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Structural basis for the interaction and processing of β-Lactam antibiotics by l,d-transpeptidase 3 (LdtMt3) from mycobacterium tuberculosis

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Libreros-Zúñiga, Gerardo Andrés, dos Santos Silva, Catharina, Salgado Ferreira, Rafaela and Dias, Marcio Vinicius Bertacine (2019) Structural basis for the interaction and processing of β-Lactam antibiotics by l,d-transpeptidase 3 (LdtMt3) from mycobacterium tuberculosis. ACS Infectious Diseases, 5 (2). pp. 260-271. doi:10.1021/acsinfecdis.8b00244 ISSN 2373-8227.

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Official URL: http://dx.doi.org/10.1021/acsinfecdis.8b00244

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Abstract

Targeting Mycobacterium tuberculosis peptidoglycans with β-lactam antibiotics represents a strategy to address increasing resistance to antitubercular drugs. β-Lactams inhibit peptidoglycan synthases such as l,d-transpeptidases, a group of carbapenem-sensitive enzymes that stabilize peptidoglycans through 3 → 3 cross-links. M. tuberculosis encodes five l,d-transpeptidases (LdtMt1–5), of which LdtMt3 is one of the less understood. Herein, we structurally characterized the apo and faropenem-acylated forms of LdtMt3 at 1.3 and 1.8 Å resolution, respectively. These structures revealed a fold and catalytic diad similar to those of other LdtsMt enzymes, supporting its involvement in transpeptidation reactions despite divergences in active site size and charges. The LdtMt3–faropenem structure indicated that faropenem is degraded after Cys-246 acylation, and possibly only a β-OH-butyrate or an acetyl group (C2H3O) covalently attached to the enzyme remains, an observation that strongly supports the notion that LdtMt3 is inactivated by β-lactams. Docking simulations with intact β-lactams predicted key LdtMt3 residues that interact with these antibiotics. We also characterized the heat of acylation involved in the binding and reaction of LdtMt3 for ten β-lactams belonging to four different classes, and imipenem had the highest inactivation constant. This work provides key insights into the structure, binding mechanisms, and degradation of β-lactams by LdtMt3, which may be useful for the development of additional β-lactams with potential antitubercular activity.

Item Type: Journal Article
Divisions: Faculty of Science, Engineering and Medicine > Science > Chemistry
Journal or Publication Title: ACS Infectious Diseases
Publisher: American Chemical Society (ACS)
ISSN: 2373-8227
Official Date: 8 February 2019
Dates:
DateEvent
8 February 2019Published
17 December 2018Available
17 September 2018Accepted
Volume: 5
Number: 2
Page Range: pp. 260-271
DOI: 10.1021/acsinfecdis.8b00244
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Restricted or Subscription Access

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