title: 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 (α-KPA) showed maximum inhibition of 88% and IC50 of 21 μM in the presence of pyruvate (500 μM) and ASA (400 μM). Competition experiments with pyruvate and ASA revealed competition of α-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 α-KPA. The 2.4 Å crystal structure of Mtb-rDapA-α-KPA complex showed the interaction of critical residues at the active site with α-KPA. Molecular dynamics simulations over 500 ns of pyruvate docked to Mtb-DapA and of α-KPA-bound Mtb-rDapA revealed formation of hydrogen bonds with pyruvate throughout in contrast to α-KPA. Molecular descriptors analysis showed that ligands with polar surface area of 91.7 Å(2) are likely inhibitors. In summary, α-hydroxypimelic acid and other analogues could be explored further as inhibitors of Mtb-DapA.
authors: Functional Genomics Unit, Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB), South Campus, New Delhi 110025, India.|Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, New Delhi 110025, India.
authors: Priyanka
authors: P
authors: Shrivastava
authors: Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India.
authors: Vikas
authors: V
authors: Navratna
authors: Biotechnology Group (BIF center), Biological Science &Technology Division (BSTD), CSIR-North-East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India.
authors: Yumnam
authors: Y
authors: Silla
authors: Functional Genomics Unit, Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB), South Campus, New Delhi 110025, India.
authors: Rikeshwer P
authors: RP
authors: Dewangan
authors: Functional Genomics Unit, Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB), South Campus, New Delhi 110025, India.
authors: Atreyi
authors: A
authors: Pramanik
authors: Functional Genomics Unit, Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB), South Campus, New Delhi 110025, India.
authors: Sarika
authors: S
authors: Chaudhary
authors: Open Source Drug Discovery Unit (OSDD), CSIR-IGIB, New Delhi, 110001, India.
authors: GeethaVani
authors: G
authors: Rayasam
authors: Open Source Drug Discovery Unit (OSDD), CSIR-IGIB, New Delhi, 110001, India.
authors: Anuradha
authors: A
authors: Kumar
authors: Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India.
authors: Balasubramanian
authors: B
authors: Gopal
authors: Functional Genomics Unit, Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB), South Campus, New Delhi 110025, India.|Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, New Delhi 110025, India.
authors: Srinivasan
authors: S
authors: Ramachandran
mesh_terms: D001224:Aspartic Acid / Q000031:analogs & derivatives / Q000737:chemistry / Q000378:metabolism; D001426:Bacterial Proteins / Q000037:antagonists & inhibitors / Q000235:genetics / Q000378:metabolism*; D001665:Binding Sites; D001952:Bridged-Ring Compounds / Q000737:chemistry / Q000378:metabolism / Q000494:pharmacology*; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D004789:Enzyme Activation / Q000187:drug effects; D004791:Enzyme Inhibitors / Q000494:pharmacology; D006836:Hydro-Lyases / Q000037:antagonists & inhibitors / Q000235:genetics / Q000378:metabolism*; D006860:Hydrogen Bonding; D020128:Inhibitory Concentration 50; D007659:Ketones / Q000737:chemistry / Q000378:metabolism / Q000494:pharmacology*; D007700:Kinetics; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D009169:Mycobacterium tuberculosis / Q000187:drug effects* / Q000201:enzymology*; D019289:Pyruvic Acid / Q000737:chemistry / Q000378:metabolism; D011994:Recombinant Proteins / Q000096:biosynthesis / Q000235:genetics / Q000302:isolation & purification
chemical_list: D001426:Bacterial Proteins; D001952:Bridged-Ring Compounds; D004791:Enzyme Inhibitors; D007659:Ketones; D011994:Recombinant Proteins; C431983:ketopinic acid; D001224:Aspartic Acid; C006644:aspartic semialdehyde; D019289:Pyruvic Acid; D006836:Hydro-Lyases; C020040:4-hydroxy-tetrahydrodipicolinate synthase