Genomics and Tuberculosis Research
The completion of the genome of Mycobacterium tuberculosis presents
an enormous opportunity for understanding its pathogenesis,
exploring drug resistance mechanisms
identifying drug targets, and developing more effective new drugs.
This scenario is further reinforced by
high throughput gene expression analysis based on a microarray,
a chip on which tens of thousands of genes are implanted.
How the tubercle bacillus develops resistance to INH (isoniazid) is
a classical example to illustrate a common mechanism of drug resistance.
As INH is activated by an enzyme called
catalase-peroxidase of the bacillus, lack or alteration of this
enzyme leads to drug resistance.
An estimated 50% or more of INH resistance is caused
by deletion or mutation in the katG gene, which encodes
the sole catalase-peroxidase activity in the cell.
It is thus possible to demonstrate the altered expression level
of the katG gene for at least some INH-resistant strains
in the microarray experiment.
The hope here is that we can discover more drug-resistance
associated genes much quicker than before.
Drug Discovery based on Genomics
Of the estimated 4000 proteins in M. tuberculosis genome,
about 40% have known biochemical functions, another 44%
have some sequence homology, and 16% are completely unknown.
The focus of mycobacterial research now has shifted from gene
hunting to understanding of genome behavior in an attempt to
find clues for new drugs.
Potential drug targets can be selected using a variety of
bioinformatic methods such as protein phylogenetic profiling,
and screened for certain physical and chemical properties.
Since Mycobacteria are prokaryotic organisms (without cell nucleus membrane)
and the human host is an eukaryote (with cell nucleus membrane),
the basic idea here is to select genes which are
linked to essential prokaryotic genes but non-essential or absent
The traditional approach focuses on
rate-limiting steps in metabolic pathways unique to prokaryotes.
Many such targets are obvious given the genome sequence.
which are specific to M. tuberculosis can be recognized by bioinformatic
analysis and confirmed by molecular biology methods.
Criteria based on protein solubility, domain size, and so on
are also required for target selection.
Differential gene expression as monitored by
DNA microarrays coupled with the discipline of combinatorial chemistry
(ref. 1) is the emerging fundamental principle
for high throughput drug discovery.
The metabolism of the tubercle bacillus in the in vivo
environment can be studied by taking the specimen from
infected cells by bronchial lavage, for example.
This will provide additional information on top of
that from the in vitro bacterial culture study.
Many current antimycobacterials require some form of cellular activation
such as hydrolysis, oxidation, or reduction
to convert an inactive prodrug to active drug.
Understanding the processes involved in drug activation will
facilitate the development of analogs with
alternative activation mechanisms or even none.
Barry, C.E., Slayden, R.A., Sampson, A.E., Lee, R.E. 2000.
Use of genomics and combinatorial chemistry in the
development of new antimycobacterial drugs.
Biochem Pharmacol 59(3):221-31.