Toward the Virtual Screening of Potential Drugs in the Homology Modeled NAD+ Dependent DNA Ligase From Mycobacterium Tuberculosis

Protein Pept Lett. 2010 Feb;17(2):269-76. doi: 10.2174/092986610790225950.

Abstract

DNA ligase is an important enzyme and it plays vital role in the replication and repair; also catalyzes nick joining between adjacent bases of DNA. The NAD(+) dependent DNA ligase is selectively present in eubacteria and few viruses; but missing in humans. Homology modeling was used to generate 3-D structure of NAD(+) dependent DNA ligase (LigA) of Mycobacterium tuberculosis using the known template (PDB: 2OWO). Furthermore, the stereochemical quality and torsion angle of 3-D structure was validated. Numerous effective drugs were selected and the active amino acid residue in LigA was targeted and virtual screening through molecular docking was done. In this analysis, four drugs Chloroquine, Hydroxychloroquine, Putrienscine and Adriamycin were found more potent in inhibition of M. tuberculosis through the robust binding affinity between protein-drug interactions in comparison with the other studied drugs. A phylogenetic tree was constructed and it was observed that homology of LigA in M. tuberculosis resembled with other Mycobacterium species. The conserved active amino acids of LigA may be useful to target these drugs. These findings could be used as the starting point of a rational design of novel antibacterial drugs and its analogs.

Publication types

  • Comparative Study
  • Validation Study

MeSH terms

  • Amino Acid Sequence
  • Antitubercular Agents / chemistry
  • Antitubercular Agents / metabolism*
  • Antitubercular Agents / pharmacology
  • Bacterial Proteins / antagonists & inhibitors
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / metabolism*
  • Catalytic Domain
  • Computational Biology / methods
  • DNA Ligases / antagonists & inhibitors
  • DNA Ligases / chemistry*
  • DNA Ligases / metabolism*
  • Databases, Protein
  • Drug Design
  • Enzyme Inhibitors / chemistry
  • Enzyme Inhibitors / metabolism
  • Enzyme Inhibitors / pharmacology
  • Escherichia coli / enzymology
  • Escherichia coli Proteins / chemistry
  • Hydrogen Bonding
  • Microbial Sensitivity Tests
  • Models, Molecular
  • Molecular Sequence Data
  • Molecular Structure
  • Mycobacterium tuberculosis / drug effects
  • Mycobacterium tuberculosis / enzymology*
  • NAD / metabolism
  • Phylogeny
  • Protein Binding
  • Protein Conformation
  • Sequence Alignment
  • Sequence Homology, Amino Acid
  • Tuberculosis / drug therapy

Substances

  • Antitubercular Agents
  • Bacterial Proteins
  • Enzyme Inhibitors
  • Escherichia coli Proteins
  • NAD
  • DNA Ligases
  • DNA ligase (NAD)
  • LigA protein, E coli