Computational Investigations for Identification of Bioactive Molecules from Baccaurea ramiflora and Bergenia ciliata as Inhibitors of SARS-CoV-2 Mpro
Polycyclic Aromatic Compounds
; 43(3):2459-2487, 2023.
Article
in English
| ProQuest Central | ID: covidwho-2306657
ABSTRACT
In this study, a hybrid compound library of 72 phytocompounds from two antiviral medicinal plants (Baccaurea ramiflora and Bergenia ciliata) was computationally investigated for their inhibitory potential against SARS-CoV-2 Mpro. Molecular docking showed that 6-O-vanilloylicariside B5, 6-O-vanilloylisotachioside, leucoanthocyanidin 4-(2-galloyl), and p-hydroxybenzoyl bergenin has good binding affinity for Mpro. However, p-hydroxybenzoyl bergenin did not bind at the catalytic cavity. The RMSD and RMSF data obtained from 100 ns MD simulations revealed stable protein–ligand complexes for 6-O-vanilloylicariside B5, 6-O-vanilloylisotachioside, leucoanthocyanidin 4-(2-galloyl). Ligand trajectory study found 6-O-vanilloylisotachioside and leucoanthocyanidin 4-(2-galloyl) to be stable. Studies on ligand interaction profile and timeline interaction profile showed that 6-O-vanilloylisotachioside and leucoanthocyanidin 4-(2-galloyl) interacted with HIS41–CYS145 dyad and other crucial amino acids of the catalytic site cavity during the entire 100 ns MD simulations. Molecular mechanics generalized born solvent accessibility binding free energy calculations, density functional theory analysis, quantitative structure–property relationship studies, and ADMET profiling of 6-O-vanilloylisotachioside and leucoanthocyanidin 4-(2-galloyl) supported the results generated by molecular docking and MD simulations studies. Based on the current computational investigations, we conclude that that 6-O-vanilloylisotachioside of B. ramiflora and leucoanthocyanidin 4-(2-galloyl) of B. ciliata are two potential inhibitors of SARS-CoV-2 Mpro that are worthy of further investigations.
Chemistry--Organic Chemistry; Baccaurea ramiflora; Bergenia ciliata; SARS-CoV-2 M pro; COVID-19; In silico; Simulation; Amino acids; Binding; Molecular docking; Severe acute respiratory syndrome coronavirus 2; Medicinal plants; Herbal medicine; Inhibitors; Ligands; Free energy; Computer applications; Density functional theory
Full text:
Available
Collection:
Databases of international organizations
Database:
ProQuest Central
Language:
English
Journal:
Polycyclic Aromatic Compounds
Year:
2023
Document Type:
Article
Similar
MEDLINE
...
LILACS
LIS