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Alipour Z, Zarezadeh S, Ghotbi-Ravandi AA. The Potential of Anti-coronavirus Plant Secondary Metabolites in COVID-19 Drug Discovery as an Alternative to Repurposed Drugs: A Review. PLANTA MEDICA 2024; 90:172-203. [PMID: 37956978 DOI: 10.1055/a-2209-6357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2023]
Abstract
In early 2020, a global pandemic was announced due to the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), known to cause COVID-19. Despite worldwide efforts, there are only limited options regarding antiviral drug treatments for COVID-19. Although vaccines are now available, issues such as declining efficacy against different SARS-CoV-2 variants and the aging of vaccine-induced immunity highlight the importance of finding more antiviral drugs as a second line of defense against the disease. Drug repurposing has been used to rapidly find COVID-19 therapeutic options. Due to the lack of clinical evidence for the therapeutic benefits and certain serious side effects of repurposed antivirals, the search for an antiviral drug against SARS-CoV-2 with fewer side effects continues. In recent years, numerous studies have included antiviral chemicals from a variety of plant species. A better knowledge of the possible antiviral natural products and their mechanism against SARS-CoV-2 will help to develop stronger and more targeted direct-acting antiviral agents. The aim of the present study was to compile the current data on potential plant metabolites that can be investigated in COVID-19 drug discovery and development. This review represents a collection of plant secondary metabolites and their mode of action against SARS-CoV and SARS-CoV-2.
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Affiliation(s)
- Zahra Alipour
- Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Somayeh Zarezadeh
- Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Ali Akbar Ghotbi-Ravandi
- Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
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2
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Saha C, Naskar R, Chakraborty S. Antiviral Flavonoids: A Natural Scaffold with Prospects as Phytomedicines against SARS-CoV2. Mini Rev Med Chem 2024; 24:39-59. [PMID: 37138419 DOI: 10.2174/1389557523666230503105053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 03/01/2023] [Accepted: 03/13/2023] [Indexed: 05/05/2023]
Abstract
Flavonoids are vital candidates to fight against a wide range of pathogenic microbial infections. Due to their therapeutic potential, many flavonoids from the herbs of traditional medicine systems are now being evaluated as lead compounds to develop potential antimicrobial hits. The emergence of SARS-CoV-2 caused one of the deadliest pandemics that has ever been known to mankind. To date, more than 600 million confirmed cases of SARS-CoV2 infection have been reported worldwide. Situations are worse due to the unavailability of therapeutics to combat the viral disease. Thus, there is an urgent need to develop drugs against SARS-CoV2 and its emerging variants. Here, we have carried out a detailed mechanistic analysis of the antiviral efficacy of flavonoids in terms of their potential targets and structural feature required for exerting their antiviral activity. A catalog of various promising flavonoid compounds has been shown to elicit inhibitory effects against SARS-CoV and MERS-CoV proteases. However, they act in the high-micromolar regime. Thus a proper leadoptimization against the various proteases of SARS-CoV2 can lead to high-affinity SARS-CoV2 protease inhibitors. To enable lead optimization, a quantitative structure-activity relationship (QSAR) analysis has been developed for the flavonoids that have shown antiviral activity against viral proteases of SARS-CoV and MERS-CoV. High sequence similarities between coronavirus proteases enable the applicability of the developed QSAR to SARS-CoV2 proteases inhibitor screening. The detailed mechanistic analysis of the antiviral flavonoids and the developed QSAR models is a step forward toward the development of flavonoid-based therapeutics or supplements to fight against COVID-19.
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Affiliation(s)
- Chiranjeet Saha
- Amity Institute of Biotechnology, Amity University, Kolkata, 700135, India
| | - Roumi Naskar
- Amity Institute of Biotechnology, Amity University, Kolkata, 700135, India
| | - Sandipan Chakraborty
- Center for Innovation in Molecular and Pharmaceutical Sciences (CIMPS), Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad, 500046, India
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3
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Li X, Song Y. Targeting SARS-CoV-2 nonstructural protein 3: Function, structure, inhibition, and perspective in drug discovery. Drug Discov Today 2024; 29:103832. [PMID: 37977285 PMCID: PMC10872262 DOI: 10.1016/j.drudis.2023.103832] [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: 09/22/2023] [Revised: 11/06/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
As a highly contagious human pathogen, severe acute respiratory syndrome-associated coronavirus-2 (SARS-CoV-2) has infected billions of people worldwide with more than 6 million deaths. With several effective vaccines and antiviral drugs now available, the SARS-CoV-2 pandemic been brought under control. However, a new pathogenic coronavirus could emerge in the future, given the zoonotic nature of this virus. Natural evolution and drug-induced mutations of SARS-CoV-2 also require continued efforts for new anti-coronavirus drugs. Nonstructural protein (nsp) 3 of CoVs is a large, multifunctional protein, containing a papain-like protease (PLpro) and a macrodomain (Mac1), which are essential for viral replication. Here, we provide a comprehensive review of the function, structure, and inhibition of SARS-CoV/-CoV-2 PLpro and Mac1. We also discuss advances in, and challenges to, the discovery of drugs against these targets.
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Affiliation(s)
- Xin Li
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA.
| | - Yongcheng Song
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA.
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4
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Singh M, Lo SH, Dubey R, Kumar S, Chaubey KK, Kumar S. Plant-Derived Natural Compounds as an Emerging Antiviral in Combating COVID-19. Indian J Microbiol 2023; 63:429-446. [PMID: 38031604 PMCID: PMC10682353 DOI: 10.1007/s12088-023-01121-5] [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: 09/02/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a human virus that burst at Wuhan in China and spread quickly over the world, leading to millions of deaths globally. The journey of this deadly virus to different mutant strains is still ongoing. The plethora of drugs and vaccines have been tested to cope up this pandemic. The herbal plants and different spices have received great attention during pandemic, because of their anti-inflammatory, and immunomodulatory properties in treating viruses and their symptoms. Also, it has been shown that nano-formulation of phytochemicals has potential therapeutic effect against COVID-19. Furthermore, the plant derived compound nano-formulation specifically increases its antiviral property by enhancing its bioavailability, solubility, and target-specific delivery system. This review highlights the potentiality of herbal plants and their phytochemical against SARS-CoV-2 utilizing different mechanisms such as blocking the ACE-2 receptors, inhibiting the main proteases, binding spike proteins and reducing the cytokine storms.
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Affiliation(s)
- Mansi Singh
- Department of Pharmacy, Institute of Pharmaceutical Research, GLA University, Mathura, UP 281406 India
| | - Shih-Hsiu Lo
- Department of Urology, Taipei Medical University Hospital, Taipei, Taiwan
| | - Rajni Dubey
- Division of Cardiology, Department of Internal Medicine, Taipei Medical University Hospital, No. 252, Wuxing Street, Taipei, 11031 Taiwan
| | - Sudhashekhar Kumar
- Department of Physiology, School of Medical Sciences and Research, Sharda University, Greater Noida, UP 201310 India
| | - Kundan Kumar Chaubey
- Division of Research and Innovation, School of Applied and Life Sciences, Uttaranchal University, Arcadia Grant, P.O. Chandanwari, Premnagar, Dehradun, Uttarakhand 248007 India
- School of Basic and Applied Sciences, Sanskriti University, Mathura, UP 281401 India
| | - Sanjay Kumar
- Biological and Bio-Computational Lab, Department of Life Science, Sharda School of Basic Sciences and Research, Sharda University, Greater Noida, UP 201310 India
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Abou Baker DH, Hassan EM, El Gengaihi S. An overview on medicinal plants used for combating coronavirus: Current potentials and challenges. JOURNAL OF AGRICULTURE AND FOOD RESEARCH 2023; 13:100632. [PMID: 37251276 PMCID: PMC10198795 DOI: 10.1016/j.jafr.2023.100632] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 05/01/2023] [Accepted: 05/09/2023] [Indexed: 05/31/2023]
Abstract
Worldwide, Severe acute respiratory syndrome Coronavirus (SARS-CoV-2) pandemic crisis, causing many morbidities, mortality, and devastating impact on economies, so the current outbreak of the CoV-2 is a major concern for global health. The infection spread quickly and caused chaos in many countries around the world. The slow discovery of CoV-2 and the limited treatment options are among the main challenges. Therefore, the development of a drug that is safe and effective against CoV-2 is urgently needed. The present overview briefly summarizes CoV-2 drug targets ex: RNA-dependent RNA polymerase (RdRp), papain-like protease (PLpro), 3-chymotrypsin-like protease (3CLpro), transmembrane serine protease enzymes (TMPRSS2), angiotensin-converting enzyme 2 (ACE2), structural protein (N, S, E, and M), and virulence factors (NSP1, ORF7a, and NSP3c) for which drug design perspective can be considered. In addition, summarize all anti-COVID-19 medicinal plants and phytocompounds and their mechanisms of action to be used as a guide for further studies.
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Affiliation(s)
- Doha H Abou Baker
- Medicinal and Aromatic Plants Dept., Pharmaceutical and Drug Industries Institute, National Research Centre, Cairo, Egypt
| | - Emad M Hassan
- Medicinal and Aromatic Plants Dept., Pharmaceutical and Drug Industries Institute, National Research Centre, Cairo, Egypt
| | - Souad El Gengaihi
- Medicinal and Aromatic Plants Dept., Pharmaceutical and Drug Industries Institute, National Research Centre, Cairo, Egypt
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Rout M, Mishra S, Dey S, Singh MK, Dehury B, Pati S. Exploiting the potential of natural polyphenols as antivirals against monkeypox envelope protein F13 using machine learning and all-atoms MD simulations. Comput Biol Med 2023; 162:107116. [PMID: 37302336 PMCID: PMC10239311 DOI: 10.1016/j.compbiomed.2023.107116] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/12/2023] [Accepted: 05/30/2023] [Indexed: 06/13/2023]
Abstract
The re-emergence of monkeypox (MPX), in the era of COVID-19 pandemic is a new global menace. Regardless of its leniency, there are chances of MPX expediting severe health deterioration. The role of envelope protein, F13 as a critical component for production of extracellular viral particles makes it a crucial drug target. Polyphenols, exhibiting antiviral properties have been acclaimed as an effective alternative to the traditional treatment methods for management of viral diseases. To facilitate the development of potent MPX specific therapeutics, herein, we have employed state-of-the-art machine learning techniques to predict a highly accurate 3-dimensional structure of F13 as well as identify binding hotspots on the protein surface. Additionally, we have effectuated high-throughput virtual screening methodology on 57 potent natural polyphenols having antiviral activities followed by all-atoms molecular dynamics (MD) simulations, to substantiate the mode of interaction of F13 protein and polyphenol complexes. The structure-based virtual screening based on Glide SP, XP and MM/GBSA scores enables the selection of six potent polyphenols having higher binding affinity towards F13. Non-bonded contact analysis, of pre- and post- MD complexes propound the critical role of Glu143, Asp134, Asn345, Ser321 and Tyr320 residues in polyphenol recognition, which is well supported by per-residue decomposition analysis. Close-observation of the structural ensembles from MD suggests that the binding groove of F13 is mostly hydrophobic in nature. Taken together, this structure-based analysis from our study provides a lead on Myricetin, and Demethoxycurcumin, which may act as potent inhibitors of F13. In conclusion, our study provides new insights into the molecular recognition and dynamics of F13-polyphenol bound states, offering new promises for development of antivirals to combat monkeypox. However, further in vitro and in vivo experiments are necessary to validate these results.
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Affiliation(s)
- Madhusmita Rout
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Chandrasekharpur, Bhubaneswar, 751023, Odisha, India
| | - Sarbani Mishra
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Chandrasekharpur, Bhubaneswar, 751023, Odisha, India
| | - Suchanda Dey
- Biomics and Biodiversity Lab, Siksha 'O' Anusandhan (deemed to be) University, Kalinga Nagar, Ghatikia, Bhubaneswar, 751003, Odisha, India
| | - Mahender Kumar Singh
- Data Science Laboratory, National Brain Research Centre, Gurgaon, Haryana, 122052, India
| | - Budheswar Dehury
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Chandrasekharpur, Bhubaneswar, 751023, Odisha, India.
| | - Sanghamitra Pati
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Chandrasekharpur, Bhubaneswar, 751023, Odisha, India.
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Xue Y, Mei H, Chen Y, Griffin JD, Liu Q, Weisberg E, Yang J. Repurposing clinically available drugs and therapies for pathogenic targets to combat SARS-CoV-2. MedComm (Beijing) 2023; 4:e254. [PMID: 37193304 PMCID: PMC10183156 DOI: 10.1002/mco2.254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 02/11/2023] [Accepted: 03/07/2023] [Indexed: 05/18/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has affected a large portion of the global population, both physically and mentally. Current evidence suggests that the rapidly evolving coronavirus subvariants risk rendering vaccines and antibodies ineffective due to their potential to evade existing immunity, with enhanced transmission activity and higher reinfection rates that could lead to new outbreaks across the globe. The goal of viral management is to disrupt the viral life cycle as well as to relieve severe symptoms such as lung damage, cytokine storm, and organ failure. In the fight against viruses, the combination of viral genome sequencing, elucidation of the structure of viral proteins, and identifying proteins that are highly conserved across multiple coronaviruses has revealed many potential molecular targets. In addition, the time- and cost-effective repurposing of preexisting antiviral drugs or approved/clinical drugs for these targets offers considerable clinical advantages for COVID-19 patients. This review provides a comprehensive overview of various identified pathogenic targets and pathways as well as corresponding repurposed approved/clinical drugs and their potential against COVID-19. These findings provide new insight into the discovery of novel therapeutic strategies that could be applied to the control of disease symptoms emanating from evolving SARS-CoV-2 variants.
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Affiliation(s)
- Yiying Xue
- Department of Hematology, Tongji Hospital, Frontier Science Center for Stem Cell Research, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Husheng Mei
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical ScienceChinese Academy of SciencesHefeiChina
- University of Science and Technology of ChinaHefeiAnhuiChina
| | - Yisa Chen
- Department of Hematology, Tongji Hospital, Frontier Science Center for Stem Cell Research, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - James D. Griffin
- Department of Medical Oncology, Dana‐Farber Cancer InstituteBostonMassachusettsUSA
- Department of Medicine, Harvard Medical SchoolBostonMassachusettsUSA
| | - Qingsong Liu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical ScienceChinese Academy of SciencesHefeiChina
- University of Science and Technology of ChinaHefeiAnhuiChina
- Hefei Cancer HospitalChinese Academy of SciencesHefeiChina
| | - Ellen Weisberg
- Department of Medical Oncology, Dana‐Farber Cancer InstituteBostonMassachusettsUSA
- Department of Medicine, Harvard Medical SchoolBostonMassachusettsUSA
| | - Jing Yang
- Department of Hematology, Tongji Hospital, Frontier Science Center for Stem Cell Research, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and TechnologyTongji UniversityShanghaiChina
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical ScienceChinese Academy of SciencesHefeiChina
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8
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Patel M, Bazaid AS, Azhar EI, Gattan HS, Binsaleh NK, Patel M, Surti M, Adnan M. Novel phytochemical inhibitors targeting monkeypox virus thymidine and serine/threonine kinase: integrating computational modeling and molecular dynamics simulation. J Biomol Struct Dyn 2023; 41:13679-13695. [PMID: 36852556 DOI: 10.1080/07391102.2023.2179547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 02/06/2023] [Indexed: 03/01/2023]
Abstract
Due to the rapid spread of the monkeypox virus and rise in the number of cases, there is an urgent need for the development of effective drugs against the infection. Serine/threonine protein kinase (Ser/Thr kinase) and Thymidine Kinase (TK) plays an imperative role in the replication and virulence of monkeypox virus and thus is deliberated as an attractive target in anti-viral drug development. In the present study, the 3D structure of monkeypox virus Ser/Thr kinase and TK was generated via molecular modeling techniques and performed their thorough structural analysis. We have screened potent anti-viral phytochemicals from the literature to inhibit Ser/Thr kinase and TK. As part of the initial screening, the physicochemical properties of the compounds were examined. Following this, a structure-based molecular docking technique was used to select compounds based on their binding affinity towards Ser/Thr kinase and TK. In order to find more potent hits against Ser/Thr kinase and TK, further examinations of ADMET properties, PAINS patterns and blood-brain barrier permeability were conducted. As a result, thalimonine and galanthamine were identified from the screening process bearing appreciable binding affinity towards Ser/Thr kinase and TK respectively, which showed a worthy set of drug-like properties. In the end, molecular dynamics simulations were performed for 100 ns, which showed decent stability of both protein-ligand complex throughout the trajectory. Due to the possibility that both monkeypox virus target proteins may be inhibited by thalimonine and galanthamine, our study highlights the need to investigate in vivo effects of thalimonine and galanthamine.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mitesh Patel
- Department of Biotechnology, Parul Institute of Applied Sciences and Centre of Research for Development, Parul University, Vadodara, India
| | - Abdulrahman S Bazaid
- Department of Medical Laboratory Science, College of Applied Medical Sciences, University of Hail, Hail, Saudi Arabia
- Molecular Diagnostics and Personalized Therapeutics Unit, University of Hail, Hail, Saudi Arabia
| | - Esam I Azhar
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Saudi Arabia
- Special Infectious Agents Unit - BSL3, King Fahd Medical Research Center, King Abdulaziz University, Saudi Arabia
| | - Hattan S Gattan
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Saudi Arabia
- Special Infectious Agents Unit - BSL3, King Fahd Medical Research Center, King Abdulaziz University, Saudi Arabia
| | - Naif K Binsaleh
- Department of Medical Laboratory Science, College of Applied Medical Sciences, University of Hail, Hail, Saudi Arabia
- Molecular Diagnostics and Personalized Therapeutics Unit, University of Hail, Hail, Saudi Arabia
| | - Mirav Patel
- Department of Biotechnology, Parul Institute of Applied Sciences and Centre of Research for Development, Parul University, Vadodara, India
| | - Malvi Surti
- Bapalal Vaidya Botanical Research Centre, Department of Biosciences, Veer Narmad South Gujarat University, Surat, Gujarat, India
| | - Mohd Adnan
- Molecular Diagnostics and Personalized Therapeutics Unit, University of Hail, Hail, Saudi Arabia
- Department of Biology, College of Science, University of Hail, Hail, Saudi Arabia
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Huq AKMM, Roney M, Imran S, Khan SU, Uddin MN, Htar TT, Baig AA, Bhuiyan MA, Zakaria ZA, Aluwi MFFM, Tajuddin SN. Virtual screening of bioactive anti-SARS-CoV natural products and identification of 3β,12-diacetoxyabieta-6,8,11,13-tetraene as a potential inhibitor of SARS-CoV-2 virus and its infection related pathways by MD simulation and network pharmacology. J Biomol Struct Dyn 2023; 41:13923-13936. [PMID: 36786766 DOI: 10.1080/07391102.2023.2176926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/28/2023] [Indexed: 02/15/2023]
Abstract
Since the first prevalence of COVID-19 in 2019, it still remains the most devastating pandemic throughout the world. The current research aimed to find potential natural products to inhibit the novel coronavirus and associated infection by MD simulation and network pharmacology approach. Molecular docking was performed for 39 natural products having potent anti-SARS-CoV activity. Five natural products showed high binding interaction with the viral main protease for the SARS-CoV-2 virus, where 3β,12-diacetoxyabieta-6,8,11,13 tetraene showed stable binding in MD simulation until 100 ns. Both 3β,12-diacetoxyabieta-6,8,11,13 tetraene and tomentin A targeted 11 common genes that are related to COVID-19 and interact with each other. Gene ontology development analysis further showed that all these 11 genes are attached to various biological processes. The KEGG pathway analysis also showed that the proteins that are targeted by 3β,12-diacetoxyabieta-6,8,11,13 tetraene and tomentin A are associated with multiple pathways related to COVID-19 infection. Furthermore, the ADMET and MDS studies reveals 3β,12-diacetoxyabieta-6,8,11,13 as the best-suited compound for oral drug delivery.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- A K M Moyeenul Huq
- Bio Aromatic Research Centre, Universiti Malaysia Pahang, Kuantan, Pahang, Malaysia
- School of Medicine, Department of Pharmacy, University of Asia Pacific, Dhaka, Bangladesh
| | - Miah Roney
- Bio Aromatic Research Centre, Universiti Malaysia Pahang, Kuantan, Pahang, Malaysia
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Kuantan, Pahang, Malaysia
| | - Syahrul Imran
- Atta-ur-Rahman Institute for Natural Product Discovery (AuRIns), Universiti Teknologi MARA Cawangan Selangor Kampus Puncak Alam, Puncak Alam, Selangor, Malaysia
- Faculty of Applied Science, Universiti Teknologi MARA (UiTM), Shah Alam, Selangor, Malaysia
| | - Shafi Ullah Khan
- Product & Process Innovation Department, Qarshi Brands (Pvt) Ltd, Haripur, KPK, Pakistan
| | - Md Nazim Uddin
- Institute of Food Science and Technology, Bangladesh Council of Scientific and Industrial Research, Dhaka, Bangladesh
| | - Thet Thet Htar
- School of Pharmacy, Monash University Malaysia, Subang Jaya, Selangor, Malaysia
| | - Atif Amin Baig
- Faculty of Medicine, Universiti Sultan Zainal Abidin, Kuala Terengganu, Terengannu, Malaysia
| | | | - Zainul Amiruddin Zakaria
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu, Sabah, Malaysia
| | - Mohd Fadhlizil Fasihi Mohd Aluwi
- Bio Aromatic Research Centre, Universiti Malaysia Pahang, Kuantan, Pahang, Malaysia
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Kuantan, Pahang, Malaysia
| | - Saiful Nizam Tajuddin
- Bio Aromatic Research Centre, Universiti Malaysia Pahang, Kuantan, Pahang, Malaysia
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Kuantan, Pahang, Malaysia
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10
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Gurjar V, Iqra Kamil S, Chandra A, Qamar I, Singh N. Drugs swapping in coronavirus strains: a structural biology view. J Biomol Struct Dyn 2023; 41:13488-13495. [PMID: 36744537 DOI: 10.1080/07391102.2023.2175037] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 01/26/2023] [Indexed: 02/07/2023]
Abstract
Coronavirus belongs to the coronaviridae family, having a single-stranded RNA as genetic material of 26-42 kb in size. The first coronavirus infection emerged in 2002, caused by SARS-CoV1. Since then, genome sequences and three-dimensional structures of crucial proteins and enzymes of the virus have been studied in detail. The novel coronavirus (nCoV) outbreak has caused the COVID19 pandemic, which is responsible for the deaths of millions of people worldwide. The nCoV was later renamed as SARS-CoV2. The details of most of the COV proteins are available at the atomic and molecular levels. The entire genome is made up of 12 open reading frames that code for 27 different proteins. The spike surface glycoprotein, the envelope protein, the nucleocapsid protein, and the membrane protein are the four structural proteins which are required for virus attachment, entrance, assembly, and pathogenicity. The remaining proteins encoded are called non-structural (NSPs) and support the survival of the virus. Several non-structural proteins are also validated targets for drug development against coronavirus and are being used for drug design purposes. To perform a comparative study, sequences and three-dimensional structures of four crucial viral enzymes, Mpro, PLpro, RdRp, and EndoU from SARS-CoV1 and SARS-CoV2 variants were analyzed. The key structural elements and ligands recognizing amino acid residues were found to be similar in enzymes from both strains. The significant sequences and structural resemblance also suggest that a drug developed either for SARS-CoV1 or SARS-CoV2 using these enzymes may also have the potential to cross-react.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vaishali Gurjar
- School of Biotechnology, Gautam Buddha University, Gautam Budh Nagar, Uttar Pradesh, India
| | - Saiyada Iqra Kamil
- School of Biotechnology, Gautam Buddha University, Gautam Budh Nagar, Uttar Pradesh, India
| | - Anshuman Chandra
- School of Biotechnology, Gautam Buddha University, Gautam Budh Nagar, Uttar Pradesh, India
| | - Imteyaz Qamar
- School of Biotechnology, Gautam Buddha University, Gautam Budh Nagar, Uttar Pradesh, India
| | - Nagendra Singh
- School of Biotechnology, Gautam Buddha University, Gautam Budh Nagar, Uttar Pradesh, India
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Essa AF, El-Hawary SS, Kubacy TM, El-Din A M El-Khrisy E, El-Desoky AH, Elshamy AI, Younis IY. Integration of LC/MS, NMR and Molecular Docking for Profiling of Bioactive Diterpenes from Euphorbia mauritanica L. with in Vitro Anti-SARS-CoV-2 Activity. Chem Biodivers 2023; 20:e202200918. [PMID: 36602020 DOI: 10.1002/cbdv.202200918] [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: 09/28/2022] [Revised: 01/04/2023] [Accepted: 01/04/2023] [Indexed: 01/06/2023]
Abstract
In spite of tremendous efforts exerted in the management of COVID-19, the absence of specific treatments and the prevalence of delayed and long-term complications termed post-COVID syndrome still urged all concerned researchers to develop a potent inhibitor of SARS-Cov-2. The hydromethanolic extracts of different parts of E. mauritanica were in vitro screened for anti-SARS-Cov-2 activity. Then, using an integrated strategy of LC/MS/MS, molecular networking and NMR, the chemical profile of the active extract was determined. To determine the optimum target for these compounds, docking experiments of the active extract's identified compounds were conducted at several viral targets. The leaves extract showed the best inhibitory effect with IC50 8.231±0.04 μg/ml. The jatrophane diterpenes were provisionally annotated as the primary metabolites of the bioactive leaves extract based on multiplex of LC/MS/MS, molecular network, and NMR. In silico studies revealed the potentiality of the compounds in the most active extract to 3CLpro, where compound 20 showed the best binding affinity. Further attention should be paid to the isolation of various jatrophane diterpenes from Euphorbia and evaluating their effects on SARS-Cov-2 and its molecular targets.
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Affiliation(s)
- Ahmed F Essa
- Chemistry of Natural Compounds Department, National Research Center, 33 El Bohouth St., Dokki, Giza, 12622, Egypt
| | - Seham S El-Hawary
- Pharmacognosy Department, Faculty of Pharmacy, Cairo University, Cairo, 12613, Egypt
| | - Tahia M Kubacy
- Chemistry of Natural Compounds Department, National Research Center, 33 El Bohouth St., Dokki, Giza, 12622, Egypt
| | - Ezz El-Din A M El-Khrisy
- Chemistry of Natural Compounds Department, National Research Center, 33 El Bohouth St., Dokki, Giza, 12622, Egypt
| | - Ahmed H El-Desoky
- Pharmacognosy Department, National Research Center, 33 El Bohouth St., Dokki, Giza, 12622, Egypt
| | - Abdelsamed I Elshamy
- Chemistry of Natural Compounds Department, National Research Center, 33 El Bohouth St., Dokki, Giza, 12622, Egypt
| | - Inas Y Younis
- Pharmacognosy Department, Faculty of Pharmacy, Cairo University, Cairo, 12613, Egypt
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12
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Magurano F, Micucci M, Nuzzo D, Baggieri M, Picone P, Gioacchini S, Fioravanti R, Bucci P, Kojouri M, Mari M, Retini M, Budriesi R, Mattioli LB, Corazza I, Di Liberto V, Todaro L, Giuseppetti R, D’Ugo E, Marchi A, Mecca M, D’Auria M. A potential host and virus targeting tool against COVID-19: Chemical characterization, antiviral, cytoprotective, antioxidant, respiratory smooth muscle relaxant effects of Paulownia tomentosa Steud. Biomed Pharmacother 2023; 158:114083. [PMID: 36495668 PMCID: PMC9721285 DOI: 10.1016/j.biopha.2022.114083] [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: 09/14/2022] [Revised: 11/23/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
COronaVIrus Disease 2019 (COVID-19) is a newly emerging infectious disease that spread across the world, caused by the novel coronavirus Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2). Despite the advancements in science that led to the creation of the vaccine, there is still an urgent need for new antiviral drugs effective against SARS-CoV-2. This study aimed to investigate the antiviral effect of Paulownia tomentosa Steud extract against SARS-CoV-2 and to evaluate its antioxidant properties, including respiratory smooth muscle relaxant effects. Our results showed that P. tomentosa extract can inhibit viral replication by directly interacting with both the 3-chymotrypsin-like protease and spike protein. In addition, the phyto complex does not reduce lung epithelial cell viability and exerts a protective action in those cells damaged by tert-butyl hydroperoxide , a toxic agent able to alter cells' functions via increased oxidative stress. These data suggest the potential role of P. tomentosa extract in COVID-19 treatment, since this extract is able to act both as an antiviral and a cytoprotective agent in vitro.
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Affiliation(s)
- Fabio Magurano
- Department of Infectious Diseases, Istituto Superiore di Sanità (ISS), Rome, Italy.
| | - Matteo Micucci
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Piazza Rinascimento 6, 61029 Urbino, PU, Italy
| | - Domenico Nuzzo
- Istituto per la Ricerca e l’Innovazione Biomedica, CNR, via U. La Malfa 153, 90146 Palermo, Italy
| | - Melissa Baggieri
- Department of Infectious Diseases, Istituto Superiore di Sanità (ISS), Rome, Italy
| | - Pasquale Picone
- Istituto per la Ricerca e l’Innovazione Biomedica, CNR, via U. La Malfa 153, 90146 Palermo, Italy
| | - Silvia Gioacchini
- Department of Infectious Diseases, Istituto Superiore di Sanità (ISS), Rome, Italy
| | - Raoul Fioravanti
- Department of Infectious Diseases, Istituto Superiore di Sanità (ISS), Rome, Italy
| | - Paola Bucci
- Department of Infectious Diseases, Istituto Superiore di Sanità (ISS), Rome, Italy
| | - Maedeh Kojouri
- Department of Infectious Diseases, Istituto Superiore di Sanità (ISS), Rome, Italy
| | - Michele Mari
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Piazza Rinascimento 6, 61029 Urbino, PU, Italy
| | - Michele Retini
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Piazza Rinascimento 6, 61029 Urbino, PU, Italy
| | - Roberta Budriesi
- Department of Pharmacy and Biotechnology, Food Chemistry and Nutraceutical Lab, Alma Mater Studiorum-University of Bologna, 40126 Bologna, Italy
| | - Laura Beatrice Mattioli
- Department of Pharmacy and Biotechnology, Food Chemistry and Nutraceutical Lab, Alma Mater Studiorum-University of Bologna, 40126 Bologna, Italy
| | - Ivan Corazza
- Department of Specialistic, Diagnostic and Experimental Medicine (DIMES), University of Bologna, S. Orsola-Malpighi University Hospital, Alma Mater Studiorum-University of Bologna, Bologna, Italy
| | - Valentina Di Liberto
- Department of Biomedicine, Neuroscience and Advanced Diagnostic, University of Palermo, 90128 Palermo, Italy
| | - Luigi Todaro
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Università della Basilicata, Via dell’Ateneo Lucano 10, 85100 Potenza, Italy
| | - Roberto Giuseppetti
- Department of Infectious Diseases, Istituto Superiore di Sanità (ISS), Rome, Italy
| | - Emilio D’Ugo
- Department of Infectious Diseases, Istituto Superiore di Sanità (ISS), Rome, Italy
| | - Antonella Marchi
- Department of Infectious Diseases, Istituto Superiore di Sanità (ISS), Rome, Italy
| | - Marisabel Mecca
- Dipartimento di Scienze, Università della Basilicata, Via dell’Ateneo Lucano 10, 85100 Potenza, Italy
| | - Maurizio D’Auria
- Dipartimento di Scienze, Università della Basilicata, Via dell’Ateneo Lucano 10, 85100 Potenza, Italy
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13
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Sławińska N, Zając J, Olas B. Paulownia Organs as Interesting New Sources of Bioactive Compounds. Int J Mol Sci 2023; 24:ijms24021676. [PMID: 36675191 PMCID: PMC9860774 DOI: 10.3390/ijms24021676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/09/2023] [Accepted: 01/12/2023] [Indexed: 01/19/2023] Open
Abstract
Paulownia spp. is a genus of trees in the Paulowniaceae family. It is native to southeastern Asia (especially China), where it has been cultivated for decorative, cultural, and medicinal purposes for over 2000 years. Depending on taxonomic classification, there are 6 to 17 species of Paulownia; P. tomentosa, P. elongata, P. fortunei, and P. catalpifolia are considered the most popular. Nowadays, Paulownia trees are planted in Asia, Europe, North America, and Australia for commercial, medical, and decorative purposes. Lately, growing interest in Paulownia has led to the development of various hybrids, the best-known being Clone in vitro 112, Shan Tong, Sundsu 11, and Cotevisa 2. Paulownia Clone in vitro 112 is an artificially created hybrid of two species of Paulownia: P. elongata and P. fortunei. The present review of selected papers from electronic databases including PubMed, ScienceDirect, and SCOPUS before 15 November 2022 describes the phytochemical characteristics, biological properties, and economic significance of various organs from different Paulownia species and hybrids, including P. tomentosa, P. elongata, P. fortunei, and Paulownia Clone in vitro 112. Many compounds from Paulownia demonstrate various biological activities and are promising candidates for natural preparations; for example, the leaves of Clone in vitro 112 have anti-radical and anticoagulant potential. However, further in vivo studies are needed to clarify the exact mechanism of action of the active substances and their long-term effects.
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14
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Shoaib S, Ansari MA, Kandasamy G, Vasudevan R, Hani U, Chauhan W, Alhumaidi MS, Altammar KA, Azmi S, Ahmad W, Wahab S, Islam N. An Attention towards the Prophylactic and Therapeutic Options of Phytochemicals for SARS-CoV-2: A Molecular Insight. Molecules 2023; 28:molecules28020795. [PMID: 36677853 PMCID: PMC9864057 DOI: 10.3390/molecules28020795] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/05/2023] [Accepted: 01/07/2023] [Indexed: 01/15/2023] Open
Abstract
The novel pathogenic virus was discovered in Wuhan, China (December 2019), and quickly spread throughout the world. Further analysis revealed that the pathogenic strain of virus was corona but it was distinct from other coronavirus strains, and thus it was renamed 2019-nCoV or SARS-CoV-2. This coronavirus shares many characteristics with other coronaviruses, including SARS-CoV and MERS-CoV. The clinical manifestations raised in the form of a cytokine storm trigger a complicated spectrum of pathophysiological changes that include cardiovascular, kidney, and liver problems. The lack of an effective treatment strategy has imposed a health and socio-economic burden. Even though the mortality rate of patients with this disease is lower, since it is judged to be the most contagious, it is considered more lethal. Globally, the researchers are continuously engaged to develop and identify possible preventive and therapeutic regimens for the management of disease. Notably, to combat SARS-CoV-2, various vaccine types have been developed and are currently being tested in clinical trials; these have also been used as a health emergency during a pandemic. Despite this, many old antiviral and other drugs (such as chloroquine/hydroxychloroquine, corticosteroids, and so on) are still used in various countries as emergency medicine. Plant-based products have been reported to be safe as alternative options for several infectious and non-infectious diseases, as many of them showed chemopreventive and chemotherapeutic effects in the case of tuberculosis, cancer, malaria, diabetes, cardiac problems, and others. Therefore, plant-derived products may play crucial roles in improving health for a variety of ailments by providing a variety of effective cures. Due to current therapeutic repurposing efforts against this newly discovered virus, we attempted to outline many plant-based compounds in this review to aid in the fight against SARS-CoV-2.
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Affiliation(s)
- Shoaib Shoaib
- Department Biochemistry, Faculty of Medicine, J. N. Medical College, Aligarh Muslim University, Aligarh 202002, India
| | - Mohammad Azam Ansari
- Department of Epidemic Disease Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
- Correspondence: (M.A.A.); (N.I.)
| | - Geetha Kandasamy
- Department of Clinical Pharmacy, College of Pharmacy, King Khalid University (KKU), Abha 62529, Saudi Arabia
| | - Rajalakshimi Vasudevan
- Department of Pharmacology, College of Pharmacy, King Khalid University (KKU), Abha 62529, Saudi Arabia
| | - Umme Hani
- Department of Pharmaceutics, College of Pharmacy, King Khalid University (KKU), Abha 62529, Saudi Arabia
| | - Waseem Chauhan
- Department of Zoology, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India
| | - Maryam S. Alhumaidi
- Department of Biology, College of Science, University of Hafr Al Batin, Hafr Al Batin 31991, Saudi Arabia
| | - Khadijah A. Altammar
- Department of Biology, College of Science, University of Hafr Al Batin, Hafr Al Batin 31991, Saudi Arabia
| | - Sarfuddin Azmi
- Molecular Microbiology Biology Division, Scientific Research Centre (SRC), Prince Sultan Military Medical City (PSMMC), Riyadh 11159, Saudi Arabia
| | - Wasim Ahmad
- Department of Pharmacy, Mohammed Al-Mana College for Medical Sciences, Dammam 34222, Saudi Arabia
| | - Shadma Wahab
- Deparment of Pharmacognosy, College of Pharmacy, King Khalid University, Abha 61421, Saudi Arabia
| | - Najmul Islam
- Department Biochemistry, Faculty of Medicine, J. N. Medical College, Aligarh Muslim University, Aligarh 202002, India
- Correspondence: (M.A.A.); (N.I.)
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15
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Arung ET, Syafrizal, Kusuma IW, Paramita S, Amen Y, Kim YU, Naibaho NM, Ramadhan R, Ariyanta HA, Fatriasari W, Shimizu K. Antioxidant, anti-inflammatory and anti-acne activities of stingless bee (Tetragonula biroi) propolis. Fitoterapia 2023; 164:105375. [PMID: 36511341 DOI: 10.1016/j.fitote.2022.105375] [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: 11/06/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 11/27/2022]
Abstract
We collected stingless bee propolis Tetragonula biroi in order to find materials for medicine and cosmetics applications from tropical rainforest resources. Even though this bee has some biological functions including a cancer cell line, hair growth promotion, asthma remedy, α-glucosidase enzyme inhibition, and antiviral action, the investigation on anti-acne has not been reported yet. This study was to focus on propolis Tetragonula biroi extracts and leads us to isolate active compounds for antioxidant, anti-inflammatory, and anti-acne. We used methanol to obtain the extract from this propolis and assayed it with antioxidants, anti-inflammation, and anti-acne. The extract showed strong activity in antioxidants by DPPH radical scavenging activity (82.31% in 6.25 μg/ml). Via a column chromatography and Reveleris PREP purification system, we isolated 3'-O-methyldiplacone, nymphaeol A, and 5,7,3',4'-tetrahydroxy-6-geranyl flavonol. These compounds showed potential biological activity with IC50 for antioxidant 6.33, 15.49, 17.32 μM; and antiinflammatory 121.54, 121.20, 117.31 μM. The isolated compounds showed anti-acne properties with properties 0.00, 14.11, and 13.78 mm for the inhibition zone (at a concentration of 1 μg/well), respectively. The results indicated that the propolis extract of Tetragonula biroi has the potential to be developed as a cosmetic agent; however, further work needs to be done to clarify its application.
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Affiliation(s)
- Enos Tangke Arung
- Laboratory of Forest Product Chemistry, Faculty of Forestry, Mulawarman University, Samarinda, Indonesia; Research Center for Medicine and Cosmetic from Tropical Rainforest Resources, Mulawarman University, Samarinda, Indonesia; Research Collaboration Center for Biomass-Based Nano Cosmetics, in Collaboration with Mulawarman University and BRIN, Samarinda, East Kalimantan 75119, Indonesia.
| | - Syafrizal
- Mathematics and Science Faculty, Mulawarman University, Samarinda, Indonesia
| | - Irawan Wijaya Kusuma
- Laboratory of Forest Product Chemistry, Faculty of Forestry, Mulawarman University, Samarinda, Indonesia; Research Center for Medicine and Cosmetic from Tropical Rainforest Resources, Mulawarman University, Samarinda, Indonesia
| | - Swandari Paramita
- Research Center for Medicine and Cosmetic from Tropical Rainforest Resources, Mulawarman University, Samarinda, Indonesia; Faculty of Medicine, Mulawarman University, Samarinda, Indonesia
| | - Yhiya Amen
- Department of Pharmacognosy, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Yong-Ung Kim
- Department of Pharmaceutical Engineering, Daegu Haany University, Gyeongsan, South Korea
| | - Netty Maria Naibaho
- Department of Plantation Processing Technology, State Agricultural Polytechnic of Samarinda, Jl. Samratulangi PO Box 75131, Samarinda, Indonesia
| | - Rico Ramadhan
- Division for Exploration and Synthesis of Bioactive Compounds, CoE-University Research Center for Bio-Molecule Engineering, Universitas Airlangga, Surabaya 60115, Indonesia; Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga, Surabaya 60115, Indonesia
| | - Harits Atika Ariyanta
- Research Center for Biomass and Bioproducts, National Research and Innovation Agency, Bogor 16911, Indonesia; Research Collaboration Center for Biomass-Based Nano Cosmetics, in Collaboration with Mulawarman University and BRIN, Samarinda, East Kalimantan 75119, Indonesia; Department of Pharmacy, University of Gunadarma, Depok, Indonesia
| | - Widya Fatriasari
- Research Center for Biomass and Bioproducts, National Research and Innovation Agency, Bogor 16911, Indonesia; Research Collaboration Center for Biomass-Based Nano Cosmetics, in Collaboration with Mulawarman University and BRIN, Samarinda, East Kalimantan 75119, Indonesia
| | - Kuniyoshi Shimizu
- Department of Agro-Environmental Sciences, Faculty of Agriculture, Kyushu University, Fukuoka, Japan; Kyushu University Institute for Asian and Oceanian Studies, Fukuoka, Japan.
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16
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Chen TH, Tsai MJ, Chang CS, Xu L, Fu YS, Weng CF. The exploration of phytocompounds theoretically combats SARS-CoV-2 pandemic against virus entry, viral replication and immune evasion. J Infect Public Health 2023; 16:42-54. [PMID: 36470006 PMCID: PMC9675089 DOI: 10.1016/j.jiph.2022.11.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/12/2022] [Accepted: 11/16/2022] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The novel coronavirus disease-2019 (COVID-19) that emerged in China, is an extremely contagious and pathogenic viral infection caused by the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) that has sparked a global pandemic. The few and limited availability of approved therapeutic agents or vaccines is of great concern. Urgently, Remdesivir, Nirmatrelvir, Molnupiravir, and some phytochemicals including polyphenol, flavonoid, alkaloid, and triterpenoid are applied to develop as repurposing drugs against the SARS-CoV-2 invasion. METHODS This study was conducted to perform molecular docking and absorption, distribution, metabolism, excretion and toxicity (ADMET) analysis of the potential phytocompounds and repurposing drugs against three targets of SARS-CoV-2 proteins (RNA dependent RNA polymerase, RdRp, Endoribonclease, S-protein of ACE2-RBD). RESULTS The docking data illustrated Arachidonic acid, Rutin, Quercetin, and Curcumin were highly bound with coronavirus polyprotein replicase and Ebolavirus envelope protein. Furthermore, anti- Ebolavirus molecule Remedesivir, anti-HIV molecule Chloroquine, and Darunavir were repurposed with coronavirus polyprotein replicase as well as Ebolavirus envelope protein. The strongest binding interaction of each targets are Rutin with RdRp, Endoribonclease with Amentoflavone, and ACE2-RBD with Epigallocatechin gallate. CONCLUSIONS Taken altogether, these results shed a light on that phytocompounds have a therapeutic potential for the treatment of anti-SARS-CoV-2 may base on multi-target effects or cocktail formulation for blocking viral infection through invasion/activation, transcription/reproduction, and posttranslational cleavage to battle COVID-19 pandemic.
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Affiliation(s)
- Ting-Hsu Chen
- Functional Physiology Section, Department of Basic Medical Science, Xiamen Medical College, Xiamen 361023, Fujian, China
| | - May-Jywan Tsai
- Department of Neurosurgery, Neurological Institute, Neurological Institute, Taipei 11217, Taiwan
| | - Chun-Sheng Chang
- Department of biotechnology and food technology, Southern Taiwan University of Science and Technology, Yungkang City 701, Taiwan
| | - Linxi Xu
- Functional Physiology Section, Department of Basic Medical Science, Xiamen Medical College, Xiamen 361023, Fujian, China
| | - Yaw-Syan Fu
- Functional Physiology Section, Department of Basic Medical Science, Xiamen Medical College, Xiamen 361023, Fujian, China,Institute of Respiratory Disease, Department of Basic Medical Science, Xiamen Medical College, Xiamen 361023, Fujian, China,Corresponding author
| | - Ching-Feng Weng
- Functional Physiology Section, Department of Basic Medical Science, Xiamen Medical College, Xiamen 361023, Fujian, China,Institute of Respiratory Disease, Department of Basic Medical Science, Xiamen Medical College, Xiamen 361023, Fujian, China,Corresponding author
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17
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Sruthi D, Dhanalakshmi M, Rao HCY, Parthasarathy R, Deepanraj SP, Jayabaskaran C. Curative Potential of High-Value Phytochemicals on COVID-19 Infection. BIOCHEMISTRY (MOSCOW) 2023; 88:64-72. [PMID: 37068882 PMCID: PMC9937517 DOI: 10.1134/s0006297923010066] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Medicinal plants and their therapeutically promising chemical compounds belonging to the valued category of 'traditional medicine' are potential remedies for various health problems. Due to their complex structure and enormous health benefits, the high-value plant-derived metabolites collectively termed as 'phytochemicals' have emerged as a crucial source for novel drug discovery and development. Indeed, several medicinal plants from diverse habitats are still in the 'underexplored' category in terms of their bioactive principles and therapeutic potential. COVID-19, infection caused by the SARS-CoV-2, first reported in November 2019, resulted in the alarming number of deaths (6.61 million), was further declared 'pandemic', and spread of the disease has continued till today. Even though the well-established scientific world has successfully implemented vaccines against COVID-19 within the short period of time, the focus on alternative remedies for long-term symptom management and immunity boosting have been increased. At this point, interventions based on traditional medicine, which include medicinal plants, their bioactive metabolites, extracts and formulations, attracted a lot of attention as alternative solutions for COVID-19 management. Here, we reviewed the recent research findings related to the effectiveness of phytochemicals in treatment or prevention of COVID-19. Furthermore, the literature regarding the mechanisms behind the preventive or therapeutic effects of these natural phytochemicals were also discussed. In conclusion, we suggest that the active plant-derived components could be used alone or in combination as an alternative solution for the management of SARS-CoV-2 infection. Moreover, the structure of these natural productomes may lead to the emergence of new prophylactic strategies for SARS-CoV-2-caused infection.
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Affiliation(s)
- Damodaran Sruthi
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, 560012, India.
| | - Menamadathil Dhanalakshmi
- Research and Development Centre, Bharathiar University, Marudhamalai Road, Coimbatore, Tamil Nadu, 641046, India
| | | | | | - Shashikala Paranthaman Deepanraj
- Department of Biological Sciences, Tata Institute for Genetics and Society, Instem building, National Centre for Biological Sciences Campus, Bengaluru, Karnataka, 560065, India
| | - Chelliah Jayabaskaran
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, 560012, India
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18
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De A, Bhattacharya S, Debroy B, Bhattacharya A, Pal K. Exploring the pharmacological aspects of natural phytochemicals against SARS-CoV-2 Nsp14 through an in silico approach. In Silico Pharmacol 2023; 11:12. [PMID: 37131867 PMCID: PMC10141836 DOI: 10.1007/s40203-023-00143-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 03/13/2023] [Indexed: 05/04/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), possesses an important bifunctional nonstructural protein (nsp14) with a C-terminal N7-methyltransferase (N7-MTase) domain and an N-terminal domain with exoribonuclease (ExoN) activity that is required for maintaining high-fidelity viral replication. Viruses use the error-prone replication mechanism, which results in high mutation rates, to adapt quickly to stressful situations. The efficiency with which nsp14 removes mismatched nucleotides due to the presence of ExoN activity protects viruses from mutagenesis. We investigated the pharmacological role of the phytochemicals (Baicalein, Bavachinin, Emodin, Kazinol F, Lycorine, Sinigrin, Procyanidin A2, Tanshinone IIA, Tanshinone IIB, Tomentin A, and Tomentin E) against the highly conserved nsp14 protein using docking-based computational analyses in search of new potential natural drug targets. The selected eleven phytochemicals failed to bind the active site of N7-Mtase in the global docking study, while the local docking study identified the top five phytochemicals with high binding energy scores ranging from - 9.0 to - 6.4 kcal/mol. Procyanidin A2 and Tomentin A showed the highest docking score of - 9.0 and - 8.1 kcal/mol, respectively. Local docking of isoform variants was also conducted, yielding the top five phytochemicals, with Procyanidin A1 having the highest binding energy value of - 9.1 kcal/mol. The phytochemicals were later tested for pharmacokinetics and pharmacodynamics analysis for Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) which resulted in choosing Tomentin A as a potential candidate. The molecular dynamics simulations studies of nsp14 revealed significant conformational changes upon complex formation with the identified compound, implying that these phytochemicals could be used as safe nutraceuticals which will impart long-term immunological competence in the human population against CoVs. Graphical Abstract Supplementary Information The online version contains supplementary material available at 10.1007/s40203-023-00143-7.
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Affiliation(s)
- Arkajit De
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Barasat-Barrackpore Road, Kolkata, West Bengal 700126 India
| | - Somdatta Bhattacharya
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Barasat-Barrackpore Road, Kolkata, West Bengal 700126 India
- Cancer Biology Laboratory, Adamas University, Barasat-Barrackpore Road, Kolkata, West Bengal 700126 India
| | - Bishal Debroy
- Department of Biological Sciences, School of Life Science and Biotechnology, Adamas University, Barasat-Barrackpore Road, Kolkata, West Bengal 700126 India
| | - Arijit Bhattacharya
- Department of Biological Sciences, School of Life Science and Biotechnology, Adamas University, Barasat-Barrackpore Road, Kolkata, West Bengal 700126 India
- Anti-Microbial Resistance Laboratory, Adamas University, Barasat-Barrackpore Road, Kolkata, West Bengal 700126 India
| | - Kuntal Pal
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Barasat-Barrackpore Road, Kolkata, West Bengal 700126 India
- Cancer Biology Laboratory, Adamas University, Barasat-Barrackpore Road, Kolkata, West Bengal 700126 India
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19
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Ouassaf M, Belaidi S, Chtita S, Lanez T, Abul Qais F, Md Amiruddin H. Combined molecular docking and dynamics simulations studies of natural compounds as potent inhibitors against SARS-CoV-2 main protease. J Biomol Struct Dyn 2022; 40:11264-11273. [PMID: 34315340 DOI: 10.1080/07391102.2021.1957712] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Main protease (Mpro) of SARS-CoV-2 is a key CoV enzyme that plays a pivotal role in mediating viral replication and transcription, making it an attractive drug target for SARS-CoV-2 the new strain of coronavirus. In this study, we evaluated biologically active compounds present in medicinal plants as potential SARS-CoV-2 Mpro inhibitors, using a molecular docking study with Autodock Vina software. Top seven compounds Afzelin, Phloroglucinol, Myricetin-3-O- rutinosid Tricin 7-neohesperidoside, Silybin, Kaempferol and Silychristin among 50 molecules of natural Origin (Algerian Medicinal plants) were selected which had better and significantly low binding energy as compared to the reference molecule with binding affinities of -9.3, -9.3, -9, -8.9, -8.5, 8.3 and -8.3 kcal mol-1 respectively. Then, we analyzed the ADME properties of the best 7 ligands using the Web server SwissADME. Two of small molecules have been shown to be the ideal candidates for further drug development. Finally, the stability of the both compounds complexed with Mpro was validated through molecular dynamics (MD) simulation, they displayed stable trajectory (RMSD, RMSF) and molecular properties with consistent interaction profile in molecular dynamics simulations, moreover, Silybin could form more stable complex with Mpro than Silychristin.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mebarka Ouassaf
- Group of Computational and Medicinal Chemistry, LMCE Laboratory, University of Biskra, Biskra, Algeria
| | - Salah Belaidi
- Group of Computational and Medicinal Chemistry, LMCE Laboratory, University of Biskra, Biskra, Algeria.,Centre de Recherche en Sciences Pharmaceutiques (CRSP) la nouvelle ville Ali Mendjeli, Constantine, Algeria
| | - Samir Chtita
- Laboratory of Physical Chemistry of Materials, Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca, Casablanca, Morocco
| | - Touhami Lanez
- VTRS Laboratory, Faculty of Sciences and Technology, University of El Oued, El Oued, Algeria
| | - Faizan Abul Qais
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Hashmi Md Amiruddin
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
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Molecular Docking and Dynamics Simulation of Several Flavonoids Predict Cyanidin as an Effective Drug Candidate against SARS-CoV-2 Spike Protein. Adv Pharmacol Pharm Sci 2022; 2022:3742318. [DOI: 10.1155/2022/3742318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/13/2022] [Accepted: 10/15/2022] [Indexed: 11/10/2022] Open
Abstract
The in silico method has provided a versatile process of developing lead compounds from a large database in a short duration. Therefore, it is imperative to look for vaccinations and medications that can stop the havoc caused by SARS-CoV-2. The spike protein of SARS-CoV-2 is required for the viral entry into the host cells, hence inhibiting the virus from fusing and infecting the host. This study determined the binding interactions of 36 flavonoids along with two FDA-approved drugs against the spike protein receptor-binding domain of SARS-CoV-2 through molecular docking and molecular dynamics (MD) simulations. In addition, the molecular mechanics generalized Born surface area (MM/GBSA) approach was used to calculate the binding-free energy (BFE). Flavonoids were selected based on their in vitro assays on SARS-CoV and SARS-CoV-2. Our pharmacokinetics study revealed that cyanidin showed good drug-likeness, fulfilled Lipinski’s rule of five, and conferred favorable toxicity parameters. Furthermore, MD simulations showed that cyanidin interacts with spike protein and alters the conformation and binding-free energy suited. Finally, an in vitro assay indicated that about 50% reduction in the binding of hACE2 with S1-RBD in the presence of cyanidin-containing red grapes crude extract was achieved at approximately 1.25 mg/mL. Hence, cyanidin may be a promising adjuvant medication for the SARS-CoV-2 spike protein based on in silico and in vitro research.
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21
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Jamal QMS. Antiviral Potential of Plants against COVID-19 during Outbreaks-An Update. Int J Mol Sci 2022; 23:13564. [PMID: 36362351 PMCID: PMC9655040 DOI: 10.3390/ijms232113564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 10/06/2022] [Accepted: 11/02/2022] [Indexed: 12/01/2023] Open
Abstract
Several human diseases are caused by viruses, including cancer, Type I diabetes, Alzheimer's disease, and hepatocellular carcinoma. In the past, people have suffered greatly from viral diseases such as polio, mumps, measles, dengue fever, SARS, MERS, AIDS, chikungunya fever, encephalitis, and influenza. Recently, COVID-19 has become a pandemic in most parts of the world. Although vaccines are available to fight the infection, their safety and clinical trial data are still questionable. Social distancing, isolation, the use of sanitizer, and personal productive strategies have been implemented to prevent the spread of the virus. Moreover, the search for a potential therapeutic molecule is ongoing. Based on experiences with outbreaks of SARS and MERS, many research studies reveal the potential of medicinal herbs/plants or chemical compounds extracted from them to counteract the effects of these viral diseases. COVID-19's current status includes a decrease in infection rates as a result of large-scale vaccination program implementation by several countries. But it is still very close and needs to boost people's natural immunity in a cost-effective way through phytomedicines because many underdeveloped countries do not have their own vaccination facilities. In this article, phytomedicines as plant parts or plant-derived metabolites that can affect the entry of a virus or its infectiousness inside hosts are described. Finally, it is concluded that the therapeutic potential of medicinal plants must be analyzed and evaluated entirely in the control of COVID-19 in cases of uncontrollable SARS infection.
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Affiliation(s)
- Qazi Mohammad Sajid Jamal
- Department of Health Informatics, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia
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22
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Plant Molecular Pharming and Plant-Derived Compounds towards Generation of Vaccines and Therapeutics against Coronaviruses. Vaccines (Basel) 2022; 10:vaccines10111805. [DOI: 10.3390/vaccines10111805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/14/2022] [Accepted: 10/19/2022] [Indexed: 11/17/2022] Open
Abstract
The current century has witnessed infections of pandemic proportions caused by Coronaviruses (CoV) including severe acute respiratory syndrome-related CoV (SARS-CoV), Middle East respiratory syndrome-related CoV (MERS-CoV) and the recently identified SARS-CoV2. Significantly, the SARS-CoV2 outbreak, declared a pandemic in early 2020, has wreaked devastation and imposed intense pressure on medical establishments world-wide in a short time period by spreading at a rapid pace, resulting in high morbidity and mortality. Therefore, there is a compelling need to combat and contain the CoV infections. The current review addresses the unique features of the molecular virology of major Coronaviruses that may be tractable towards antiviral targeting and design of novel preventative and therapeutic intervention strategies. Plant-derived vaccines, in particular oral vaccines, afford safer, effectual and low-cost avenues to develop antivirals and fast response vaccines, requiring minimal infrastructure and trained personnel for vaccine administration in developing countries. This review article discusses recent developments in the generation of plant-based vaccines, therapeutic/drug molecules, monoclonal antibodies and phytochemicals to preclude and combat infections caused by SARS-CoV, MERS-CoV and SARS-CoV-2 viruses. Efficacious plant-derived antivirals could contribute significantly to combating emerging and re-emerging pathogenic CoV infections and help stem the tide of any future pandemics.
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23
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Molčanová L, Treml J, Brezáni V, Maršík P, Kurhan S, Trávníček Z, Uhrin P, Šmejkal K. C-geranylated flavonoids from Paulownia tomentosa Steud. fruit as potential anti-inflammatory agents. JOURNAL OF ETHNOPHARMACOLOGY 2022; 296:115509. [PMID: 35760257 DOI: 10.1016/j.jep.2022.115509] [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: 04/14/2022] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Paulownia tomentosa Steud., a traditional Chinese medicinal plant, was used for many centuries in Chinese herbal medicine as a component of remedies for many illnesses, including inflammatory diseases. It is a rich source of phenolic compounds, mainly geranylated flavonoids, which are currently studied for their promising biological activities. AIM OF THE STUDY The study aimed to isolate minor geranylated flavanones and flavones from P. tomentosa fruit and evaluate their cytotoxicity and possible anti-inflammatory effects in a cell-based model of inflammation. MATERIALS AND METHODS Chromatographic separation of chloroform portion of the ethanolic extract of P. tomentosa fruit led to the isolation of twenty-seven flavonoids (1-27), twenty-six of them geranylated with different modifications and one non-geranylated flavanone, and two phenolic compounds. Compounds were identified using UV, IR, HRMS, NMR, and CD spectroscopy. Ten of these compounds (7-10, 12, 21, 22, 24, 25, and 27) were determined to be new flavonoid derivatives obtained from a natural source for the first time. Selected compounds were analyzed for cytotoxicity and anti-inflammatory potential to affect the activation of nuclear factor κB/activator protein 1 (NF-κB/AP-1) after lipopolysaccharide (LPS) stimulation. RESULTS All the test compounds (1-21 and 23-26) reduced the activation of NF-κB/AP-1 24 h after the addition of LPS. Eight compounds (5, 14-18, 21, and 26) were more active than prednisone, a widely used anti-inflammatory drug. However, this effect was not seen significantly on the level of TNF-α and IL-1β, which can be explained by the plurality of possible outcomes of activation of the NF-κB pathway in cells. CONCLUSIONS Results of the presented study confirmed that constituents from traditional Chinese medicinal plant P. tomentosa Steud. have promising anti-inflammatory activities and can serve as a potential source of inspiration for new anti-inflammatory medications.
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Affiliation(s)
- Lenka Molčanová
- Department of Natural Drugs, Faculty of Pharmacy, Masaryk University, Palackého tř. 1946/1, CZ-61200, Brno, Czech Republic.
| | - Jakub Treml
- Department of Molecular Pharmacy, Faculty of Pharmacy, Masaryk University, Palackého tř. 1946/1, CZ-61200, Brno, Czech Republic.
| | - Veronika Brezáni
- Department of Molecular Pharmacy, Faculty of Pharmacy, Masaryk University, Palackého tř. 1946/1, CZ-61200, Brno, Czech Republic; Veterinary Research Institute, Hudcova 296/70, CZ-62100, Brno, Czech Republic.
| | - Petr Maršík
- Department of Food Quality and Safety, Czech University of Life Sciences Prague, Kamýcká 129, CZ-16500, Prague 6-Suchdol, Czech Republic.
| | - Sebnem Kurhan
- Department of Food Quality and Safety, Czech University of Life Sciences Prague, Kamýcká 129, CZ-16500, Prague 6-Suchdol, Czech Republic.
| | - Zdeněk Trávníček
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University, Šlechtitelů 27, CZ-77900, Olomouc, Czech Republic.
| | - Pavel Uhrin
- Institute of Vascular Biology and Thrombosis Research, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria.
| | - Karel Šmejkal
- Department of Natural Drugs, Faculty of Pharmacy, Masaryk University, Palackého tř. 1946/1, CZ-61200, Brno, Czech Republic.
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Evaluation of flavonoids as potential inhibitors of the SARS-CoV-2 main protease and spike RBD: Molecular docking, ADMET evaluation and molecular dynamics simulations. J INDIAN CHEM SOC 2022. [PMCID: PMC9428111 DOI: 10.1016/j.jics.2022.100697] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The 3CLpro main protease and the RDB spike (s) protein of SARS-CoV-2 are critical targets in the treatment of coronavirus 19 disease (COVID-19), as they are responsible for the COVID-19 replication and infection. With this in mind, Molecular docking of 26 natural compounds belonging to the flavonoid family with the 3CLpro and RBD sites of SARS-CoV-2 has been performed. The docking results revealed that the ligands Silibinin, Tomentin A, Tomentin B, 4′-O-methyldiplacone, Hesperidin Amentoflavone and Bilobetin act as a potential inhibitor of SARS-CoV-2 3CLpro, and that the ligands Herbacetin, Morin, Silibinin, Tomentin E, Amentoflavone, Bilobetin, Baicalein and Quercetin can be potential inhibitors of SARS-CoV-2 RBD. It has been noticed that three ligands can inhibit both sites of SARS-CoV-2, indicating a great potential of these compounds to combat COVID-19. Moreover, molecular docking has been validated by a new validation method based on visual inspiration. Evaluation of ADMET pharmacokinetic properties and the drug likeness in silico revealed that six compounds could be effective drugs against COVID-19. Finally, the docking results were verified by molecular dynamics simulations and MM-GBSA calculation to confirm the stability of hydrogen bonding interactions with crucial residues, which are essential to overcome SARS-CoV-2. These results could direct researchers toward plant-derived compounds that could be further investigated as therapeutic targets against COVID-19 replication and infection.
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25
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Gasmi A, Mujawdiya PK, Lysiuk R, Shanaida M, Peana M, Gasmi Benahmed A, Beley N, Kovalska N, Bjørklund G. Quercetin in the Prevention and Treatment of Coronavirus Infections: A Focus on SARS-CoV-2. Pharmaceuticals (Basel) 2022; 15:1049. [PMID: 36145270 PMCID: PMC9504481 DOI: 10.3390/ph15091049] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/17/2022] [Accepted: 08/20/2022] [Indexed: 12/15/2022] Open
Abstract
The COVID-19 outbreak seems to be the most dangerous challenge of the third millennium due to its highly contagious nature. Amongst natural molecules for COVID-19 treatment, the flavonoid molecule quercetin (QR) is currently considered one of the most promising. QR is an active agent against SARS and MERS due to its antimicrobial, antiviral, anti-inflammatory, antioxidant, and some other beneficial effects. QR may hold therapeutic potential against SARS-CoV-2 due to its inhibitory effects on several stages of the viral life cycle. In fact, QR inhibits viral entry, absorption, and penetration in the SARS-CoV virus, which might be at least partly explained by the ability of QR and its derivatives to inhibit 3-chymotrypsin-like protease (3CLpro) and papain-like protease (PLpro). QR is a potent immunomodulatory molecule due to its direct modulatory effects on several immune cells, cytokines, and other immune molecules. QR-based nanopreparations possess enhanced bioavailability and solubility in water. In this review, we discuss the prospects for the application of QR as a preventive and treatment agent for COVID-19. Given the multifactorial beneficial action of QR, it can be considered a very valid drug as a preventative, mitigating, and therapeutic agent of COVID-19 infection, especially in synergism with zinc, vitamins C, D, and E, and other polyphenols.
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Affiliation(s)
- Amin Gasmi
- Société Francophone de Nutrithérapie et de Nutrigénétique Appliquée, 69100 Villeurbanne, France
| | | | - Roman Lysiuk
- Department of Pharmacognosy and Botany, Danylo Halytsky Lviv National Medical University, 79010 Lviv, Ukraine
- CONEM Ukraine Life Science Research Group, Danylo Halytsky Lviv National Medical University, 79010 Lviv, Ukraine
| | - Mariia Shanaida
- I. Horbachevsky Ternopil National Medical University, 46001 Ternopil, Ukraine
| | - Massimiliano Peana
- Department of Chemical, Physics, Mathematics and Natural Sciences, University of Sassari, 07100 Sassari, Italy
| | - Asma Gasmi Benahmed
- Académie Internationale de Médecine Dentaire Intégrative, 75000 Paris, France
| | - Nataliya Beley
- I. Horbachevsky Ternopil National Medical University, 46001 Ternopil, Ukraine
| | | | - Geir Bjørklund
- Council for Nutritional and Environmental Medicine (CONEM), Toften 24, 8610 Mo i Rana, Norway
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26
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Bhargav A, Chaurasia P, Kumar R, Ramachandran S. Phytovid19: a compilation of phytochemicals research in coronavirus. Struct Chem 2022; 33:2169-2177. [PMID: 36039155 PMCID: PMC9402405 DOI: 10.1007/s11224-022-02035-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 08/09/2022] [Indexed: 01/31/2023]
Abstract
The COVID-19 pandemic has immensely impacted global health causing colossal damage. The recent outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has increased the quest to explore phytochemicals as treatment options. We summarize phytochemicals with activity against various coronaviruses including SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV). We compiled 705 phytochemical compounds through text mining of 893 PubMed articles. The physicochemical properties including molecular weight, lipophilicity, and the number of hydrogen bond donors and acceptors were determined from the structures of these compounds. A structure-based evaluation of these properties with respect to drug likeness showed that most compounds have a positive score of drug likeness. QSAR analysis showed that 5 descriptors, namely polar surface area, relative polar surface area, number of hydrogen bond donors, solubility, and lipophilicity, are significantly related to IC50. We envisage that these phytochemicals could be further explored for developing new potential therapeutic molecules for COVID-19.
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Affiliation(s)
- Anasuya Bhargav
- Informatics and Big Data, Council of Scientific and Industrial Research - Institute of Genomics and Integrative Biology (CSIR-IGIB), Room No. 130, Mathura Road, New Delhi, 110025 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
| | - Pratibha Chaurasia
- Informatics and Big Data, Council of Scientific and Industrial Research - Institute of Genomics and Integrative Biology (CSIR-IGIB), Room No. 130, Mathura Road, New Delhi, 110025 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
| | - Rohit Kumar
- Informatics and Big Data, Council of Scientific and Industrial Research - Institute of Genomics and Integrative Biology (CSIR-IGIB), Room No. 130, Mathura Road, New Delhi, 110025 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
| | - Srinivasan Ramachandran
- Informatics and Big Data, Council of Scientific and Industrial Research - Institute of Genomics and Integrative Biology (CSIR-IGIB), Room No. 130, Mathura Road, New Delhi, 110025 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
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Rahman MM, Islam MR, Akash S, Mim SA, Rahaman MS, Emran TB, Akkol EK, Sharma R, Alhumaydhi FA, Sweilam SH, Hossain ME, Ray TK, Sultana S, Ahmed M, Sobarzo-Sánchez E, Wilairatana P. In silico investigation and potential therapeutic approaches of natural products for COVID-19: Computer-aided drug design perspective. Front Cell Infect Microbiol 2022; 12:929430. [PMID: 36072227 PMCID: PMC9441699 DOI: 10.3389/fcimb.2022.929430] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/03/2022] [Indexed: 12/07/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a substantial number of deaths around the world, making it a serious and pressing public health hazard. Phytochemicals could thus provide a rich source of potent and safer anti-SARS-CoV-2 drugs. The absence of approved treatments or vaccinations continues to be an issue, forcing the creation of new medicines. Computer-aided drug design has helped to speed up the drug research and development process by decreasing costs and time. Natural compounds like terpenoids, alkaloids, polyphenols, and flavonoid derivatives have a perfect impact against viral replication and facilitate future studies in novel drug discovery. This would be more effective if collaboration took place between governments, researchers, clinicians, and traditional medicine practitioners’ safe and effective therapeutic research. Through a computational approach, this study aims to contribute to the development of effective treatment methods by examining the mechanisms relating to the binding and subsequent inhibition of SARS-CoV-2 ribonucleic acid (RNA)-dependent RNA polymerase (RdRp). The in silico method has also been employed to determine the most effective drug among the mentioned compound and their aquatic, nonaquatic, and pharmacokinetics’ data have been analyzed. The highest binding energy has been reported -11.4 kcal/mol against SARS-CoV-2 main protease (7MBG) in L05. Besides, all the ligands are non-carcinogenic, excluding L04, and have good water solubility and no AMES toxicity. The discovery of preclinical drug candidate molecules and the structural elucidation of pharmacological therapeutic targets have expedited both structure-based and ligand-based drug design. This review article will assist physicians and researchers in realizing the enormous potential of computer-aided drug design in the design and discovery of therapeutic molecules, and hence in the treatment of deadly diseases.
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Affiliation(s)
- Md. Mominur Rahman
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Md. Rezaul Islam
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Shopnil Akash
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Sadia Afsana Mim
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Md. Saidur Rahaman
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Talha Bin Emran
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, Bangladesh
- *Correspondence: Eduardo Sobarzo-Sánchez, ; Talha Bin Emran, ; Polrat Wilairatana,
| | - Esra Küpeli Akkol
- Department of Pharmacognosy, Faculty of Pharmacy, Gazi University, Ankara, Turkey
| | - Rohit Sharma
- Department of Rasashastra and Bhaishajya Kalpana, Faculty of Ayurveda, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Fahad A. Alhumaydhi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Sherouk Hussein Sweilam
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
- Department of Pharmacognosy, Faculty of Pharmacy, Egyptian Russian University, Badr City, Egypt
| | - Md. Emon Hossain
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Tanmay Kumar Ray
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Sharifa Sultana
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Muniruddin Ahmed
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Eduardo Sobarzo-Sánchez
- Instituto de Investigación y Postgrado, Facultad de Ciencias de la Salud, Universidad Central de Chile, Santiago, Chile
- Department of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela, Spain
- *Correspondence: Eduardo Sobarzo-Sánchez, ; Talha Bin Emran, ; Polrat Wilairatana,
| | - Polrat Wilairatana
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- *Correspondence: Eduardo Sobarzo-Sánchez, ; Talha Bin Emran, ; Polrat Wilairatana,
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28
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Role of natural products towards the SARS-CoV-2: A critical review. Ann Med Surg (Lond) 2022; 80:104062. [PMID: 35814035 PMCID: PMC9249430 DOI: 10.1016/j.amsu.2022.104062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/11/2022] [Accepted: 06/22/2022] [Indexed: 11/23/2022] Open
Abstract
Despite the fact that various therapeutic compounds are being investigated, there is still a scarcity of effective and reliable therapeutic regimens to treat COVID-19. Ever since the COVID-19 pandemic, a diversity of traditional herbal treatments has been investigated to cure infected people, either alone or in conjunction with mainstream pharmaceuticals, with encouraging outcomes. In this article, we look at the latest research on the usage of natural products to alleviate the severity of COVID-19. To determine the activity of the natural products, act against SARS-CoV-2 to various targets like Mpro, ACE-II, papain-like, chymotrypsin-like proteases, and some antiviral targets. The processes underlying this preventative or therapeutic action are also examined. We used PubMed, Scopus, Google Scholar, and the WHO site to perform our review. The anti-SARS-CoV-2 impacts of various herbal extracts and purified compounds may be mediated via direct prevention of viral replication or entrance. Interestingly, certain items might avert SARS-CoV-2 from infecting human cells by blocking the ACE-2 protein or the serine protease TMPRRS2. Natural products have also been stated to suppress proteins intricate in the virus life cycle, like papain-like and chymotrypsin-like proteases. To conclude, natural products can be used alone or in combination as remedies or treatments for COVID-19. In addition, their compositions may provide insight into the development of effective and reliable antiviral drugs. The COVID-19 pandemic caused by a novel coronavirus SARS-CoV-2, resulted in thousands of deaths across the world. Globally, numerous studies and researchers have recently started fighting this virus. In this article, we look at the latest research on the usage of natural products to alleviate the severity of COVID-19. The anti-SARS-CoV-2 impacts of various herbal extracts and purified compounds may be mediated via direct prevention of viral replication or entrance.
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29
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Parva N, Omid S, Sadegh AJ, Mohammad HA, Mehrdad K. Antiviral Activity of Medicinal Plants against Human Coronavirus: a systematic scoping review of and experimentations. J TRADIT CHIN MED 2022; 42:332-343. [PMID: 35610002 PMCID: PMC9924666 DOI: 10.19852/j.cnki.jtcm.2022.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2023]
Abstract
OBJECTIVE To investigate the and studies of natural compounds and medicinal plants with anti-coronavirus activity. METHODS A systematic review was performed based on Preferred Reporting Items for Systematic Reviews and Meta-Analyses and Animal Research: Reporting of experiments guidelines to find data for medicinal plants and natural products effective against human coronaviruses in or studies. Studies published up to September 6, 2020 were included. Studies ( or ) reporting the effect of medicinal plants and natural products or their derivatives on human coronavirus were included RESULTS: Promising anti-coronavirus effects are seen with different herbal compounds like some diterpenoids, sesquiterpenoids, and three compounds in tea with 3CLpro inhibiting effect of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV); Hirsutenone, Six cinnamic amides and bavachinin are PLpro inhibitors and Tanshinones are active on both 3CLpro and PLpro. Some flavonoid compounds of Citrus fruits act on Immun-oregulation and target angiotensin-converting enzyme 2 which is used by SARS-COV for entry. Virus helicase is possibly inhibited by two compounds myricetin and scutellarein. CONCLUSION This review shows that complementary medicine have the potential for new drug discovery against coronavirus. Further research is needed before definitive conclusions can be made concerning the safety and efficacy of the use of these medicinal plants.
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Affiliation(s)
- Namiranian Parva
- 1 Department of Traditional Medicine, School of Persian Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Sadatpour Omid
- 2 Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Azimzadeh Jamalkandi Sadegh
- 3 Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Hossein Ayati Mohammad
- 1 Department of Traditional Medicine, School of Persian Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Karimi Mehrdad
- 1 Department of Traditional Medicine, School of Persian Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Mehrdad Karimi MD, Department of Traditional Medicine, School of Persian Medicine, Tehran University of Medical Sciences, Sarparast St, Taleghani St, Tehran, 1668753961, Iran. , Telephone: +98-21-88974535
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Medicinal plants with anti-SARS-CoV activity repurposing for treatment of COVID-19 infection: A systematic review and meta-analysis. ACTA PHARMACEUTICA (ZAGREB, CROATIA) 2022; 72:199-224. [PMID: 36651508 DOI: 10.2478/acph-2022-0021] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/14/2021] [Indexed: 01/20/2023]
Abstract
The novel SARS-CoV-2 (severe acute respiratory syndrome coronavirus) has emerged as a significant threat to public health with startling drawbacks in all sectors globally. This study investigates the practicality of some medicinal plants for SARS-CoV-2 therapy using a systematic review and meta-analysis of their reported SARS-CoV-1 inhibitory potencies. Relevant data were systematically gathered from three databases, viz., Web of Science, PubMed and Scopus. The information obtained included botanical information, extraction method and extracts concentrations, as well as the proposed mechanisms. Fourteen articles describing 30 different plants met our eligibility criteria. Random effects model and subgroup analysis were applied to investigate heterogeneity. According to subgroup analysis, the substantial heterogeneity of the estimated mean based on the IC 50 values reporting the most potent anti-SARS-CoV 3C--like protease (3CLpro) inhibitors (10.07 %, p < 0.0001), was significantly higher compared to the most active anti-SARS-CoV papain-like protease (PLpro) inhibitors (6.12 %, p < 0.0001). More importantly, the literature analysis revealed that fruit extracts of Rheum palmatum L. and the compound cryptotanshinone isolated from the root of Salvia miltiorrhiza (IC 50 = 0.8 ± 0.2 μmol L-1) were excellent candidates for anti--SARS-CoV targeting PLpro. Meanwhile, iguesterin (IC 50 = 2.6 ± 0.6 μmol L-1) isolated from the bark of Tripterygium regelii emerged as the most excellent candidate for anti-SARS--CoV targeting 3CLpro. The present systematic review and meta-analysis provide valuable and comprehensive information about potential medicinal plants for SARS-CoV-2 inhibition. The chemotypes identified herein can be adopted as a starting point for developing new drugs to contain the novel virus.
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Promising inhibitors against main protease of SARS CoV-2 from medicinal plants: In silico identification. ACTA PHARMACEUTICA (ZAGREB, CROATIA) 2022; 72:159-169. [PMID: 36651513 DOI: 10.2478/acph-2022-0020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/13/2021] [Indexed: 01/20/2023]
Abstract
Some compounds reported as active against SARS CoV were selected, and docking studies were performed using the main protease of SARS CoV-2 as the receptor. The docked complex analysis shows that the ligands selectively bind with the target residues and binding affinity of amentoflavone (-10.1 kcal mol-1), isotheaflavin-3'-gallate (-9.8 kcal mol-1), tomentin A and D (-8.0 and -8.8 kcal mol-1), theaflavin-3,3'-digallate (-8.6 kcal mol-1), papyriflavonol A (-8.4 kcal mol-1), iguesterin (-8.0 kcal mol-1) and savinin (-8.3 kcal mol-1) were ranked above the binding affinity of the reference, co-crystal ligand, ML188, a furan-2-carboxamide-based compound. To pinpoint the drug-like compound among the top-ranked compounds, the Lipinski's rule of five and pharmacokinetic properties of all the selected compounds were evaluated. The results detailed that savinin exhibits high gastrointestinal absorption and can penetrate through the blood-brain barrier. Also, modifying these natural scaffolds with excellent binding affinity may lead to discovering of anti-SARS CoV agents with promising safety profiles.
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Bibi S, Khan MS, El-Kafrawy SA, Alandijany TA, El-Daly MM, Yousafi Q, Fatima D, Faizo AA, Bajrai LH, Azhar EI. Virtual screening and molecular dynamics simulation analysis of Forsythoside A as a plant-derived inhibitor of SARS-CoV-2 3CLpro. Saudi Pharm J 2022; 30:979-1002. [PMID: 35637849 PMCID: PMC9132386 DOI: 10.1016/j.jsps.2022.05.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 05/20/2022] [Indexed: 12/24/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a more severe strain of coronavirus (CoV) that was first emerged in China in 2019. Available antiviral drugs could be repurposed and natural compounds with antiviral activity could be safer and cheaper source of medicine for SARS-CoV-2. 78 natural antiviral compounds database was identified from literature and virtual screening technique was applied to identify potential 3-chymotrypsin-like protease (3CLpro) inhibitors. Molecular docking studies were conducted to analyze the main protease (3CLpro) and inhibitors interactions with key residues of active site of target protein (PDB ID: 6LU7), active site constitute the part of active domain I and II of 3CLpro. 10 compounds with highest dock score were subjected to calculate ADMET parameters to figure out drug-likeness. Molecular dynamic (MD) simulation of the selected lead was performed by Amber simulation package to understand the conformational changes in docked complex. MD simulations analysis (RMSD, RMSF, Rg, BF, HBs, and SASA plots) of lead bounded with 3CLpro, hence revealed the important structural turns and twists during MD simulations from 0 to 100 ns. MM-PBSA/GBSA methods has also been applied for the estimation binding free energy (BFE) of the selected lead-complex. The present study has identified lead compound “Forsythoside A” an active extract of Forsythia suspense as SARS-CoV-2 3CLpro inhibitor that can block the viral replication and translation. Structural analysis of target protein and lead compound performed in this study could contribute to the development of potential drug against SARS-CoV-2 infection.
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Affiliation(s)
- Shabana Bibi
- Department of Biosciences, Shifa-Tameer-e-Milat University, Islamabad, Pakistan
- Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming 650091, Yunnan, China
- Corresponding authors at: Department of Biosciences, Shifa-Tameer-e-Milat University, Islamabad, Pakistan. Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming 650091, Yunnan, China (S. Bibi). Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia (E.I. Azhar).
| | - Muhammad Saad Khan
- Department of Biosciences, COMSATS University Islamabad, Sahiwal, Pakistan
| | - Sherif A. El-Kafrawy
- Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Thamir A. Alandijany
- Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mai M. El-Daly
- Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Qudsia Yousafi
- Department of Biosciences, COMSATS University Islamabad, Sahiwal, Pakistan
| | - Dua Fatima
- Department of Biosciences, COMSATS University Islamabad, Sahiwal, Pakistan
| | - Arwa A. Faizo
- Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Leena H. Bajrai
- Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
- Biochemistry Department, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Esam I. Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Corresponding authors at: Department of Biosciences, Shifa-Tameer-e-Milat University, Islamabad, Pakistan. Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming 650091, Yunnan, China (S. Bibi). Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia (E.I. Azhar).
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Chhetri BK, Tedbury PR, Sweeney-Jones AM, Mani L, Soapi K, Manfredi C, Sorscher E, Sarafianos SG, Kubanek J. Marine Natural Products as Leads against SARS-CoV-2 Infection. JOURNAL OF NATURAL PRODUCTS 2022; 85:657-665. [PMID: 35290044 PMCID: PMC8936055 DOI: 10.1021/acs.jnatprod.2c00015] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Indexed: 05/13/2023]
Abstract
Since early 2020, disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a global pandemic, causing millions of infections and deaths worldwide. Despite rapid deployment of effective vaccines, it is apparent that the global community lacks multipronged interventions to combat viral infection and disease. A major limitation is the paucity of antiviral drug options representing diverse molecular scaffolds and mechanisms of action. Here we report the antiviral activities of three distinct marine natural products─homofascaplysin A (1), (+)-aureol (2), and bromophycolide A (3)─evidenced by their ability to inhibit SARS-CoV-2 replication at concentrations that are nontoxic toward human airway epithelial cells. These compounds stand as promising candidates for further exploration toward the discovery of novel drug leads against SARS-CoV-2.
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Affiliation(s)
- Bhuwan Khatri Chhetri
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Philip R. Tedbury
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | | | - Luke Mani
- Institute of Applied Sciences, University of South Pacific, Suva, Fiji
| | - Katy Soapi
- Institute of Applied Sciences, University of South Pacific, Suva, Fiji
| | - Candela Manfredi
- Department of Pediatrics, Division of Pulmonary Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Eric Sorscher
- Department of Pediatrics, Division of Pulmonary Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Stefan G. Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Julia Kubanek
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30332, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
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Tian X, Zhao Q, Chen X, Peng Z, Tan X, Wang Q, Chen L, Yang Y. Discovery of Novel and Highly Potent Inhibitors of SARS CoV-2 Papain-Like Protease Through Structure-Based Pharmacophore Modeling, Virtual Screening, Molecular Docking, Molecular Dynamics Simulations, and Biological Evaluation. Front Pharmacol 2022; 13:817715. [PMID: 35264955 PMCID: PMC8899470 DOI: 10.3389/fphar.2022.817715] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/03/2022] [Indexed: 01/09/2023] Open
Abstract
Background and Objective: COVID-19 has struck our society as a great calamity, and the need for effective anti-viral drugs is more urgent than ever. Papain-like protease (PLpro) of SARS CoV-2 plays important roles in virus maturation, dysregulation of host inflammation, and antiviral immune responses, which is being regarded as a promising druggable target for the treatment of COVID-19. Here, we carried out a combined screening approach to identify novel and highly potent PLpro inhibitors for the treatment of COVID-19. Methods: We used a combined screening approach of structure-based pharmacophore modeling and molecular docking to screen an in-house database containing 35,000 compounds. SARS CoV-2 PLpro inhibition assay was used to carry out the biological evaluation of hit compounds. Molecular dynamics (MD) simulations were conducted to check the stability of the PLpro-hit complexes predicted by molecular docking. Results: We found that four hit compounds showed excellent inhibitory activities against PLpro with IC50 values ranging from 0.6 to 2.4 μM. Among them, the most promising compound, hit 2 is the best PLpro inhibitor and its inhibitory activity was about 4 times higher than that of the positive control (GRL0617). The study of MD simulations indicated that four hits could bind stably to the active site of PLpro. Further study of interaction analysis indicated that hit 2 could form hydrogen-bond interactions with the key amino acids such as Gln269 and Asp164 in the PLpro-active site. Conclusion: Hit 2 is a novel and highly potent PLpro inhibitor, which will open the way for the development of clinical PLpro inhibitors for the treatment of COVID-19.
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Affiliation(s)
- Xiaoyan Tian
- Department of Pharmacology, Chongqing Health Center for Women and Children, Chongqing, China
| | - Quanfeng Zhao
- Department of Pharmacy, Southwest Hospital, First Affiliated Hospital to TMMU, Third Military Medical University (Army Medical University), Chongqing, China
| | - Xiaohong Chen
- Department of Pharmacology, Chongqing Health Center for Women and Children, Chongqing, China
| | - Zhe Peng
- Department of Pharmacology, Chongqing Health Center for Women and Children, Chongqing, China
| | - Xiaodan Tan
- Department of Pharmacology, Chongqing Health Center for Women and Children, Chongqing, China
| | - Qin Wang
- Department of Pharmacology, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, China
| | - Lin Chen
- Department of Pharmacology, Chongqing Health Center for Women and Children, Chongqing, China
| | - Yang Yang
- Department of Pharmacology, Chongqing Health Center for Women and Children, Chongqing, China
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35
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Coronavirus enzyme inhibitors-experimentally proven natural compounds from plants. J Microbiol 2022; 60:347-354. [PMID: 35089586 PMCID: PMC8795716 DOI: 10.1007/s12275-022-1499-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/09/2021] [Accepted: 11/09/2021] [Indexed: 11/04/2022]
Abstract
Coronavirus disease (COVID-19) can cause critical conditions that require efficient therapeutics. Several medicines are derived from plants, and researchers are seeking natural compounds to ameliorate the symptoms of COVID-19. Viral enzymes are popular targets of antiviral medicines; the genome of coronaviruses encodes several enzymes, including RNA-dependent RNA polymerase and viral proteases. Various screening systems have been developed to identify potential inhibitors. In this review, we describe the natural compounds that have been shown to exert inhibitory effects on coronavirus enzymes. Although computer-aided molecular structural studies have predicted several antiviral compound candidates, the current review focuses on experimentally proven natural compounds.
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36
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Abou Baker DH. An ethnopharmacological review on the therapeutical properties of flavonoids and their mechanisms of actions: A comprehensive review based on up to date knowledge. Toxicol Rep 2022; 9:445-469. [PMID: 35340621 PMCID: PMC8943219 DOI: 10.1016/j.toxrep.2022.03.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 12/11/2022] Open
Abstract
Flavonoids -a class of low molecular weight secondary metabolites- are ubiquitous and cornucopia throughout the plant kingdom. Structurally, the main structure consists of C6-C3-C6 rings with different substitution patterns so that many sub-classes are obtained, for example: flavonols, flavonolignans, flavonoid glycosides, flavans, anthocyanidins, aurones, anthocyanidins, flavones, neoflavonoids, chalcones, isoflavones, flavones and flavanones. Flavonoids are evaluated to have drug like nature since they possess different therapeutic activities, and can act as cardioprotective, antiviral, antidiabetic, anti-inflammatory, antibacterial, anticancer, and also work against Alzheimer's disease and others. However, information on the relationship between their structure and biological activity is scarce. Therefore, the present review tries to summarize all the therapeutic activities of flavonoids, their mechanisms of action and the structure activity relationship. Latest updated ethnopharmacological review of the therapeutic effects of flavonoids. Flavonoids are attracting attention because of their therapeutic properties. Flavonoids are valuable candidates for drug development against many dangerous diseases. This overview summarizes the most important therapeutic effect and mechanism of action of flavonoids. General knowledge about the structure activity relationship of flavonoids is summarized. Substitution of chemical groups in the structure of flavonoids can significantly change their biological and chemical properties. The chemical properties of the basic flavonoid structure should be considered in a drug-based structural program.
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Vere G, Alam MR, Farrar S, Kealy R, Kessler BM, O’Brien DP, Pinto-Fernández A. Targeting the Ubiquitylation and ISGylation Machinery for the Treatment of COVID-19. Biomolecules 2022; 12:biom12020300. [PMID: 35204803 PMCID: PMC8869442 DOI: 10.3390/biom12020300] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 02/09/2022] [Accepted: 02/10/2022] [Indexed: 12/15/2022] Open
Abstract
Ubiquitylation and ISGylation are protein post-translational modifications (PTMs) and two of the main events involved in the activation of pattern recognition receptor (PRRs) signals allowing the host defense response to viruses. As with similar viruses, SARS-CoV-2, the virus causing COVID-19, hijacks these pathways by removing ubiquitin and/or ISG15 from proteins using a protease called PLpro, but also by interacting with enzymes involved in ubiquitin/ISG15 machinery. These enable viral replication and avoidance of the host immune system. In this review, we highlight potential points of therapeutic intervention in ubiquitin/ISG15 pathways involved in key host-pathogen interactions, such as PLpro, USP18, TRIM25, CYLD, A20, and others that could be targeted for the treatment of COVID-19, and which may prove effective in combatting current and future vaccine-resistant variants of the disease.
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Affiliation(s)
- George Vere
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (G.V.); (M.R.A.); (S.F.); (B.M.K.)
- MRC Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Md Rashadul Alam
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (G.V.); (M.R.A.); (S.F.); (B.M.K.)
| | - Sam Farrar
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (G.V.); (M.R.A.); (S.F.); (B.M.K.)
| | - Rachel Kealy
- Environmental Futures & Big Data Impact Lab, University of Exeter, Stocker Rd., Exeter EX4 4PY, UK;
| | - Benedikt M. Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (G.V.); (M.R.A.); (S.F.); (B.M.K.)
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Darragh P. O’Brien
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (G.V.); (M.R.A.); (S.F.); (B.M.K.)
- Correspondence: (D.P.O.); (A.P.-F.)
| | - Adán Pinto-Fernández
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (G.V.); (M.R.A.); (S.F.); (B.M.K.)
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
- Correspondence: (D.P.O.); (A.P.-F.)
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Gorai S, Junghare V, Kundu K, Gharui S, Kumar M, Patro BS, Nayak SK, Hazra S, Mula S. Synthesis of Dihydrobenzofuro[3,2-b]chromenes as a potential 3CLpro inhibitors of SARS-CoV-2: A molecular docking and dynamics simulation study. ChemMedChem 2022; 17:e202100782. [PMID: 35112482 PMCID: PMC9015348 DOI: 10.1002/cmdc.202100782] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Indexed: 11/29/2022]
Abstract
The recent emergence of pandemic of coronavirus (COVID‐19) caused by SARS‐CoV‐2 has raised significant global health concerns. More importantly, there is no specific therapeutics currently available to combat against this deadly infection. The enzyme 3‐chymotrypsin‐like cysteine protease (3CLpro) is known to be essential for viral life cycle as it controls the coronavirus replication. 3CLpro could be a potential drug target as established before in the case of severe acute respiratory syndrome coronavirus (SARS‐CoV) and Middle East respiratory syndrome coronavirus (MERS‐CoV). In the current study, we wanted to explore the potential of fused flavonoids as 3CLpro inhibitors. Fused flavonoids (5a,10a‐dihydro‐11H‐benzofuro[3,2‐b]chromene) are unexplored for their potential bioactivities due to their low natural occurrences. Their synthetic congeners are also rare due to unavailability of general synthetic methodology. Here we designed a simple strategy to synthesize 5a,10a‐dihydro‐11H‐benzofuro[3,2‐b]chromene skeleton and it's four novel derivatives. Our structural bioinformatics study clearly shows excellent potential of the synthesized compounds in comparison to experimentally validated inhibitor N3. Moreover, in‐silico ADMET study displays excellent druggability and extremely low level of toxicity of the synthesized molecules. Further, for better understanding, the molecular dynamic approach was implemented to study the change in dynamicity after the compounds bind to the protein. A detailed investigation through clustering analysis and distance calculation gave us sound comprehensive data about their molecular interaction. In summary, we anticipate that the currently synthesized molecules could not only be a potential set of inhibitors against 3CLpro but also the insights acquired from the current study would be instrumental in further developing novel natural flavonoid based anti‐COVID therapeutic spectrums.
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Affiliation(s)
- Sudip Gorai
- Bhabha Atomic Research Centre, Department of Atomic Energy, INDIA
| | - Vivek Junghare
- IIT Roorkee: Indian Institute of Technology Roorkee, Biotechnology, INDIA
| | - Kshama Kundu
- Bhabha Atomic Research Centre, Department of Atomic Energy, INDIA
| | | | - Mukesh Kumar
- Bhabha Atomic Research Centre, Department of Atomic Energy, INDIA
| | | | - Sandip K Nayak
- Bhabha Atomic Research Centre, Department of Atomic Energy, INDIA
| | - Saugata Hazra
- IIT Roorkee: Indian Institute of Technology Roorkee, Biotechnology, INDIA
| | - Soumyaditya Mula
- Bhabha Atomic Research Centre, Bio-Organic Division, 1-28H, Modular Laboratory, 400085, Mumbai, INDIA
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Stochmal A, Moniuszko-Szajwaj B, Zuchowski J, Pecio Ł, Kontek B, Szumacher-Strabel M, Olas B, Cieslak A. Qualitative and Quantitative Analysis of Secondary Metabolites in Morphological Parts of Paulownia Clon In Vitro 112 ® and Their Anticoagulant Properties in Whole Human Blood. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27030980. [PMID: 35164250 PMCID: PMC8840654 DOI: 10.3390/molecules27030980] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/19/2022] [Accepted: 01/25/2022] [Indexed: 12/17/2022]
Abstract
It is not easy to find data in the scientific literature on the quantitative content of individual phytochemicals. It is possible to find groups of compounds and even individual compounds rather easily, but it is not known what their concentration is in cultivated or wild plants. Therefore, the subject of this study was to determine the content of individual compounds in the new Paulownia species, Oxytree, developed in a biotechnology laboratory in 2008 at La Mancha University in Spain. Six secondary metabolites were isolated, and their chemical structure was confirmed by spectral methods. An analytical method was developed, which was then used to determine the content of individual compounds in leaves, twigs, flowers and fruits of Paulownia Clon in Vitro 112®. No flavonoids were found in twigs and fruits of Oxytree, while the highest phenylethanoid glycosides were found in twigs. In this study, we also focused on biological properties (anticoagulant or procoagulant) of extract and four fractions (A–D) of different chemical composition from Paulownia Clon in Vitro 112 leaves using whole human blood. These properties were determined based on the thrombus-formation analysis system (T-TAS), which imitates in vivo conditions to assess whole blood thrombogenecity. We observed that three fractions (A, C and D) from leaves decrease AUC10 measured by T-TAS. In addition, fraction D rich in triterpenoids showed the strongest anticoagulant activity. However, in order to clarify the exact mechanism of action of the active substances present in this plant, studies closer to physiological conditions, i.e., in vivo studies, should be performed, which will also allow to determine the effects of their long-term effects.
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Affiliation(s)
- Anna Stochmal
- Department of Biochemistry and Crop Quality, Institute of Soil Science and Plant Cultivation—State Research Institute, Czartoryskich 8, 24-100 Puławy, Poland; (A.S.); (B.M.-S.); (J.Z.); (Ł.P.)
| | - Barbara Moniuszko-Szajwaj
- Department of Biochemistry and Crop Quality, Institute of Soil Science and Plant Cultivation—State Research Institute, Czartoryskich 8, 24-100 Puławy, Poland; (A.S.); (B.M.-S.); (J.Z.); (Ł.P.)
| | - Jerzy Zuchowski
- Department of Biochemistry and Crop Quality, Institute of Soil Science and Plant Cultivation—State Research Institute, Czartoryskich 8, 24-100 Puławy, Poland; (A.S.); (B.M.-S.); (J.Z.); (Ł.P.)
| | - Łukasz Pecio
- Department of Biochemistry and Crop Quality, Institute of Soil Science and Plant Cultivation—State Research Institute, Czartoryskich 8, 24-100 Puławy, Poland; (A.S.); (B.M.-S.); (J.Z.); (Ł.P.)
| | - Bogdan Kontek
- Department of General Biochemistry, Faculty of Biology and Environmental Protection, University of Lodz, 90-236 Łódź, Poland;
| | - Malgorzata Szumacher-Strabel
- Department of Animal Nutrition, Poznań University of Life Sciences, Wołyńska 33, 60-637 Poznań, Poland; (M.S.-S.); (A.C.)
| | - Beata Olas
- Department of General Biochemistry, Faculty of Biology and Environmental Protection, University of Lodz, 90-236 Łódź, Poland;
- Correspondence:
| | - Adam Cieslak
- Department of Animal Nutrition, Poznań University of Life Sciences, Wołyńska 33, 60-637 Poznań, Poland; (M.S.-S.); (A.C.)
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40
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Suresh P, Gupta S, Anmol, Sharma U. Insight into coronaviruses and natural products-based approach for COVID-19 treatment. BIOACTIVE NATURAL PRODUCTS 2022. [PMCID: PMC9294970 DOI: 10.1016/b978-0-323-91099-6.00005-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
There is a deep-rooted belief in mankind that for every illness, somewhere in the world, there exists a botanical-based healing agent in nature in the form of a natural product. Natural products are better equipped to become successful drugs because of their million years of coevolution in a biological milieu. Generally, most herbal formulations and natural products obtained from traditionally used medicinal plants are nontoxic and have rarely shown any adverse side effects on humans. Plants synthesize secondary metabolites primarily for their defense against microbes and herbivores, and because of this, these metabolites have good specificity and potency against harmful pathogens. Nowadays, mankind is facing the contagion effect of SARS-CoV-2 that has caused the ongoing pandemic of COVID-19, which has no specific and effective treatment. Hence this is the time to explore nature for effective, safe, and affordable remedies against this disease. This chapter includes an overview of coronaviruses, their therapeutic targets, and the progress made in identifying lead natural products against the coronaviruses. Additionally, molecular docking and pharmacokinetics analysis of anticoronaviral natural products have been performed to narrow down the possible lead molecules.
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Li L, Ma L, Hu Y, Li X, Yu M, Shang H, Zou Z. Natural biflavones are potent inhibitors against SARS-CoV-2 papain-like protease. PHYTOCHEMISTRY 2022; 193:112984. [PMID: 34757253 PMCID: PMC8506144 DOI: 10.1016/j.phytochem.2021.112984] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 10/01/2021] [Accepted: 10/09/2021] [Indexed: 06/02/2023]
Abstract
Papain-like protease (PLpro) is a key enzyme encoded by SARS-CoV-2 that is essential for viral replication and immune evasion. Significant suppression of viral spread and promotion of antiviral immunity can be achieved by inhibition of PLpro, revealing an inspiring strategy for COVID-19 treatment. This study aimed to discover PLpro inhibitors by investigating the national compound library of traditional Chinese medicines (NCLTCMs), a phytochemical library comprising over 9000 TCM-derived compounds. Through virtual screening and enzymatic evaluations, nine natural biflavones were confirmed to be effective PLpro inhibitors with IC50 values ranging from 9.5 to 43.2 μM. Pro-ISG15 cleavage assays further demonstrated that several biflavones exhibited potent inhibitory effects against PLpro-mediated deISGylation, a key process involved in viral immune evasion. Herein, we report the discovery, antiviral evaluation, structure-activity relationship elucidation and molecular docking investigation of biflavones as potent inhibitors of SARS-CoV-2 PLpro.
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Affiliation(s)
- Lingyu Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, PR China
| | - Liyan Ma
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, PR China
| | - Yue Hu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, PR China
| | - Xiaoxue Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, PR China; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, PR China
| | - Meng Yu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, PR China
| | - Hai Shang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, PR China.
| | - Zhongmei Zou
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, PR China.
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Guo DA, Yao CL, Wei WL, Zhang JQ, Bi QR, Li JY, Khan I, Bauer R. Traditional Chinese medicines against COVID-19: A global overview. WORLD JOURNAL OF TRADITIONAL CHINESE MEDICINE 2022. [DOI: 10.4103/2311-8571.353502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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In Silico Screening of Natural Products as Potential Inhibitors of SARS-CoV-2 Using Molecular Docking Simulation. Chin J Integr Med 2021; 28:249-256. [PMID: 34913151 PMCID: PMC8672856 DOI: 10.1007/s11655-021-3504-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2021] [Indexed: 12/23/2022]
Abstract
Objective To explore potential natural products against severe acute respiratory syndrome coronavirus (SARS-CoV-2) via the study of structural and non-structural proteins of human coronaviruses. Methods In this study, we performed an in-silico survey of 25 potential natural compounds acting against SARS-CoV-2. Molecular docking studies were carried out using compounds against 3-chymotrypsin-like protease (3CLPRO), papain-like protease (PLPRO), RNA-dependent RNA polymerase (RdRp), non-structural protein (nsp), human angiotensin converting enzyme 2 receptor (hACE2R), spike glycoprotein (S protein), abelson murine leukemia viral oncogene homolog 1 (ABL1), calcineurin-nuclear factor of activated T-cells (NFAT) and transmembrane protease serine 2. Results Among the screened compounds, amentoflavone showed the best binding affinity with the 3CLPRO, RdRp, nsp13, nsp15, hACE2R. ABL1 and calcineurin-NFAT; berbamine with hACE2R and ABL1; cepharanthine with nsp10, nsp14, nsp16, S protein and ABL1; glucogallin with nsp15; and papyriflavonol A with PLPRO protein. Other good interacting compounds were juglanin, betulinic acid, betulonic acid, broussooflavan A, tomentin A, B and E, 7-methoxycryptopleurine, aloe emodin, quercetin, tanshinone I, tylophorine and furruginol, which also showed excellent binding affinity towards a number of target proteins. Most of these compounds showed better binding affinities towards the target proteins than the standard drugs used in this study. Conclusion Natural products or their derivatives may be one of the potential targets to fight against SARS-CoV-2. Electronic Supplementary Material Supplementary materials (Appendixes 1–6) are available in the online version of this article at DOI: 10.1007/s11655-021-3504-5
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Agrawal PK, Agrawal C, Blunden G. Naringenin as a Possible Candidate Against SARS-CoV-2 Infection and in the Pathogenesis of COVID-19. Nat Prod Commun 2021. [DOI: 10.1177/1934578x211066723] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Naringenin, widely distributed in fruits and vegetables, is endowed with antiviral and other health beneficial activities, such as immune-stimulating and anti-inflammatory actions that could play a role in contributing, to some extent, to either preventing or alleviating coronavirus infection. Several computational studies have identified naringenin as one of the prominent flavonoids that can possibly inhibit internalization of the virus, virus-host interactions that trigger the cytokine storm, and replication of the virus. This review highlights the antiviral potential of naringenin in COVID-19 associated risk factors and its predicted therapeutic targets against SARS-CoV-2 infection.
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Affiliation(s)
- Pawan K. Agrawal
- Natural Product Inc., 7963 Anderson Park Lane, Westerville, OH 43081, USA
| | - Chandan Agrawal
- Natural Product Inc., 7963 Anderson Park Lane, Westerville, OH 43081, USA
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Yapasert R, Khaw-on P, Banjerdpongchai R. Coronavirus Infection-Associated Cell Death Signaling and Potential Therapeutic Targets. Molecules 2021; 26:7459. [PMID: 34946543 PMCID: PMC8706825 DOI: 10.3390/molecules26247459] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/29/2021] [Accepted: 12/06/2021] [Indexed: 12/12/2022] Open
Abstract
COVID-19 is the name of the disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection that occurred in 2019. The virus-host-specific interactions, molecular targets on host cell deaths, and the involved signaling are crucial issues, which become potential targets for treatment. Spike protein, angiotensin-converting enzyme 2 (ACE2), cathepsin L-cysteine peptidase, transmembrane protease serine 2 (TMPRSS2), nonstructural protein 1 (Nsp1), open reading frame 7a (ORF7a), viral main protease (3C-like protease (3CLpro) or Mpro), RNA dependent RNA polymerase (RdRp) (Nsp12), non-structural protein 13 (Nsp13) helicase, and papain-like proteinase (PLpro) are molecules associated with SARS-CoV infection and propagation. SARS-CoV-2 can induce host cell death via five kinds of regulated cell death, i.e., apoptosis, necroptosis, pyroptosis, autophagy, and PANoptosis. The mechanisms of these cell deaths are well established and can be disrupted by synthetic small molecules or natural products. There are a variety of compounds proven to play roles in the cell death inhibition, such as pan-caspase inhibitor (z-VAD-fmk) for apoptosis, necrostatin-1 for necroptosis, MCC950, a potent and specific inhibitor of the NLRP3 inflammasome in pyroptosis, and chloroquine/hydroxychloroquine, which can mitigate the corresponding cell death pathways. However, NF-κB signaling is another critical anti-apoptotic or survival route mediated by SARS-CoV-2. Such signaling promotes viral survival, proliferation, and inflammation by inducing the expression of apoptosis inhibitors such as Bcl-2 and XIAP, as well as cytokines, e.g., TNF. As a result, tiny natural compounds functioning as proteasome inhibitors such as celastrol and curcumin can be used to modify NF-κB signaling, providing a responsible method for treating SARS-CoV-2-infected patients. The natural constituents that aid in inhibiting viral infection, progression, and amplification of coronaviruses are also emphasized, which are in the groups of alkaloids, flavonoids, terpenoids, diarylheptanoids, and anthraquinones. Natural constituents derived from medicinal herbs have anti-inflammatory and antiviral properties, as well as inhibitory effects, on the viral life cycle, including viral entry, replication, assembly, and release of COVID-19 virions. The phytochemicals contain a high potential for COVID-19 treatment. As a result, SARS-CoV-2-infected cell death processes and signaling might be of high efficacy for therapeutic targeting effects and yielding encouraging outcomes.
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Affiliation(s)
- Rittibet Yapasert
- Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand;
| | - Patompong Khaw-on
- Faculty of Nursing, Chiang Mai University, Chiang Mai 50200, Thailand;
| | - Ratana Banjerdpongchai
- Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand;
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Wu Y, Crich D, Pegan SD, Lou L, Hansen MC, Booth C, Desrochers E, Mullininx LN, Starling EB, Chang KY, Xie ZR. Polyphenols as Potential Inhibitors of SARS-CoV-2 RNA Dependent RNA Polymerase (RdRp). Molecules 2021; 26:7438. [PMID: 34946521 PMCID: PMC8706955 DOI: 10.3390/molecules26247438] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/08/2021] [Accepted: 12/02/2021] [Indexed: 01/18/2023] Open
Abstract
An increasing number of studies have demonstrated the antiviral nature of polyphenols, and many polyphenols have been proposed to inhibit SARS-CoV or SARS-CoV-2. Our previous study revealed the inhibitory mechanisms of polyphenols against DNA polymerase α and HIV reverse transcriptase to show that polyphenols can block DNA elongation by competing with the incoming NTPs. Here we applied computational approaches to examine if some polyphenols can also inhibit RNA polymerase (RdRp) in SARS-CoV-2, and we identified some better candidates than remdesivir, the FDA-approved drug against RdRp, in terms of estimated binding affinities. The proposed compounds will be further examined to develop new treatments for COVID-19.
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Affiliation(s)
- Yifei Wu
- School of Electrical and Computer Engineering, College of Engineering, University of Georgia, Athens, GA 30602, USA; (Y.W.); (L.L.)
| | - David Crich
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, USA;
| | - Scott D. Pegan
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, Riverside, CA 92521, USA;
| | - Lei Lou
- School of Electrical and Computer Engineering, College of Engineering, University of Georgia, Athens, GA 30602, USA; (Y.W.); (L.L.)
| | - Madelyn C. Hansen
- Franklin College of Arts and Sciences, University of Georgia, Athens, GA 30602, USA; (M.C.H.); (C.B.); (E.D.); (L.N.M.); (E.B.S.)
| | - Carson Booth
- Franklin College of Arts and Sciences, University of Georgia, Athens, GA 30602, USA; (M.C.H.); (C.B.); (E.D.); (L.N.M.); (E.B.S.)
| | - Ellison Desrochers
- Franklin College of Arts and Sciences, University of Georgia, Athens, GA 30602, USA; (M.C.H.); (C.B.); (E.D.); (L.N.M.); (E.B.S.)
| | - Lauren Nicole Mullininx
- Franklin College of Arts and Sciences, University of Georgia, Athens, GA 30602, USA; (M.C.H.); (C.B.); (E.D.); (L.N.M.); (E.B.S.)
| | - Edward B. Starling
- Franklin College of Arts and Sciences, University of Georgia, Athens, GA 30602, USA; (M.C.H.); (C.B.); (E.D.); (L.N.M.); (E.B.S.)
| | - Kuan Y. Chang
- Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung 202, Taiwan
| | - Zhong-Ru Xie
- School of Electrical and Computer Engineering, College of Engineering, University of Georgia, Athens, GA 30602, USA; (Y.W.); (L.L.)
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Demeke CA, Woldeyohanins AE, Kifle ZD. Herbal medicine use for the management of COVID-19: A review article. Metabol Open 2021; 12:100141. [PMID: 34693242 PMCID: PMC8519661 DOI: 10.1016/j.metop.2021.100141] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 10/15/2021] [Accepted: 10/15/2021] [Indexed: 12/23/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause pandemic of coronavirus disease 2019 (COVID-19). For many thousands of years, herbal products and dietary plants have been prescribed for various diseases by traditional healers. Thus, the aim of this review is to present main herbal products, their source, characteristics, and potential antiviral actions concerning COVID-19. Publications on herbal products related to antiviral effects were searched from different databases, such as Web of Science, Google Scholar, Medline, Scopus, and PubMed, until August 2021, using English key terms. According to different studies, there are so many important medicinal plants with antiviral activity, which can be used for viral infections or can be prescribed as supportive treatment. lack of information on the safety profile and amount of dose for different diseases is some of the limitations of medicinal plants. herbal medicine can interfere with COVID-19 pathogenesis by inhibiting SARS-CoV-2 replication and entry to host cells. Some of the antiviral medicinal plant species are citrus Spp., orange (C. Sinensis), Allium sativum, Allium cepa, Mentha piperita, and nigella sativa are the most desirable herbal drink or fruit that can introduce effective adjuvant components in COVID-19 management.
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Affiliation(s)
- Chilot Abiyu Demeke
- Department of Pharmaceutics, School of Pharmacy, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Alem Endashaw Woldeyohanins
- Department of Social Pharmacy, School of Pharmacy, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Zemene Demelash Kifle
- Department of Pharmacology, School of Pharmacy, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
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Lima NM, Fernandes BL, Alves GF, de Souza JC, Siqueira MM, Patrícia do Nascimento M, Moreira OB, Sussulini A, de Oliveira MA. Mass spectrometry applied to diagnosis, prognosis, and therapeutic targets identification for the novel coronavirus SARS-CoV-2: A review. Anal Chim Acta 2021; 1195:339385. [PMID: 35090661 PMCID: PMC8687343 DOI: 10.1016/j.aca.2021.339385] [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: 04/27/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 12/27/2022]
Abstract
Mass spectrometry (MS) has found numerous applications in medicine and has been widely used in the detection and characterization of biomolecules associated with viral infections such as COVID-19. COVID-19 is a multisystem disease and, therefore, the need arises to carry out a careful and conclusive assessment of the pathophysiological parameters involved in the infection, to develop an effective therapeutic approach, assess the prognosis of the disease, and especially the early diagnosis of the infected population. Thus, the urgent need for highly accurate methods of diagnosis and prognosis of this infection presents new challenges for the development of laboratory medicine, whose methods require sensitivity, speed, and accuracy of the techniques for analyzing the biological markers involved in the infection. In this context, MS stands out as a robust analytical tool, with high sensitivity and selectivity, accuracy, low turnaround time, and versatility for the analysis of biological samples. However, it has not yet been adopted as a frontline clinical laboratory technique. Therefore, this review explores the potential and trends of current MS methods and their contribution to the development of new strategies to COVID-19 diagnosis and prognosis and how this tool can assist in the discovery of new therapeutic targets, in addition, to comment what could be the future of MS in medicine.
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Islam SS, Midya S, Sinha S, Saadi SMAI. Natural medicinal plant products as an immune-boosters: A possible role to lessen the impact of Covid-19. CASE STUDIES IN CHEMICAL AND ENVIRONMENTAL ENGINEERING 2021; 4:100105. [PMID: 38620656 PMCID: PMC8096520 DOI: 10.1016/j.cscee.2021.100105] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 04/21/2021] [Accepted: 04/23/2021] [Indexed: 05/27/2023]
Abstract
Transmissible Covid-19, caused by novel corona virus since last of 2019 has outspread widely until now. Where, India was the second most affected country and 3rd in mortality rate. In world ancient history, medicinal plants were played a crucial role to cure several diseases. In present study, we show some novel natural medicinal plant metabolites as the potential inhibitors against papain-like protease (PLpro), main protease (Mpro) and RNA-dependent RNA polymerase (RdRp), transmembrane proteinase Serine 2 (TMPRSS2) and angiotensin converting enzyme-2 (ACE-2) of Covid-19. Plant metabolites were having been proven to inhibit SARS-CoVs, which also actively walkable against Covid-19.
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Key Words
- ACE-2, angiotensin converting enzyme-2
- CSG, Coronavirus Study Group
- Covid-19
- Covid-19, corona virus disease-2019
- E, small envelope protein
- IC, Inhibitory concentration
- ICTV, International Committee on Taxonomy of Viruses
- M, matrix protein
- Medicinal plant
- Mpro, main protease
- N, nucleocapsid protein
- PLpro, papain-like protease
- Plant metabolites
- RBD, receptor binding domain
- RdRp, RNA-dependent RNA polymerase
- S, spike protein
- SARS-CoV
- ST, swine testicular
- TMPRSS2, transmembrane proteinase Serine 2
- WHO, world health organization
- nsps, non-structural proteins
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Affiliation(s)
- Sk Saruk Islam
- Department of Plant Pathology, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, 741235, West Bengal, India
| | - Sujoy Midya
- Department of Zoology, Raja N.L. Khan Women's College, Midnapore, West Bengal, 721102, India
| | - Sanjit Sinha
- Department of Botany and Forestry, Vidyasagar University, Midnapore, West Bengal, 721102, India
| | - Sk Md Abu Imam Saadi
- Department of Biological Sciences, Aliah University, IIA/27, New Town, Kolkata, 700160, West Bengal, India
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Peng S, Fang C, He H, Song X, Zhao X, Zou Y, Li L, Jia R, Yin Z. Myricetin exerts its antiviral activity against infectious bronchitis virus by inhibiting the deubiquitinating activity of papain-like protease. Poult Sci 2021; 101:101626. [PMID: 34995876 PMCID: PMC8741506 DOI: 10.1016/j.psj.2021.101626] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 11/02/2022] Open
Abstract
Infectious bronchitis virus (IBV) is a causative agent that causes severe economic losses in the poultry industry worldwide. Papain-like protease (PLpro) is a nonstructural protein encoded by IBV. It has deubiquitinating enzyme activity, which can remove the ubiqutin modification from the protein in nuclear factor kappa-B (NF-κB) and interferon regulatory factor 7 (IRF7) signaling pathway, so as to negatively regulate the host's innate immune response to promote viral replication. In this study, PLpro was selected as the target to screen antiviral agents against IBV. Through protein prokaryotic expression technology, we successfully expressed the active IBV PLpro. Among the 16 natural products, myricetin showed the strongest inhibitory effect on IBV PLpro. Next, we tested the antiviral activity of myricetin against IBV and verified whether it can exert antiviral activity by inhibiting the deubiquitinating activity of PLpro. The results showed that myricetin can significantly inhibit IBV replication in primary chicken embryo kidney (CEK) cells and it can significantly upregulate the transcription levels in the NF-κB and IRF7 signaling pathways. Moreover, we verified that myricetin can increase the ubiquitin modification level on tumor necrosis factor receptor-associated factor 3 and 6 (TRAF3 and TRAF6) reduced by IBV PLpro. In conclusion, these results indicated that myricetin exerts antiviral activity against IBV by inhibiting the deubiquitinating activity of PLpro, which can provide new perspective for the prevention and treatment of IBV.
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Affiliation(s)
- Shuwei Peng
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, People's Republic of China
| | - Chunlin Fang
- Chengdu Agricultural College, Chengdu 611130, People's Republic of China; Chengdu QianKun Veterinary Pharmaceutical Co., Ltd, Chengdu 611130, People's Republic of China
| | - Heng He
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, People's Republic of China
| | - Xu Song
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, People's Republic of China
| | - Xinghong Zhao
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, People's Republic of China
| | - Yuanfeng Zou
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, People's Republic of China
| | - Lixia Li
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, People's Republic of China
| | - Renyong Jia
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, People's Republic of China
| | - Zhongqiong Yin
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, People's Republic of China.
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