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This article is part of the supplement: Selected articles from the Twelfth Asia Pacific Bioinformatics Conference (APBC 2014): Genomics

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Structural insights into mode of actions of novel natural Mycobacterium protein tyrosine phosphatase B inhibitors

Jaspreet Kaur Dhanjal1, Sonam Grover1, Sudhanshu Sharma2, Ajeet Kumar Singh3 and Abhinav Grover1*

Author Affiliations

1 School of Biotechnology, Jawaharlal Nehru University, New Delhi, India - 110067

2 Department of Biotechnology, Delhi Technological University, New Delhi, India - 110042

3 School of Life Sciences, Jawaharlal Nehru University, New Delhi, India - 110067

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BMC Genomics 2014, 15(Suppl 1):S3  doi:10.1186/1471-2164-15-S1-S3

Published: 24 January 2014



Tuberculosis has become a major health problem being the second leading cause of death worldwide. Mycobacterium tuberculosis secretes a virulence factor, protein tyrosine phosphatase B (mPTPB) in the cytoplasm of host macrophage which suppresses its natural innate immune response and helps the pathogen survive and proliferate in the phagosome. The present study aims at indentifying potent inhibitors of mPTPB by using computational approaches of ligand based molecular modeling and docking studies.


A 3D QSAR model was developed using a set of benzofuran salicylic acid based mPTPB inhibitors with experimentally known IC50 values. The model was generated using the statistical method of principle component regression analysis in combination with step wise forward variable selection algorithm. It was observed that steric and hydrophobic descriptors positively contribute towards the inhibitory activity of the ligands. The developed model had a robust internal as well as external predictive power as indicated by the q2 value of 0.8920 and predicted r2 value of 0.8006 respectively. Hence, the generated model was used to screen a large set of naturally occurring chemical compounds and predict their biological activity to identify more potent natural compounds targeting mPTPB. The two top potential hits (with pIC50 value of 1.459 and 1.677 respectively) had a similar interaction pattern as that of the most potent compound (pIC50 = 1.42) of the congeneric series.


The contour plot provided a better understanding of the relationship between structural features of substituted benzofuran salicylic acid derivatives and their activities which would facilitate design of novel mPTPB inhibitors. The QSAR modeling was used to obtain an equation, correlating the important steric and hydrophobic descriptors with the pIC50 value. Thus, we report two natural compounds of inhibitory nature active against mPTPB enzyme of Mycobacterium tuberculosis. These inhibitors have the potential to evolve as lead molecules in the development of drugs for the treatment of tuberculosis.

QSAR; PTPB; Tuberculosis; Virtual screening; Tyrosine phosphatase; Inhibitor