In Silico Screening for Novel Inhibitors of DNA Polymerase III Alpha Subunit of Mycobacterium tuberculosis (MtbDnaE2, H37Rv)

• Published in: PloS one Vol. 10; no. 3; p. e0119760
• Main Authors: Jadaun, Alka, Sudhakar D, Raja, Subbarao, N., Dixit, Aparna
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 26.03.2015; Public Library of Science (PLoS)
• Subjects: Affinity; Amino acid sequence; Amino acids; Analysis; Antitubercular Agents - chemistry; Antitubercular Agents - metabolism; Bacillus subtilis; Bacterial Proteins - antagonists & inhibitors; Bacterial Proteins - metabolism; Binding; Binding Sites; Coding; Deoxyribonucleic acid; DNA; DNA biosynthesis; DNA polymerase; DNA Polymerase III - antagonists & inhibitors; DNA Polymerase III - metabolism; DNA polymerases; DNA replication; DNA structure; DNA-directed DNA polymerase; Docking; Drug Design; E coli; Enzyme Inhibitors - chemistry; Enzyme Inhibitors - metabolism; Enzymes; Epidemics; Escherichia coli - enzymology; Fitness; Genetic algorithms; Gold; Ligands; Medical screening; Molecular Docking Simulation; Mycobacterium tuberculosis; Mycobacterium tuberculosis - enzymology; Pandemics; Pathogens; Pharmaceutical sciences; Protein Structure, Tertiary; Proteins; Pyrimidinones - chemistry; Pyrimidinones - metabolism; Three dimensional models; Tuberculosis; India
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0119760

Tuberculosis, a pandemic disease is caused by Mycobacterium tuberculosis (Mtb). DNA polymerase III encoded by DnaE2 of Mtb is specifically required for its survival in vivo, and hence can be considered to be a potential drug target. Amino acid sequence analysis of the MtbDnaE2 and its human counterpart does not show any significant similarity. Therefore, a 3D model of the MtbDnaE2 was generated using Modeller 9v10 with the template structure of E. Coli DNA polymerase III alpha subunit (2HNH_A). The generated models were validated using a number of programmes such as RAMPAGE/PROCHECK, VERIFY_3D, and ProSA. MtbDnaE2 has few conserved residues and four conserved domains similar to that present in DNA polymerase III of E. coli. In silico screening was performed with bioactive anti-tuberculosis compounds and 6-AU (a known inhibitor of DNA polymerase III of Bacillus subtilis) and its analogues against the modeled MtbDnaE2 structure. Docking was performed using GOLD v5.2 software which resulted in the identification of top ten compounds with high GOLD fitness scores and binding affinity (X-Score). To further evaluate the efficacy of these compounds, in silico ADMET analysis was performed using MedChem Designer v3. Given their high binding affinity to the targeted MtbDnaE2, which is essential for DNA replication in the Mtb and good ADMET properties, these compounds are promising candidates for further evaluation and development as anti-tubercular agents.