|
Internet Electronic Journal of Molecular Design - IEJMD, ISSN 1538-6414, CODEN IEJMAT
| ABSTRACT - Internet Electron. J. Mol. Des. January 2008, Volume 7, Number 1, 12-29 |
Comparative Modeling and Docking Studies of Mycobacterium tuberculosis H37RV rpoB Protein
P. Nataraj Sekhar, P. B. Kavi Kishor, V. C. K. Reddy, E. Prem Kumar, A. Anitha, Ranjith Kumar M., and L. Ananda Reddy
Internet Electron. J. Mol. Des. 2008, 7, 12-29
|
Abstract:
Recently the entire rpoB genes of Mycobacterium leprae and M. tuberculosis
have been sequenced and several mutations associated with rifampin resistance
have been identified in both species. Since no crystal structure was available for
the rpoB protein, a three-dimensional (3D) structure of rpoB protein (a protein
complex involved in the polymerization of ribonucleotides) was generated
computationally in order to understand the mechanisms of ligand binding and the
interactions between the ligand and the protein. Docking experiments for rpoB
were performed with its inhibitors to better understand the drug interactions and
rifampin resistance, thus allowing us to predict the mutations with respect to the
active site of the enzyme and its inhibitor and binding domain. This study may
thus help in the development of rapid diagnostic tests for tuberculosis. A three-dimensional
model of the rpoB protein (NP_215181) is generated based on the
crystal structure of the Thermus thermophilus (PDB: 2CW0) by using the
software MODELLER6v2. The structure having the lowest score was used as
starting point for further minimization computations. The structure having the
lowest energy generated by the conjugate gradient energy minimization, with less
than 0.05 kcal/mol energy gradient, was further assessed by PROCHECK, which
showed that the refined model is reliable. In order to understand the mechanisms
of ligand binding and the interaction between the ligand and the rpoB protein
complex, a flexible docking study was performed using GOLD software. Docking
results indicated that the fourth binding pocket falls in the active site of the
protein. They also indicated that ciprofloxacin is the more preferred inhibitor and
that the residues Gln429, Arg448, Ser450 are determinant residues in binding as
they have strong hydrogen bonding contacts with the ligand. Thus, this study is
useful for the synthesis of novel rpoB inhibitors. Based on docking studies, the
bioactive conformations of the ligands obtained will be useful in building
structure-based 3-D QSAR models. Our results indicate that ciproflaxin is the best
inhibitor against rifampicin resistant rpoB protein.
|