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 8

Molecular docking results of isolated compounds against pyruvate kinase M2, PKM2 (PDB ID: 4G1N), and human topoisomerase IIβ (PDB ID: 3QX3) (binding affinity in kcal/mol).


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

4G1N	3	−7.1	—	Alkyl: Pro-403, Met-22, Leu-392	Leu-401, Ala-402, 21, Ile-404, Lys-422, Phe-421, 395, Arg-399, Glu-418, 400
	4	−7.5	Tyr-390	Pi-alkyl: Tyr-390	Gln-393, 393, 393, Arg-400, 400, 400, Thr-25, 25, Asp-24, 24, Glu-397, 396, 396, 396, Leu-392
	5	−8.5	Asp-24, Arg-400, 400, Gln-393	Pi-anion and pi-cation: Arg-400, Glu-396, 396; carbon hydrogen bond: Glu-396, Gln-393	Thr-25, 390, Gln-393, Glu-397, Leu-392, Arg-400, Asp-24, Tyr-390, Phe-26
	6	−8.3	Arg-400, 400, Glu-396	Carbon hydrogen bond: Gly-393, 393, Thr-25; pi-anion: Glu-397, 396	Thr-25, 25, 25, Glu-396, 396, 397, 397, 397, Phe-26, 26, 26, 26, Asp-24, 24, 24, 24, Tyr-390, 390, 390, Gln-393, 393 Leu-392, Arg-400, 400
	7	−8.1	Arg-400, 399, 447, His-391	Pi-anaion: Asp-24; pi-sigma: Ile-404; pi-sulfur: Met-22; pi-pi T-shaped: Phe-421; alkyl and pi-alkyl: Ala-21, Lys-422, Ile-404; carbon hydrogen bond: Met-22	Arg-32, Leu-401, 392, 18, Glu-418, Ala-402, Pro-403
	Abiraterone	−9.5	Asn-350	Carbon hydrogen bond: Glu-397; pi-sigma: Leu-394; alkyl and pi-alkyl: Phe-26, Leu-353, 353	Leu-27, Ile-389, Tyr-390, Lys-311, 311, Asn-350, Asp-354, 354, Met-30, Phe-26, Gln-393

3QX3	3	−7.9	—	Alkyl and pi-alkyl: His-774, 775, Pro-740	Glu-853, 855, 728, Leu-845, Arg-743, Trp-856, His-1021, Asp-1020, Ser-733, Gly-1023, Phe-1019, Lys-744, Tyr-773, Ala-772
	4	−8.4	His- 775	Pi-sigma: Phe-1019; alkyl and pi-alkyl: Phe-1019, Pro-740, Leu-845	Gly-1023, Ser-733, Trp-856, Arg-743, 729, Glu-855, 853, 728, Lys-744, His-744
	5	−8.5	Arg-688, 743, His-775, Lys-744	Carbon hydrogen bond: Gly-1023, Asp-847, Asp-1020, Ser-733, Glu-728; pi-pi stacked: Phe-1019; alkyl and pi-alkyl: Val-852, Pro-740, Arg-729	Phe-738, Lys-739, Trp-856, Glu-855, 853, Gln-560, Ser-725, His-774, Leu-845, Arg-692, Met-1022
	6	−8.1	Arg-743, 688, Phe-738	Pi-cation: Arg-688; pi-pi stacked: Phe-1019; carbon hydrogen bond: Glu-728, Asp-1020; alkyl and pi-alkyl: Trp-856, Leu-721, 845, Pro-740, Arg-692	Ser-733, 725, Lys-739, Pro-732, 854, Glu-855, 853, Gln-560, Asn-724, Phe-684, Gly-1023
	7	−8.2	Phe-738, Arg-743, 688, Glu-728, Lys-744, Ser-725	Pi-anion: Glu-728; alkyl and pi-alkyl: Pro-740, Leu-845, pi-pi stacked: Phe-1019; carbon hydrogen bond: Asp-1020, 847, Glu-855, 728	Trp-856, Tyr-846, Val-852, Ala-772, His-775, Gln-560, Arg-729, Ile-731, Gly-1023, Lys-739, Ser-733, Pro-732
	Abiraterone	−9.3	Arg-743, Ser-733	Alkyl and pi-alkyl: Arg-692, Phe-1019, Pro-740; pi-cation: Arg-688	Gly-1023, Glu-855, 728, Trp-856, Lys-739, Phe-738, Ile-731, Pro-732, Arg-689