Molecular docking, molecular dynamic and drug-likeness studies of natural flavonoids as inhibitors for SARS-CoV-2 main protease (Mpro). (COVID-19 dedicated issue.)
Journal of Research in Pharmacy
; 25(6):998-1009, 2021.
Article
in English
| CAB Abstracts | ID: covidwho-1761622
ABSTRACT
The emergence of the global pandemic COVID-19 lead to a huge demand for the therapeutic agent to combat the disease. Since the FDA approval of some of HIV-1 main protease inhibitors such as ritonavir lopinavir to treat COVID-19, the investigation of anti-HIV inhibitor to inhibit SARS-CoV-2 main protease (Mpro) is getting considerably much attention. This study evaluates the potency of sixteen selected natural flavonoids which were previously reported active to block HIV-1 protease as potential inhibitors of SARS-CoV-2 Mpro. The molecular docking and dynamic study were completed to know the binding affinity and stability of the protein-ligand complex via docking study along with molecular dynamic simulations. Moreover, drug-likeness was also evaluated through via ADMET evaluation. This study revealed robinin (6), a flavonol molecule with linked to galactose-rhamnose at C3 and rhamnose molecule at C7, exhibited the highest binding affinity (-9 kcal/mol) among others. The amino acids that interacted with robinin were Asn142;Gly143;Arg188;Thr190. The binding affinity of robinin surpassed the binding affinity of ritonavir (-7.7 kcal/mol) and lopinavir (-8.2 kcal/mol). The replacement of the hydroxyl group from the flavonoid skeleton at C-7, C-4' was proposed to affect the binding affinity. The free hydroxyl group particularly in A ring and the position of the hydroxyl group were important to improve the binding affinity. The molecular dynamic simulation showed the stability of Mpro-robinin during the simulation period. The ADME evaluation referring to Lipinski's rule of 5 revealed that the flavonoids (2,5,6,9,10,13,14,15) show low oral bioavailability and absorption. Robinin exhibited a good drug-likeness score (value1) with an unconcerned level of acute toxicity. From this study, it was concluded that robinin showed the most potent natural flavonoids studied to inhibit SASR-CoV-2 Mpro by both docking study and ADME/tox properties evaluation.
Prion, Viral, Bacterial and Fungal Pathogens of Humans [VV210]; Non-food/Non-feed Plant Products [SS200]; Composition and Quality of Non-food/Non-feed Plant Products [SS230]; Animal and in vitro Models for Pharmaceuticals [VV450]; Pesticides and Drugs; Control [HH405]; flavonoids; coronavirus disease 2019; human diseases; viral diseases; antiviral properties; plant composition; chemical composition; ligands; flavonols; amino acids; man; Severe acute respiratory syndrome coronavirus 2; Homo; Hominidae; primates; mammals; vertebrates; Chordata; animals; eukaryotes; Severe acute respiratory syndrome-related coronavirus; Betacoronavirus; Coronavirinae; Coronaviridae; Nidovirales; positive-sense ssRNA Viruses; ssRNA Viruses; RNA Viruses; viruses; SARS-CoV-2; viral infections; anti-viral properties; chemical constituents of plants
Full text:
Available
Collection:
Databases of international organizations
Database:
CAB Abstracts
Language:
English
Journal:
Journal of Research in Pharmacy
Year:
2021
Document Type:
Article
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