Inhibition of Mycobacterium tuberculosis dihydrodipicolinate synthase by alpha-ketopimelic acid and its other structural analogues.

ABSTRACT: The Mycobacterium tuberculosis dihydrodipicolinate synthase (Mtb-dapA) is an essential gene. Mtb-DapA catalyzes the aldol condensation between pyruvate and L-aspartate-beta-semialdehyde (ASA) to yield dihydrodipicolinate. In this work we tested the inhibitory effects of structural analogues of pyruvate on recombinant Mtb-DapA (Mtb-rDapA) using a coupled assay with recombinant dihydrodipicolinate reductase (Mtb-rDapB). Alpha-ketopimelic acid (?-KPA) showed maximum inhibition of 88% and IC50 of 21??M in the presence of pyruvate (500??M) and ASA (400??M). Competition experiments with pyruvate and ASA revealed competition of ?-KPA with pyruvate. Liquid chromatography-mass spectrometry (LC-MS) data with multiple reaction monitoring (MRM) showed that the relative abundance peak of final product, 2,3,4,5-tetrahydrodipicolinate, was decreased by 50%. Thermal shift assays showed 1?°C Tm shift of Mtb-rDapA upon binding ?-KPA. The 2.4?Å crystal structure of Mtb-rDapA-?-KPA complex showed the interaction of critical residues at the active site with ?-KPA. Molecular dynamics simulations over 500?ns of pyruvate docked to Mtb-DapA and of ?-KPA-bound Mtb-rDapA revealed formation of hydrogen bonds with pyruvate throughout in contrast to ?-KPA. Molecular descriptors analysis showed that ligands with polar surface area of 91.7?Å(2) are likely inhibitors. In summary, ?-hydroxypimelic acid and other analogues could be explored further as inhibitors of Mtb-DapA.

SUBMITTER: Shrivastava P 

PROVIDER: S-EPMC4977564 | biostudies-literature | 2016 Aug

REPOSITORIES: biostudies-literature