Advances in Pharmacological and Pharmaceutical Sciences

Research Article

In Vitro Antibacterial, DPPH Radical Scavenging Activities, and In Silico Molecular Modeling of Isolated Compounds from the Roots of Clematis hirsuta

Table 7

Molecular docking results of isolated compounds against E. coli DNA gyrase B (PDB ID: 7P2M) and Pseudomonas quinolone signal A, PqsA (PDB ID: 5OE4) (binding affinity in kcal/mol).


Target	Ligand	Binding affinity	H-bonding	Hydrophobic and electrostatic	Van der Waals

7P2M	3	−7.8	Thr-165	Alkyl: Ile-78, 94	Leu-98, Val-93, 97, 120, Gly-119, 75, 77, Asn-46, Asp-73, Glu-50, Arg-76, Pro-79
	4	−6.8	—	Pi-sigma: Phe-196; alkyl and pi-alkyl: Arg-192, Leu-197, Phe-196	Glu-193, Ser-195, His-217, Phe-216, Tyr-218
	5	−6.4	Asn-46, Arg-76, Asp-49	Pi-sigma: Ile-78; alkyl and pi-alkyl: Ala-47, Ile-94, Val-120, Ala-53; carbon hydrogen bond: Asp-73	Gly-119, Val-93, 167, 97, Pro-79, Thr-165, Met-95, Glu-50, Leu-98
	6	−7.6	Arg-76, Asn-46, Val-120	Pi-sigma: Thr-165; alkyl and pi-alkyl: Val-167, 120, 43, Ile-78, 84; carbon hydrogen bond: Val-71, 97, Thr-165	Pro-79, Arg-136, Ala-90, 53, 47, Gly-77, 119, Asp-49, 73, Val-93, Leu-98, Met-166, Glu-50
	7	−7.9	Asp-73, Val-120, Ser-121	Pi-sigma: Thr-165; alkyl and pi-alkyl: Ala-47, Val-43, 97, 93, Ile-94, 78; carbon hydrogen bond: Val-71, Thr-165, Asp-73, Gly-119	Val-167, Asn-46, Asp-49, His-83, Arg-76, 136, Pro-79, Gly-77, Glu-50
	Ciprofloxacin	−7.4	Arg-76	Halogen: Asp-73; amide-pi stacked: Gly-77; alkyl and pi-alkyl: Ile-78, 94, Pro-79; carbon hydrogen bond: Asp-73	Arg-136, Ala-47, Asn-46, Val-43, 167, 120, Glu-50, Trh-165

5OE4	3	−9.0	—	Pi-sigma: Phe-209, Trp-233; alkyl and pi-alkyl: Pro-205, Trp-233	Val-254, Ile-204, Pro-234, 236, Ser-235, Phe-208
	4	−8.8	—	Pi-sigma: Phe-209, Trp-233; alkyl and pi-alkyl: Pro-205, Phe-209, Trp-233	Val-254, Pro-234, Phe-208, Lys-206, Ile-204
	5	−8.3	Ser-226, Gly-198, Arg-200, 200	Pi-anion: Asp-17, 19; pi-sigma: Ala-21; alkyl and pi-alkyl: Arg-249, 200, Ala-21; pi-donor and carbon hydrogen bond: Asp-199, 19, Ala-21, Arg-247	Thr-29, 29, 20, 20, His-24, 24, Asp-199, 19, 17, Gly-198, Pro-248, Ser-31, 226
	6	−8.7	Arg-200, 200, His-24, Ser-226	Pi-anion and cation: Arg-200, Asp-19; alkyl, pi-alkyl, and pi-sigma: Arg-249, Ala-21; carbon and pi-donor hydrogen bond: Gly-198, 224, Arg-247, Asp-19, Ala-21	Pro-248, Thr-20, 20, 29, 29, Gly-198, Ala-125, 21, 197, Asp-199, 19, 17, His-24
	7	−8.4	Gln-34, Ser-31, Arg-200, 200, Ala-21	Pi-cation: Arg-200; pi-sigma: Thr-29; alkyl and pi-alkyl: Ala-245, 21, 21; carbon hydrogen bond: His-24, Asp-117	Leu-228, 30, Phe-246, His-24, Thr-29, 20, 20, Ser-31, Asp-19, 19, Gly-198, 27
	Ciprofloxacin	−7.2	Arg-200	Halogen: Asp-19, Arg-200; alkyl: Ala-21; carbon hydrogen bond: Gly-198, Asp-17	His-24, Ser-226, Thr-29, 20, Arg-249, Gly-198