title: Mycobacterium tuberculosis NAD+-dependent DNA ligase is selectively inhibited by glycosylamines compared with human DNA ligase I.
abstract: DNA ligases are important enzymes which catalyze the joining of nicks between adjacent bases of double-stranded DNA. NAD+-dependent DNA ligases (LigA) are essential in bacteria and are absent in humans. They have therefore been identified as novel, validated and attractive drug targets. Using virtual screening against an in-house database of compounds and our recently determined crystal structure of the NAD+ binding domain of the Mycobacterium tuberculosis LigA, we have identified N1, N(n)-bis-(5-deoxy-alpha-D-xylofuranosylated) diamines as a novel class of inhibitors for this enzyme. Assays involving M.tuberculosis LigA, T4 ligase and human DNA ligase I show that these compounds specifically inhibit LigA from M.tuberculosis. In vitro kinetic and inhibition assays demonstrate that the compounds compete with NAD+ for binding and inhibit enzyme activity with IC50 values in the microM range. Docking studies rationalize the observed specificities and show that among several glycofuranosylated diamines, bis xylofuranosylated diamines with aminoalkyl and 1, 3-phenylene carbamoyl spacers mimic the binding modes of NAD+ with the enzyme. Assays involving LigA-deficient bacterial strains show that in vivo inhibition of ligase by the compounds causes the observed antibacterial activities. They also demonstrate that the compounds exhibit in vivo specificity for LigA over ATP-dependent ligase. This class of inhibitors holds out the promise of rational development of new anti-tubercular agents.
authors.affiliation: Molecular and Structural Biology Division, Central Drug Research Institute, PO Box 173, Chattar Manzil, Mahatma Gandhi Marg, Lucknow 226001, India.
authors.forename: Sandeep Kumar
authors.initials: SK
authors.lastname: Srivastava
authors.forename: Divya
authors.initials: D
authors.lastname: Dube
authors.forename: Neetu
authors.initials: N
authors.lastname: Tewari
authors.forename: Namrata
authors.initials: N
authors.lastname: Dwivedi
authors.forename: Rama Pati
authors.initials: RP
authors.lastname: Tripathi
authors.forename: Ravishankar
authors.initials: R
authors.lastname: Ramachandran
mesh_terms: D000995:Antitubercular Agents / Q000737:chemistry* / Q000494:pharmacology*; D001665:Binding Sites; D004247:DNA / Q000378:metabolism; D000072481:DNA Ligase ATP; D011088:DNA Ligases / Q000037:antagonists & inhibitors* / Q000737:chemistry / Q000378:metabolism; D003959:Diamines / Q000737:chemistry / Q000494:pharmacology*; D004791:Enzyme Inhibitors / Q000737:chemistry / Q000494:pharmacology; D005663:Furans / Q000737:chemistry; D006801:Humans; D008958:Models, Molecular; D009169:Mycobacterium tuberculosis / Q000201:enzymology*; D009243:NAD / Q000737:chemistry; D014994:Xylose / Q000737:chemistry
chemical_list: D000995:Antitubercular Agents; D003959:Diamines; D004791:Enzyme Inhibitors; D005663:Furans; C000607892:LIG1 protein, human; D009243:NAD; D004247:DNA; D014994:Xylose; D011088:DNA Ligases; D000072481:DNA Ligase ATP; C120640:DNA ligase (NAD)