PROJECT REPORT

ON
Homology Modeling of Mycobacterium tuberculosis H37Rv gyra Protein :
Design and Evaluation of novel gyrA inhibitors
Submitted in partial fulfillment of the requirements for
the award of degree of

BACHELOR OF TECHNOLOGY
IN
BIOINFORMATICS
By
Anurag Yadav
MRT07UGBBI009

Under the supervision of

Prof. Dwijendra K. Gupta
Co-ordinator, Bioinformatics
Department of Biochemistry
University of Allahabad

Ms.Sarika Sahu
Assistant Professor
School of Biotechnology
Center of Bioinformatics

Session: 2007 2011

SHOBHIT UNIVERSITY
Modipuram Meerut-250110

School of Biotechnology &

Centre for Bioinformatics
Shobhit University, Meerut

Certificate
This is to certify that the work embodied in the project report entitled Homology
Modeling of

Mycobacterium tuberculosis H37Rv gyrA Protein : Design and

Evaluation of novel gyrA inhibitors has been carried out by Mr. Anurag Yadav
under our supervision for the partial fulfillment of the requirements for the degree of
Bachelor of Technology in Biotechnology.

(Prof. D.V. Rai)

Director

(Ms. Sarika Sahu)

Supervisor

DECLARATION

I Anurag Yadav, confirm that this work submitted for assessment is my original
work and is expressed in my own words. Any uses made within it of the works of
other authors in any form (e.g. ideas, equations, figures, text, tables,
programmes) are properly acknowledged at the point of their use. A full list of
the references employed has been included.
I also declare that this project report has not been submitted any where in any
form for the partial fulfillment of the award of degree.
I understand that my project report may be made electronically to the public.

(Anurag Yadav)

Abstract
The present study focuses on determining and validating the structure of a protein target and
conducting a preliminary in silico study on Trovofloxacin and Moxifloxacin compounds for the
design of a putative drug.

gyrA

encodes

Dna

gyrase subunit A,

important

for cell

DNA

replication and

multiplication of bacteria. The crystal structure of gyrA is not available in any structural database.
In this study we modeled a 3D structure of gyrA by X-ray crystal structure of N-terminal domain of
Dna gyrase subunit A of Mycobcterium tuberculosis (PDB ID: 3IFZ, Chain A), used as the template.

The receptor was docked to the gyrA inhibitor drugs and final energy value of each confer obtained
as follows Gatifloxacin (-11.2837), Ciprofloxacin (-11.2814), Norfloxacin (-9.7557), Moxifloxacin (11.3729), Trovafloxacin (-11.4397), Gemifloxacin (-11.0109) and Tamifloxacin (-8.4628) using the
docking suite of MOE. Depending on the energy values the best two drugs, they are Trovafloxacin
and Moxifloxacin are chosen. We tried to improve the binding efficiency and steric compatibility of
these two drugs namely Trovafloxacin and Moxifloxacin.

Several modifications were made to the probable functional groups which were interacting with the
receptor molecule. Analogs of these drug molecule were prepared using ACD ChemSketch and
docked using MOE docking . Trovafloxacin Analog 6 and Moxifloxacin analog 6 were detected with
significant energy values.

ACKNOWLEDGEMENT
First and foremost, I would like to thank my supervisors, Mrs. Sarika Sahu, for his guidance,
support and for sharing his knowledge with me throughout my B.tech and Mr. Surya Pratap
Singh and Mrs. Nutan Chauhan, for proof-reading my thesis and for the great enthusiasm and
motivation that every meeting with her brought..

I am thankful to Prof. Anoop Swarup Vice Chancellor, Shobhit University,

Meerut, for providing all the necessary requirements and for his moral support for this
dissertation work as well during the whole course of B. Tech. I am also thankful to Prof. R.P.
Agarwal, Pro-vice chancellor Shobhit University, Meerut for his honest dedication towards our
education and career and for being with us in various levels of academic pursuits.
In this project, I was greatly assisted, inspired by Prof. Dwijendra Gupta
without them, the completion of this project was almost impossible. With great reverence, I
acknowledge them for providing me an environment to involve as an independent researcher.
Their constant encouragement and affection gave me courage to tackle the failure days, which is
inevitable in a researchers life.
My primary thanks goes to Surya Pratap Singh and Ansul Tiwari for his
deep commitment & guidance. I am also grateful to Dr. Rekha Dixit, Mr. Maneesh Gupta and
Mr.Vikas Gupta for their motivation throughout my project work. It is my pleasure to thank all
the people who helped to turn this project a success.

Contents
List of figures

List of Tables

Abbrevations

10

Abstract

11

1 : Introduction
1.1
1.2
1.3
1.4
1.5
1.6

Motivation
Problem Statement
Introduction to Trovafloxacin
Introduction to Moxifloxacin
Target of Trovafloxacin and Moxifloxacin
Dna gyrase

2 : Literature review
2.1

Intoduction to Mycobacterium genome

2.1.1 Disease caused by Mycobaacterium tuberculosis
2.1.2 Sign and Symptom

2.2 Computer aided drug design

2.2.1 Introduction
2.2.2 Drug design cycle
2.3 Homology modeling
2.3.1 General Procedures
2.4 Docking

3: Materials and Tools

3.1 : ACD/ChemSkecth
3.2 : MOE(Molecular Operating Enviroment)
3.3 : Drug Bank
3.4 : PDB
3.5 : Pubmed
3.6 : Modeller 9v7

4: Methodology
4.1 : Screening for best homologoues templates
4.2 : In silico Comprative Modelling of gyrA protein
4.3 : Model refinement, validation and evaluation
4.4 : Submission of Modeled structure to PMDB
4.5 : Selection of potential drug candidate against gyrA
4.6 : Ligand
4.7 : Docking in MOE
4.7.1 : Methodology Overview

5: Result
5.1 : Docking result with Trovafloxacin Derivative
5.2 : Docking result with Moxifloxacin Derivative

6: Discussion
7: Conclusion
8: Future work
9: References

List of figures

Figure 1: Structure of Trovafloxacin

Figure 2: Structure of Moxifloxacin
Figure 3: M.tuberculosis colonies
Figure 4: Symptoms of M.tuberculosis in Human lung
Figure 5: 3 D structure of target protein
Figure 6: Ramachandran plot of target protein

List of tables

Table 1:

Structure of Trovafloxacin derivatives

Table 2:

Structure of Moxifloxacin derivatives

Table 3:

Docking result with Trovafloxacin derivatives

Table 4:

Docking result with Moxifloxacin derivatives

Abbreviations

gyrA

Dna gyrase subunit A

RMSD

Root Mean Square Deviation

E_conf

Energy of Conformer

Final Energy

PDB

Protein Data Bank

PMDB

Protein Model Database

MW

Molecular Weight

H-Bond

Hydrogen Bond

H-acc

Hydrogen Bond Acceptor

H-don

Hydrogen Bond donor

T.B

Tuberculosis

MDR

Multi Drug Resistance

MTB

Mycobacterium tuberculosis