Target-Based Antimicrobial Drug Discovery - Bacterial Pathogenesis: Methods and Protocols - page 255

It is generally accepted that a target must be essential for survival (in
a laboratory setting), broadly represented among the target organisms, and
preferably not homologous, or overly so, to a eukaryotic counterpart (4) .It
must also be “druggable,” that is, amenable to inhibition by a small molecule
or biotherapeutic, as well as accessible to such interaction in vivo (5) . When
deciding whether the method used to detect target inhibitors should occur in
the test tube or in whole cells, one must take into account whether the target
is a pathway or a single gene product, whether the target can be isolated, and
whether the cellular environment needs to be considered for target activity.
Until recently, there were only a handful of cellular targets that were proven to
lead to successful antibacterial chemotherapy when inhibited. More recently,
other types of targets have been exploited, and representatives of both sets will
be given below. In addition, assay types that are amenable to use with such
targets will be reviewed. Whether target-driven antimicrobial drug discovery
will ultimately prove more fruitful than tried and true methods remains to be
determined.
2. Methods of Target Identification
One need not look farther than any bacterial physiology text to identify
potential targets for antimicrobial drug discovery. These targets include well-
characterized components of essential biological processes whose usefulness
in chemotherapic intervention of bacterial infection has been validated by
assorted means (discussed below). In general, any enzyme that is proven to be
essential for cellular survival (either in vitro or in vivo) constitutes a starting
platform for drug discovery efforts. A second “class” of targets, which are also
described below, includes virulence factors and their regulatory molecules. A
third “class,” novel targets, generically refers to gene products that are essential
for cellular survival but whose function(s) is poorly understood. Benefits of
focusing drug discovery efforts on a novel target include freedom of intellectual
property issues and increased probability of avoiding compound inactivation
by commonly encountered antibiotic resistance determinants. However, there
are several drawbacks associated with work with novel targets. Perhaps, the
largest obstacle includes developing a functional assay to screen for compounds
that inhibit protein function and thus constitute a potential antimicrobial agent.
Nonetheless, it is exciting to consider that with each deposit of bacterial
genomic sequence content into publicly available databases lies potential novel
targets for antimicrobial drug discovery. To one degree or another, the identi-
fication of potential novel targets includes a bioinformatics-based comparison
of bacterial genomes to delineate genes that are conserved across pathogens of