  Antibiotic resistance is a worldwide challenge. A potential approach to block
resistance is to simultaneously inhibit WT and known escape variants of the
target bacterial protein. Here we applied an integrated computational and
experimental approach to discover compounds that inhibit both WT and
trimethoprim (TMP) resistant mutants of E. coli dihydrofolate reductase (DHFR).
We identified a novel compound (CD15-3) that inhibits WT DHFR and its TMP
resistant variants L28R, P21L and A26T with IC50 50-75 micromoles against WT
and TMP-resistant strains. Resistance to CD15-3 was dramatically delayed
compared to TMP in in vitro evolution. Whole genome sequencing of CD15-3
resistant strains showed no mutations in the target folA locus. Rather, gene
duplication of several efflux pumps gave rise to weak (about twofold increase
in IC50) resistance against CD15-3. Altogether, our results demonstrate the
promise of strategy to develop evolution drugs - compounds which block
evolutionary escape routes in pathogens.
