Table 3 Summary of the best docking interactions of the FDA-approved drug and natural compounds against the RdRp domain of DENV-2.

From: Repurposing FDA-approved drugs and natural compounds to inhibit the RNA-dependent RNA polymerase domain of dengue virus 2 or dengue virus 3

Compound

2D interaction diagrams

3D interaction diagrams

Bonds (Ångströms (Å))

Binding energy (kcal/mol)

Lumacaftor(VX_809)

Hydrogen bond: Met883 (4.14 Å)

Pi–anion: Asp808 (6.22 Å)

Pi–sulfur: Cys780 (5.58 Å)

Pi–Pi stacked: Tyr882 (4 Å)

Alkyl: Ala776 (6.6 Å), Met809 (4.37 Å), Tyr882 (5.68 Å)

− 10.2421

Clofazimine

Hydrogen bond: Thr806 (3.82 Å), Ser832 (4.85 Å)

Pi–Pi stacked: Trp833 (5.19 Å), Tyr882 (4.79 Å, 4.98 Å)

Pi–alkyl: Met883 (5.2 Å), Met 809 (4.76 Å), Cys780 (6.71 Å), Tyr882 (5.92 Å)

Pi–sulfur: Cys780 (5.95 Å)

− 9.9683

Valdecoxibe

Hydrogen bond: Thr806 (3.43 Å), Tyr882 (6.76 Å)

Pi–donor hydrogen bond: Met809 (5.2 Å), Tyr882 (4.56 Å)

Pi–Pi stacked: Trp833 (5.58 Å)

Pi–alkyl: Ala776 (6.63 Å), Cys780 (6.16 Å), Thr882 (4.46 Å)

Pi–sulfur: Cys780 (6.47 Å)

− 9.95223

Chlorthalidone

Hydrogen bond: Met883 (4.06 Å), Glu807 (4.87 Å), Gln760 (4.49 Å), Met809 (4.40 Å)

Pi–Pi stacked: Trp833 (6.69 Å)

Pi–alkyl: (4.99 Å)

− 9.94339

ZINC13378516

Carbon hydrogen bond: Ser832 (3.91 Å)

Pi–Pi stacked: Trp833 (6.46 Å, 6.30 Å)

Tyr 882 (3.91 Å, 4.82 Å, 4.48 Å)

Pi–anion: Asp808 (4.92 Å)

Pi–alkyl: Leu810 (7.12 Å), Met809 (4.52 Å) Cys780 (5.84 Å)

− 11.4121

ZINC14824819

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Hydrogen bond: Gln760 (4.81 Å)

Attractive charge: Asp808 (6.27 Å, 6.87 Å, 5.53 Å)

Pi–sulfur: Cys780 (5.94 Å)

Pi–Pi stacked: Tyr882 (4.08 Å, 5.26 Å, 5.35 Å)

Carbon hydrogen bond: Thr806 (5.46 Å)

− 11.3939

ZINC01532028

Hydrogen bond: Trp833 (5.21 Å), Asp808 (4.95 Å)

Carbon hydrogen bond: Met809 (4.69 Å), Gln760 (5 Å)

Alkyl: Met883 (4.61 Å, 5.57 Å), Cys780 (4.74 Å, 6.21 Å), Met882 (6.21 Å)

Pi–anion: Asp808 (4.95 Å)

− 11.3831

ZINC95913991

Hydrogen bond: Trp833 (5 Å)

Pi–anion: Asp808 (5.23 Å, 5.6 Å), Cys780 (5.62 Å), Tyr882 (3.93 Å, 5.5 Å, 5.45 Å)

Pi–Pi stacked: Trp833 (6.45 Å), Tyr882 (4.73 Å, 5.5 Å)

− 11.2163

ZINC01619649

Hydrogen bond: Met883 (4.11 Å)

Carbon hydrogen bond: Thr806 (5.68 Å), Met809 (5.42 Å), Tyr882 (4.57 Å)

Pi–anion: Asp808 (4.98 Å)

Alkyl: Met883 (4.37 Å), Cys780 (7.01 Å)

Pi–Pi stacked: Tyr882 (4.20 Å)

− 11.176

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