Cellular Microbiology

Research Article

Molecular Docking, Dynamics Simulations, ADMET, and DFT Calculations: Combined In Silico Approach to Screen Natural Inhibitors of 3CL and PL Proteases of SARS-CoV-2

Table 2

The amino acids of 3CL protease involved in bonding.
LigandDetails of hydrogen bondOther interactions
No. of bondsAmino acids involvedNo. of bondsAmino acids involvedBond
Caricaxanthin——3TYR154, HIS246, PHE294Hydrophobic bond
Catechin1GLU1661CYS145Pi–sulfur bond
1HIS41Hydrophobic bond
Chlorogenic acid4TYR239, ASP289, LEU271, GLU2882LEU287, MET276Hydrophobic bond
Coumaric acid2TYR154, GLN3062TYR154, PHE294Hydrophobic bond
Dasyscyphin C3LYS137, ASN238, LEU287———
Gingerol3SER144, ARG188, ASN1422HIS41, MET165Hydrophobic bond
1CYS145Pi–sulfur bond
Glycyrrhizin7CYS145, ARG131, LYS137, THR199, LEU287, ASP289, GLU2881LYS137Electrostatic bond
Hyperoside6GLN189, GLN192, MET165, VAL186, LEU141, GLU1661CYS145Pi–sulfur bond
2HIS41, MET165Hydrophobic bond
Kaempferol1GLU1664HIS41, LEU141, ASN142, CYS145Hydrophobic bond
Naringin4GLN110, TYR154, THR111, THR292———
Nimbaflavone2GLN192, GLN1895CYS145, MET49, HIS41, PRO168, MET165Hydrophobic bond
Quercetin2PHE140, LEU1412HIS41, CYS145Hydrophobic bond
1CYS145Pi–sulfur bond
Rutin6SER144, GLN189, THR26, ASP187, GLU166, ASN1421CYS44Pi–sulfur bond
2HIS41, MET49Hydrophobic bond
Violaxanthin——3ILE249, TYR154, PHE294Hydrophobic bond
Zeaxanthin——2PRO241, HIS246Hydrophobic bond
Zingiberene——1PHE294Hydrophobic bond