Molecular Docking and Dynamics Simulation of Several Flavonoids Predict Cyanidin as an Effective Drug Candidate against SARS-CoV-2 Spike Protein

Table 4

Binding free energies, GOLD fitness score, interacting residues of spike protein with their interaction distance, and IC₅₀ values of potent metabolites which were obtained from previous studies through in vitro analysis.

Compounds	Binding free energies (Kcal/mol)	GOLD fitness score	Interacting residues of the spike protein	Interaction distance (Å)	IC50 value (μM) and citations
Cyanidin	−25.09	51.91	Asn 343	2.77	65.1 ± 14.6 μM (SARS-CoV-2) [48]
			Ser 371	2.37
			Ser 372	4.16
			Asn 437	2.97
			Asn 440	2.22
Malvidin	−22.03	52.01	Arg 346	2.72	0.04573 μM (SARS-CoV-2) [49]
			Phe 347	1.83
			Ser 349	2.24
			Asp 442	2.68
			Lys 444	2.20
Tomentin E	−25.02	50.91	Glu 340	2.30	5.0 μM (SARS-CoV) [50]
			Lys 356	2.37
			Ser 399	2.07
4′-O-Methyldiplacol	−18.40	63.83	Ala 344	4.05	9.2 μM (SARS-CoV) [50]
			Arg 346	4.36
			Ala 348	3.77
			Ser 349	2.35
			Ser 399	2.43
			Asn 450	2.52
Mimulone	−21.23	61.60	Ala 344	4.27	14.4 μM (SARS-CoV) [50]
			Arg 346	2.40
			Ala 348	3.90
			Ser 349	2.24
			Asn 450	2.54
Neobavaisoflavone	−19.49	53.90	Ser 469	2.72	18.3 μM (SARS-CoV) [51]
			Gln 474	2.54
Lopinavir	−22.75	59.82	Gly 339	4.23	26.63 μM (SARS-CoV-2) [52]
			Val 341	4.97
			Ala 344	5.44
			Arg 346	2.10
			Phe 347	2.05
			Asn 354	2.16
			Lys 356	5.10
Remdesivir	−18.03	56.33	Leu 335	5.47	23.15 μM (SARS-CoV-2) [52]
			Pro 337	2.44
			Gly 339	2.44
			Asn 343	2.21
			Asp 364	2.15
			Val 367	4.41