Target-Based Antimicrobial Drug Discovery - Bacterial Pathogenesis: Methods and Protocols - page 258

Different classes of antibiotics have been defined that target various structures
and functions of the protein synthetic apparatus. For example, the aminogly-
cosides target the 30S ribosomal subunit, whereas the 50S subunit is the target
of many antibiotic classes, including the phenyl propanoids, streptogramins,
the macrolides, and the ketolides to name a few (19) . An interesting aspect
of ribosomal-based antimicrobial antibiotics is the critical role of agent-RNA
interaction in this macromolecular structure. In addition, the fact that the
ribosomal RNA is primarily the target and that it is so remarkably conserved
among bacteria makes ribosome-based antimicrobial chemotherapy amenable
to empirical use. The exquisitely detailed understanding of ribosomal three-
dimensional structure makes this a particularly rich source for target-based drug
design (21) . Additional components of the translational machinery have also
recently been explored, and these will be described below.
3.4. Transcription and Replication
Two multipart molecular machines (holoenzymes) that continue to be
exploited for potential antimicrobial inhibition are RNA polymerase, an enzyme
comprised of multiple conserved subunits and required for the transcription
of the bacterial genome (22) , and the replisome, required for its replication
(23) . The 1950s witnessed the identification of the rifamycins, which target the
RpoB subunit of RNA polymerase and of which rifampicin is one of the most
potent antibiotics yet discovered (14) . Unfortunately, resistance to this class of
antibiotics can occur readily, limiting their usefulness. Thus far, this enzyme
complex has remained somewhat intractable to target-based drug discovery but
may yet prove to have an Achilles' heel. Somewhat later than the rifamycins,
members of the quinolone class were described, which target DNA gyrase and
topoisomerase activities of the replisome. Quinolones have been exploited and
expanded extensively by synthetic modification; however, it is likely that much
could be done to identify novel inhibitors of the replicative machinery as better
tools to probe the dynamic structure of the complexes come into use.
3.5. Other Validated Antibacterial Targets
Two other validated targets for antimicrobial chemotherapy will be mentioned
here, both of which are defined by pathway inhibition. The earliest antibi-
otics, the sulfonamides, are inhibitors of the folate biosynthetic pathway (24) .
Sulfamethoxazole and trimethoprim, targeting dihydropteroate synthase and
dihydrofolate reductase, respectively, are each susceptible to rapid emergence
of resistance but have been used successfully in combination. Recently, other
enzymes in the pathway have begun to engender interest for target-based
screening. Fatty acid biosynthesis is another pathway that has previously been