A Computational Study on Selected Alkaloids as SARS-CoV-2 Inhibitors: PASS Prediction, Molecular Docking, ADMET Analysis, DFT, and Molecular Dynamics Simulations

Table 3

Interactions of the protein (M^pro) with the top ten alkaloids.

Serial No.	Compound	Hydrogen bond		Hydrophobic bond
		Residues	Distance (Å)	Residues	Distance (Å)
1	L-1	THR111	3.10	PHE305	5.04
		ASP153	3.68	VAL303	3.71
				PHE294	3.27
2	L-7	GLN110	2.03	ARG298	5.10
		PHE294	3.43	VAL104	3.93
				ILE106	5.23
3	L-16	Absent	Absent	VAL303	4.70
				VAL297	5.30
				ARG298	4.31
				PHE305	5.18
				PHE8	5.87
4	L-18	ASP295	2.86	ARG298	4.30
				PHE294	4.44
5	L-21	ARG131	3.05	MET276	5.03
		LYS137	5.58
		LEU287	2.00	LEU272	5.42
		TYR237	3.56
6	L-25	THR 292	2.74	PHE305	5.20
		GLN110	2.25	VAL104	4.98
		ASN151	3.32	ASP295	4.99
		ASP153	3.55
7	L-30	THR292	2.44	PHE294	2.44
		ASP153	3.78
8	L-35	THR292	4.31	PHE294	5.93
		ASP153	1.53
9	L-40	GLN110	1.95	ARG298	4.83
				PHE294	4.47
				PHE294	5.23
10	L-50	GLY143	2.47	MET49	4.49
		ASN142	2.17	CYS145	5.20
		HIS 41	2.15	MET165	5.12
11	Remdesivir	PHE294	2.92	ASN131	2.90
		ASP293	3.17	VAL208	3.78
		THR111	2.16	PRO292	2.92
		GLN110	2.94	VAL 308	4.52
				PHE305	5.13