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Vajdi M, Karimi A, Hassanizadeh S, Farhangi MA, Bagherniya M, Askari G, Roufogalis BD, Davies NM, Sahebkar A. Effect of polyphenols against complications of COVID-19: current evidence and potential efficacy. Pharmacol Rep 2024; 76:307-327. [PMID: 38498260 DOI: 10.1007/s43440-024-00585-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 03/01/2024] [Accepted: 03/03/2024] [Indexed: 03/20/2024]
Abstract
The COVID-19 pandemic that started in 2019 and resulted in significant morbidity and mortality continues to be a significant global health challenge, characterized by inflammation, oxidative stress, and immune system dysfunction.. Developing therapies for preventing or treating COVID-19 remains an important goal for pharmacology and drug development research. Polyphenols are effective against various viral infections and can be extracted and isolated from plants without losing their therapeutic potential. Researchers have developed methods for separating and isolating polyphenols from complex matrices. Polyphenols are effective in treating common viral infections, including COVID-19, and can also boost immunity. Polyphenolic-based antiviral medications can mitigate SARS-CoV-2 enzymes vital to virus replication and infection. Individual polyphenolic triterpenoids, flavonoids, anthraquinonoids, and tannins may also inhibit the SARS-CoV-2 protease. Polyphenol pharmacophore structures identified to date can explain their action and lead to the design of novel anti-COVID-19 compounds. Polyphenol-containing mixtures offer the advantages of a well-recognized safety profile with few known severe side effects. However, studies to date are limited, and further animal studies and randomized controlled trials are needed in future studies. The purpose of this study was to review and present the latest findings on the therapeutic impact of plant-derived polyphenols on COVID-19 infection and its complications. Exploring alternative approaches to traditional therapies could aid in developing novel drugs and remedies against coronavirus infection.
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Affiliation(s)
- Mahdi Vajdi
- Department of Community Nutrition, School of Nutrition and Food Science, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Arash Karimi
- Traditional Medicine and Hydrotherapy Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Shirin Hassanizadeh
- Department of Community Nutrition, School of Nutrition and Food Science, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mahdieh Abbasalizad Farhangi
- Department of Community Nutrition, Faculty of Nutrition and Food Science, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Bagherniya
- Department of Community Nutrition, Food Security Research Center, School of Nutrition and Food Science, Isfahan University of Medical Sciences, Isfahan, Iran
- Anesthesia and Critical Care Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Gholamreza Askari
- Department of Community Nutrition, Food Security Research Center, School of Nutrition and Food Science, Isfahan University of Medical Sciences, Isfahan, Iran
- Anesthesia and Critical Care Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Basil D Roufogalis
- Discipline of Pharmacology, School of Medical Sciences, University of Sydney, Sydney, NSW, Australia
- NICM Health Research Institute, Western Sydney University, Penrith, NSW, Australia
| | - Neal M Davies
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
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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 Med 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Rohman N, Ardiansah B, Wukirsari T, Judeh Z. Recent Trends in the Synthesis and Bioactivity of Coumarin, Coumarin-Chalcone, and Coumarin-Triazole Molecular Hybrids. Molecules 2024; 29:1026. [PMID: 38474540 DOI: 10.3390/molecules29051026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/08/2024] [Accepted: 02/10/2024] [Indexed: 03/14/2024] Open
Abstract
Molecular hybridization represents a new approach in drug discovery in which specific chromophores are strategically combined to create novel drugs with enhanced therapeutic effects. This innovative strategy leverages the strengths of individual chromophores to address complex biological challenges, synergize beneficial properties, optimize pharmacokinetics, and overcome limitations associated with single-agent therapies. Coumarins are documented to possess several bioactivities and have therefore been targeted for combination with other active moieties to create molecular hybrids. This review summarizes recent (2013-2023) trends in the synthesis of coumarins, as well as coumarin-chalcone and coumarin-triazole molecular hybrids. To cover the wide aspects of this area, we have included differently substituted coumarins, chalcones, 1,2,3- and 1,2,4-triazoles in this review and considered the point of fusion/attachment with coumarin to show the diversity of these hybrids. The reported syntheses mainly relied on well-established chemistry without the need for strict reaction conditions and usually produced high yields. Additionally, we discussed the bioactivities of the reported compounds, including antioxidative, antimicrobial, anticancer, antidiabetic, and anti-cholinesterase activities and commented on their IC50 where possible. Promising bioactivity results have been obtained so far. It is noted that mechanistic studies are infrequently found in the published work, which was also mentioned in this review to give the reader a better understanding. This review aims to provide valuable information to enable further developments in this field.
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Affiliation(s)
- Nur Rohman
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok 16424, Indonesia
| | - Bayu Ardiansah
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok 16424, Indonesia
| | - Tuti Wukirsari
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok 16424, Indonesia
| | - Zaher Judeh
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 62 Nanyang Drive, N1.2-B1-14, Singapore 637459, Singapore
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Bianconi E, Gidari A, Souma M, Sabbatini S, Grifagni D, Bigiotti C, Schiaroli E, Comez L, Paciaroni A, Cantini F, Francisci D, Macchiarulo A. The hope and hype of ellagic acid and urolithins as ligands of SARS-CoV-2 Nsp5 and inhibitors of viral replication. J Enzyme Inhib Med Chem 2023; 38:2251721. [PMID: 37638806 PMCID: PMC10464554 DOI: 10.1080/14756366.2023.2251721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 08/14/2023] [Accepted: 08/19/2023] [Indexed: 08/29/2023] Open
Abstract
Non-structural protein 5 (Nsp5) is a cysteine protease that plays a key role in SARS-CoV-2 replication, suppressing host protein synthesis and promoting immune evasion. The investigation of natural products as a potential strategy for Nsp5 inhibition is gaining attention as a means of developing antiviral agents. In this work, we have investigated the physicochemical properties and structure-activity relationships of ellagic acid and its gut metabolites, urolithins A-D, as ligands of Nsp5. Results allow us to identify urolithin D as promising ligand of Nsp5, with a dissociation constant in the nanomolar range of potency. Although urolithin D is able to bind to the catalytic cleft of Nsp5, the appraisal of its viral replication inhibition against SARS-CoV-2 in Vero E6 assay highlights a lack of activity. While these results are discussed in the framework of the available literature reporting conflicting data on polyphenol antiviral activity, they provide new clues for natural products as potential viral protease inhibitors.
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Affiliation(s)
- Elisa Bianconi
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Anna Gidari
- Department of Medicine and Surgery, Clinic of Infectious Diseases, University of Perugia, Perugia, Italy
| | - Maria Souma
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Samuele Sabbatini
- Medical Microbiology Section, Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Deborah Grifagni
- Centre for Magnetic Resonance, University of Florence, Sesto Fiorentino, Italy
- Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - Carlo Bigiotti
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Elisabetta Schiaroli
- Department of Medicine and Surgery, Clinic of Infectious Diseases, University of Perugia, Perugia, Italy
| | - Lucia Comez
- Istituto Officina dei Materiali-IOM, National Research Council-CNR, Perugia, Italy
| | | | - Francesca Cantini
- Centre for Magnetic Resonance, University of Florence, Sesto Fiorentino, Italy
- Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - Daniela Francisci
- Department of Medicine and Surgery, Clinic of Infectious Diseases, University of Perugia, Perugia, Italy
| | - Antonio Macchiarulo
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
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Li X, Song Y. Structure and function of SARS-CoV and SARS-CoV-2 main proteases and their inhibition: A comprehensive review. Eur J Med Chem 2023; 260:115772. [PMID: 37659195 PMCID: PMC10529944 DOI: 10.1016/j.ejmech.2023.115772] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/24/2023] [Accepted: 08/26/2023] [Indexed: 09/04/2023]
Abstract
Severe acute respiratory syndrome-associated coronavirus (SARS-CoV) identified in 2003 infected ∼8000 people in 26 countries with 800 deaths, which was soon contained and eradicated by syndromic surveillance and enhanced quarantine. A closely related coronavirus SARS-CoV-2, the causative agent of COVID-19 identified in 2019, has been dramatically more contagious and catastrophic. It has infected and caused various flu-like symptoms of billions of people in >200 countries, including >6 million people died of or with the virus. Despite the availability of several vaccines and antiviral drugs against SARS-CoV-2, finding new therapeutics is needed because of viral evolution and a possible emerging coronavirus in the future. The main protease (Mpro) of these coronaviruses plays important roles in their life cycle and is essential for the viral replication. This article represents a comprehensive review of the function, structure and inhibition of SARS-CoV and -CoV-2 Mpro, including structure-activity relationships, protein-inhibitor interactions and clinical trial status.
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Affiliation(s)
- Xin Li
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
| | - Yongcheng Song
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
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Liu M, Wang Q, Xu W, Wu J, Xu X, Yang H, Li X. Natural products for treating cytokine storm-related diseases: Therapeutic effects and mechanisms. Biomed Pharmacother 2023; 167:115555. [PMID: 37776639 DOI: 10.1016/j.biopha.2023.115555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/18/2023] [Accepted: 09/18/2023] [Indexed: 10/02/2023] Open
Abstract
BACKGROUND A cytokine storm (CS) is a rapidly occurring, complex, and highly lethal systemic acute inflammatory response induced by pathogens and other factors. Currently, no clinical therapeutic drugs are available with a significant effect and minimal side effects. Given the pathogenesis of CS, natural products have become important resources for bioactive agents in the discovery of anti-CS drugs. PURPOSE This study aimed to provide guidance for preventing and treating CS-related diseases by reviewing the natural products identified to inhibit CS in recent years. METHODS A comprehensive literature review was conducted on CS and natural products, utilizing databases such as PubMed and Web of Science. The quality of the studies was evaluated and summarized for further analysis. RESULTS This study summarized more than 30 types of natural products, including 9 classes of flavonoids, phenols, and terpenoids, among others. In vivo and in vitro experiments demonstrated that these natural products could effectively inhibit CS via nuclear factor kappa-B, mitogen-activated protein kinase, and Mammalian target of rapamycin (mTOR) signaling pathways. Moreover, the enzyme inhibition assays revealed that more than 20 chemical components had the potential to inhibit ACE2, 3CL-protease, and papain-like protease activity. The experimental results were obtained using advanced technologies such as biochips and omics. CONCLUSIONS Various natural compounds in traditional Chinese medicine (TCM) extracts could directly or indirectly inhibit CS occurrence, potentially serving as effective drugs for treating CS-related diseases. This study may guide further exploration of the therapeutic effects and biochemical mechanisms of natural products on CS.
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Affiliation(s)
- Mei Liu
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Qing Wang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Wanai Xu
- School of Pharmacy, Jiangxi University of Traditional Chinese Medicine, China
| | - Jingyu Wu
- School of Pharmacy, Jiangxi University of Traditional Chinese Medicine, China
| | - Xingyue Xu
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China; China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Hongjun Yang
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China; China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Xianyu Li
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China; China Academy of Chinese Medical Sciences, Beijing 100700, China.
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Nematollahi MH, Mehrabani M, Hozhabri Y, Mirtajaddini M, Iravani S. Antiviral and antimicrobial applications of chalcones and their derivatives: From nature to greener synthesis. Heliyon 2023; 9:e20428. [PMID: 37810815 PMCID: PMC10556610 DOI: 10.1016/j.heliyon.2023.e20428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/10/2023] Open
Abstract
Chalcones and their derivatives have been widely studied due to their versatile pharmacological and biological activities, such as anti-inflammatory, antibacterial, antiviral, and antitumor effects. These compounds have shown suitable antiviral effects through the selective targeting of a variety of viral enzymes, including lactate dehydrogenase, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), fumarate reductase, protein tyrosine phosphatase, topoisomerase-II, protein kinases, integrase/protease, and lactate/isocitrate dehydrogenase, among others. Chalcones and their derivatives have displayed excellent potential for combating pathogenic bacteria and fungi (especially, multidrug-resistant bacteria). However, relevant mechanisms should be further explored, focusing on inhibitory effects against DNA gyrase B, UDP-N-acetylglucosamine enolpyruvyl transferase (MurA), and efflux pumps (e.g., NorA), among others. In addition, the antifungal and antiparasitic activities of these compounds (e.g., antitrypanosomal and antileishmanial properties) have prompted additional explorations. Nonetheless, systematic analysis of the relevant mechanisms, biosafety issues, and pharmacological properties, as well as clinical translation studies, are vital for practical applications. Herein, recent advancements pertaining to the antibacterial, antiviral, antiparasitic, and antifungal activities of chalcones and their derivatives are deliberated, focusing on the relevant mechanisms of action, crucial challenges, and future prospects. Furthermore, due to the great importance of greener and more sustainable synthesis of these valuable compounds, especially on an industrial scale, the progress made in this field has been briefly discussed. Hopefully, this review can serve as a catalyst for researchers to delve deeper into the exploration and designing of novel chalcone compounds with medicinal properties, especially against pathogenic viruses and multidrug-resistant bacteria as major causes of concern for human health.
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Affiliation(s)
- Mohammad Hadi Nematollahi
- Herbal and Traditional Medicines Research Center, School of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | - Mehrnaz Mehrabani
- Physiology Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
| | - Yaser Hozhabri
- Applied Cellular and Molecular Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Maryamossadat Mirtajaddini
- Physiology Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
| | - Siavash Iravani
- Independent Researcher, W Nazar ST, Boostan Ave, Isfahan, Iran
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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. J Agric Food Res 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Pojtanadithee P, Hengphasatporn K, Suroengrit A, Boonyasuppayakorn S, Wilasluck P, Deetanya P, Wangkanont K, Sukanadi IP, Chavasiri W, Wolschann P, Langer T, Shigeta Y, Maitarad P, Sanachai K, Rungrotmongkol T. Identification of Promising Sulfonamide Chalcones as Inhibitors of SARS-CoV-2 3CL pro through Structure-Based Virtual Screening and Experimental Approaches. J Chem Inf Model 2023; 63:5244-5258. [PMID: 37581276 DOI: 10.1021/acs.jcim.3c00663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
3CLpro is a viable target for developing antiviral therapies against the coronavirus. With the urgent need to find new possible inhibitors, a structure-based virtual screening approach was developed. This study recognized 75 pharmacologically bioactive compounds from our in-house library of 1052 natural product-based compounds that satisfied drug-likeness criteria and exhibited good bioavailability and membrane permeability. Among these compounds, three promising sulfonamide chalcones were identified by combined theoretical and experimental approaches, with SWC423 being the most suitable representative compound due to its competitive inhibition and low cytotoxicity in Vero E6 cells (EC50 = 0.89 ± 0.32 μM; CC50 = 25.54 ± 1.38 μM; SI = 28.70). The binding and stability of SWC423 in the 3CLpro active site were investigated through all-atom molecular dynamics simulation and fragment molecular orbital calculation, indicating its potential as a 3CLpro inhibitor for further SARS-CoV-2 therapeutic research. These findings suggested that inhibiting 3CLpro with a sulfonamide chalcone such as SWC423 may pave the effective way for developing COVID-19 treatments.
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Affiliation(s)
- Piyatida Pojtanadithee
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
| | - Kowit Hengphasatporn
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Aphinya Suroengrit
- Center of Excellence in Applied Medical Virology, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Siwaporn Boonyasuppayakorn
- Center of Excellence in Applied Medical Virology, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Patcharin Wilasluck
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Center of Excellence for Molecular Crop, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Peerapon Deetanya
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Center of Excellence for Molecular Crop, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Kittikhun Wangkanont
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Center of Excellence for Molecular Crop, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - I Putu Sukanadi
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Warinthorn Chavasiri
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Peter Wolschann
- Department of Pharmaceutical Chemistry, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
- Institute of Theoretical Chemistry, University of Vienna, Vienna 1090, Austria
| | - Thierry Langer
- Department of Pharmaceutical Chemistry, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Phornphimon Maitarad
- Research Center of Nano Science and Technology, Department of Chemistry, College of Science, Shanghai University, Shanghai 200444, P. R. China
| | - Kamonpan Sanachai
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Thanyada Rungrotmongkol
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
- Center of Excellence in Structural and Computational Biology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
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12
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Soleimani Asl S, Roozbahani MH. A novel robust inhibitor of papain-like protease (PLpro) as a COVID-19 drug. J Biomol Struct Dyn 2023:1-8. [PMID: 37578047 DOI: 10.1080/07391102.2023.2245474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 07/08/2023] [Indexed: 08/15/2023]
Abstract
Regarding the significance of SARS-CoV-2, scientists have shown considerable interest in developing effective drugs. Inhibitors for PLpro are the primary strategies for locating suitable COVID-19 drugs. Natural compounds comprise the majority of COVID-19 drugs. Due to limitations on the safety of clinical trials in cases of COVID, computational methods are typically utilized for inhibition studies. Whereas papain is highly similar to PLpro and is entirely safe, the current study aimed to examine several plant secondary metabolites to identify the most effective papain inhibitor and validate the results using molecular dynamics and docking. This simulation was conducted identically for PLpro and the optimal inhibitor. The results indicated that the experimental results are comparable to those obtained In-Silico, and the inhibition effects of Chlorogenic acid (CGA) on papain attained in the experiment were validated (IC50=0.54 mM). CGA as an inhibitor was located in the active site of PLpro and papain (total energy -2009410 and -456069 kJ/mol, respectively) at the desired location and distance. The study revealed that CGA and its derivatives are effective PLpro inhibitors against SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Saeed Soleimani Asl
- Iran Digital Twin Laboratory (IDT-Lab)- Incubator Center, Iran University of Science and Technology, Tehran, Iran
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13
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Ruatta SM, Prada Gori DN, Fló Díaz M, Lorenzelli F, Perelmuter K, Alberca LN, Bellera CL, Medeiros A, López GV, Ingold M, Porcal W, Dibello E, Ihnatenko I, Kunick C, Incerti M, Luzardo M, Colobbio M, Ramos JC, Manta E, Minini L, Lavaggi ML, Hernández P, Šarlauskas J, Huerta García CS, Castillo R, Hernández-Campos A, Ribaudo G, Zagotto G, Carlucci R, Medrán NS, Labadie GR, Martinez-Amezaga M, Delpiccolo CML, Mata EG, Scarone L, Posada L, Serra G, Calogeropoulou T, Prousis K, Detsi A, Cabrera M, Alvarez G, Aicardo A, Araújo V, Chavarría C, Mašič LP, Gantner ME, Llanos MA, Rodríguez S, Gavernet L, Park S, Heo J, Lee H, Paul Park KH, Bollati-Fogolín M, Pritsch O, Shum D, Talevi A, Comini MA. Garbage in, garbage out: how reliable training data improved a virtual screening approach against SARS-CoV-2 MPro. Front Pharmacol 2023; 14:1193282. [PMID: 37426813 PMCID: PMC10323144 DOI: 10.3389/fphar.2023.1193282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 05/31/2023] [Indexed: 07/11/2023] Open
Abstract
Introduction: The identification of chemical compounds that interfere with SARS-CoV-2 replication continues to be a priority in several academic and pharmaceutical laboratories. Computational tools and approaches have the power to integrate, process and analyze multiple data in a short time. However, these initiatives may yield unrealistic results if the applied models are not inferred from reliable data and the resulting predictions are not confirmed by experimental evidence. Methods: We undertook a drug discovery campaign against the essential major protease (MPro) from SARS-CoV-2, which relied on an in silico search strategy -performed in a large and diverse chemolibrary- complemented by experimental validation. The computational method comprises a recently reported ligand-based approach developed upon refinement/learning cycles, and structure-based approximations. Search models were applied to both retrospective (in silico) and prospective (experimentally confirmed) screening. Results: The first generation of ligand-based models were fed by data, which to a great extent, had not been published in peer-reviewed articles. The first screening campaign performed with 188 compounds (46 in silico hits and 100 analogues, and 40 unrelated compounds: flavonols and pyrazoles) yielded three hits against MPro (IC50 ≤ 25 μM): two analogues of in silico hits (one glycoside and one benzo-thiazol) and one flavonol. A second generation of ligand-based models was developed based on this negative information and newly published peer-reviewed data for MPro inhibitors. This led to 43 new hit candidates belonging to different chemical families. From 45 compounds (28 in silico hits and 17 related analogues) tested in the second screening campaign, eight inhibited MPro with IC50 = 0.12-20 μM and five of them also impaired the proliferation of SARS-CoV-2 in Vero cells (EC50 7-45 μM). Discussion: Our study provides an example of a virtuous loop between computational and experimental approaches applied to target-focused drug discovery against a major and global pathogen, reaffirming the well-known "garbage in, garbage out" machine learning principle.
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Affiliation(s)
- Santiago M. Ruatta
- Laboratory Redox Biology of Trypanosomes, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Denis N. Prada Gori
- Laboratory of Bioactive Compound Research and Development (LIDeB), Faculty of Exact Sciences, National University of La Plata, Buenos Aires, Argentina
| | - Martín Fló Díaz
- Laboratory of Immunovirology, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Departamento de Inmunobiología, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Franca Lorenzelli
- Laboratory Redox Biology of Trypanosomes, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Karen Perelmuter
- Cell Biology Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Lucas N. Alberca
- Laboratory of Bioactive Compound Research and Development (LIDeB), Faculty of Exact Sciences, National University of La Plata, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Carolina L. Bellera
- Laboratory of Bioactive Compound Research and Development (LIDeB), Faculty of Exact Sciences, National University of La Plata, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Andrea Medeiros
- Laboratory Redox Biology of Trypanosomes, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Gloria V. López
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
- Vascular Biology and Drug Discovery Lab, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Mariana Ingold
- Vascular Biology and Drug Discovery Lab, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Williams Porcal
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
- Vascular Biology and Drug Discovery Lab, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Estefanía Dibello
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Irina Ihnatenko
- PVZ—Center of Pharmaceutical Engineering, Institute of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Conrad Kunick
- PVZ—Center of Pharmaceutical Engineering, Institute of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Marcelo Incerti
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Martín Luzardo
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Maximiliano Colobbio
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
- Laboratorio de Química Fina, Facultad de Química, Instituto Polo Tecnológico de Pando, Universidad de la República, Montevideo, Uruguay
| | - Juan Carlos Ramos
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
- Laboratorio de Química Fina, Facultad de Química, Instituto Polo Tecnológico de Pando, Universidad de la República, Montevideo, Uruguay
| | - Eduardo Manta
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
- Laboratorio de Química Fina, Facultad de Química, Instituto Polo Tecnológico de Pando, Universidad de la República, Montevideo, Uruguay
| | - Lucía Minini
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - María Laura Lavaggi
- Laboratorio de Química Biológica Ambiental, Sede Rivera, Centro Universitario Regional Noreste, Universidad de la República, Montevideo, Uruguay
| | - Paola Hernández
- Departamento de Genética, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Jonas Šarlauskas
- Life Sciences Centre, Department of Xenobiotic Biochemistry, Institute of Biochemistry, Vilnius University, Vilnius, Lithuania
| | | | - Rafael Castillo
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de Mexico, Mexico
| | - Alicia Hernández-Campos
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de Mexico, Mexico
| | - Giovanni Ribaudo
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Giuseppe Zagotto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Renzo Carlucci
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Química Rosario (IQUIR) UNR, CONICET, Universidad Nacional de Rosario, Rosario, Argentina
| | - Noelia S. Medrán
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Química Rosario (IQUIR) UNR, CONICET, Universidad Nacional de Rosario, Rosario, Argentina
| | - Guillermo R. Labadie
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Química Rosario (IQUIR) UNR, CONICET, Universidad Nacional de Rosario, Rosario, Argentina
| | - Maitena Martinez-Amezaga
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Química Rosario (IQUIR) UNR, CONICET, Universidad Nacional de Rosario, Rosario, Argentina
| | - Carina M. L. Delpiccolo
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Química Rosario (IQUIR) UNR, CONICET, Universidad Nacional de Rosario, Rosario, Argentina
| | - Ernesto G. Mata
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Química Rosario (IQUIR) UNR, CONICET, Universidad Nacional de Rosario, Rosario, Argentina
| | - Laura Scarone
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Laura Posada
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Gloria Serra
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | | | - Kyriakos Prousis
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Anastasia Detsi
- Laboratory of Organic Chemistry, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Mauricio Cabrera
- Laboratorio de Moléculas Bioactivas, Departamento de Ciencias Biológicas, CENUR Litoral Norte, Universidad de la República, Paysandú, Uruguay
| | - Guzmán Alvarez
- Laboratorio de Moléculas Bioactivas, Departamento de Ciencias Biológicas, CENUR Litoral Norte, Universidad de la República, Paysandú, Uruguay
| | - Adrián Aicardo
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
- Departamento de Nutrición Clínica, Escuela de Nutrición, Universidad de la República, Montevideo, Uruguay
| | - Verena Araújo
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
- Departamento de Alimentos, Escuela de Nutrición, Universidad de la República, Montevideo, Uruguay
| | - Cecilia Chavarría
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
| | | | - Melisa E. Gantner
- Laboratory of Bioactive Compound Research and Development (LIDeB), Faculty of Exact Sciences, National University of La Plata, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Manuel A. Llanos
- Laboratory of Bioactive Compound Research and Development (LIDeB), Faculty of Exact Sciences, National University of La Plata, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Santiago Rodríguez
- Laboratory of Bioactive Compound Research and Development (LIDeB), Faculty of Exact Sciences, National University of La Plata, Buenos Aires, Argentina
| | - Luciana Gavernet
- Laboratory of Bioactive Compound Research and Development (LIDeB), Faculty of Exact Sciences, National University of La Plata, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Soonju Park
- Screening Discovery Platform, Institut Pasteur Korea, Seongnam, Republic of Korea
| | - Jinyeong Heo
- Screening Discovery Platform, Institut Pasteur Korea, Seongnam, Republic of Korea
| | - Honggun Lee
- Screening Discovery Platform, Institut Pasteur Korea, Seongnam, Republic of Korea
| | - Kyu-Ho Paul Park
- Screening Discovery Platform, Institut Pasteur Korea, Seongnam, Republic of Korea
| | | | - Otto Pritsch
- Laboratory of Immunovirology, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Departamento de Inmunobiología, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - David Shum
- Screening Discovery Platform, Institut Pasteur Korea, Seongnam, Republic of Korea
| | - Alan Talevi
- Laboratory of Bioactive Compound Research and Development (LIDeB), Faculty of Exact Sciences, National University of La Plata, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Marcelo A. Comini
- Laboratory Redox Biology of Trypanosomes, Institut Pasteur de Montevideo, Montevideo, Uruguay
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14
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Valipour M, Di Giacomo S, Di Sotto A, Irannejad H. Discovery of Chalcone-Based Hybrid Structures as High Affinity and Site-Specific Inhibitors against SARS-CoV-2: A Comprehensive Structural Analysis Based on Various Host-Based and Viral Targets. Int J Mol Sci 2023; 24:ijms24108789. [PMID: 37240149 DOI: 10.3390/ijms24108789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 05/01/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
Previous studies indicated that natural-based chalcones have significant inhibitory effects on the coronavirus enzymes 3CLpro and PLpro as well as modulation of some host-based antiviral targets (HBATs). In this study, a comprehensive computational and structural study was performed to investigate the affinity of our compound library consisting of 757 chalcone-based structures (CHA-1 to CHA-757) for inhibiting the 3CLpro and PLpro enzymes and against twelve selected host-based targets. Our results indicated that CHA-12 (VUF 4819) is the most potent and multi-target inhibitor in our chemical library over all viral and host-based targets. Correspondingly, CHA-384 and its congeners containing ureide moieties were found to be potent and selective 3CLpro inhibitors, and benzotriazole moiety in CHA-37 was found to be a main fragment for inhibiting the 3CLpro and PLpro. Surprisingly, our results indicate that the ureide and sulfonamide moieties are integral fragments for the optimum 3CLpro inhibition while occupying the S1 and S3 subsites, which is fully consistent with recent reports on the site-specific 3CLpro inhibitors. Finding the multi-target inhibitor CHA-12, previously reported as an LTD4 antagonist for the treatment of inflammatory pulmonary diseases, prompted us to suggest it as a concomitant agent for relieving respiratory symptoms and suppressing COVID-19 infection.
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Affiliation(s)
- Mehdi Valipour
- Razi Drug Research Center, Iran University of Medical Sciences, Tehran 1545913487, Iran
| | - Silvia Di Giacomo
- Department of Physiology and Pharmacology "V. Erspamer", Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Antonella Di Sotto
- Department of Physiology and Pharmacology "V. Erspamer", Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Hamid Irannejad
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari 4847116547, Iran
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15
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Xiao Q, Zhong B, Hou Y, Wang M, Guo B, Lin L, Zhou Y, Chen X. Fighting cancer by triggering non-canonical mitochondrial permeability transition-driven necrosis through reactive oxygen species induction. Free Radic Biol Med 2023; 202:35-45. [PMID: 36963639 DOI: 10.1016/j.freeradbiomed.2023.03.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 03/03/2023] [Accepted: 03/20/2023] [Indexed: 03/26/2023]
Abstract
Non-apoptotic necrosis shows therapeutic potential for the treatment of various diseases, especially cancer. Mitochondrial permeability transition (MPT)-driven necrosis is a form of non-apoptotic cell death triggered by oxidative stress and cytosolic Ca2+ overload, and relies on cyclophilin D (CypD). Previous reports demonstrated that isobavachalcone (IBC), a natural chalcone, has anticancer effect by apoptosis induction. Here, we found that IBC induced regulated necrosis in cancer cells. IBC triggered non-apoptotic cell death in lung and breast cancer cells mediated by reactive oxygen species (ROS). IBC caused mitochondrial injury and dysfunction as evidenced by mitochondrial Ca2+ overload, the opening of MPT pore, mitochondrial membrane potential collapse, and structural damages. IBC-triggered cell death could be remarkably reversed by the ROS scavengers, cyclosporin A (CsA) and hemin, whereas CypD silence and heme oxygenase-1 overexpression failed to do so. Protein kinase B, dihydroorotate dehydrogenase, and mitogen-activated protein kinases were not involved in IBC-induced necrosis as well. In addition, IBC showed an anticancer effect in a 4T1 breast cancer cell-derived allograft mouse model, and this effect was considerably reversed by CsA. Collectively, our results showed that IBC triggered non-canonical MPT-driven necrosis mediated by ROS in cancer cells, which might provide a novel strategy for fighting against cancer.
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Affiliation(s)
- Qingwen Xiao
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao
| | - Bingling Zhong
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao
| | - Ying Hou
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao
| | - Miaojuan Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao
| | - Baojian Guo
- Institute of New Drug Research, Jinan University College of Pharmacy, Guangzhou, 510632, China
| | - Ligen Lin
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao; Department of Pharmaceutical Sciences, Faculty of Health Sciences, University of Macau, Macao
| | - Yinning Zhou
- Institute of Applied Physics and Materials Engineering, University of Macau, Macao
| | - Xiuping Chen
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao; Department of Pharmaceutical Sciences, Faculty of Health Sciences, University of Macau, Macao; MoE Frontiers Science Center for Precision Oncology, University of Macau, Macao.
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16
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Ershov PV, Yablokov EO, Mezentsev YV, Chuev GN, Fedotova MV, Kruchinin SE, Ivanov AS. SARS-COV-2 Coronavirus Papain-like Protease PLpro as an Antiviral Target for Inhibitors of Active Site and Protein-Protein Interactions. Biophysics (Nagoya-shi) 2023; 67:902-912. [PMID: 36883182 PMCID: PMC9984130 DOI: 10.1134/s0006350922060082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 08/09/2022] [Accepted: 08/12/2022] [Indexed: 03/06/2023] Open
Abstract
The papain-like protease PLpro of the SARS-CoV-2 coronavirus is a multifunctional enzyme that catalyzes the proteolytic processing of two viral polyproteins, pp1a and pp1ab. PLpro also cleaves peptide bonds between host cell proteins and ubiquitin (or ubiquitin-like proteins), which is associated with a violation of immune processes. Nine structures of the most effective inhibitors of the PLpro active center were prioritized according to the parameters of biochemical (IC 50) and cellular tests to assess the suppression of viral replication (EC 50) and cytotoxicity (CC 50). A literature search has shown that PLpro can interact with at least 60 potential protein partners in cells, 23 of which are targets for other viral proteins (human papillomavirus and Epstein-Barr virus). The analysis of protein-protein interactions showed that the proteins USP3, UBE2J1, RCHY1, and FAF2 involved in deubiquitinylation and ubiquitinylation processes contain the largest number of bonds with other proteins; the interaction of viral proteins with them can affect the architecture of the entire network of protein-protein interactions. Using the example of a spatial model of the PLpro/ubiquitin complex and a set of 154 naturally occurring compounds with known antiviral activity, 13 compounds (molecular masses in the range of 454-954 Da) were predicted as potential PLpro inhibitors. These compounds bind to the "hot" amino acid residues of the protease at the positions Gly163, Asp164, Arg166, Glu167, and Tyr264 involved in the interaction with ubiquitin. Thus, pharmacological effects on peripheral PLpro sites, which play important roles in binding protein substrates, may be an additional target-oriented antiviral strategy.
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Affiliation(s)
- P. V. Ershov
- Institute of Biomedical Chemistry, 119121 Moscow, Russia
| | - E. O. Yablokov
- Institute of Biomedical Chemistry, 119121 Moscow, Russia
| | | | - G. N. Chuev
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Moscow oblast Russia
| | - M. V. Fedotova
- Krestov Institute of Solution Chemistry, Russian Academy of Sciences, 153045 Ivanovo, Russia
| | - S. E. Kruchinin
- Krestov Institute of Solution Chemistry, Russian Academy of Sciences, 153045 Ivanovo, Russia
| | - A. S. Ivanov
- Institute of Biomedical Chemistry, 119121 Moscow, Russia
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17
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Guterres Fernandes OL, Tizziani T, Dambrós BP, Ferreira de Sousa N, Mansur Pontes CL, da Silva LAL, Escorteganha Pollo LA, de Assis FF, Scotti MT, Scotti L, Braga AL, Steindel M, Sandjo LP. Studies of Cytotoxicity Effects, SARS-CoV-2 Main Protease Inhibition, and in Silico Interactions of Synthetic Chalcones. Chem Biodivers 2023; 20:e202201151. [PMID: 36740573 DOI: 10.1002/cbdv.202201151] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 02/07/2023]
Abstract
SARS-CoV-2 main protease (Mpro ) plays an essential role in proteolysis cleavage that promotes coronavirus replication. Thus, attenuating the activity of this enzyme represents a strategy to develop antiviral agents. We report inhibitory effects against Mpro of 40 synthetic chalcones, and cytotoxicity activities, hemolysis, and in silico interactions of active compounds. Seven of them bearing a (E)-3-(furan-2-yl)-1-arylprop-2-en-1-one skeleton (10, 28, and 35-39) showed enzyme inhibition with IC50 ranging from 13.76 and 36.13 μM. Except for 35 and 36, other active compounds were not cytotoxic up to 150 μM against THP-1 and Vero cell lines. Compounds 10, and 35-39 showed no hemolysis while 28 was weakly hemotoxic at 150 μM. Moreover, molecular docking showed interactions between compound 10 and Mpro (PDBID 5RG2 and 5RG3) with proximity to cys145 and His41, suggesting a covalent binding. Products of the reaction between chalcones and cyclohexanethiol indicated that this binding could be a Michael addition type.
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Affiliation(s)
- Octavio L Guterres Fernandes
- Postgraduate Program in Chemistry, Department of Chemistry, Universidade Federal de Santa Catarina, Campus Universitário da Trindade, 88040-900, Florianópolis, SC, Brazil
| | - Tiago Tizziani
- Postgraduate Program in Chemistry, Department of Chemistry, Universidade Federal de Santa Catarina, Campus Universitário da Trindade, 88040-900, Florianópolis, SC, Brazil
| | - Bibiana P Dambrós
- Department of Microbiology, Immunology and Parasitology, Universidade Federal de Santa Catarina, 88040-900, Florianópolis, Santa Catarina, Brazil
| | - Natália Ferreira de Sousa
- Postgraduate Program in Natural and Bioactive Synthetic Products, Department of Pharmaceutical Sciences, Universidade Federal de Paraíba, 50670-910, João Pessoa, Paraíba, Brazil
| | - Carime L Mansur Pontes
- Postgraduate Program in Chemistry, Department of Chemistry, Universidade Federal de Santa Catarina, Campus Universitário da Trindade, 88040-900, Florianópolis, SC, Brazil
| | - Layzon A L da Silva
- Postgraduate Program in Pharmacy, Department of Pharmaceutical Sciences, Universidade Federal de Santa Catarina, Campus Universitário-Trindade, 88040-900, Florianópolis, SC, Brazil
| | - Luiz A Escorteganha Pollo
- Postgraduate Program in Pharmacy, Department of Pharmaceutical Sciences, Universidade Federal de Santa Catarina, Campus Universitário-Trindade, 88040-900, Florianópolis, SC, Brazil
| | - Francisco F de Assis
- Postgraduate Program in Chemistry, Department of Chemistry, Universidade Federal de Santa Catarina, Campus Universitário da Trindade, 88040-900, Florianópolis, SC, Brazil
| | - Marcus T Scotti
- Postgraduate Program in Natural and Bioactive Synthetic Products, Department of Pharmaceutical Sciences, Universidade Federal de Paraíba, 50670-910, João Pessoa, Paraíba, Brazil
| | - Luciana Scotti
- Postgraduate Program in Natural and Bioactive Synthetic Products, Department of Pharmaceutical Sciences, Universidade Federal de Paraíba, 50670-910, João Pessoa, Paraíba, Brazil
| | - Antonio L Braga
- Postgraduate Program in Chemistry, Department of Chemistry, Universidade Federal de Santa Catarina, Campus Universitário da Trindade, 88040-900, Florianópolis, SC, Brazil
| | - Mario Steindel
- Department of Microbiology, Immunology and Parasitology, Universidade Federal de Santa Catarina, 88040-900, Florianópolis, Santa Catarina, Brazil
| | - Louis P Sandjo
- Postgraduate Program in Chemistry, Department of Chemistry, Universidade Federal de Santa Catarina, Campus Universitário da Trindade, 88040-900, Florianópolis, SC, Brazil
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18
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El Aissouq A, Bouachrine M, Bouayyadi L, Ouammou A, Khalil F. Structure-based virtual screening of novel natural products as chalcone derivatives against SARS-CoV-2 M pro. J Biomol Struct Dyn 2023; 41:13235-13249. [PMID: 36752320 DOI: 10.1080/07391102.2023.2172456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 01/19/2023] [Indexed: 02/09/2023]
Abstract
Coronavirus disease 2019 (COVID-19), which is caused by SARS-CoV-2, has spread quickly around the world, causing a global pandemic. It has infected more than 500 million people as of April 28, 2022. Much research has been reported to stop the virus from spreading, but there are currently no approved medicines to treat COVID-19. In this work, a dataset of 142 natural products collected from various medicinal plants was used to perform structure-based virtual screening (SBVS) through the combined application of molecular docking and molecular dynamics (MD) simulation methods. First, the dataset of compounds was optimized using the density functional theory (DFT) approach. The optimized compounds were then submitted to the first screening, which was done by the pKCM web server to look for drug-likeness and the PyRx to look for binding affinity. Among the 142 natural substances, 10 compounds were selected for docking validation. Compounds that interact with CYS145 and LEU141, the essential catalytic residues, as well as compounds with binding affinities less than -8.0 kcal/mol, are considered promising anti-SARS-CoV-2 drug candidates. The top-ranked compounds were then evaluated by MD simulations and MM-GBSA method. These results could help researchers come up with new natural compounds that could be used to treat SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abdellah El Aissouq
- Laboratory of Processes, Materials, and Environment (LPME), Faculty of Science and Technology, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Mohammed Bouachrine
- MCNS Laboratory, Faculty of Sciences, Moulay Ismail University, Meknes, Morocco
| | | | - Abdelkrim Ouammou
- LIMOME Laboratory, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Fouad Khalil
- Laboratory of Processes, Materials, and Environment (LPME), Faculty of Science and Technology, Sidi Mohamed Ben Abdellah University, Fez, Morocco
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19
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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20
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Peng W, Xu Y, Han D, Feng F, Wang Z, Gu C, Zhou X, Wu Q. Potential mechanism underlying the effect of matrine on COVID-19 patients revealed through network pharmacological approaches and molecular docking analysis. Arch Physiol Biochem 2023; 129:253-260. [PMID: 32915649 PMCID: PMC7544918 DOI: 10.1080/13813455.2020.1817944] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND The clinical efficacy of matrine in treating coronavirus disease (COVID-19) has been confirmed; however, its underlying mechanism of action remains unknown. METHODS TCMSP, SwissTargetPrediction, SEA, GeneCards, CTD, and TTD were used to identify potential targets for matrine in SARS-CoV-2. Cytoscape software was used to determine the target-pathway network for topographical analysis. The online STRING analysis platform and Cytoscape were together used to generate a PPI network and for GO and KEGG pathway enrichment analysis. Finally, molecular docking simulations were performed to study matrine-Mpro, matrine-ACE2, and matrine-RdRp interactions. RESULTS Ten common matrine targets were obtained, particularly including TNF-α, IL-6, and CASP3. GO and KEGG pathway enrichment analysis revealed five significantly enriched signalling pathways involved in cell proliferation, apoptosis, programmed cell death, and immune responses. CONCLUSIONS During COVID-19 treatment, matrine regulates viral replication, host cell apoptosis, and inflammation by targeting the TNF-α, IL-6, and CASP3 in the TNF signalling pathway.
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Affiliation(s)
- Wenpan Peng
- Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Yong Xu
- Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Di Han
- Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Fanchao Feng
- Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
- Department of Respiratory Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Zhichao Wang
- Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Cheng Gu
- Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Xianmei Zhou
- Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
- Department of Respiratory Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
- CONTACT Xianmei Zhou Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, China; Department of Respiratory Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, 210029, China
| | - Qi Wu
- Department of Physiology, Xuzhou Medical University, Xuzhou, China
- Qi Wu Department of Physiology, Xuzhou Medical University, Xuzhou, 221009, China
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21
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Heleno SA, Carocho M, Reis FS, Pires TCSP, Pintado M, Ferreira ICFR, Barros L. Plant Extracts and SARS-CoV-2: Research and Applications. Life (Basel) 2023; 13. [PMID: 36836744 DOI: 10.3390/life13020386] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/29/2022] [Accepted: 01/28/2023] [Indexed: 02/01/2023] Open
Abstract
The recent pandemic of COVID-19 caused by the SARS-CoV-2 virus has brought upon the world an unprecedented challenge. During its acute dissemination, a rush for vaccines started, making the scientific community come together and contribute to the development of efficient therapeutic agents and vaccines. Natural products have been used as sources of individual molecules and extracts capable of inhibiting/neutralizing several microorganisms, including viruses. Natural extracts have shown effective results against the coronavirus family, when first tested in the outbreak of SARS-CoV-1, back in 2002. In this review, the relationship between natural extracts and SARS-CoV is discussed, while also providing insight into misinformation regarding the use of plants as possible therapeutic agents. Studies with plant extracts on coronaviruses are presented, as well as the main inhibition assays and trends for the future regarding the yet unknown long-lasting effects post-infection with SARS-CoV-2.
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22
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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23
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Naidu SAG, Tripathi YB, Shree P, Clemens RA, Naidu AS. Phytonutrient Inhibitors of SARS-CoV-2/NSP5-Encoded Main Protease (M pro) Autocleavage Enzyme Critical for COVID-19 Pathogenesis. J Diet Suppl 2023; 20:284-311. [PMID: 34821532 DOI: 10.1080/19390211.2021.2006388] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The genomic reshuffling, mutagenicity, and high transmission rate of the SARS-CoV-2 pathogen highlights an urgent need for effective antiviral interventions for COVID-19 control. Targeting the highly conserved viral genes and/or gene-encoded viral proteins such as main proteinase (Mpro), RNA-dependent RNA polymerase (RdRp) and helicases are plausible antiviral approaches to prevent replication and propagation of the SARS-CoV-2 infection. Coronaviruses (CoVs) are prone to extensive mutagenesis; however, any genetic alteration to its highly conserved Mpro enzyme is often detrimental to the viral pathogen. Therefore, inhibitors that target the Mpro enzyme could reduce the risk of mutation-mediated drug resistance and provide effective antiviral protection. Several existing antiviral drugs and dietary bioactives are currently repurposed to treat COVID-19. Dietary bioactives from three ayurvedic medicinal herbs, 18 β-glycyrrhetinic acid (ΔG = 8.86 kcal/mol), Solanocapsine (ΔG = 8.59 kcal/mol), and Vasicoline (ΔG = 7.34 kcal/mol), showed high-affinity binding to Mpro enzyme than the native N3 inhibitor (ΔG = 5.41 kcal/mol). Flavonoids strongly inhibited SARS-CoV-2 Mpro with comparable or higher potency than the antiviral drug, remdesivir. Several tannin hydrolysates avidly bound to the receptor-binding domain and catalytic dyad (His41 and Cys145) of SARS-CoV-2 Mpro through H-bonding forces. Quercetin binding to Mpro altered the thermostability of the viral protein through redox-based mechanism and inhibited the viral enzymatic activity. Interaction of quercetin-derivatives with the Mpro seem to be influenced by the 7-OH group and the acetoxylation of sugar moiety on the ligand molecule. Based on pharmacokinetic and ADMET profiles, several phytonutrients could serve as a promising redox nutraceutical for COVID-19 management.
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Affiliation(s)
- Sreus A G Naidu
- N-terminus Research Laboratory, Yorba Linda, California, USA
| | - Yamini B Tripathi
- Department of Medicinal Chemistry, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Priya Shree
- Department of Medicinal Chemistry, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Roger A Clemens
- Department of International Regulatory Science, University of Southern California School of Pharmacy, Los Angeles, California, USA
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24
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Boonthaworn K, Hengphasatporn K, Shigeta Y, Chavasiri W, Rungrotmongkol T, Ounjai P. In silico screening of chalcones and flavonoids as potential inhibitors against yellow head virus 3C-like protease. PeerJ 2023; 11:e15086. [PMID: 37123012 PMCID: PMC10135407 DOI: 10.7717/peerj.15086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 02/26/2023] [Indexed: 05/02/2023] Open
Abstract
Yellow head virus (YHV) is one of the most important pathogens in prawn cultivation. The outbreak of YHV could potentially result in collapses in aquaculture industries. Although a flurry of development has been made in searching for preventive and therapeutic approaches against YHV, there is still no effective therapy available in the market. Previously, computational screening has suggested a few cancer drugs to be used as YHV protease (3CLpro) inhibitors. However, their toxic nature is still of concern. Here, we exploited various computational approaches, such as deep learning-based structural modeling, molecular docking, pharmacological prediction, and molecular dynamics simulation, to search for potential YHV 3CLpro inhibitors. A total of 272 chalcones and flavonoids were in silico screened using molecular docking. The bioavailability, toxicity, and specifically drug-likeness of hits were predicted. Among the hits, molecular dynamics simulation and trajectory analysis were performed to scrutinize the compounds with high binding affinity. Herein, the four selected compounds including chalcones cpd26, cpd31 and cpd50, and a flavonoid DN071_f could be novel potent compounds to prevent YHV and GAV propagation in shrimp. The molecular mechanism at the atomistic level is also enclosed that can be used to further antiviral development.
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Affiliation(s)
- Kanpong Boonthaworn
- Department of Biology, Faculty of Science, Mahidol University, Ratchathewi, Bangkok, Thailand
- Center of Excellence on Environmental Health and Toxicology, Ministry of Education, Ratchathewi, Bangkok, Thailand
| | - Kowit Hengphasatporn
- Center of Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yasuteru Shigeta
- Center of Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Warinthorn Chavasiri
- Department of Chemistry, Faculty of Science, Center of Excellence in Natural Products Chemistry, Chulalongkorn University, Pathum Wan, Bangkok, Thailand
| | - Thanyada Rungrotmongkol
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathum Wan, Bangkok, Thailand
| | - Puey Ounjai
- Department of Biology, Faculty of Science, Mahidol University, Ratchathewi, Bangkok, Thailand
- Center of Excellence on Environmental Health and Toxicology, Ministry of Education, Ratchathewi, Bangkok, Thailand
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25
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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26
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Wang L, Yu Z, Wang S, Guo Z, Sun Q, Lai L. Discovery of novel SARS-CoV-2 3CL protease covalent inhibitors using deep learning-based screen. Eur J Med Chem 2022; 244:114803. [PMID: 36209629 PMCID: PMC9528019 DOI: 10.1016/j.ejmech.2022.114803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/20/2022] [Accepted: 09/26/2022] [Indexed: 11/28/2022]
Abstract
SARS-CoV-2 3CL protease is one of the key targets for drug development against COVID-19. Most known SARS-CoV-2 3CL protease inhibitors act by covalently binding to the active site cysteine. Yet, computational screens against this enzyme were mainly focused on non-covalent inhibitor discovery. Here, we developed a deep learning-based stepwise strategy for selective covalent inhibitor screen. We used a deep learning framework that integrated a directed message passing neural network with a feed-forward neural network to construct two different classifiers for either covalent or non-covalent inhibition activity prediction. These two classifiers were trained on the covalent and non-covalent 3CL protease inhibitors dataset, respectively, which achieved high prediction accuracy. We then successively applied the covalent inhibitor model and the non-covalent inhibitor model to screen a chemical library containing compounds with covalent warheads of cysteine. We experimentally tested the inhibition activity of 32 top-ranking compounds and 12 of them were active, among which 6 showed IC50 values less than 12 μM and the strongest one inhibited SARS-CoV-2 3CL protease with an IC50 of 1.4 μM. Further investigation demonstrated that 5 of the 6 active compounds showed typical covalent inhibition behavior with time-dependent activity. These new covalent inhibitors provide novel scaffolds for developing highly active SARS-CoV-2 3CL covalent inhibitors.
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Affiliation(s)
- Liying Wang
- BNLMS, Peking-Tsinghua Center for Life Sciences at the College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, PR China
| | - Zhongtian Yu
- BNLMS, Peking-Tsinghua Center for Life Sciences at the College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, PR China
| | - Shiwei Wang
- BNLMS, Peking-Tsinghua Center for Life Sciences at the College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, PR China
| | - Zheng Guo
- BNLMS, Peking-Tsinghua Center for Life Sciences at the College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, PR China
| | - Qi Sun
- BNLMS, Peking-Tsinghua Center for Life Sciences at the College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, PR China,Research Unit of Drug Design Method, Chinese Academy of Medical Sciences (2021RU014), Beijing, 100871, PR China,Corresponding author. BNLMS, Peking-Tsinghua Center for Life Sciences at the College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, PR China
| | - Luhua Lai
- BNLMS, Peking-Tsinghua Center for Life Sciences at the College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, PR China,Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, PR China,Research Unit of Drug Design Method, Chinese Academy of Medical Sciences (2021RU014), Beijing, 100871, PR China,Corresponding author. BNLMS, Peking-Tsinghua Center for Life Sciences at the College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, PR China
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27
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Valipour M. Recruitment of chalcone's potential in drug discovery of anti-SARS-CoV-2 agents. Phytother Res 2022; 36:4477-4490. [PMID: 36208000 PMCID: PMC9874432 DOI: 10.1002/ptr.7651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/09/2022] [Accepted: 09/22/2022] [Indexed: 01/27/2023]
Abstract
Chalcone is an interesting scaffold found in the structure of many naturally occurring molecules. Medicinal chemists are commonly interested in designing new chalcone-based structures because of having the α, β-unsaturated ketone functional group, which allows these compounds to participate in Michael's reaction and create strong covalent bonds at the active sites of the targets. Some studies have identified several natural chalcone-based compounds with the ability to inhibit the severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome coronavirus proteases. A few years after the advent of the coronavirus disease 2019 pandemic and the publication of many findings in this regard, there is some evidence that suggests chalcone scaffolding has great potential for use in the design and development of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) inhibitors. Artificial placement of this scaffold in the structure of optimized anti-SARS-CoV-2 compounds can potentially provide irreversible inhibition of the viral cysteine proteases 3-chymotrypsin-like protease and papain-like protease by creating Michael interaction. Despite having remarkable capabilities, the use of chalcone scaffold in drug design and discovery of SARS-CoV-2 inhibitors seems to have been largely neglected. This review addresses issues that could lead to further consideration of chalcone scaffolding in the structure of SARS-CoV-2 protease inhibitors in the future.
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Affiliation(s)
- Mehdi Valipour
- Razi Drug Research Center, Iran University of Medical SciencesTehranIran
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28
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Gandhi Y, Mishra SK, Rawat H, Grewal J, Kumar R, Shakya SK, Jain VK, Babu G, Singh A, Singh R, Acharya R, Kumar V. Phytomedicines explored under in vitro and in silico studies against coronavirus: An opportunity to develop traditional medicines. S Afr J Bot 2022; 151:451-483. [PMID: 35530267 PMCID: PMC9057940 DOI: 10.1016/j.sajb.2022.04.053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 04/07/2022] [Accepted: 04/29/2022] [Indexed: 05/21/2023]
Abstract
The widespread COVID-19 pandemic, caused by novel coronavirus SARS-CoV-2, has emanated as one of the most life-threatening transmissible diseases. Currently, the repurposed drugs such as remdesivir, azithromycine, chloroquine, and hydroxychloroquine are being employed in the management of COVID-19 but their adverse effects are a matter of concern. In this regard, alternative treatment options i.e., traditional medicine, medicinal plants, and their phytochemicals, which exhibit significant therapeutic efficacy and show a low toxicity profile, are being explored. The current review aims at unraveling the promising medicinal plants, phytochemicals, and traditional medicines against SARS-CoV-2 to discover phytomedicines for the management of COVID-19 on the basis of their potent antiviral activities against coronaviruses, as demonstrated in various biochemical and computational chemical biology studies. The review consists of integrative and updated information on the potential traditional medicines against COVID-19 and will facilitate researchers to develop traditional medicines for the management of COVID-19.
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Affiliation(s)
- Yashika Gandhi
- Department of Chemistry, Central Ayurveda Research Institute Jhansi, Uttar Pradesh, 284003, India
| | - Sujeet K Mishra
- Department of Chemistry, Central Ayurveda Research Institute Jhansi, Uttar Pradesh, 284003, India
| | - Hemant Rawat
- Department of Chemistry, Central Ayurveda Research Institute Jhansi, Uttar Pradesh, 284003, India
| | - Jyotika Grewal
- Department of Chemistry, Central Ayurveda Research Institute Jhansi, Uttar Pradesh, 284003, India
| | - Ravi Kumar
- Department of Chemistry, Central Ayurveda Research Institute Jhansi, Uttar Pradesh, 284003, India
| | - Santosh K Shakya
- Department of Chemistry, Central Ayurveda Research Institute Jhansi, Uttar Pradesh, 284003, India
| | - Vipin Kumar Jain
- Department of Chemistry, Central Ayurveda Research Institute Jhansi, Uttar Pradesh, 284003, India
| | - G Babu
- Department of Ayurveda, Central Ayurveda Research Institute Jhansi, Uttar Pradesh, 284003, India
| | - Arjun Singh
- Central Council for Research in Ayurvedic Sciences, New Delhi, 110058, India
| | - Ravindra Singh
- Central Council for Research in Ayurvedic Sciences, New Delhi, 110058, India
| | - Rabinarayan Acharya
- Central Council for Research in Ayurvedic Sciences, New Delhi, 110058, India
| | - Vijay Kumar
- Department of Chemistry, Central Ayurveda Research Institute Jhansi, Uttar Pradesh, 284003, India
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Kuttithodi AM, Nikhitha D, Jacob J, Narayanankutty A, Mathews M, Olatunji OJ, Rajagopal R, Alfarhan A, Barcelo D. Antioxidant, Antimicrobial, Cytotoxicity, and Larvicidal Activities of Selected Synthetic Bis-Chalcones. Molecules 2022; 27:molecules27238209. [PMID: 36500302 PMCID: PMC9740027 DOI: 10.3390/molecules27238209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/16/2022] [Accepted: 11/18/2022] [Indexed: 11/26/2022]
Abstract
Plants are known to have numerous phytochemicals and other secondary metabolites with numerous pharmacological and biological properties. Among the various compounds, polyphenols, flavonoids, anthocyanins, alkaloids, and terpenoids are the predominant ones that have been explored for their biological potential. Among these, chalcones and bis-chalcones are less explored for their biological potential under in vitro experiments, cell culture models, and animal studies. In the present study, we evaluated six synthetic bis-chalcones that were different in terms of their aromatic cores, functional group substitution, and position of substitutions. The results indicated a strong antioxidant property in terms of DPPH and ABTS radical-scavenging potentials and ferric-reducing properties. In addition, compounds 1, 2, and 4 exhibited strong antibacterial activities against Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, and Salmonella enteritidis. The disc diffusion assay values were indicative of the antibacterial properties of these compounds. Overall, the study indicated the antioxidant and antimicrobial properties of the compounds. Our preliminary studies point to the potential of this class of compounds for further in vivo investigation.
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Affiliation(s)
- Aswathi Moothakoottil Kuttithodi
- Molecular Microbial Ecology Lab, PG and Research Department of Zoology, St. Joseph’s College (Autonomous), Devagiri, Calicut 680 555, Kerala, India
| | - Divakaran Nikhitha
- Molecular Microbial Ecology Lab, PG and Research Department of Zoology, St. Joseph’s College (Autonomous), Devagiri, Calicut 680 555, Kerala, India
| | - Jisha Jacob
- Molecular Microbial Ecology Lab, PG and Research Department of Zoology, St. Joseph’s College (Autonomous), Devagiri, Calicut 680 555, Kerala, India
| | - Arunaksharan Narayanankutty
- Division of Cell and Molecular Biology, PG and Research Department of Zoology, St. Joseph’s College (Autonomous), Devagiri, Calicut 673 008, Kerala, India
- Correspondence: (A.N.); (O.J.O.)
| | - Manoj Mathews
- PG and Research Department of Chemistry, St. Joseph’s College (Autonomous), Devagiri, Calicut 673 008, Kerala, India
| | - Opeyemi Joshua Olatunji
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir 43150, Morocco
- Correspondence: (A.N.); (O.J.O.)
| | - Rajakrishnan Rajagopal
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Ahmed Alfarhan
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Damia Barcelo
- Water and Soil Research Group, Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18–26, 08034 Barcelona, Spain
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Yang F, Jiang XL, Tariq A, Sadia S, Ahmed Z, Sardans J, Aleem M, Ullah R, Bussmann RW. Potential medicinal plants involved in inhibiting 3CL pro activity: A practical alternate approach to combating COVID-19. J Integr Med 2022; 20:488-496. [PMID: 35985974 PMCID: PMC9359926 DOI: 10.1016/j.joim.2022.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 06/29/2022] [Indexed: 01/25/2023]
Abstract
At present, a variety of vaccines have been approved, and existing antiviral drugs are being tested to find an effective treatment for coronavirus disease 2019 (COVID-19). However, no standardized treatment has yet been approved by the World Health Organization. The virally encoded chymotrypsin-like protease (3CLpro) from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which facilitates the replication of SARS-CoV in the host cells, is one potential pharmacological target for the development of anti-SARS drugs. Online search engines, such as Web of Science, Google Scholar, Scopus and PubMed, were used to retrieve data on the traditional uses of medicinal plants and their inhibitory effects against the SARS-CoV 3CLpro. Various pure compounds, including polyphenols, terpenoids, chalcones, alkaloids, biflavonoids, flavanones, anthraquinones and glycosides, have shown potent inhibition of SARS-CoV-2 3CLpro activity with 50% inhibitory concentration (IC50) values ranging from 2-44 µg/mL. Interestingly, most of these active compounds, including xanthoangelol E (isolated from Angelica keiskei), dieckol 1 (isolated from Ecklonia cava), amentoflavone (isolated from Torreya nucifera), celastrol, pristimerin, tingenone and iguesterin (isolated from Tripterygium regelii), tannic acid (isolated from Camellia sinensis), and theaflavin-3,3'-digallate, 3-isotheaflav1in-3 gallate and dihydrotanshinone I (isolated from Salvia miltiorrhiza), had IC50 values of less than 15 µg/mL. Kinetic mechanistic studies of several active compounds revealed that their mode of inhibition was dose-dependent and competitive, with Ki values ranging from 2.4-43.8 μmol/L. Given the significance of plant-based compounds and the many promising results obtained, there is still need to explore the phytochemical and mechanistic potentials of plants and their products. These medicinal plants could serve as an effective inexpensive nutraceutical for the general public to help manage COVID-19.
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Affiliation(s)
- Fan Yang
- The Medical Center of General Practice, Sichuan Academy of Medical Science and Sichuan Provincial People's Hospital, Chengdu 610041, Sichuan Province, China
| | - Xiao-Lan Jiang
- The Medical Center of General Practice, Sichuan Academy of Medical Science and Sichuan Provincial People's Hospital, Chengdu 610041, Sichuan Province, China.
| | - Akash Tariq
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830041, Xinjiang Uygur Autonomous Region, China.
| | - Sehrish Sadia
- Department of Biological Sciences, University of Veterinary and Animal Sciences, Ravi Campus, Pattoki 55300, Pakistan
| | - Zeeshan Ahmed
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830041, Xinjiang Uygur Autonomous Region, China
| | - Jordi Sardans
- Consejo Superior de Investigaciones Científicas, Global Ecology Unit, Centre for Ecological Research and Forestry Applications-Consejo Superior de Investigaciones Científicas-Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Catalonia, Spain; Centre for Ecological Research and Forestry Applications, Cerdanyola del Vallès 08193, Catalonia, Spain
| | - Muhammad Aleem
- Department of Biological Sciences, University of Veterinary and Animal Sciences, Ravi Campus, Pattoki 55300, Pakistan
| | - Riaz Ullah
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Rainer W Bussmann
- Department of Ethnobotany, Institute of Botany, llia State University, Tbilisi 0105, Georgia
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Dey R, Samadder A, Nandi S. Exploring the Targets of Novel Corona Virus and Docking-based Screening of Potential Natural Inhibitors to Combat COVID-19. Curr Top Med Chem 2022; 22:2410-2434. [PMID: 36281864 DOI: 10.2174/1568026623666221020163831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 09/07/2022] [Accepted: 09/21/2022] [Indexed: 01/20/2023]
Abstract
There is a need to explore natural compounds against COVID-19 due to their multitargeted actions against various targets of nCoV. They act on multiple sites rather than single targets against several diseases. Thus, there is a possibility that natural resources can be repurposed to combat COVID-19. However, the biochemical mechanisms of these inhibitors were not known. To reveal the mode of anti-nCoV action, structure-based docking plays a major role. The present study is an attempt to explore various potential targets of SARS-CoV-2 and the structure-based screening of various potential natural inhibitors to combat the novel coronavirus.
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Affiliation(s)
- Rishita Dey
- Department of Zoology, Cytogenetics and Molecular Biology Lab., University of Kalyani, Kalyani, Nadia, 741235, India.,Department of Pharmaceutical Chemistry, Global Institute of Pharmaceutical Education and Research (Affiliated to Uttarakhand Technical University), Kashipur, 244713, India
| | - Asmita Samadder
- Department of Zoology, Cytogenetics and Molecular Biology Lab., University of Kalyani, Kalyani, Nadia, 741235, India
| | - Sisir Nandi
- Department of Pharmaceutical Chemistry, Global Institute of Pharmaceutical Education and Research (Affiliated to Uttarakhand Technical University), Kashipur, 244713, India
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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] [What about the content of this article? (0)] [Affiliation(s)] [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] [What about the content of this article? (0)] [Affiliation(s)] [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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Zhai J, Sun B, Sang F. Progress of isolation, chemical synthesis and biological activities of natural chalcones bearing 2-hydroxy-3-methyl-3-butenyl group. Front Chem 2022; 10:964089. [PMID: 36046729 PMCID: PMC9420912 DOI: 10.3389/fchem.2022.964089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/20/2022] [Indexed: 11/13/2022] Open
Abstract
Chalcones have a three-carbon α,β-unsaturated carbonyl system composed of two phenolic rings. Many chalcones have shown broad spectrum of biological activities with clinical potentials against various diseases. They are usually abundant in seeds, fruit skin, bark and flowers of most edible plants. Among them, chalcones bearing 2-hydroxy-3-methyl-3-butenyl (HMB) group have been reported several times in the past few decades due to their novel scaffolds and numerous interesting biological activities. In this paper, we reviewed the isolation of twelve natural chalcones and a natural chalcone-type compound bearing 2-hydroxy-3-methyl-3-butenyl group discovered so far, and reviewed their synthesis methods and biological activities reported in the literature. We anticipate that this review will inspire further research of natural chalcones.
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Affiliation(s)
- Jiadai Zhai
- Research Center of Chemical Biology and Pharmaceutical Chemistry, School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Bingxia Sun
- Research Center of Chemical Biology and Pharmaceutical Chemistry, School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China
| | - Feng Sang
- Research Center of Chemical Biology and Pharmaceutical Chemistry, School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China
- *Correspondence: Feng Sang,
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Su J, Yang F, Kang X, Liu J, Tao Y, Diao Q, Meng X, Liu D, Zhang Y. Chalcone Derivatives From Abelmoschus manihot Seeds Restrain NLRP3 Inflammasome Assembly by Inhibiting ASC Oligomerization. Front Pharmacol 2022; 13:932198. [PMID: 35873581 PMCID: PMC9301202 DOI: 10.3389/fphar.2022.932198] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Three chalcone derivatives, abelmanihotols A−C (1–3), and nine known compounds were isolated from A. manihot seeds, and their structures were determined using HRESIMS and NMR spectroscopic analysis. Compound 1 exhibited the most potent inhibitory effect (IC50 = 4.79 ± 0.72 μM) against lipopolysaccharide (LPS)-induced NO release in THP-1 cells, and significantly inhibited interleukin 1β (IL-1β) secretion, which is stimulated by LPS plus nigericin (IC50 = 11.86 ± 1.20 μM), ATP or MSU, in THP-1 cells. A preliminary mechanism of action study indicated that compound 1 blocked the formation of nucleotide oligomerization domain-like receptor protein-3 (NLRP3) inflammasome formation by suppressing apoptosis-associated speck-like protein oligomerization, thereby attenuating caspase-1 activation and IL-1β release. These results reveal that compound 1 is not only a potent and efficacious NLRP3 inflammasome inhibitor but also a promising drug for the treatment of NLRP3-related diseases.
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Affiliation(s)
- Jinsong Su
- School of Ethnic Medicine, and Research Institute of Integrated TCM and Western Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China.
| | - Fujing Yang
- Chongqing Clinical Research Center for Dermatology, Chongqing Key Laboratory of Integrative Dermatology Research, Key Laboratory of External Therapies of Traditional Chinese Medicine in Eczema, Department of Dermatology, Chongqing Traditional Chinese Medicine Hospital, Chongqing, China.
| | - Xuemei Kang
- Hospital Administration Office, The First People’s Hospital of Ziyang, Ziyang, China.
| | - Jia Liu
- School of Ethnic Medicine, and Research Institute of Integrated TCM and Western Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China.
| | - Yiwen Tao
- School of Ethnic Medicine, and Research Institute of Integrated TCM and Western Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China.
| | - Qingchun Diao
- Chongqing Clinical Research Center for Dermatology, Chongqing Key Laboratory of Integrative Dermatology Research, Key Laboratory of External Therapies of Traditional Chinese Medicine in Eczema, Department of Dermatology, Chongqing Traditional Chinese Medicine Hospital, Chongqing, China.
| | - Xianli Meng
- School of Ethnic Medicine, and Research Institute of Integrated TCM and Western Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China.
| | - Deming Liu
- Chongqing Clinical Research Center for Dermatology, Chongqing Key Laboratory of Integrative Dermatology Research, Key Laboratory of External Therapies of Traditional Chinese Medicine in Eczema, Department of Dermatology, Chongqing Traditional Chinese Medicine Hospital, Chongqing, China.
- *Correspondence: Deming Liu, ; Yi Zhang,
| | - Yi Zhang
- School of Ethnic Medicine, and Research Institute of Integrated TCM and Western Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China.
- *Correspondence: Deming Liu, ; Yi Zhang,
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Bagde H, Dhopte A. Effects of Plant Metabolites on the Growth of COVID-19 (Coronavirus Disease-19) Including Omicron Strain. Cureus 2022; 14:e26549. [PMID: 35936126 PMCID: PMC9348519 DOI: 10.7759/cureus.26549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 07/04/2022] [Indexed: 11/10/2022] Open
Abstract
According to recent reports out of India, a new strain of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) B1.1.529 Omicron virus has emerged. In comparison to the Wuhan (WHU) strain and the delta variant, this variant showed a far stronger effect on the angiotensin converting enzyme2 (ACE2) receptor. There are several medicinal compounds in plant metabolites, and their diverse chemical structures make them ideal for the treatment of serious illnesses. It's possible that some of these could be useful alternative pharmaceuticals, as well as a starting point for the repurposing of existing medications and new chemical discoveries. SARS-CoV-2 infection triggered a worldwide epidemic of the severe acute respiratory syndrome (SARS). There have been trials for different therapies for SARS-CoV-2 and so also there are recent announcements of extensive research into the development of viable medicines for this global health calamity. After a thorough examination of plant-derived treatments for COVID-19, investigators in the current study decided to focus on plant-derived secondary metabolites (PSMs). According to some researchers, new MDR (Multi-Drug Resistant) antibiotics may one day be developed due to the adaptability of secondary metabolites. Identifying plant metabolites that can treat a wide range of viral infections was one of the study's aims. Many natural medications that could be recommended for the treatment of COVID-19 were discovered as a result of this research, including remedies from plant families, viral candidates that are susceptible, antiviral assays, and mechanisms of therapeutic action. The findings of this study will inspire further research and speed up the development of new antiviral plant-based medications.
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Zhou M, Liu Y, Cao J, Dong S, Hou Y, Yu Y, Zhang Q, Zhang Y, Jia X, Zhang B, Xiao G, Li G, Wang W. Bergamottin, a bioactive component of bergamot, inhibits SARS-CoV-2 infection in golden Syrian hamsters. Antiviral Res 2022; 204:105365. [PMID: 35732228 PMCID: PMC9212731 DOI: 10.1016/j.antiviral.2022.105365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 06/13/2022] [Accepted: 06/13/2022] [Indexed: 11/02/2022]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has caused an ongoing pandemic, coronavirus disease-2019 (COVID-19), which has become a major global public health event. Antiviral compounds remain the predominant means of treating COVID-19. Here, we reported that bergamottin, a furanocoumarin originally found in bergamot, exhibited inhibitory activity against SARS-CoV-2 in vitro, ex vivo, and in vivo. Bergamottin interfered with multiple stages of virus life cycles, specifically blocking the SARS-CoV-2 spike-mediated membrane fusion and effectively reducing viral RNA synthesis. Oral delivery of bergamottin to golden Syrian hamsters at dosages of both 50 mg/kg and 75 mg/kg reduced the SARS-CoV-2 load in nasal turbinates and lung tissues. Pathological damage caused by viral infection was also ameliorated after bergamottin treatment. Overall, our study provides evidence of bergamottin as a promising natural compound, with broad-spectrum anti-coronavirus activity, that could be further developed in the fight against COVID-19 infection during the current pandemic.
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Affiliation(s)
- Minmin Zhou
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang Liu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Junyuan Cao
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Siqi Dong
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuxia Hou
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan Yu
- Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China; Guangdong Engineering and Technology Research Centre of Organoid, Guangzhou, 510515, China
| | - Qiuyan Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Yueli Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; College of Pharmacy and State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300450, China
| | - Xiaoying Jia
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Bo Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Gengfu Xiao
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Gang Li
- Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Wei Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; University of the Chinese Academy of Sciences, Beijing, 100049, China.
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Zaman N, Parvaiz N, Farid R, Navid A, Abbas G, Azam SS. Senna makki and other active phytochemicals: Myths and realities behind covid19 therapeutic interventions. PLoS One 2022; 17:e0268454. [PMID: 35700199 PMCID: PMC9197063 DOI: 10.1371/journal.pone.0268454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 04/30/2022] [Indexed: 11/19/2022] Open
Abstract
This study aims to investigate the binding potential of chemical compounds of Senna in comparison with the experimentally tested active phytochemicals against SARS-CoV-2 protein targets to assist in prevention of infection by exploring multiple treatment options. The entire set of phytochemicals from both the groups were subjected to advanced computational analysis that explored functional molecular descriptors from a set of known medicinal-based active therapeutics followed by MD simulations on multiple SARS-CoV-2 target proteins. Our findings manifest the importance of hydrophobic substituents in chemical structures of potential inhibitors through cross-validation with the FDA-approved anti-3CLpro drugs. Noteworthy improvement in end-point binding free energies and pharmacokinetic profiles of the proposed compounds was perceived in comparison to the control drug, vizimpro. Moreover, the identification of common drug targets namely; AKT1, PTGS1, TNF, and DPP4 between proposed active phytochemicals and Covid19 using network pharmacological analysis further substantiate the importance of medicinal scaffolds. The structural dynamics and binding affinities of phytochemical compounds xanthoangelol_E, hesperetin, and beta-sitosterol reported as highly potential against 3CLpro in cell-based and cell-free assays are consistent with the computational analysis. Whereas, the secondary metabolites such as sennosides A, B, C, D present in higher amount in Senna exhibited weak binding affinity and instability against the spike protein, helicase nsp13, RdRp nsp12, and 3CLpro. In conclusion, the results contravene fallacious efficacy claims of Senna tea interventions circulating on electronic/social media as Covid19 cure; thus emphasizing the importance of well-examined standardized data of the natural products in hand; thereby preventing unnecessary deaths under pandemic hit situations worldwide.
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Affiliation(s)
- Naila Zaman
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Nousheen Parvaiz
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Rabia Farid
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Afifa Navid
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Ghulam Abbas
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Syed Sikander Azam
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
- * E-mail: ,
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Ebenezer O, Bodede O, Awolade P, Jordaan MA, Ogunsakin RE, Shapi M. Medicinal plants with anti-SARS-CoV activity repurposing for treatment of COVID-19 infection: A systematic review and meta-analysis. Acta Pharm 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] [What about the content of this article? (0)] [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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Ebenezer O, Shapi M. Promising inhibitors against main protease of SARS CoV-2 from medicinal plants: In silico identification. Acta Pharm 2022; 72:159-69. [PMID: 36651513 DOI: 10.2478/acph-2022-0020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [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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Kumar A, Sharma M, Richardson CD, Kelvin DJ. Potential of Natural Alkaloids From Jadwar ( Delphinium denudatum) as Inhibitors Against Main Protease of COVID-19: A Molecular Modeling Approach. Front Mol Biosci 2022; 9:898874. [PMID: 35620478 PMCID: PMC9127362 DOI: 10.3389/fmolb.2022.898874] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 04/08/2022] [Indexed: 02/05/2023] Open
Abstract
The ongoing pandemic coronavirus disease (COVID-19) caused by a novel corona virus, namely, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has had a major impact on global public health. COVID-19 cases continue to increase across the globe with high mortality rates in immunocompromised patients. There is still a pressing demand for drug discovery and vaccine development against this highly contagious disease. To design and develop antiviral drugs against COVID-19, the main protease (Mpro) has emerged as one of the important drug targets. In this context, the present work explored Jadwar (Delphinium denudatum)-derived natural alkaloids as potential inhibitors against Mpro of SARS-CoV-2 by employing a combination of molecular docking and molecular dynamic simulation-based methods. Molecular docking and interaction profile analysis revealed strong binding on the Mpro functional domain with four natural alkaloids viz. panicutine (-7.4 kcal/mol), vilmorrianone (-7.0 kcal/mol), denudatine (-6.0 kcal/mol), and condelphine (-5.9 kcal/mol). The molecular docking results evaluated by using the MD simulations on 200 nanoseconds confirmed highly stable interactions of these compounds with the Mpro. Additionally, mechanics/generalized Born/Poisson-Boltzmann surface area (MM/G/P/BSA) free energy calculations also affirmed the docking results. Natural alkaloids explored in the present study possess the essential drug-likeness properties, namely, absorption, distribution, metabolism, and excretion (ADME), and are in accordance with Lipinski's rule of five. The results of this study suggest that these four bioactive molecules, namely, condelphine, denudatine, panicutine, and vilmorrianone, might be effective candidates against COVID-19 and can be further investigated using a number of experimental methods.
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Affiliation(s)
- Anuj Kumar
- Laboratory of Immunity, Shantou University Medical College, Shantou, China
- Department of Microbiology and Immunology, Canadian Centre for Vaccinology CCfV, Faculty of Medicine, Dalhousie University, Halifax, Canada
| | - Mansi Sharma
- Laboratory of Immunity, Shantou University Medical College, Shantou, China
- Department of Microbiology and Immunology, Canadian Centre for Vaccinology CCfV, Faculty of Medicine, Dalhousie University, Halifax, Canada
| | - Christopher D. Richardson
- Department of Microbiology and Immunology, Canadian Centre for Vaccinology CCfV, Faculty of Medicine, Dalhousie University, Halifax, Canada
| | - David J. Kelvin
- Laboratory of Immunity, Shantou University Medical College, Shantou, China
- Department of Microbiology and Immunology, Canadian Centre for Vaccinology CCfV, Faculty of Medicine, Dalhousie University, Halifax, Canada
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Oriola AO, Oyedeji AO. Plant-Derived Natural Products as Lead Agents against Common Respiratory Diseases. Molecules 2022; 27:3054. [PMID: 35630531 DOI: 10.3390/molecules27103054] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/23/2022] [Accepted: 05/07/2022] [Indexed: 12/16/2022]
Abstract
Never has the world been more challenged by respiratory diseases (RDs) than it has witnessed in the last few decades. This is evident in the plethora of acute and chronic respiratory conditions, ranging from asthma and chronic obstructive pulmonary disease (COPD) to multidrug-resistant tuberculosis, pneumonia, influenza, and more recently, the novel coronavirus (COVID-19) disease. Unfortunately, the emergence of drug-resistant strains of pathogens, drug toxicity and side effects are drawbacks to effective chemotherapeutic management of RDs; hence, our focus on natural sources because of their unique chemical diversities and novel therapeutic applications. This review provides a summary on some common RDs, their management strategies, and the prospect of plant-derived natural products in the search for new drugs against common respiratory diseases.
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Fang S, Zheng R, Lei C, Wang J, Zhou R, Li M. In Silico Prediction of New Mutations That Can Improve the Binding Abilities Between 2019-nCoV Coronavirus and Human ACE2. IEEE/ACM Trans Comput Biol Bioinform 2022; 19:1694-1702. [PMID: 33560990 PMCID: PMC9328728 DOI: 10.1109/tcbb.2021.3058265] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 01/27/2021] [Accepted: 02/06/2021] [Indexed: 06/12/2023]
Abstract
The Coronavirus Disease 2019 (COVID-19) has become an international public health emergency, posing a serious threat to human health and safety around the world. The 2019-nCoV coronavirus spike protein was confirmed to be highly susceptible to various mutations, which can trigger apparent changes of virus transmission capacity and the pathogenic mechanism. In this article, the binding interface was obtained by analyzing the interaction modes between 2019-nCoV coronavirus and the human ACE2. Based on the "SIFT server" and the "bubble" identification mechanism, 9 amino acid sites were selected as potential mutation-sites from the 2019-nCoV-S1-ACE2 binding interface. Subsequently, a total number of 171 mutant systems for 9 mutation-sites were optimized for binding-pattern comparsion analysis, and 14 mutations that may improve the binding capacity of 2019-nCoV-S1 to ACE2 were selected. The Molecular Dynamic Simulations were conducted to calculate the binding free energies of all the 14 mutant systems. Finally, we found that most of the 14 mutations on the 2019-nCoV-S1 protein could enhance the binding ability between 2019-nCoV coronavirus and human ACE2. Among which, the binding capacities for G446R, Y449R and F486Y mutations could be increased by 20 percent, and that for S494R mutant increased even by 38.98 percent. We hope this research could provide significant help for the future epidemic detection, drug and vaccine development.
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Affiliation(s)
- Senbiao Fang
- Hunan Provincial Key Lab on BioinformaticsSchool of Computer Science and EngineeringCentral South UniversityChangsha410083China
| | - Ruoqian Zheng
- Hunan Provincial Key Lab on BioinformaticsSchool of Computer Science and EngineeringCentral South UniversityChangsha410083China
| | - Chuqi Lei
- Hunan Provincial Key Lab on BioinformaticsSchool of Computer Science and EngineeringCentral South UniversityChangsha410083China
| | - Jianxin Wang
- Hunan Provincial Key Lab on BioinformaticsSchool of Computer Science and EngineeringCentral South UniversityChangsha410083China
| | - Renyi Zhou
- Hunan Provincial Key Lab on BioinformaticsSchool of Computer Science and EngineeringCentral South UniversityChangsha410083China
| | - Min Li
- Hunan Provincial Key Lab on BioinformaticsSchool of Computer Science and EngineeringCentral South UniversityChangsha410083China
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Shoman ME, Abd El-Hafeez AA, Khobrani M, Assiri AA, Al Thagfan SS, Othman EM, Ibrahim ARN. Molecular docking and dynamic simulations study for repurposing of multitarget coumarins against SARS-CoV-2 main protease, papain-like protease and RNA-dependent RNA polymerase. PHAR 2022. [DOI: 10.3897/pharmacia.69.e77021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Proteases and RNA-Dependent RNA polymerase, major enzymes which are essential targets involved in the life and replication of SARS-CoV-2. This study aims at in silico examination of the potential ability of coumarins and their derivatives to inhibit the replication of SARS-Cov-2 through multiple targets, including the main protease, papain-like protease and RNA-Dependent RNA polymerase. Several coumarins as biologically active compounds were studied, including coumarin antibiotics and some naturally reported antiviral coumarins. Aminocoumarin antibiotics, especially coumermycin, showed a high potential to bind to the enzymes’ active site, causing possible inhibition and termination of viral life. They demonstrate the ability to bind to residues essential for triggering the crucial cascades within the viral cell. Molecular dynamics simulations for 50 ns supported these data pointing out the formation of rigid, stable Coumermycin/enzyme complexes. These findings strongly suggest the possible use of Coumermycin, Clorobiocin or Novobiocin in the fight against COVID-19, but biological evidence is still required to support such suggestions.
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Park J, Park R, Jang M, Park YI, Park Y. Coronavirus enzyme inhibitors-experimentally proven natural compounds from plants. J Microbiol 2022; 60:347-54. [PMID: 35089586 DOI: 10.1007/s12275-022-1499-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [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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Mottin M, Caesar LK, Brodsky D, Mesquita NCMR, de Oliveira KZ, Noske GD, Sousa BKP, Ramos PRPS, Jarmer H, Loh B, Zorn KM, Foil DH, Torres PM, Guido RVC, Oliva G, Scholle F, Ekins S, Cech NB, Andrade CH, Laster SM. Chalcones from Angelica keiskei (ashitaba) inhibit key Zika virus replication proteins. Bioorg Chem 2022; 120:105649. [PMID: 35124513 DOI: 10.1016/j.bioorg.2022.105649] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 01/21/2022] [Accepted: 01/25/2022] [Indexed: 12/25/2022]
Abstract
Zika virus (ZIKV) is a dangerous human pathogen and no antiviral drugs have been approved to date. The chalcones are a group of small molecules that are found in a number of different plants, including Angelica keiskei Koidzumi, also known as ashitaba. To examine chalcone anti-ZIKV activity, three chalcones, 4-hydroxyderricin (4HD), xanthoangelol (XA), and xanthoangelol-E (XA-E), were purified from a methanol-ethyl acetate extract from A. keiskei. Molecular and ensemble docking predicted that these chalcones would establish multiple interactions with residues in the catalytic and allosteric sites of ZIKV NS2B-NS3 protease, and in the allosteric site of the NS5 RNA-dependent RNA-polymerase (RdRp). Machine learning models also predicted 4HD, XA and XA-E as potential anti-ZIKV inhibitors. Enzymatic and kinetic assays confirmed chalcone inhibition of the ZIKV NS2B-NS3 protease allosteric site with IC50s from 18 to 50 µM. Activity assays also revealed that XA, but not 4HD or XA-E, inhibited the allosteric site of the RdRp, with an IC50 of 6.9 µM. Finally, we tested these chalcones for their anti-viral activity in vitro with Vero cells. 4HD and XA-E displayed anti-ZIKV activity with EC50 values of 6.6 and 22.0 µM, respectively, while XA displayed relatively weak anti-ZIKV activity with whole cells. With their simple structures and relative ease of modification, the chalcones represent attractive candidates for hit-to-lead optimization in the search of new anti-ZIKV therapeutics.
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Abstract
The pandemic of coronavirus disease 2019 (COVID-19) caused by the SARS-coronavirus 2(SARS-CoV-2) virus has become the greatest global public health crisis in recent years,and the COVID-19 epidemic is still continuing. However, due to the lack of effectivetherapeutic drugs, the treatment of corona viruses is facing huge challenges. In thiscontext, countries with a tradition of using herbal medicine such as China have beenwidely using herbal medicine for prevention and nonspecific treatment of corona virusesand achieved good responses. In this review, we will introduce the application of herbalmedicine in the treatment of corona virus patients in China and other countries, andreview the progress of related molecular mechanisms and antiviral activity ingredients ofherbal medicine, in order to provide a reference for herbal medicine in the treatment ofcorona viruses. We found that herbal medicines are used in the prevention and fightagainst COVID-19 in countries on all continents. In China, herbal medicine has beenreported to relieve some of the clinical symptoms of mild patients and shorten the length of hospital stay. However, as most herbal medicines for the clinical treatment of COVID-19still lack rigorous clinical trials, the clinical and economic value of herbal medicines in theprevention and treatment of COVID-19 has not been fully evaluated. Future work basedon large-scale randomized, double-blind clinical trials to evaluate herbal medicines andtheir active ingredients in the treatment of new COVID-19 will be very meaningful.
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Affiliation(s)
- Yan-Xia Liu
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Yan-He Zhou
- Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, 510623 China
- Department of Gastroenterology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Chang-Hong Jiang
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Junyan Liu
- Department of Civil and Environmental Engineering, University of Maryland, College Park, MD, USA
| | - Ding-Qiang Chen
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
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Mathpal S, Joshi T, Sharma P, Pande V, Chandra S. Assessment of activity of chalcone compounds as inhibitors of 3-chymotrypsin like protease (3CLPro) of SARS-CoV-2: in silico study. Struct Chem. [PMID: 35153452 PMCID: PMC8818839 DOI: 10.1007/s11224-022-01887-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 01/24/2022] [Indexed: 11/02/2022]
Abstract
The COVID-19 is still pandemic due to emerging of various variant of concern of SARS-CoV2. Hence, it is devastating the world, causing significant economic as well as social chaos. This needs great effort to search and develop effective alternatives along with vaccination. Therefore, to continue drug discovery endeavors, we used chalcone derivatives to find an effective drug candidate against SARS-CoV2. Chalcone is a common simple scaffold that exists in many diets as well as in traditional medicine. Natural as well as synthetic chalcones have shown numerous interesting biological activities and are also effective in fighting various diseases. Hence, various computational methods were applied to find out potential inhibitors of 3CLPro using a library of 3000 compounds of chalcones. Firstly, the screening by structure-based pharmacophore model yielded 84 hits that were subjected to molecular docking. The top 10 docked compounds were characterized for stability by using 100 ns molecular dynamic (MD) simulation approach. Further, the binding free energy calculation by MMPBSA showed that four compounds bind to 3CLPro enzyme with high affinity, i.e., − 87.962 (kJ/mol), − 66.125 (kJ/mol), − 59.589 (kJ/mol), and − 66.728 (kJ/mol), respectively. Since chalcone is a common simple scaffold that is present in many diets as well as in traditional medicine, we suggest that screened compounds may emerge as promising drug candidates for SARS-CoV-2. These compounds may be investigated in vitro to evaluate the efficacy against SARS-CoV-2.
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Abstract
The recent outbreak of coronavirus disease 2019 (COVID-19) is a respiratory infection and it can spread from animal to person, person to person through coughing or physical contact. Recent studies revealed that the genome sequence of this pandemic disease is very similar to that of SARS-CoV, thus, there are not yet effective treatments that target the 2019-nCoV virus. Medicinal plants present a potential solution to resolve the drug problem. In fact, the bioactive compounds such as phenols, flavonoids, monoterpenes, and phenylpropanoids, derived from several herbs such as Eucalyptus globulus, Mentha spicata, Nigella sativa, Rosmarinus officinalis, Thymus capitatus and Zingiber officinale could be used to develop formal drugs against several diseases with no or minimal side effects. In this paper, we describe the potential antiviral properties of several medicinal plants against Coronaviridae family viruses such as SARS, MERS, and IBV. Besides, we review various species of medicinal herbs and their derived phytochemical compounds in terms of their immunomodulatory bioactivities and antiviral activity.
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