Abstract
Inhibition of protein–protein interaction is considered as an innovative approach in the drug development field. In the present study, this strategy has been handled computationally using in-silico tools to identify potential leads against M. tuberculosis, a still undefeatable pathogen. CarD, a translational regulator protein seems to be indispensible for the survival and pathogenicity of M. tuberculosis. Many mutational studies have recommended that inhibition of its interaction with RNA polymerase using small molecules would be a promising therapy against tuberculosis. Hence in this study, using CarD–RNA polymerase complex structure, hotspot residues which favor complex formation were identified with BioLuminate program and Anchor tool. Based on this information, peptide similarity search was carried out by pepMMsMIMIC tool in MMsINC database and virtual screening was done against ZINC database molecules using DOCK Blaster tool. The small molecule hits from both the studies were collected to create a library. Docking studies were carried out with the library molecules against CarD using Glide program and eight molecules were identified as potential hits. Of them, molecules MMs02420750, MMs02489191 and MMs02514414 were found to interact with the important hotspot residues of CarD and thereby are considered to be capable of inhibiting CarD–RNA polymerase complex formation. The binding free energies of the Glide hit complexes were calculated by MM/GBSA approach and molecule MMs02420750 was identified to have more affinity towards CarD and hence taken for molecular dynamics simulation studies to check the stability of the complex. Finally, the ADME profile of this small molecule hit was predicted by QikProp program. This small molecule ligand which interacts with hot spots on CarD to form a stable complex may inhibit CarD from interacting with RNA polymerase and hence can be considered as an initial lead for the development of novel anti-tuberculosis agents.
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Acknowledgements
VGS is thankful to KLEDr.M.S.S.CET for the infrastructural and computational facilities provided. We thank Bioinformatics Resources and Application Facility (BRAF) under C-DAC, Pune, India for computational resources and we thank Schrodinger team for the software facility provided. PMF & RSP are thankful to UGC for fellowship under UGC-BSR-SRF. KDS is thankful to UGC for financial support under UGC-SAP-DRS-II sanctioned to Dept. of Biochemistry, Shivaji University, Kolhapur. KDS is also thankful to DST-PURSE-II sanctioned to Dept. of Microbiology, Shivaji University, Kolhapur. We thank Mr. Vishwambhar Bhandare, Research Associate, Bose Institute, Kolkata for his valuable inputs in this work.
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Shanmuga Priya, V.G., Swaminathan, P., Muddapur, U.M. et al. Peptide Similarity Search Based and Virtual Screening Based Strategies to Identify Small Molecules to Inhibit CarD–RNAP Interaction in M. tuberculosis. Int J Pept Res Ther 25, 697–709 (2019). https://doi.org/10.1007/s10989-018-9716-7
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DOI: https://doi.org/10.1007/s10989-018-9716-7