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1.
Eur Rev Med Pharmacol Sci ; 25(21): 6741-6744, 2021 Nov.
Article in English | MEDLINE | ID: covidwho-1524862

ABSTRACT

OBJECTIVE: Coronaviruses are large, enveloped, positive-stranded RNA viruses. These viruses contain spike-like projections of glycoprotein on their surface, which appear like a crown. Millions of infections and thousands of deaths have been reported worldwide to date. Hence, the objective of the present study was to look for in silico evaluation of certain commercially available flavonoids against SARS-CoV-2 enzyme. MATERIALS AND METHODS: The in silico docking calculations were carried out using AutoDock 4.2 software. For the computational investigation, Apigenin, Catechin, Galangin, Luteolin, Naringenin were selected. An anti-viral drug Remdesivir was selected as reference drug. RESULTS: In the present study we found that Naringenin showed excellent binding score with the SARS-CoV-2 enzyme compared to the reference drug and other selected flavonoids. CONCLUSIONS: Based on the docking results, we conclude that Naringenin can be considered worthwhile to check its antiviral activity for the management of Coronavirus disease.


Subject(s)
Antiviral Agents/chemistry , Molecular Docking Simulation , SARS-CoV-2/metabolism , Spike Glycoprotein, Coronavirus/chemistry , Antiviral Agents/metabolism , Binding Sites , COVID-19/pathology , COVID-19/virology , Catechin/chemistry , Catechin/metabolism , Flavanones/chemistry , Flavanones/metabolism , Flavonoids/chemistry , Flavonoids/metabolism , Humans , SARS-CoV-2/isolation & purification , Spike Glycoprotein, Coronavirus/metabolism
2.
Sci Rep ; 11(1): 16307, 2021 08 11.
Article in English | MEDLINE | ID: covidwho-1354117

ABSTRACT

Structure-based drug design targeting the SARS-CoV-2 virus has been greatly facilitated by available virus-related protein structures. However, there is an urgent need for effective, safe small-molecule drugs to control the spread of the virus and variants. While many efforts are devoted to searching for compounds that selectively target individual proteins, we investigated the potential interactions between eight proteins related to SARS-CoV-2 and more than 600 compounds from a traditional Chinese medicine which has proven effective at treating the viral infection. Our original ensemble docking and cooperative docking approaches, followed by a total of over 16-micorsecond molecular simulations, have identified at least 9 compounds that may generally bind to key SARS-CoV-2 proteins. Further, we found evidence that some of these compounds can simultaneously bind to the same target, potentially leading to cooperative inhibition to SARS-CoV-2 proteins like the Spike protein and the RNA-dependent RNA polymerase. These results not only present a useful computational methodology to systematically assess the anti-viral potential of small molecules, but also point out a new avenue to seek cooperative compounds toward cocktail therapeutics to target more SARS-CoV-2-related proteins.


Subject(s)
Antiviral Agents/pharmacology , Drug Evaluation, Preclinical , Drugs, Chinese Herbal/pharmacology , Medicine, Chinese Traditional , SARS-CoV-2/drug effects , Viral Proteins/metabolism , Angiotensin-Converting Enzyme 2/metabolism , Animals , Antiviral Agents/chemistry , Antiviral Agents/metabolism , Cats , Computational Biology , Drugs, Chinese Herbal/chemistry , Drugs, Chinese Herbal/metabolism , Flavonoids/metabolism , Humans , Molecular Dynamics Simulation , Protein Binding , RNA-Dependent RNA Polymerase/metabolism , Spike Glycoprotein, Coronavirus/metabolism , Structure-Activity Relationship
3.
Curr Opin Virol ; 49: 151-156, 2021 08.
Article in English | MEDLINE | ID: covidwho-1271612

ABSTRACT

Intestinal microbiota have profound effects on viral infections locally and systemically. While they can directly influence enteric virus infections, there is also an increasing appreciation for the role of microbiota-derived metabolites in regulating virus infections. Because metabolites diffuse across the intestinal epithelium and enter circulation, they can influence host response to pathogens at extraintestinal sites. In this review, we summarize the effects of three types of microbiota-derived metabolites on virus infections. While short-chain fatty acids serve to regulate the extent of inflammation associated with viral infections, the flavonoid desaminotyrosine and bile acids generally regulate interferon responses. A common theme that emerges is that microbiota-derived metabolites can have proviral and antiviral effects depending on the virus in question. Understanding the molecular mechanisms by which microbiota-derived metabolites impact viral infections and the highly conditional nature of these responses should pave the way to developing novel rational antivirals.


Subject(s)
Bacteria/metabolism , Gastrointestinal Microbiome/physiology , Virus Diseases/microbiology , Virus Diseases/physiopathology , Bile Acids and Salts/metabolism , Fatty Acids, Volatile/metabolism , Flavonoids/metabolism , Humans , Inflammation , Interferons/metabolism , Virus Diseases/immunology
4.
Eur J Pharmacol ; 886: 173448, 2020 Nov 05.
Article in English | MEDLINE | ID: covidwho-1005587

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is distinctly infective and there is an ongoing effort to find a cure for this pandemic. Flavonoids exist in many diets as well as in traditional medicine, and their modern subset, indole-chalcones, are effective in fighting various diseases. Hence, these flavonoids and structurally similar indole chalcones derivatives were studied in silico for their pharmacokinetic properties including absorption, distribution, metabolism, excretion, toxicity (ADMET) and anti-SARS-CoV-2 properties against their proteins, namely, RNA dependent RNA polymerase (rdrp), main protease (Mpro) and Spike (S) protein via homology modelling and docking. Interactions were studied with respect to biology and function of SARS-CoV-2 proteins for activity. Functional/structural roles of amino acid residues of SARS-CoV-2 proteins and, the effect of flavonoid and indole chalcone interactions which may cause disease suppression are discussed. The results reveal that out of 23 natural flavonoids and 25 synthetic indole chalcones, 30 compounds are capable of Mpro deactivation as well as potentially lowering the efficiency of Mpro function. Cyanidin may inhibit RNA polymerase function and, Quercetin is found to block interaction sites on the viral spike. These results suggest flavonoids and their modern pharmaceutical cousins, indole chalcones are capable of fighting SARS-CoV-2. The in vitro anti-SARS-CoV-2 activity of these 30 compounds needs to be studied further for complete understanding and confirmation of their inhibitory potential.


Subject(s)
Betacoronavirus/drug effects , Chalcones/chemistry , Chalcones/pharmacology , Flavonoids/pharmacology , Indoles/chemistry , Molecular Docking Simulation , Viral Proteins/metabolism , Betacoronavirus/metabolism , Chalcones/metabolism , Chalcones/pharmacokinetics , Computer Simulation , Flavonoids/metabolism , Flavonoids/pharmacokinetics , Protein Conformation , SARS-CoV-2 , Safety , Tissue Distribution , Viral Proteins/chemistry
5.
Mol Divers ; 25(3): 1745-1759, 2021 Aug.
Article in English | MEDLINE | ID: covidwho-942592

ABSTRACT

Although vaccine development is being undertaken at a breakneck speed, there is currently no effective antiviral drug for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing COVID-19. Therefore, the present study aims to explore the possibilities offered by naturally available and abundant flavonoid compounds, as a prospective antiviral drug to combat the virus. A library of 44 citrus flavonoids was screened against the highly conserved Main Protease (Mpro) of SARS-CoV-2 using molecular docking. The compounds which showed better CDocker energy than the co-crystal inhibitor of Mpro were further revalidated by flexible docking within the active site; followed by assessment of drug likeness and toxicity parameters. The non-toxic compounds were further subjected to molecular dynamics simulation and predicted activity (IC50) using 3D-QSAR analysis. Subsequently, hydrogen bonds and dehydration analysis of the best compound were performed to assess the binding affinity to Mpro. It was observed that out of the 44 citrus flavonoids, five compounds showed lower binding energy with Mpro than the co-crystal ligand. Moreover, these compounds also formed H-bonds with two important catalytic residues His41 and Cys145 of the active sites of Mpro. Three compounds which passed the drug likeness filter showed stable conformation during MD simulations. Among these, the lowest predicted IC50 value was observed for Taxifolin. Therefore, this study suggests that Taxifolin, could be a potential inhibitor against SARS-CoV-2 main protease and can be further analysed by in vitro and in vivo experiments for management of the ongoing pandemic.


Subject(s)
Citrus/chemistry , Coronavirus 3C Proteases/antagonists & inhibitors , Drug Discovery , Flavonoids/pharmacology , Protease Inhibitors/pharmacology , SARS-CoV-2/enzymology , Coronavirus 3C Proteases/chemistry , Coronavirus 3C Proteases/metabolism , Flavonoids/metabolism , Molecular Docking Simulation , Protease Inhibitors/metabolism , Protein Conformation , Quercetin/analogs & derivatives , Quercetin/metabolism , Quercetin/pharmacology , SARS-CoV-2/drug effects
6.
Comb Chem High Throughput Screen ; 24(6): 874-878, 2021.
Article in English | MEDLINE | ID: covidwho-895209

ABSTRACT

BACKGROUND: COVID-19 which is known as the novel coronavirus was reported in December 2019 in Wuhan city, China and many people have been contaminated by environmental contamination and transmission from one human to another until now. OBJECTIVE: The objective of the present work is to establish the inhibitory potential of nicotiflorin, a Kaempferol 3-O-rutinoside flavonoid, against the deadly coronavirus (COVID-19) 6W63 (main protease 3Clpro protein), using molecular docking approach. METHODS: The Molegro Virtual Docker software (MVD) with a 30 Å grid resolution was used. The structure was drawn by Chem 3D software and energy minimization was done by the MM2 force field. The protein 6W63 was downloaded from the protein data bank. Molegro modeller was used for score calculations. RESULT: The molecular docking studies were carried out on nicotiflorin and standard inhibitor X77, where standard inhibitor was observed in a co-crystallized state with main protease 3Clpro protein 6W63. The MolDock score, Rerank Sore, and H Bond score of nicotiflorin and standard inhibitor X77 were observed as -173.058, -127.302, -21.9398 and -156.913,-121.296,-5.7369, respectively. CONCLUSION: Molecular docking studies have confirmed that the affinity of flavonoid nicotiflorin with the amino acids of the viral protein 6W63 was relatively more than the standard X77. For the effective treatment of novel coronavirus COVID-19, the effectiveness of the identified flavonoid nicotiflorin can further be evaluated for safety and efficacy parameters at both preclinical and clinical stages.


Subject(s)
Coronavirus 3C Proteases/chemistry , Coronavirus 3C Proteases/metabolism , Flavonoids/chemistry , Phenols/chemistry , Antiviral Agents/chemistry , Antiviral Agents/metabolism , Catalytic Domain , Coronavirus 3C Proteases/antagonists & inhibitors , Flavonoids/metabolism , Molecular Docking Simulation , Phenols/metabolism
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