title: Homology modelling, docking, pharmacophore and site directed mutagenesis analysis to identify the critical amino acid residue of PknI from Mycobacterium tuberculosis.
abstract: Tuberculosis is caused by Mycobacterium tuberculosis, an intracellular pathogen. PknI is one of the 11 functional Serine/Threonine Protein Kinases which is predicted to regulate the cell division of M. tuberculosis. In order to find newer drugs and vaccine we need to understand the pathogenesis of the disease. We have used the bioinformatics approach to identify the functionally active residues of PknI and to confirm the same with wet lab experiments. In the current study, we have created homology model for PknI and have done comparative structural analysis of PknI with other kinases. Molecular docking studies were done with a library of kinase inhibitors and T95 was found as the potent inhibitor for PknI. Based on structure based pharmacophore analysis of kinase substrate complexes, Lys 41 along with Asp90, Val92 and Asp96 were identified as functionally important residues. Further, we used site directed mutagenesis technique to mutate Lys 41 to Met resulting in defective cell division of Mycobacterium smegmatis mc(2). Overall, the proposed model together with its binding features gained from pharmacophore docking studies helped in identifying ligand inhibitor specific to PknI which was confirmed by laboratory experiments.
authors: Department of Immunology, National Institute for Research in Tuberculosis (NIRT) (ICMR), Chetput, Chennai 600 031, Tamilnadu, India.
authors: Srinivasan
authors: S
authors: Kandasamy
authors: Department of Biomedical Informatics, National Institute for Research in Tuberculosis (NIRT) (ICMR), Chetput, Chennai 600 031, Tamilnadu, India.
authors: Sameer
authors: S
authors: Hassan
authors: Department of Immunology, National Institute for Research in Tuberculosis (NIRT) (ICMR), Chetput, Chennai 600 031, Tamilnadu, India.
authors: Radha
authors: R
authors: Gopalaswamy
authors: Department of Immunology, National Institute for Research in Tuberculosis (NIRT) (ICMR), Chetput, Chennai 600 031, Tamilnadu, India. Electronic address: sujatha.sujatha36@gmail.com.
authors: Sujatha
authors: S
authors: Narayanan
mesh_terms: D000255:Adenosine Triphosphate / Q000378:metabolism; D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry*; D001426:Bacterial Proteins / Q000737:chemistry*; D015153:Blotting, Western; D062105:Molecular Docking Simulation; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D009169:Mycobacterium tuberculosis / Q000201:enzymology* / Q000254:growth & development; D011494:Protein Kinases / Q000737:chemistry* / Q000378:metabolism; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D040681:Structural Homology, Protein
chemical_list: D000596:Amino Acids; D001426:Bacterial Proteins; D000255:Adenosine Triphosphate; D011494:Protein Kinases
keywords: Docking; Homology modelling; Pharmacophore analysis; Protein kinases; Site directed mutagenesis; Substrate