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 3

Details of amino acids of PL protease involved in bonding.

Name of the ligandDetails of hydrogen bondDetails of other interactions
No. of bondsAmino acids involvedNo. of bondsAmino acids involvedBond

Caricaxanthin5ARG65, ALA68, PRO77, PRO59, PHE69Hydrophobic bond
Catechin6TYR213, GLU214, LYS254, GLU252, SER212, THR2571TYR251Hydrophobic bond
1GLU214Electrostatic interaction
Chlorogenic acid5TYR213, LYS217, TYR305, LYS306, SER2121TYR305Hydrophobic bond
Coumaric acid2TYR305, TYR2511GLU214Electrostatic interaction
Dasyscyphin C5ARG166, GLN174, SER170, MET206, GLU2031TYR207Hydrophobic bond
Gingerol4TYR213, GLU214, TYR305, TYR2511GLU214Electrostatic interaction
3TYR305, LYS254, TYR213Hydrophobic bond
Glycyrrhizin3LEU211, TYR305, GLY209
Hyperoside5LYS217, GLY256, THR257, GLU307, ASN3081TYR310Hydrophobic bond
2GLU214, GLU307Electrostatic interaction
Kaempferol3THR257, GLU252, TYR2511TYR305Hydrophobic bond
1GLU214Electrostatic interaction
Naringin4PRO247, THR257, GLU252, LEU2114TYR305, LEU211, ALA246, ALA249Hydrophobic bond
Nimbaflavone1GLU3072LYS217, GLU214Electrostatic interaction
5THR257, LEU253, VAL303, PHE258, TYR305Hydrophobic bond
Quercetin1TYR2732TYR264, PRO248Hydrophobic bond
Rutin4LYS217, PHE258, THR257, GLU2521GLU307Electrostatic interaction
6LEU253, VAL303, TYR251, PHE258, TYR305, LYS306Hydrophobic bond
Violaxanthin1GLN2502TYR251, TYR305Hydrophobic bond
Zeaxanthin2LYS279, LYS306Hydrophobic bond
Zingiberene4VAL188, ILE314, PRO316, TYR233Hydrophobic bond