Alkaloids from Cryptolepis sanguinolenta as Potential Inhibitors of SARS-CoV-2 Viral Proteins: An In Silico Study

Table 3

Ligand-driven molecular dynamics simulation data of ligands with best binding affinities recorded from docking study using explicit water model.

P-L complex	RMSD (avg.) (Å)		Rg (Å)	ΔPBSAbind (kcal/mol)	ΔGBSAbind (kcal/mol)	H-bonding	Dist. (Å)	Ang. (°)
	Ligand	Protein
M^pro
Cryptospirolepine	0.39	1.95	22.17	-15.65	-22.87	Gly^143, OH	3.04	154.02
Cryptomisirine	0.51	1.74	22.19	-14.32	-24.37	Arg^188, N-H	3.30	143.14
Biscryptolepine	0.60	1.43	22.14	-12.68	-21.16	Gln^189, N-H	3.29	147.33
Cryptoquindoline	0.62	1.67	22.03	-8.43	-15.14	Gln^189, N-H	3.27	153.77
RdRp
Cryptomisirine	0.30	1.87	28.59	-53.54	-60.15	Thr^556, N-H	3.06	152.95
Cryptospirolepine	0.68	1.85	28.76	-44.94	-54.45	Asn^691, N	3.20	141.31
Cryptoquindoline	0.69	1.80	28.63	-44.91	-55.68	Lys^621, N-H	3.33	151.55
RemTP	0.47	1.94	28.78	89.22	32.7	Asp^623, O-H	3.07	149.90
RdRpol
Cryptospirolepine	0.51	2.94	32.37	-17.07	-20.35	Arg^553, N-H	3.27	143.58
Cryptomisirine	0.42	3.16	32.05	-12.24	-16.92	Asp^623, N-H	3.13	151.01
Cryptoquindoline	0.47	2.99	38.65	-4.98	-10.66	Lys^621, N-H	3.35	148.11

RMSD (avg): average root mean square deviation; Rg: average radius of gyration; ΔPBSA: binding free energy using Poisson-Boltzmann surface area continuum solvation; ΔGBSA: binding free energy Generalized Born surface area continuum solvation; H-bonding: most frequent interacting pocket residue; Dist.: average distance; Ang.: average interaction angle.