Comprehensive Identification of β‑Lactam Antibiotic Polypharmacology in Mycobacterium tuberculosis

Infections with Mycobacterium tuberculosis (Mtb) cause tuberculosis (TB), which requires at
least 6 months of treatment with multiple antibiotics. There is emergent
interest in using β-lactam antibiotics to improve treatment
outcomes for patients. These drugs target cell wall biosynthesis,
but a comprehensive list of enzymes inhibited by β-lactams in Mtb is lacking. In the current study, we sought to identify
and characterize Mtb enzymes inhibited by β-lactam
antibiotics using physiological conditions representative of both
acute and chronic TB disease. We used new activity-based probes based
on the β-lactam antibiotic meropenem due to its approval by
the World Health Organization for TB treatment. Activity-based probes
label enzymes based on both substrate specificity and catalytic mechanism,
enabling precise identification of drug targets. We identified previously
undiscovered targets of meropenem in addition to known cell wall biosynthetic
enzymes. We validated β-lactam binding and hydrolysis for six
newly identified targets: Rv1723, Rv2257c, Rv0309, DapE (Rv1202),
MurI (Rv1338), and LipD (Rv1923). Our results demonstrate that there
are at least 30 enzymes in Mtb vulnerable to inhibition
by meropenem. This is many more β-lactam targets than historically
described, suggesting that efficacy in Mtb is a direct
result of polypharmacology.