Structural basis for the inhibition of Mycobacterium tuberculosis L,D‐transpeptidase by meropenem, a drug effective against extensively drug‐resistant strains

Difficulty in the treatment of tuberculosis and growing drug resistance in Mycobacterium tuberculosis ( Mtb ) are a global health issue. Carbapenems inactivate L,D‐transpeptidases; meropenem, when administered with clavulanate, showed in vivo activity against extensively drug‐resistant Mtb strains. Ldt Mt2 (Rv2518c), one of two functional L,D‐transpeptidases in Mtb , is predominantly expressed over Ldt Mt1 (Rv0116c). Here, the crystal structure of N‐terminally truncated Ldt Mt2 (residues Leu131–Ala408) is reported in both ligand‐free and meropenem‐bound forms. The structure of meropenem‐inhibited Ldt Mt2 provides a detailed structural view of the interactions between a carbapenem drug and Mtb L,D‐transpeptidase. The structures revealed that the catalytic L,D‐transpeptidase domain of Ldt Mt2 is preceded by a bacterial immunogloblin‐like Big_5 domain and is followed by an extended C‐terminal tail that interacts with both domains. Furthermore, it is shown using mass analyses that meropenem acts as a suicide inhibitor of Ldt Mt2 . Upon acylation of the catalytic Cys354 by meropenem, the `active‐site lid' undergoes a large conformational change to partially cover the active site so that the bound meropenem is accessible to the bulk solvent via three narrow paths. This work will facilitate structure‐guided discovery of L,D‐transpeptidase inhibitors as novel antituberculosis drugs against drug‐resistant Mtb .