) along with main protease (Mpro). Our molecular docking results reveal that a gallocatechin analogue (GC-2) namely (2R,3R)-2-(3,4-dihydroxyphenyl)chroman-3-yl-3,4,5-trihydroxy benzoate has shown potential to inhibit multiple targets of SARS CoV-2. Further, the molecular dynamics study was carried out to ascertain the stability of the GC-2 and RdRp complex.
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Affiliation(s)
- Jubie Selvaraj
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research Rockland's, Ooty, Nilgiris 643001 Tamil Nadu India
| | - Shyam Sundar P
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research Rockland's, Ooty, Nilgiris 643001 Tamil Nadu India
| | - Logesh Rajan
- TIFAC CORE in Herbal Drugs, Department of Pharmacognosy, JSS College of Pharmacy, JSS Academy of Higher Education & Research Rockland's, Ooty, Nilgiris 643001 Tamil Nadu India
| | - Divakar Selvaraj
- Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education & Research Rockland's, Ooty, Nilgiris 643001 Tamil Nadu India
| | - Dhanabal Palanisamy
- TIFAC CORE in Herbal Drugs, Department of Pharmacognosy, JSS College of Pharmacy, JSS Academy of Higher Education & Research Rockland's, Ooty, Nilgiris 643001 Tamil Nadu India
| | - Krishnan Namboori Pk
- Amrita Molecular Modelling and Synthesis (AMMAS) Research Lab, Amrita Vishwavidyapeetham Amrita Nagar, Ettimadai Coimbatore Tamil Nadu India
| | - Suresh Kumar Mohankumar
- TIFAC CORE in Herbal Drugs, Department of Pharmacognosy, JSS College of Pharmacy, JSS Academy of Higher Education & Research Rockland's, Ooty, Nilgiris 643001 Tamil Nadu India
- Swansea University Medical School, Swansea University Singleton Park Swansea Wales SA2 8PP UK
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Park J, Park R, Jang M, Park YI. Therapeutic Potential of EGCG, a Green Tea Polyphenol, for Treatment of Coronavirus Diseases. Life (Basel) 2021; 11:197. [PMID: 33806274 PMCID: PMC8002208 DOI: 10.3390/life11030197] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 02/28/2021] [Accepted: 03/02/2021] [Indexed: 02/06/2023] Open
Abstract
Epigallocatechin gallate (EGCG) is a major catechin found in green tea, and there is mounting evidence that EGCG is potentially useful for the treatment of coronavirus diseases, including coronavirus disease 2019 (COVID-19). Coronaviruses encode polyproteins that are cleaved by 3CL protease (the main protease) for maturation. Therefore, 3CL protease is regarded as the main target of antivirals against coronaviruses. EGCG is a major constituent of brewed green tea, and several studies have reported that EGCG inhibits the enzymatic activity of the coronavirus 3CL protease. Moreover, EGCG has been reported to regulate other potential targets, such as RNA-dependent RNA polymerase and the viral spike protein. Finally, recent studies have demonstrated that EGCG treatment interferes with the replication of coronavirus. In addition, the bioavailability of EGCG and future research prospects are discussed.
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Affiliation(s)
- Junsoo Park
- Division of Biological Science and Technology, Yonsei University, Wonju 26493, Korea; (R.P.); (M.J.); (Y.-I.P.)
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Jang M, Park R, Park YI, Cha YE, Yamamoto A, Lee JI, Park J. EGCG, a green tea polyphenol, inhibits human coronavirus replication in vitro. Biochem Biophys Res Commun 2021; 547:23-28. [PMID: 33588235 PMCID: PMC7874949 DOI: 10.1016/j.bbrc.2021.02.016] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 02/04/2021] [Indexed: 01/27/2023]
Abstract
COVID-19 pandemic results in record high deaths in many countries. Although a vaccine for SARS-CoV-2 is now available, effective antiviral drugs to treat coronavirus diseases are not available yet. Recently, EGCG, a green tea polyphenol, was reported to inhibit SARS-CoV-2 3CL-protease, however the effect of EGCG on coronavirus replication is unknown. In this report, human coronavirus HCoV-OC43 (beta coronavirus) and HCoV-229E (alpha coronavirus) were used to examine the effect of EGCG on coronavirus. EGCG treatment decreases 3CL-protease activity of HCoV-OC43 and HCoV-229E. Moreover, EGCG treatment decreased HCoV-OC43-induced cytotoxicity. Finally, we found that EGCG treatment decreased the levels of coronavirus RNA and protein in infected cell media. These results indicate that EGCG inhibits coronavirus replication.
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Affiliation(s)
- Minsu Jang
- Division of Biological Science and Technology, Yonsei University, Wonju, Republic of Korea
| | - Rackhyun Park
- Division of Biological Science and Technology, Yonsei University, Wonju, Republic of Korea
| | - Yea-In Park
- Division of Biological Science and Technology, Yonsei University, Wonju, Republic of Korea
| | - Yeo-Eun Cha
- Division of Biological Science and Technology, Yonsei University, Wonju, Republic of Korea
| | - Ayane Yamamoto
- Division of Biological Science and Technology, Yonsei University, Wonju, Republic of Korea
| | - Jin I Lee
- Division of Biological Science and Technology, Yonsei University, Wonju, Republic of Korea
| | - Junsoo Park
- Division of Biological Science and Technology, Yonsei University, Wonju, Republic of Korea.
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49
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Huy N, Tam DH, Qarawi A, Luu M, Turnage M, Tran L, Tawfik G, Minh LN, Iiyama T, Kita K, Hirayama K. Favipiravir and its potentials in COVID-19 pandemic: An update. ASIAN PAC J TROP MED 2021. [DOI: 10.4103/1995-7645.329005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
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