Potential drug targets in Mycobacterium tuberculosis through metabolic pathway analysis

The emergence of multidrug resistant varieties of Mycobacterium tuberculosis has led to a search for novel drug targets. We have performed an insilico comparative analysis of metabolic pathways of the host Homo sapiens and the pathogen M. tuberculosis. Enzymes from the biochemical pathways of M. tuberculosis from the KEGG metabolic pathway database were compared with proteins from the host H. sapiens, by performing a BLASTp search against the non-redundant database restricted to the H. sapiens subset. The e-value threshold cutoff was set to 0.005. Enzymes, which do not show similarity to any of the host proteins, below this threshold, were filtered out as potential drug targets. We have identified six pathways unique to the pathogen M. tuberculosis when compared to the host H. sapiens. Potential drug targets from these pathways could be useful for the discovery of broad spectrum drugs. Potential drug targets were also identified from pathways related to lipid metabolism, carbohydrate metabolism, amino acid metabolism, energy metabolism, vitamin and cofactor biosynthetic pathways and nucleotide metabolism. Of the 185 distinct targets identified from these pathways, many are in various stages of progress at the TB Structural Genomics Consortium. However, 67 of our targets are new and can be considered for rational drug design. As a case study, we have built a homology model of one of the potential drug targets MurD ligase using WHAT IF software. The model could be further explored for insilico docking studies with suitable inhibitors. The study was successful in listing out potential drug targets from the M. tuberculosis proteome involved in vital aspects of the pathogen's metabolism, persistence, virulence and cell wall biosynthesis. This systematic evaluation of metabolic pathways of host and pathogen through reliable and conventional bioinformatic methods can be extended to other pathogens of clinical interest.

[1]  G Vriend,et al.  WHAT IF: a molecular modeling and drug design program. , 1990, Journal of molecular graphics.

[2]  E. Work,et al.  Biochemistry of the Bacterial Cell Wall , 1957, Nature.

[3]  P. R. Sibbald,et al.  The P-loop--a common motif in ATP- and GTP-binding proteins. , 1990, Trends in biochemical sciences.

[4]  E. Fanchon,et al.  "Open" structures of MurD: domain movements and structural similarities with folylpolyglutamate synthetase. , 2000, Journal of molecular biology.

[5]  R. Slayden,et al.  Use of genomics and combinatorial chemistry in the development of new antimycobacterial drugs. , 2000, Biochemical pharmacology.

[6]  Michael Y. Galperin,et al.  Searching for drug targets in microbial genomes. , 1999, Current opinion in biotechnology.

[7]  H. Su,et al.  The salicylate-derived mycobactin siderophores of Mycobacterium tuberculosis are essential for growth in macrophages. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[8]  Darren A. Natale,et al.  The COG database: an updated version includes eukaryotes , 2003, BMC Bioinformatics.

[9]  Sean R. Eddy,et al.  Pfam: multiple sequence alignments and HMM-profiles of protein domains , 1998, Nucleic Acids Res..

[10]  U. Strych,et al.  Characterization of the alanine racemases from two mycobacteria. , 2001, FEMS microbiology letters.

[11]  K. Schleifer,et al.  Peptidoglycan Types of Bacterial Cell Walls and Their Taxonomic Implications , 1973, Bacteriological reviews.

[12]  Amos Bairoch,et al.  The PROSITE database, its status in 2002 , 2002, Nucleic Acids Res..

[13]  Berk Hess,et al.  GROMACS 3.0: a package for molecular simulation and trajectory analysis , 2001 .

[14]  J. Thompson,et al.  The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. , 1997, Nucleic acids research.

[15]  W. Yew,et al.  Adverse neurological reactions in patients with multidrug-resistant pulmonary tuberculosis after coadministration of cycloserine and ofloxacin. , 1993, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[16]  H. Rogers,et al.  Microbial cell walls and membranes , 1980 .

[17]  E. Fanchon,et al.  Crystal structure of UDP‐N‐acetylmuramoyl‐L‐alanine:D‐glutamate ligase from Escherichia coli , 1997, The EMBO journal.

[18]  K. Schleifer,et al.  Peptidoglycan types of bacterial cell walls and their taxonomic implications , 1972, Bacteriological reviews.

[19]  V. Escuyer,et al.  Emerging therapeutic targets in tuberculosis: post-genomic era , 2002, Expert opinion on therapeutic targets.

[20]  Susumu Goto,et al.  The KEGG databases at GenomeNet , 2002, Nucleic Acids Res..

[21]  Alex Bateman,et al.  The InterPro Database, 2003 brings increased coverage and new features , 2003, Nucleic Acids Res..

[22]  Stephen K Burley,et al.  Structural genomics , 1999, Current Biology.

[23]  S. Projan,et al.  New (and not so new) antibacterial targets - from where and when will the novel drugs come? , 2002, Current opinion in pharmacology.

[24]  W Köster,et al.  Bacterial iron transport: mechanisms, genetics, and regulation. , 1998, Metal ions in biological systems.

[25]  L. Wayne,et al.  An in vitro model for sequential study of shiftdown of Mycobacterium tuberculosis through two stages of nonreplicating persistence , 1996, Infection and immunity.

[26]  Scott G. Franzblau,et al.  Drug Targeting Mycobacterium tuberculosis Cell Wall Synthesis: Genetics of dTDP-Rhamnose Synthetic Enzymes and Development of a Microtiter Plate-Based Screen for Inhibitors of Conversion of dTDP-Glucose to dTDP-Rhamnose , 2001, Antimicrobial Agents and Chemotherapy.

[27]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[28]  David Eisenberg,et al.  Structural genomics of Mycobacterium tuberculosis: a preliminary report of progress at UCLA. , 2003, Biophysical chemistry.

[29]  C. Walsh,et al.  Identification of a Mycobacterium tuberculosis gene cluster encoding the biosynthetic enzymes for assembly of the virulence-conferring siderophore mycobactin. , 1998, Chemistry & biology.

[30]  E. Weinberg,et al.  Iron: mammalian defense systems, mechanisms of disease, and chelation therapy approaches. , 1995, Blood reviews.

[31]  J. Thornton,et al.  PROCHECK: a program to check the stereochemical quality of protein structures , 1993 .

[32]  P. Brennan,et al.  Biosynthesis of the arabinogalactan-peptidoglycan complex of Mycobacterium tuberculosis. , 2001, Glycobiology.

[33]  G. Besra,et al.  Biogenesis of the mycobacterial cell wall and the site of action of ethambutol , 1995, Antimicrobial agents and chemotherapy.

[34]  John F. Kennedy,et al.  Bacterial cell wall , 1996 .

[35]  L. Hayes,et al.  Nitrate reduction as a marker for hypoxic shiftdown of Mycobacterium tuberculosis. , 1998, Tubercle and lung disease : the official journal of the International Union against Tuberculosis and Lung Disease.

[36]  B. Barrell,et al.  Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence , 1998, Nature.

[37]  J. Walker,et al.  Distantly related sequences in the alpha‐ and beta‐subunits of ATP synthase, myosin, kinases and other ATP‐requiring enzymes and a common nucleotide binding fold. , 1982, The EMBO journal.

[38]  E. Weinberg,et al.  Iron and susceptibility to infectious disease. , 1974, Science.

[39]  A. Azad,et al.  Biochemistry and molecular genetics of cell‐wall lipid biosynthesis in mycobacteria , 1997, Molecular microbiology.

[40]  S. Cole,et al.  The catalase—peroxidase gene and isoniazid resistance of Mycobacterium tuberculosis , 1992, Nature.

[41]  Amos Bairoch,et al.  The PROSITE database, its status in 1997 , 1997, Nucleic Acids Res..

[42]  L G Wayne,et al.  Glyoxylate metabolism and adaptation of Mycobacterium tuberculosis to survival under anaerobic conditions , 1982, Infection and immunity.

[43]  J. E. Arceneaux,et al.  Microbial iron transport: iron acquisition by pathogenic microorganisms. , 1998, Metal ions in biological systems.