Pharmacophore modeling and molecular dynamics approach to identify putative DNA Gyrase B inhibitors for resistant tuberculosis

J Cell Biochem. 2019 Mar;120(3):3149-3159. doi: 10.1002/jcb.27579. Epub 2018 Sep 6.


One of the major mechanisms followed by the therapeutic agents to target the causative organism of TB, mycobacterium tuberculosis (Mtb), involves disruption of the replication cycle of the pathogen DNA. The process involves two steps that occur simultaneously, ie, breakage and reunion of DNA at gyrase A (GyrA) domain and ATP hydrolysis at gyrase B (GyrB) domain. Current therapy for multi-drug resistant TB involves FDA approved, Fluoroquinolone-based antibiotics, which act by targeting the replication process at GyrA domain. However, resistance against fluoroquinolones due to mutations in the GyrA domain has limited the use of this therapy and shifted the focus of the research community on the GyrB domain. Thus, this study involves in silico designing of chemotherapeutic agents for resistant TB by targeting GyrB domain. In the current study, a pharmacophore model for GyrB domain was generated using reported inhibitors. It was utilized as a query search against three commercial databases to identify GyrB domain inhibitors. Additionally, a qualitative Hip-Hop pharmacophore model for GyrA was also developed on the basis of some marketed fluoroquinolone-based GyrA inhibitors, to remove non-selective gyrase inhibitors obtained in virtual screening. Further, molecular dynamic simulations were carried out to determine the stability of the obtained molecules in complex with both the domains. Finally, Molecular mechanics with generalized Born and surface area solvation score was calculated to determine the binding affinity of obtained molecule with both domains to determine the selectivity of the obtained molecules that resulted in seven putative specific inhibitors of GyrB domain.

Keywords: DNA gyrase; molecular dynamics; pharmacophore modeling; resistance; tuberculosis (TB).

MeSH terms

  • Antitubercular Agents / chemistry
  • Antitubercular Agents / therapeutic use*
  • Drug Resistance, Bacterial
  • Fluoroquinolones / chemistry
  • Fluoroquinolones / therapeutic use
  • Microbial Sensitivity Tests
  • Molecular Dynamics Simulation
  • Mycobacterium tuberculosis / drug effects*
  • Software
  • Topoisomerase II Inhibitors / chemistry
  • Topoisomerase II Inhibitors / therapeutic use*
  • Tuberculosis / drug therapy
  • Tuberculosis / microbiology*


  • Antitubercular Agents
  • Fluoroquinolones
  • Topoisomerase II Inhibitors