Computational modeling and ligand-based design of some novel hypothetical compound as prominent inhibitors against Mycobacterium tuberculosis

Adeniji, Shola Elijah; Adalumo, Olajumoke Bosede

doi:10.1186/s43094-020-00027-z

Future Journal of Pharmaceutical Sciences

Table 6 Binding affinity, hydrogen bond, and hydrophobic interaction of the ligands (2,4-disubstituted quinolone derivatives) with M. tuberculosis target (DNA gyrase)

From: Computational modeling and ligand-based design of some novel hypothetical compound as prominent inhibitors against Mycobacterium tuberculosis

Ligand	Binding affinity (BA) Kcal/mol	Target	Hydrogen bond		Hydrophobic interaction
Ligand	Binding affinity (BA) Kcal/mol	Target	Amino acid	Bond length (Å)	Amino acid
1	− 7.2	DNA gyrase	PRO124	2.251	VAL278, TRP103, HIS220, GLN277
2	− 7.5	DNA gyrase	ARG98	2.9399	GLN277, PRO285, HIS220, VAL78
3	− 7.7	DNA gyrase	ASP94 TRP182	2.3878	PRO124, VAL138, GLN101, CYS112
4	− 7.7	DNA gyrase	ARG98	1.4999	PRO124, VAL97, HIS220
5	− 7.9	DNA gyrase	ASP94	2.1801	VAL278, PRO119, GLN101, ASP122
6	− 8.3	DNA gyrase	SER102	2.529	ASP122, ALA167, TRP182, SER247
7	− 8.2	DNA gyrase	ARG98 GLY120 SER118	4.287 2.6231, 2.8491 2.6198	TYR276, ASP94, VAL97, PRO124
8	− 8.8	DNA gyrase	HIS220	2.4765	PHE228, ALA173 , PRO119, TRP182, SER247
9	− 8.4	DNA gyrase	LEU213 ARG184	1.461	MET99, VAL78, TRP182, SER118, ASP122,
10	− 8.2	DNA gyrase	PRO119 GLY120	2.1738	VAL77, SER247, ARG98, ASP94, VAL182
11	− 9.7	DNA gyrase	ASP94 TRP103	1.383	GLY120, GLY120, SER118, PHE168, PRO285, VAL78,
12	− 8.6	DNA gyrase	SER104 VAL77	2.023	TRP162, CYS145, ASP122, VAL78, PRO126, ARG98,
13	− 8.1	DNA gyrase	PRO	2.221	PRO34, PRO285, PHE177, VAL27, MET99
14	− 8.4	DNA gyrase	VAL169 ARG134 PRO285	2.6021	MET99, ASP122, PHE232
15	− 9.1	DNA gyrase	GLY145 SER205	2.4909	VAL98, ALA223, MET145, MET99, LEU164
16	− 8.1	DNA gyrase	ARG98 SER118 GLY120	3.3701 2.8704 1.9128, 3.2821	PRO124, VAL97, VAL97, ASP94, PRO123, ASP122,
17	− 18.8	DNA gyrase	ARG98	1.99395	CYS174, ALA67, ASN74, GLY120, MET99,
18	− 9.1	DNA gyrase	LEU114 ALA78	2.3983	LEU164, VAL228, PHE168, GLY232, TYR276
19	− 9.7	DNA gyrase	ALA167 ARG94	1.3965	ALA233, LYS136, MET99, VAL228
20	− 11.6	DNA gyrase	MET99	2.3975	TRP142, PHE88, PRO169, VAL78,LEU 156
21	− 9.9	DNA gyrase	GLN223 TYR276	2.5093	ARG98, LEU103, ALA167, PHE168, MET234,
22	− 6.8	DNA gyrase	PHE212 TRP182	1.8408	VAL78, LEU123, SER119, ALA233, TYR276,
23	− 10.7	DNA gyrase	LSY146 TRP143	2.1665	PHE168, CYS254, TRP182, ALA167, VAL78, VAL82
24	− 7.9	DNA gyrase	ARG98 CYS156	1.5984	ALA167, LEU 103, TRP112, ARG386
25	− 7.1	DNA gyrase	TRP182	2.3663	ARG72, ALA143, VAL78, GLN154
26	− 8	DNA gyrase	PHE256 ARG143	1.287	TRP182, CYS345, ALA176, PHE 168,
27	− 9.2	DNA gyrase	–	–	PRO285, MET 232, SER108, ALA137
28	− 8.5	DNA gyrase	–	–	LEU164, VAL178, PRO169, PHE98, VAL228,
29	− 8.1	DNA gyrase	ARG145	1.9217	LEU234, VAL228, CYS 144, ALA233, VAL78
30	− 8.2	DNA gyrase	TRP182 MET99	2.3896	PRO34, PRO94, PHE93, VAL178, PHE241, PRO169
31	− 9.3	DNA gyrase	ARG98	1.3896	PHE168, ALA137, TRP182, VAL122, PHE220
32	− 11.4	DNA gyrase	TYR276	3.1345	VAL78, HIS220
33	− 7.1	DNA gyrase	GLN277	2.5007	PHE338, ALA233, TYR276, ASP122, CYS345
34	− 9.6	DNA gyrase	HIS220 SER104 MET99	3.2896	PHE285, GLY120, SER118
35	− 9.4	DNA gyrase	TYR276	2.5007	TRP182, PHE168, TRP182, ALA167, TYR276
36	− 8.2	DNA gyrase	ALA167 LEU137	1.3907	VAL167, CYS234, ARG165, ARG98, GLN385, TYR276, GLN385
Ethambutol	− 5.8	DNA gyrase	ALA337	2.59739	–
Isoniazid	− 14.6	DNA gyrase	SER279 ALA337	2.29943 2.52954, 2.24657	CYS345, PHE338

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