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El-Banna AA, Ibrahim RS. Metabolic profiling of milk thistle different organs using UPLC-TQD-MS/MS coupled to multivariate analysis in relation to their selective antiviral potential. BMC Complement Med Ther 2024; 24:115. [PMID: 38454377 PMCID: PMC10921647 DOI: 10.1186/s12906-024-04411-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 02/26/2024] [Indexed: 03/09/2024] Open
Abstract
INTRODUCTION Silybum marianum commonly known as milk thistle is one of the most imperative medicinal plants due to its remarkable pharmacological activities. Lately, the antiviral activities of S. marianum extract have been studied and it showed effectiveness against many viruses. OBJECTIVE Although most previous studies were concerned mainly with silymarin content of the fruit, the present study provides comprehensive comparative evaluation of S. marianum different organs' chemical profiles using UPLC-MS/MS coupled to chemometrics to unravel potentially selective antiviral compounds against human coronavirus (HCoV-229E). METHODOLOGY UPLC-ESI-TQD-MS/MS analysis was utilized to establish metabolic fingerprints for S. marianum organs namely fruits, roots, stems and seeds. Multivariate analysis, using OPLS-DA and HCA-heat map was applied to explore the main discriminatory phytoconstituents between organs. Selective virucidal activity of organs extracts against coronavirus (HCoV-229E) was evaluated for the first time using cytopathic effect (CPE) inhibition assay. Correlation coefficient analysis was implemented for detection of potential constituents having virucidal activity. RESULTS UPLC-MS/MS analysis resulted in 87 identified metabolites belonging to different classes. OPLS-DA revealed in-between class discrimination between milk thistle organs proving their significantly different metabolic profiles. The results of CPE assay showed that all tested organ samples exhibited dose dependent inhibitory activity in nanomolar range. Correlation analysis disclosed that caffeic acid-O-hexoside, gadoleic and linolenic acids were the most potentially selective antiviral phytoconstituents. CONCLUSION This study valorizes the importance of different S. marianum organs as wealthy sources of selective and effective antiviral candidates. This approach can be extended to unravel potentially active constituents from complex plant matrices.
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Affiliation(s)
- Alaa A El-Banna
- Department of Pharmacognosy, Faculty of Pharmacy, Alexandria University, Alexandria, 21521, Egypt
| | - Reham S Ibrahim
- Department of Pharmacognosy, Faculty of Pharmacy, Alexandria University, Alexandria, 21521, Egypt.
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Azimi S, Merza MS, Ghasemi F, Dhahi HA, Baradarbarjastehbaf F, Moosavi M, Kargar PG, Len C. Green and rapid and instrumental one-pot method for the synthesis of imidazolines having potential anti-SARS-CoV-2 main protease activity. SUSTAINABLE CHEMISTRY AND PHARMACY 2023; 34:101136. [PMID: 37333050 PMCID: PMC10239909 DOI: 10.1016/j.scp.2023.101136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/02/2023] [Accepted: 05/25/2023] [Indexed: 06/20/2023]
Abstract
The Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) is responsible for ongoing epidemics in humans and some other mammals and has been declared a public health emergency of international concern. In this project, several small non-peptide molecules were synthesized to inhibit the major proteinase (Mpro) of SARS-CoV-2 using rational strategies of drug design and medicinal chemistry. Mpro is a key enzyme of coronaviruses and plays an essential role in mediating viral replication and transcription in human lung epithelial and stem cells, making it an attractive drug target for SARS-CoV. The antiviral potential of imidazoline derivatives as inhibitors of (SARS-CoV-2) Mpro was evaluated using in-silico techniques such as molecular docking simulation, molecular dynamics (MD), and ADMET prediction. The docking scores of these imidazoline derivatives were compared to that of the N3 crystal inhibitor and showed that most of these compounds, particularly compound E07, interacted satisfactorily in the active site of the coronavirus and strongly interacted with the residues (Met 165, Gln 166, Met 165, His 41, and Gln 189). Furthermore, the results were confirmed by MD simulations after exposure to long-term MD simulations and ADMET predictions.
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Affiliation(s)
- Sabikeh Azimi
- Department of Chemistry, Faculty of Sciences, University of Birjand, Birjand, 97175-615, Iran
| | - Muna S Merza
- Prosthetic Dental Techniques Department, Al-Mustaqbal University College, Babylon, 51001, Iraq
| | - Fatemeh Ghasemi
- MSC in Software Engineering, Kowsar, The Institute of Higher Education, Ministry of Science, Research and Technology, Computer Engineering Department, Qazvin, Iran
| | - Hasan Ali Dhahi
- National University of Science and Technology, Dhi Qar, Iraq
| | - Farid Baradarbarjastehbaf
- Faculty of Pharmacy, Department of Pharmaceutical Technology and Biopharmacy, University of Pécs, Pécs, Hungary
| | - Mehdi Moosavi
- Department of Chemistry, Faculty of Chemistry, Mazandaran University, Babolsar, Iran
| | - Pouya Ghamari Kargar
- Department of Chemistry, Faculty of Sciences, University of Birjand, Birjand, 97175-615, Iran
| | - Christophe Len
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, 11 Rue Pierre et Marie Curie, F-75005, Paris, France
- Sorbonne Universités, Universite de Technologie de Compiegne, F- 60200, Compiegne, France
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Giordano D, Facchiano A, Carbone V. Food Plant Secondary Metabolites Antiviral Activity and Their Possible Roles in SARS-CoV-2 Treatment: An Overview. Molecules 2023; 28:molecules28062470. [PMID: 36985442 PMCID: PMC10058909 DOI: 10.3390/molecules28062470] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 02/28/2023] [Accepted: 03/06/2023] [Indexed: 03/30/2023] Open
Abstract
Natural products and plant extracts exhibit many biological activities, including that related to the defense mechanisms against parasites. Many studies have investigated the biological functions of secondary metabolites and reported evidence of antiviral activities. The pandemic emergencies have further increased the interest in finding antiviral agents, and efforts are oriented to investigate possible activities of secondary plant metabolites against human viruses and their potential application in treating or preventing SARS-CoV-2 infection. In this review, we performed a comprehensive analysis of studies through in silico and in vitro investigations, also including in vivo applications and clinical trials, to evaluate the state of knowledge on the antiviral activities of secondary metabolites against human viruses and their potential application in treating or preventing SARS-CoV-2 infection, with a particular focus on natural compounds present in food plants. Although some of the food plant secondary metabolites seem to be useful in the prevention and as a possible therapeutic management against SARS-CoV-2, up to now, no molecules can be used as a potential treatment for COVID-19; however, more research is needed.
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Affiliation(s)
- Deborah Giordano
- Institute of Food Sciences, National Research Council, via Roma 64, 83100 Avellino, Italy
| | - Angelo Facchiano
- Institute of Food Sciences, National Research Council, via Roma 64, 83100 Avellino, Italy
| | - Virginia Carbone
- Institute of Food Sciences, National Research Council, via Roma 64, 83100 Avellino, Italy
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In Silico Study of Coumarins: Wedelolactone as a Potential Inhibitor of the Spike Protein of the SARS-CoV-2 Variants. J Trop Med 2023. [DOI: 10.1155/2023/4771745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Despite the rigorous global efforts to control SARS-CoV-2 transmission, it continues to pose a serious threat to humans with the frequent emergence of new variants. Thus, robust therapeutics to combat the virus are a desperate need. The SARS-CoV-2 spike (S) protein is an important target protein as it mediates the entry of the virus inside the host cells, which is initiated by the binding of the receptor-binding domain (RBD) to its cognate receptor, angiotensin-converting enzyme 2 (ACE-2). Herein, the inhibition potential of several naturally occurring coumarins was investigated against the spike proteins of SARS-CoV-2 variants using computational approaches. Molecular docking studies revealed 26 coumarins with better binding energies than the reference ligands, molnupiravir and ceftazidime, against the S-RBD of the omicron variant. The top 10 best-docked coumarins were further analyzed to understand their binding interactions against the spike proteins of other variants (wild-type, Alpha, Beta, Gamma, and Delta), and these studies also demonstrated decent binding energies. Physicochemical, QSAR, and pharmacokinetics analyses of the coumarins revealed wedelolactone as the best inhibitor of the spike protein with ideal Lipinski’s drug-likeness and optimal ADMET properties. Furthermore, coarse-grained molecular dynamics (MD) simulation studies of spike protein-wedelolactone complexes validated the stable binding of wedelolactone in the respective binding pockets. As an outcome, wedelolactone could be utilized to develop a potent drug candidate against COVID-19 by blocking the viral entry into the host cell.
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Omar RA, Koparir P, Sarac K, Koparir M, Safin DA. A novel coumarin-triazole-thiophene hybrid: synthesis, characterization, ADMET prediction, molecular docking and molecular dynamics studies with a series of SARS-CoV-2 proteins. J CHEM SCI 2023; 135:6. [PMID: 36686402 PMCID: PMC9845830 DOI: 10.1007/s12039-022-02127-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 12/16/2022] [Accepted: 12/16/2022] [Indexed: 01/19/2023]
Abstract
Synthesis, characterization and theoretical studies of a novel coumarin-triazole-thiophene hybrid 4-(((4-ethyl-5-(thiophen-2-yl)-4H-1,2,4-triazol-3-yl)thio)methyl)-6,7-dimethyl-2H-chromen-2-one (1), which was fabricated from 4-ethyl-5-(thiophen-2-yl)-4H-1,2,4-triazole-3-thiol and 4-(chloromethyl)-6,7-dimethyl-2H-chromen-2-one, are reported. The resulting compound was characterized by microanalysis, IR, 1H, and 13C APT NMR spectroscopy. The DFT calculations examined the structure and electronic properties of 1 in gas phase. Its reactivity descriptors and molecular electrostatic potential revealed the reactivity and the reactive centers of 1. ADMET properties of 1 were evaluated using the respective online tools. It was established that 1 exhibit positive gastrointestinal absorption properties and negative human blood-brain barrier penetration. The Toxicity Model Report revealed that 1 belongs to toxicity class 4. Molecular docking was additionally applied to study the interaction of 1 with some SARS-CoV-2 proteins. It was established that the title compound is active against all the applied proteins with the most efficient interaction with Papain-like protease (PLpro). The interaction of 1 with the applied proteins was also studied using molecular dynamics simulations. Graphical abstract A novel coumarin-triazole-thiophene hybrid 4-(((4-ethyl-5-(thiophen-2-yl)-4H-1,2,4-triazol-3-yl)thio)methyl)-6,7-dimethyl-2H-chromen-2-one (1) is reported. The structure and electronic properties of 1 were examined by the DFT calculations. ADMET properties of 1 were also evaluated. Molecular docking and molecular dynamics simulations were applied to study interactions of 1 with a series of the SARS-CoV-2 proteins. Supplementary Information The online version contains supplementary material available at 10.1007/s12039-022-02127-0.
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Affiliation(s)
- Rebaz Anwar Omar
- Department of Chemistry, Faculty of Science and Health, Koya University, Koya KOY45, Kurdistan Region – F.R. Iraq Iraq
| | - Pelin Koparir
- Department of Chemistry, Institute of Forensics, Firat University, 23169 Elazig, Turkey
| | - Kamuran Sarac
- Department of Chemistry, Faculty of Art and Sciences, Bitlis Eren University, 13000 Bitlis, Turkey
| | - Metin Koparir
- Department of Chemistry, Faculty of Sciences, Firat University, 23000 Elazığ, Turkey
| | - Damir A Safin
- Scientific and Educational and Innovation Center for Chemical and Pharmaceutical Technologies, Ural Federal University named after the First President of Russia B. N. Yeltsin, Ekaterinburg, 620002 Russian Federation ,University of Tyumen, Volodarskogo Str. 6, 625003 Tyumen, Russian Federation
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Wang Z, Zhan J, Gao H. Computer-aided drug design combined network pharmacology to explore anti-SARS-CoV-2 or anti-inflammatory targets and mechanisms of Qingfei Paidu Decoction for COVID-19. Front Immunol 2022; 13:1015271. [PMID: 36618410 PMCID: PMC9816407 DOI: 10.3389/fimmu.2022.1015271] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Introduction Coronavirus Disease-2019 (COVID-19) is an infectious disease caused by SARS-CoV-2. Severe cases of COVID-19 are characterized by an intense inflammatory process that may ultimately lead to organ failure and patient death. Qingfei Paidu Decoction (QFPD), a traditional Chines e medicine (TCM) formula, is widely used in China as anti-SARS-CoV-2 and anti-inflammatory. However, the potential targets and mechanisms for QFPD to exert anti-SARS-CoV-2 or anti-inflammatory effects remain unclear. Methods In this study, Computer-Aided Drug Design was performed to identify the antiviral or anti-inflammatory components in QFPD and their targets using Discovery Studio 2020 software. We then investigated the mechanisms associated with QFPD for treating COVID-19 with the help of multiple network pharmacology approaches. Results and discussion By overlapping the targets of QFPD and COVID-19, we discovered 8 common targets (RBP4, IL1RN, TTR, FYN, SFTPD, TP53, SRPK1, and AKT1) of 62 active components in QFPD. These may represent potential targets for QFPD to exert anti-SARS-CoV-2 or anti-inflammatory effects. The result showed that QFPD might have therapeutic effects on COVID-19 by regulating viral infection, immune and inflammation-related pathways. Our work will promote the development of new drugs for COVID-19.
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Tang Y, Ou S, Ye L, Wang S. Pharmacological Activities and Pharmacokinetics of Glycycoumarin. REVISTA BRASILEIRA DE FARMACOGNOSIA : ORGAO OFICIAL DA SOCIEDADE BRASILEIRA DE FARMACOGNOSIA 2022; 33:471-483. [PMID: 36567915 PMCID: PMC9757630 DOI: 10.1007/s43450-022-00342-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/22/2022] [Indexed: 12/23/2022]
Abstract
Glycycoumarin is a representative coumarin compound with significant pharmacological activities isolated from Glycyrrhiza uralensis Fisch., Fabaceae. Studies have shown that glycycoumarin has many biological activities, such as anti-tumor, liver protection, antispasmodic, antibacterial, and antivirus. However, the poor solubility of glycycoumarin in water and the accompanying reactions of the phase I (hydroxylation) and II (glucuronidation) metabolism limit its druggability, which manifests as low absorption in the body after oral administration and low free drug concentration, ultimately leading to low bioavailability. Therefore, a comprehensive review of the pharmacological effects and pharmacokinetics of glycycoumarin is presented to provide a reference for further research and application as a therapeutic agent. Graphical Abstract Supplementary Information The online version contains supplementary material available at 10.1007/s43450-022-00342-x.
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Affiliation(s)
- Yumei Tang
- grid.417409.f0000 0001 0240 6969College of Pharmacy, Zunyi Medical University, Zunyi, Guizhou China
| | - Shuiping Ou
- grid.413390.c0000 0004 1757 6938Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou China
| | - Linhu Ye
- grid.417409.f0000 0001 0240 6969College of Pharmacy, Zunyi Medical University, Zunyi, Guizhou China
| | - Sen Wang
- grid.417409.f0000 0001 0240 6969College of Pharmacy, Zunyi Medical University, Zunyi, Guizhou China
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da Cruz Freire JE, Júnior JEM, Pinheiro DP, da Cruz Paiva Lima GE, do Amaral CL, Veras VR, Madeira MP, Freire EBL, Ozório RG, Fernandes VO, Montenegro APDR, Montenegro RC, Colares JKB, Júnior RMM. Evaluation of the anti-diabetic drug sitagliptin as a novel attenuate to SARS-CoV-2 evidence-based in silico: molecular docking and molecular dynamics. 3 Biotech 2022; 12:344. [PMCID: PMC9640538 DOI: 10.1007/s13205-022-03406-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 09/30/2022] [Indexed: 11/09/2022] Open
Abstract
The current outbreak of COVID-19 cases worldwide has been responsible for a significant number of deaths, especially in hospitalized patients suffering from comorbidities, such as obesity, diabetes, hypertension. The disease not only has prompted an interest in the pathophysiology, but also it has propelled a massive race to find new anti-SARS-CoV-2 drugs. In this scenario, known drugs commonly used to treat other diseases have been suggested as alternative or complementary therapeutics. Herein we propose the use of sitagliptin, an inhibitor of dipeptidyl peptidase-4 (DPP4) used to treat type-II diabetes, as an agent to block and inhibit the activity of two proteases, 3CLpro and PLpro, related to the processing of SARS-CoV-2 structural proteins. Inhibition of these proteases may possibly reduce the viral load and infection on the host by hampering the synthesis of new viruses, thus promoting a better outcome. In silico assays consisting in the modeling of the ligand sitagliptin and evaluation of its capacity to interact with 3CLpro and PLpro through the prediction of the ligand bioactivity, molecular docking, overlapping of crystal structures, and molecular dynamic simulations were conducted. The experiments indicate that sitagliptin can interact and bind to both targets. However, this interaction seems to be stronger and more stable to 3CLpro (ΔG = −7.8 kcal mol−1), when compared to PLpro (ΔG = −7.5 kcal mol−1). This study suggests that sitagliptin may be suitable to treat COVID-19 patients, beyond its common use as an anti-diabetic medication. In vivo studies may further support this hypothesis.
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Hokmabady L, Fani N. In silico elucidation of the interactions of thymoquinone analogues with phosphatase and tensin homolog (PTEN). J Mol Model 2022; 28:321. [DOI: 10.1007/s00894-022-05318-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 08/31/2022] [Indexed: 11/29/2022]
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Sun W, Chen H, Tao S, Li N, Xu Y, Fang Y, Chen L, Liang W, Cao G. Detection rate of SARS-CoV-2 RNA in relation to isolation time and environmental surface type. Front Public Health 2022; 10:957827. [PMID: 36187635 PMCID: PMC9515418 DOI: 10.3389/fpubh.2022.957827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 08/11/2022] [Indexed: 01/24/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV-2) causes environmental contamination via respiratory droplets and persists on contaminants and environmental surfaces for anywhere from a few hours to 6 days. Therefore, it is particularly important to understand the transmission and containment of SARS-CoV-2 on the surface of objects within isolated environments. In this study, 356 environmental surface samples were collected and 79 tested positive, with the highest contamination rate (56.96%) in the wood category (bedside tables, wood floors, and walls). This study revealed differences in the detection rates of environmental surfaces in hospitalized and discharged rooms of patients with confirmed COVID-19 in 2 isolated settings (A: p = 0.001; B: p = 0.505) and suggested that environmental contamination may be an important route of virus transmission, providing a reference to guide the enhancement of ventilation, the use of hotel isolation model, the advocacy of cotton masks, and the effective suppression of virus transmission.
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Affiliation(s)
- Weijie Sun
- Department of Clinical Laboratory, Ningbo First Hospital, Ningbo, China
| | - Huimin Chen
- School of Medicine, Medical School of Jiangsu University, Zhenjiang, China
| | - Shuan Tao
- School of Medicine, Medical School of Jiangsu University, Zhenjiang, China
| | - Na Li
- Laboratory Medical School, Bengbu Medical College, Bengbu, China
| | - Yao Xu
- School of Medicine, Medical School of Ningbo University, Ningbo, China
| | - Yewei Fang
- School of Medicine, Medical School of Ningbo University, Ningbo, China
| | - Luyan Chen
- School of Medicine, Medical School of Ningbo University, Ningbo, China
| | - Wei Liang
- Department of Clinical Laboratory, Ningbo First Hospital, Ningbo, China,*Correspondence: Wei Liang
| | - Gang Cao
- Department of Pain Clinic, Ningbo First Hospital, Ningbo, China,Gang Cao
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Coumarins as Fungal Metabolites with Potential Medicinal Properties. Antibiotics (Basel) 2022; 11:antibiotics11091156. [PMID: 36139936 PMCID: PMC9495007 DOI: 10.3390/antibiotics11091156] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 11/17/2022] Open
Abstract
Coumarins are a structurally varied set of 2H-chromen-2-one compounds categorized also as members of the benzopyrone group of secondary metabolites. Coumarin derivatives attract interest owing to their wide practical application and the unique reactivity of fused benzene and pyrone ring systems in molecular structure. Coumarins have their own specific fingerprints as antiviral, antimicrobial, antioxidant, anti-inflammatory, antiadipogenic, cytotoxic, apoptosis, antitumor, antitubercular, and cytotoxicity agents. Natural products have played an essential role in filling the pharmaceutical pipeline for thousands of years. Biological effects of natural coumarins have laid the basis of low-toxic and highly effective drugs. Presently, more than 1300 coumarins have been identified in plants, bacteria, and fungi. Fungi as cultivated microbes have provided many of the nature-inspired syntheses of chemically diverse drugs. Endophytic fungi bioactivities attract interest, with applications in fields as diverse as cancer and neuronal injury or degeneration, microbial and parasitic infections, and others. Fungal mycelia produce several classes of bioactive molecules, including a wide group of coumarins. Of promise are further studies of conditions and products of the natural and synthetic coumarins’ biotransformation by the fungal cultures, aimed at solving the urgent problem of searching for materials for biomedical engineering. The present review evaluates the fungal coumarins, their structure-related peculiarities, and their future therapeutic potential. Special emphasis has been placed on the coumarins successfully bioprospected from fungi, whereas an industry demand for the same coumarins earlier found in plants has faced hurdles. Considerable attention has also been paid to some aspects of the molecular mechanisms underlying the coumarins’ biological activity. The compounds are selected and grouped according to their cytotoxic, anticancer, antibacterial, antifungal, and miscellaneous effects.
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Phytochemicals as potential inhibitors for COVID-19 revealed by molecular docking, molecular dynamic simulation and DFT studies. Struct Chem 2022; 33:1423-1443. [PMID: 35729939 PMCID: PMC9189813 DOI: 10.1007/s11224-022-01982-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/30/2022] [Indexed: 10/26/2022]
Abstract
The COVID-19 pandemic outbreak demands the designing of potential drugs as there is no specific treatment available. Thanks to their safety and effectiveness, phytochemicals have been used to treat various diseases, including antiviral therapeutics. Molecular docking is a simple, quick, and effective way to screen a variety of molecules for structure-based drug design. Here, we investigate molecular docking experiments on compounds present in plant species, Cocculus hirsutus and Rhodiola rosea and show their potential for the treatment of COVID-19. Almost all the components showed higher binding affinity than the built-in ligand, and those with significantly higher binding affinity were explored further. Molecular mechanics-based generalized born surface area calculations were used to re-rank the top candidates, rhodionidin and cocsoline, and their stability in association with viral protease was confirmed. Density functional theory was used for detailed investigations of the geometries, and electrical properties of rhodionidin and cocsoline. Using the frontier molecular orbitals method, the charge transfer within the molecule was calculated. Chemical reactivity and intermolecular interactions were studied using molecular electrostatic potential maps. These in silico discoveries will simulate the identification of powerful COVID-19 inhibitors, and similar research is likely to make a significant contribution to antiviral drug discovery. Supplementary information The online version contains supplementary material available at 10.1007/s11224-022-01982-4.
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Kittakoop P, Darshana D, Sangsuwan R, Mahidol C. Alkaloids and Alkaloid-Like Compounds are Potential Scaffolds of Antiviral Agents against SARS-CoV-2 (COVID-19) Virus. HETEROCYCLES 2022. [DOI: 10.3987/rev-22-sr(r)3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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14
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Saied EM, El-Maradny YA, Osman AA, Darwish AMG, Abo Nahas HH, Niedbała G, Piekutowska M, Abdel-Rahman MA, Balbool BA, Abdel-Azeem AM. A Comprehensive Review about the Molecular Structure of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): Insights into Natural Products against COVID-19. Pharmaceutics 2021; 13:1759. [PMID: 34834174 PMCID: PMC8624722 DOI: 10.3390/pharmaceutics13111759] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/06/2021] [Accepted: 10/11/2021] [Indexed: 12/15/2022] Open
Abstract
In 2019, the world suffered from the emergence of COVID-19 infection, one of the most difficult pandemics in recent history. Millions of confirmed deaths from this pandemic have been reported worldwide. This disaster was caused by SARS-CoV-2, which is the last discovered member of the family of Coronaviridae. Various studies have shown that natural compounds have effective antiviral properties against coronaviruses by inhibiting multiple viral targets, including spike proteins and viral enzymes. This review presents the classification and a detailed explanation of the SARS-CoV-2 molecular characteristics and structure-function relationships. We present all currently available crystal structures of different SARS-CoV-2 proteins and emphasized on the crystal structure of different virus proteins and the binding modes of their ligands. This review also discusses the various therapeutic approaches for COVID-19 treatment and available vaccinations. In addition, we highlight and compare the existing data about natural compounds extracted from algae, fungi, plants, and scorpion venom that were used as antiviral agents against SARS-CoV-2 infection. Moreover, we discuss the repurposing of select approved therapeutic agents that have been used in the treatment of other viruses.
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Affiliation(s)
- Essa M. Saied
- Chemistry Department, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt
- Institute for Chemistry, Humboldt Universität zu Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany
| | - Yousra A. El-Maradny
- Microbiology Department, High Institute of Public Health, Alexandria University, Alexandria 21526, Egypt;
| | - Alaa A. Osman
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, New Giza University, Newgiza, km 22 Cairo-Alexandria Desert Road, Cairo 12256, Egypt;
| | - Amira M. G. Darwish
- Food Technology Department, Arid Lands Cultivation Research Institute (ALCRI), City of Scientific Research and Technological Applications (SRTA City), Alexandria 21934, Egypt;
| | - Hebatallah H. Abo Nahas
- Zoology Department, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt; (H.H.A.N.); (M.A.A.-R.)
| | - Gniewko Niedbała
- Department of Biosystems Engineering, Faculty of Environmental and Mechanical Engineering, Poznań University of Life Sciences, Wojska Polskiego 50, 60-627 Poznań, Poland;
| | - Magdalena Piekutowska
- Department of Geoecology and Geoinformation, Institute of Biology and Earth Sciences, Pomeranian University in Słupsk, Partyzantów 27, 76-200 Słupsk, Poland;
| | - Mohamed A. Abdel-Rahman
- Zoology Department, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt; (H.H.A.N.); (M.A.A.-R.)
| | - Bassem A. Balbool
- Faculty of Biotechnology, October University for Modern Sciences and Arts, Giza 12585, Egypt;
| | - Ahmed M. Abdel-Azeem
- Botany and Microbiology Department, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt
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