Anti-COVID-19 terpenoid from marine sources: A docking, admet and molecular dynamics study

•Screening more than fifty natural products for the SARS CoV-2 mpro protein target.•The compounds with higher hydrophobicity and lower flexibility can be more favorable inhibitor.•Terpenoid from marine sponge cacospongia mycofijiensis shows excellent SARS CoV-2 mpro inhibitory activity.•In the point...

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Bibliographic Details
Published in:Journal of molecular structure 2021-03, Vol.1228, p.129433-129433, Article 129433
Main Authors: Sepay, Nayim, Sekar, Aishwarya, Halder, Umesh C, Alarifi, Abdullah, Afzal, Mohd
Format: Article
Language:English
Subjects:
ADME
Docking
Molecular dynamics
Natural products
Sars cov-2 mpro
Toxicity
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Summary:•Screening more than fifty natural products for the SARS CoV-2 mpro protein target.•The compounds with higher hydrophobicity and lower flexibility can be more favorable inhibitor.•Terpenoid from marine sponge cacospongia mycofijiensis shows excellent SARS CoV-2 mpro inhibitory activity.•In the point of binding affinity, bioavailability, pharmacokinetics and toxicity, the natural product can act as a potential drug candidate against COVID-19 virus. Traditional medicines contain natural products (NPs) as main ingredient which always give new direction and paths to develop new advanced medicines. In the COVID-19 pandemic, NPs can be used or can help to find new compound against it. The SARS coronavirus-2 main protease (SARS CoV-2 Mpro) enzyme, arbitrate viral replication and transcription, is target here. The study show that, from the electronic features and binding affinity of all the NPs with the enzyme, the compounds with higher hydrophobicity and lower flexibility can be more favorable inhibitor. More than fifty NPs were screened for the target and one terpenoid (T3) from marine sponge Cacospongia mycofijiensis shows excellent SARS CoV-2 Mpro inhibitory activity in comparison with known peptide based inhibitors. The molecular dynamics simulation studies of the terpenoids with the protein indicates that the complex is stable and hydrogen bonds are involved during the complexation. Considering binding affinity, bioavailability, pharmacokinetics and toxicity of the compounds, it is proposed that the NP T3 can act as a potential drug candidate against COVID-19 virus. [Display omitted]
ISSN:0022-2860
1872-8014
DOI:10.1016/j.molstruc.2020.129433