Inhibition of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis: in silico screening and in vitro validation.
Tuberculosis, caused by Mycobacterium tuberculosis, remains a serious global health threat, highlighting the urgent need for novel antituberculosis drugs. The shikimate pathway, responsible for aromatic amino acid biosynthesis, is required for the growth of Mycobacterium tuberculosis and is a potential drug target. 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (mtDAH7Ps) catalyzes the first step in shikimate pathway. E-pharmacophore models for inhibitors of mtDAH7Ps - tyrosine, phenylalanine, phosphoenolpyruvate and (2S)-2,7-bis(phosphonooxy)heptanoic acid were screened against ZINC synthetic and natural compounds databases. The shortlisted compounds were subjected to induce fit docking and validated by Prime/Molecular Mechanics Generalized Born Surface Area calculation to predict ligand binding energy and ligand strain energy for ligand and receptor. The lead compounds were screened for their inhibitory activity against purified mtDAH7Ps enzyme. Lead compounds inhibited mtDAH7Ps in a concentration-dependent manner; with an IC50 value of 21 μM, 42 μM and 54 μM for α-Tocopherol, rutin and 3-Pyridine carboxyaldehyde respectively. Molecular Dynamics analysis for 50 ns of the active compounds-mtDAH7Ps complexes showed that the backbone of mtDAH7Ps was stable. These results suggest that α-tocopherol, 3 - Pyridine carboxyaldehyde and rutin could be novel drug leads to inhibit mtDAH7Ps in M. tuberculosis.
Department of Bioinformatics, School of Bioengineering, Faculty of Engineering & Technology, SRM University, Kattankulathur, 603203, Tamil Nadu, India.
Christy Rosaline
CR
Nirmal
Department of Bioinformatics, School of Bioengineering, Faculty of Engineering & Technology, SRM University, Kattankulathur, 603203, Tamil Nadu, India.
Rathankar
R
Rao
Department of Bioinformatics, School of Bioengineering, Faculty of Engineering & Technology, SRM University, Kattankulathur, 603203, Tamil Nadu, India. Electronic address: hod.bioinfo@ktr.srmuniv.ac.in.
Waheeta
W
Hopper
D010723:3-Deoxy-7-Phosphoheptulonate Synthase / Q000037:antagonists & inhibitors* / Q000378:metabolism; D000447:Aldehydes / Q000737:chemistry / Q000494:pharmacology*; D000995:Antitubercular Agents / Q000737:chemistry / Q000494:pharmacology; D003198:Computer Simulation; D004305:Dose-Response Relationship, Drug; D004353:Drug Evaluation, Preclinical; D056004:Molecular Dynamics Simulation; D015394:Molecular Structure; D009169:Mycobacterium tuberculosis / Q000201:enzymology*; D011725:Pyridines / Q000737:chemistry / Q000494:pharmacology*; D012431:Rutin / Q000737:chemistry / Q000494:pharmacology*; D013329:Structure-Activity Relationship; D024502:alpha-Tocopherol / Q000737:chemistry / Q000494:pharmacology*
C000609941:3-Pyridine carboxyaldehyde; D000447:Aldehydes; D000995:Antitubercular Agents; D011725:Pyridines; D012431:Rutin; D010723:3-Deoxy-7-Phosphoheptulonate Synthase; D024502:alpha-Tocopherol
E-pharmacophore model; IC(50); Molecular dynamics; Mycobacterium tuberculosis; mtDAH7Ps