Pharmacoinformatic study of inhibitory potentials of selected flavonoids against papain-like protease and 3-chymotrypsin-like protease of SARS-CoV-2

Tijjani, Habibu; Adegunloye, Adegbenro P.; Uba, Auwalu; Adebayo, Joseph O.; Gyebi, Gideon A.; Ibrahim, Ibrahim M.

doi:10.1186/s40816-022-00347-y

Clinical Phytoscience

International Journal of Phytomedicine and Phytotherapy

Table 1 Binding Energies and Amino Acid Interactions of Flavonoids with Papain-like Protease (PLpro) of SARS-CoV-2^a

From: Pharmacoinformatic study of inhibitory potentials of selected flavonoids against papain-like protease and 3-chymotrypsin-like protease of SARS-CoV-2

Compound(PubChem CID)	Hydrogen bonding–related residues	Non- hydrogen bonding–related residues	Binding Energy (Kcal/mol)
Lopinavir*(92727)	LEU162	GLU161B, VAL159, GLU161A, LEU162	-9.1
Ritonavir*(392622)	-	GLY160	-8.5
Licorice(163463)	HIS89, ASN109B, GLY160A, ASN109C, GLY160C	HIS89, VAL159, GLY160	-11.8
Ugonin M(135891244)	GLY160A	LEU162B, GLY160B	-10.1
Procyanidin(107876)	TYR268, LYS105	TYR268, LEU162, TRP106, PRO248, TYR264	-9.8
Silymarin(5213)	ASN108C, GLN2691, GLU161A	HIS29B, LEU162A	-9.7
Gallocatechin gallate(5276890)	ASN109B, ASP108, GLN269, ASN109C	LEU162B, LEU162C	-9.6
Epigallocatechin gallate(65064)	ASN109C, GLN269, ASP108, ASN109B	LEU162C, LEU162B	-9.6
Isoquercetin(5280804)	VAL159, GLN269, GLN269	LEU162C, ASN109, LEU162A	-9.3
Isonymphaeol B(10070991)	--	GLU161B, LEU162B, LEU162A, VAL159B, HIS89B	-9.3
Baicalin(64982)	ASP108, LYS157, GLU161, LEU162, TYR264	TRP106, LYS105, ASP164, ASP108	-9.2
Hyperin(5281643)	GLU161, ASN109, GLN269	ASN109	-9.1
Flavopiridol(5287969)	THR158	GLY160, GLU161A, VAL159, LEU162, GLN269, GLU161C	-9.0
Apigetrin(5280704)	ASN109, GLN269, GLN269, LEU162	ASP108, LEU162	-8.9
Houttuynoid B(57412150)	LEU162	GLU161, GLY160	-8.9
Methoxymatteucin(158031)	VAL159, LEU162, GLY160	LEU162, VAL159, GLU161, HIS89	-8.8
Rutin(5280805)	VAL159A, ASP108A, ASN109C, LEU162A, GLY160B, VAL159B, LEU162B, GLY160A	GLU161A, GLY160C, GLU161C	-8.8
Astragalin(5282102)	ASP108, LEU162	LEU162C, LEU162A, ASN109	-8.7
Kaempferol-3-O-glucorhamnoside(5318761)	LEU162A, LEU162B, ASN109	ASN109, VAL159, GLY160, GLU161	-8.7
Tomentin A(71659627)	ASN109C, GLY160C	HIS89A, GLU161C, LEU162C	-8.7
Tomentin B(71659628)	ASN109C	GLU161, LEU162	-8.7
Abyssinone II(10064832)	ASN109	LEU162	-8.6

^*Reference compounds;.^aResults presented here are for the twenty flavonoids for which the enzyme has the highest binding affinities; those for other flavonoids are presented in Supplementary material, Table S1

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