title: Disruption of redox catalytic functions of peroxiredoxin-thioredoxin complex in Mycobacterium tuberculosis H37Rv using small interface binding molecules.
abstract: Mycobacterium tuberculosis has distinctive ability to detoxify various microbicidal superoxides and hydroperoxides via a redox catalytic cycle involving thiol reductants of peroxiredoxin (Prx) and thioredoxin (Trx) systems which has conferred on it resistance against oxidative killing and survivability within host. We have used computational approach to disrupt catalytic functions of Prx-Trx complex which can possibly render the pathogen vulnerable to oxidative killing in the host. Using protein-protein docking method, we have successfully constructed the Prx-Trx complex. Statistics of interface region revealed contact area of each monomer less than 1500Å2and enriched in polar amino acids indicating transient interaction between Prx and Trx. We have identified ZINC40139449 as a potent interface binding molecule through virtual screening of drug-like compounds from ZINC database. Molecular dynamics (MD) simulation studies showed differences in structural properties of Prx-Trx complex both in apo and ligand bound states with regard to root mean square deviation (RMSD), radius of gyration (Rg), root mean square fluctuations (RMSF), solvent accessible surface area (SASA) and number of hydrogen bonds (NHBs). Interestingly, we found stability of two conserved catalytic residues Cys61 and Cys174 of Prx and conserved catalytic motif, WCXXC of Trx upon binding of ZINC40139449. The time dependent displacement study reveals that the compound is quite stable in the interface binding region till 30ns of MD simulation. The structural properties were further validated by principal component analysis (PCA). We report ZINC40139449 as promising lead which can be further evaluated by in vitro or in vivo enzyme inhibition assays.
authors.affiliation: Computational Biology Laboratory, Department of Biotechnology and Bioinformatics, North Eastern Hill University, Shillong 793022, Meghalaya, India.
authors.forename: Arun Bahadur
authors.initials: AB
authors.lastname: Gurung
authors.affiliation: Department of Biotechnology, Indian Institute of Technology, Kharagpur 721302, West Bengal, India.
authors.forename: Amit Kumar
authors.initials: AK
authors.lastname: Das
authors.affiliation: Computational Biology Laboratory, Department of Biotechnology and Bioinformatics, North Eastern Hill University, Shillong 793022, Meghalaya, India. Electronic address: atanubioinfo@gmail.com.
authors.forename: Atanu
authors.initials: A
authors.lastname: Bhattacharjee
mesh_terms: D000595:Amino Acid Sequence; D000995:Antitubercular Agents / Q000737:chemistry; D002384:Catalysis; D003545:Cysteine / Q000737:chemistry; D004791:Enzyme Inhibitors / Q000737:chemistry*; D006860:Hydrogen Bonding; D007093:Imidazoles / Q000737:chemistry*; D008024:Ligands; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D009025:Morpholines / Q000737:chemistry*; D046912:Multiprotein Complexes / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000378:metabolism; D009169:Mycobacterium tuberculosis / Q000378:metabolism*; D054464:Peroxiredoxins / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000378:metabolism*; D011485:Protein Binding; D055503:Protein Multimerization; D011725:Pyridines / Q000737:chemistry*; D013879:Thioredoxins / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000378:metabolism*
chemical_list: D000995:Antitubercular Agents; D004791:Enzyme Inhibitors; D007093:Imidazoles; D008024:Ligands; D009025:Morpholines; D046912:Multiprotein Complexes; D011725:Pyridines; D013879:Thioredoxins; D054464:Peroxiredoxins; D003545:Cysteine
keywords: Hot spots; Interface residues; Molecular docking; Molecular dynamics simulation; Peroxiredoxin; Thioredoxin