Structural Basis for the Interaction and Processing of beta-Lactam Antibiotics by L,D-Transpeptidase 3 (Ldt(Mt3)) from Mycobacterium tuberculosis

Author(s)

Libreros-Zuniga, Gerardo Andres ^{[1, 2, 3]} ; Silva, Catharina dos Santos ^[1] ; Ferreira, Rafaela Salgado ^[4] ; Bertacine Dias, Marcio Vinicius ^{[1, 2]}

Affiliation

^[1] Univ Sao Paulo, Dept Microbiol, Inst Ciencias Biomed, Ave Prof Lineu Prestes, BR-1374 Sao Paulo - Brazil

^[2] Univ Estadual Paulista, Inst Biociencias Letras & Ciencias Exatas, Rua Cristrivao Colombo, BR-2265 Sao Jose Do Rio Preto - Brazil

^[3] Univ Valle, Fac Salud, Dept Microbiol, Calle 4B 36-00, Cali - Colombia

^[4] Univ Fed Minas Gerais, Dept Bioquim & Imunol, Inst Ciencias Biol, Ave Antonio Carlos, BR-6627 Belo Horizonte, MG - Brazil

• Document type: Journal article
• Source: ACS INFECTIOUS DISEASES; v. 5, n. 2, p. 260-271, FEB 2019.
• Web of Science Citations: 1

Abstract

Targeting Mycobacterium tuberculosis peptidoglycans with beta-lactam antibiotics represents a strategy to address increasing resistance to antitubercular drugs. beta-Lactams inhibit peptidoglycan synthases such as L,D-transpeptidases, a group of carbapenem-sensitive enzymes that stabilize peptidoglycans through 3 -> 3 cross-links. M. tuber-culosis encodes five L,D-transpeptidases (Ldt(Mt1)(-5)), of which Ldt(Mt3) is one of the less understood. Herein, we structurally characterized the apo and faropenem-acylated forms of Ldt(Mt)3 at 1.3 and 1.8 A resolution, respectively. These structures revealed a fold and catalytic diad similar to those of other Ldts(Mt) enzymes, supporting its involvement in transpeptidation reactions despite divergences in active site size and charges. The Ldt(Mt3)-faropenem structure indicated that faropenem is degraded after Cys-246 acylation, and possibly only beta-OH-butyrate or an acetyl group (C2H3O) covalently attached to the enzyme remains, an observation that strongly supports the notion that Ldt(Mt3) is inactivated by beta-lactams. Docking simulations with intact beta-lactams predicted key Ldt(Mt3) residues that interact with these antibiotics. We also characterized the heat of acylation involved in the binding and reaction of Ldt(Mt3) for ten beta-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 beta-lactams by Ldt(Mt3,) which may be useful for the development of additional beta-lactams with potential antitubercular activity. (AU)

• FAPESP's process: 15/09188-8 - Biosynthesis of polyether and aminoglycoside antibiotics: structural investigation of unusual enzymes or with synthetic biology applicability
• Grantee: Marcio Vinicius Bertacine Dias
• Support type: Regular Research Grants
• FAPESP's process: 10/15971-3 - Structural characterization of enzymes from antibiotic biosynthetic pathways with biotechnological interest
• Grantee: Marcio Vinicius Bertacine Dias
• Support type: Research Grants - Young Investigators Grants
• FAPESP's process: 16/18721-4 - Structural basis of the elongation and cell division control in Mycobacterium tuberculosis and identification of new drug hits based in fragment trials
• Grantee: Catharina dos Santos Silva
• Support type: Scholarships in Brazil - Doctorate (Direct)