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

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)

Empagliflozin

Carbon hydrogen bond: Gln760 (5.94 Å), Glu807 (5.46 Å), Lys756 (5.40 Å)

Pi–Pi stacked: Tyr882 (4.77 Å, 4.83 Å)

Pi–sulfur: Cys780 (6.28 Å)

Pi–alkyl: Met809 (4.33 Å)

− 8.75267

Netarsudil

Hydrogen bond: Trp833 (5.03 Å), Asn777 (3.11 Å), Tyr882 (6.41 Å)

Pi–anion: Asp808 (5 Å)

Pi–sulfur: Cys780 (5.55 Å)

Pi–Pi stacked: Tyr882 (4.78 Å)

− 8.56397

Cromolyn

Hydrogen bond: Met809 (4.67 Å), Gln760 (5.47 Å), Thr805 (5.57 Å), Lys756 (5.59 Å)

Pi–Pi stacked: Trp833 (5.48 Å, 6.20 Å)

− 8.57158

Lumacaftor(VX_809)

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Hydrogen bond: Gln760 (4.47 Å), Asp808 (4.22 Å)

Pi–Pi T-shaped: Tyr882 (4.72 Å)

Pi–alkyl: Ala785 (6.05 Å)

− 8.55727

ZINC13375652

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Hydrogen bond: Val785 (3.06 Å), Asp808 (3.81 Å)

Pi–Pi stacked: Tyr882 (4.50 Å)

Pi–sulfur: Cys780 (7.03 Å)

Alkyl: Trp833 (6.58 Å), Met883 (5.48 Å), Val785 (4.72 Å), Cys780 (6.54 Å), Met809 (4.56 Å), Tyr882 (7.03 Å)

− 8.88069

ZINC85510542

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Pi–sulfur: Cys780 (5.9 Å)

Pi–Pi stacked: Tyr882 (4.72 Å)

Alkyl: Met809 (5.17 Å, 4.52 Å), Cys780 (5.17 Å), Tyr882 (5.54 Å, 5.7 Å), Val785 (4.82 Å, 5.41 Å, 5.23 Å), His786 (5.43 Å)

− 8.88656

ZINC85491556

Hydrogen bond: Gln760 (5.32 Å), Met809 (3.98 Å)

Pi–sulfur: Cys780 (5.14 Å)

Pi–alkyl: Cys780 (5.47 Å), Met809 (4.65 Å, 6.21 Å), Thr882 (3.85 Å)

Alkyl: Leu (4.24 Å), Met883 (5.69 Å)

− 8.67629

ZINC14679204

Hydrogen bond: Asp808 (3.39 Å), Leu810 (4.82 Å)

Pi–sulfur: Cys780 (5.46 Å)

Pi–Pi stacked: Tyr882 (4.61 Å)

Alkyl: Val785 (4.28 Å), Leu880 (6.17 Å), Met809 (4.45 Å)

− 8.71702

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