In-silico identification of potential drug targets

from different Mycobacterium sp

Dissertation submitted in partial fulfillment of the

requirements for the degree of

Master of Science

In

Biotechnology

By

Divakaran.G.K

[07MSB037]

SCHOOL OF BIOTECHNOLOGY, CHEMICAL AND

BIOMEDICAL ENGINEERING

VIT UNIVERSITY

Vellore-632014, Tamil Nadu, India

May-2009
 Certificate
This is to certify that dissertation entitled “In-silico identification of
potential drug targets from different Mycobacterium sp” submitted by
Divakaran.G.K (07MSM037) to the School of Biotechnology, Chemical
and Biomedical engineering, VIT University, Vellore in partial fulfillment
of the requirements for the degree of Master of Science in Biotechnology is
a bonafide record of work carried out by him under my supervision. The
contents of this dissertation, in full or in parts have not been submitted to
any other institute or university for the award of any degree or diploma.

Project Guide Division Leader

Division of Medical Biotechnology

SBCBE

Internal Examiner External Examiner

 Declaration
I hereby declare that the study entitled “In-silico identification of
potential drug targets from different Mycobacterium sp” is bonafide
and has been prepared under the supervision and guidance of
Dr.Sundandira doss, Professor, School of Biotechnology, Chemical and
Biomedical Engineering, VIT University, Vellore in partial fulfillment of
the requirements for the degree of Master of Science in Biotechnology.

Date: Divakaran.G.K

Place: 07MSB037
Acknowledgement
It gives me immense pleasure to acknowledge our honourable
Chancellor Mr. G. Viswanathan who is a quintessence of determination
and excellence. His penchant for being ahead of his contemporaries has set
new benchmark for both the staff and the students of VIT.

I would also like to thank Honourable Pro-Chancellors, Mr. G.

V. Sampath(Administration) and Mr. G. V. Shankar (Academic) and
Vice-Chancellor Dr. Radha Krishnan for providing amenities for my
project work.

I am very much grateful to Dr. Lazar Mathew, Dean of SBCBE

who was always for his support during the time of my project.

I extend my hearty gratitude to my Guide Dr. Sutindira doss

who has been a source of inspiration for suggesting the topic, inspiring
guidance, constructive criticism and invaluable advice for the successful
completion of the project.

I wish to thank Mr. George priya doss (research scholar), and

my friends for their support and help throughout the project.
Abstract

Infectious diseases remain as a serious threat to the mankind because of the

emergence of multidrug resistant varieties of different Mycobacterium sp has led to
a search for novel drug targets. I have performed an in-silico comparative analysis
of metabolic pathways of different Mycobacterium sp with the metabolic pathway
of the host (Homo sapiens). Enzymes involved in different metabolic pathways are
extracted from KEGG metabolic pathway and were compared with the proteins
from the host (Homo sapiens). The e-value threshold was set to 0.01 using the
option available in NCBI blast search engine. The enzymes which do not have
similarity were filtered out and listed as potential targets. These potential drug
targets can be useful in developing broad spectrum drugs. Potential drug targets
from pathways amino acid metabolism, nucleotide metabolism, energy
metabolism, carbohydrate metabolism were identified and listed out. The identified
drug-targets from M.leprae were subjected to choke point analysis for the further
identification of best targets from its whole genome. Around 3500 genes were
subjected to these analysis and about 170 genes were identified as potential drug
targets. Preference can be given to these identified targets in drug-discovery
process so that any chances for side effects will be very less and the chances of
developing drug-resistance will be low.

The study was successful in listing out the potential drugs targets from
different Mycobacterium sp involved in vital aspects of the pathogen’s metabolism,
persistence and virulence. This method can be adapted to other pathogens and
further the identified targets can be analyzed using molecular docking techniques
for screening of inhibitors.
 Contents

S.No. Title Page No.

1. INTRODUCTION 1

1.1 Impact of Leprosy on mankind 2

1.2 Global Prevalence of leprosy 3

1.3 Diagnosis and treatment methods for leprosy 5

1.4 Emergence of Drug-resistance varieties 6

1.5 Genome of Mycobacterium leprae TN 7

2. REVIEW OF LITERATURE 10

3. OBJECTIVES 24

4. MATERIALS AND METHODS

4.1.1 Identification of potential drug targets from M.leprae Genome 25

4.1.2 Identification of orthologous groups 25

4.1.3 Choke point analysis of the potential targets 25

4.1.4 Isozyme analysis 26

4.2 Identification of potential drug targets from

Mycobacterium Avium paratuberculosis k-10 genome. 27

 4.3 Identification of potential drug targets from

Mycobacterium gilvum PYR-GCK genome 27

4.4 Identification of potential drug targets from

Mycobacterium avium 104 genome 28

5. RESULTS AND DISCUSSION

5.1 Potential drug-target genes from different

Mycobacterium sp. 29

5.2.1 Pathways unique to M.leprae (pathogen) compared

to Homo sapiens (host) 29

5.2.2 Targets from Amino acid metabolism 30

5.2.3. Targets from Carbohydrate metabolism 31

5.3 Genes involved in multiple metabolic pathways 32

6. SUMMARY 59

7. BIBLIOGRAPHY 60
 Lists of tables
Table no. Particulars Page no.

Table 1 Identified potential gene targets from

Mycobacterium leprae TN 33

Table 2 Identified potential gene targets from

Mycobacterium Avium paratuberculosis k-10 genome 37

Table 3 Identified potential gene targets from

Mycobacterium gilvum PYR-GCK genome 40

Table 4 Identified potential gene targets from

Mycobacterium avium 104 genome 44

Table 5 Identified potential gene targets from

Mycobacterium leprae TN after choke point analysis 56

 Lists of figures
Fig no. Particulars Page no.

1.1 Genome of M.leprae 9

2.1 The average length of proteins present in M.leprae 30
3.1 Nucleotide composition values of Mycobacterium

leprae genome 31
ABBREVIATIONS

BB Mid –borderline

BL Borderline lepromatous

BT Borderline tuberculoid

ENL Erythema nodosum leprosum

IFN interferon

IL interleukin

LL lepromatous

MB Multibacillary

MDT Multidrug therapy

PB Paucibacillary

PGL-I Phenolic glycolipid

RR Reversal reaction

TT Tuberculoid

MDT Multiple drug treatment method

ng nanogram

ml milliliter