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Bulletin of the National Research Centre

Table 5 Interaction pattern analysis of two top ranked flavonoids (C3/luteolin and C43/abyssinone II) along with top control drug (Con-2/remdesivir) against Mpro/3CLpro, PLpro and ACE2 of COVID-19

From: Luteolin and abyssinone II as potential inhibitors of SARS-CoV-2: an in silico molecular modeling approach in battling the COVID-19 outbreak

Receptor/target

Ligand/compound

Conventional hydrogen bonds with corresponding bond length

Amino acid residues involved in hydrophobic interaction

Mpro/3CLpro (6LU7)

C3/Luteolin

O4––OG1(Thr25) (2.88 Å)

O3––(His41) (2.69 Å)

O3––O(Cys44) (3.01 Å)

O4––O(Cys44) (2.92 Å)

O1––N(Gly143) (2.86 Å)

O6––N(Glu166) (2.93 Å)

Thr45, Met49, Asn142, Cys145, Met165 and Asp187 (N = 6)

C43/Abyssinone II

O4––O(Leu141) (2.78 Å)

O4––OG(Ser144) (3.07 Å)

Thr25, Thr26, Leu27, Met49, Asn142, Gly143, Cys145, His163, His164, Met165 and Glu166 (N = 11)

Con-2/Remdesivir

O8––N(Gly143) (3.11 Å)

N6––O(Glu166) (2.83 Å)

N6––NE2(Gln189) (3.33 Å)

Thr24, Thr25, Thr26, Leu27, His41, Cys44, Thr45, Met49, Asn142, Cys145, His164 and Met165 (N = 12)

PLpro (6WX4)

C3/Luteolin

O5––OE1(Glu161) (3.18 Å)

Lys157, Leu162, Gly163, Asp164, Arg166, Tyr264, Tyr268, Gln269 and Tyr273 (N = 9)

C43/Abyssinone II

O3––OE1(Glu161) (2.85 Å)

Gly160, Leu162, Gly163, Asp164, Tyr264 and Tyr268 (N = 6)

Con-2/Remdesivir

N6––OH(Tyr112) (3.18 Å)

N3––NE(Arg166) (3.28 Å)

N3––NH2(Arg166) (3.1 Å)

O7––OE2(Glu167) (2.92 Å)

O8––OE2(Glu167) (2.71 Å)

Leu162, Gly163, Asp164, Met208, Ser245, Ala246, Pro247, Tyr264, Tyr268, Gl269 and Cys270 (N = 11)

ACE2 (1R4L)

C3/Luteolin

O3––O(Gly250) (3.21 Å)

O3––OG1(Thr258) (3.08 Å)

O3––ND2(Asn259) (2.8 Å)

O5––OE2(Glu388) (3.07 Å)

Ala135, Asp251, Phe256, Asp349, Thr353, His356, Glu357 and Thr427 (N = 8)

C43/Abyssinone II

O4––OD1(Asp350) (3.05 Å)

O3––OE2(Glu388) (2.77 Å)

Glu127, Phe156, Trp253, His327, Pro328, Asp349, Leu352, His356, Thr363, Thr427 and Tyr497 (N = 11)

Con-2/Remdesivir

O7––OE2(Glu127) (2.93 Å)

N1––ND2(Asn131) (3.11 Å)

O8––ND1(His327) (3.26 Å)

O1––OG1(Thr353) (3.03 Å)

Asp251, Met252, Trp253, Arg255, Phe256, Thr258, Pro328, Lys345, Asp349, Asp350, Leu352, His356, Glu388, Ser391, Thr427 and Tyr497 (N = 16)

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