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

Acta Crystallogr D Biol Crystallogr. 2013 Mar;69(Pt 3):420-31. doi: 10.1107/S0907444912048998. Epub 2013 Feb 16.

Abstract

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. LdtMt2 (Rv2518c), one of two functional L,D-transpeptidases in Mtb, is predominantly expressed over LdtMt1 (Rv0116c). Here, the crystal structure of N-terminally truncated LdtMt2 (residues Leu131-Ala408) is reported in both ligand-free and meropenem-bound forms. The structure of meropenem-inhibited LdtMt2 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 LdtMt2 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 LdtMt2. 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.

Keywords: LdtMt2; Mt2594; Mycobacterium tuberculosis; Rv2518c; antituberculosis drug discovery; carbapenem; l,d-transpeptidases; meropenem; peptidoglycans.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anti-Bacterial Agents / pharmacology*
  • Crystallography, X-Ray
  • Drug Resistance, Microbial / drug effects*
  • Enzyme Inhibitors / pharmacology*
  • Meropenem
  • Mycobacterium tuberculosis / drug effects
  • Mycobacterium tuberculosis / enzymology
  • Peptidyl Transferases / antagonists & inhibitors*
  • Peptidyl Transferases / chemistry*
  • Thienamycins / pharmacology*

Substances

  • Anti-Bacterial Agents
  • Enzyme Inhibitors
  • Thienamycins
  • Peptidyl Transferases
  • Meropenem

Associated data

  • PDB/4GSQ
  • PDB/4GSR
  • PDB/4GSU