BACTERIAL RNA POLYMERASE: MANY NATURAL PRODUCTS
BIND IN ADJACENT SUBSITES
Bacterial RNA polymerase has been a validated antibacterial target for
decades. It is the target for rifampicin and derivatives as front-line
agents in combination therapy against Mycobacterium tuberculosis. In
fact, a wide range of natural product scaffolds have been examined
and found to inhibit bacterial transcription by targeting
RNA polymerase.186 One of the most recently approved antibiotics
fidaxomicin, an 18 membered polyketide macrolactone (Figure 13a)
from Dactylosporangium auranticum187 likewise blocks RNA
transcription and has been approved by the FDA for the treatment
of Clostridium difficile infections.188 The drug is poorly adsorbed from
the gastrointestinal tract, supporting its use against C. difficile. As
shown in Figure 13b, rifamycins189 and the natural product
sorangicin190 bind to almost identical subsites of the enzyme while
streptolydigin191 and myxopyronin192 bind in separate subsites.193
The bicyclic phosphate metabolite tagetitoxin from the
phytopathogenic Pseudomonas syringae pv tagetis binds in yet a
fourth subsite coordinating the Mg2þ in the active site.194 Nature
clearly presents a rich variety of small molecular frameworks to target
different pockets in RNAP. The specific binding subsite for
fidaxomycin is not yet determined. One anticipates that other
scaffolds may be found for additional or overlapping RNAP subsites
and that structure-based evaluation might guide combinations
directed against RNAP beyond Tb and C. difficile colitis.