8V9H

GES-5-NA-1-157 complex

Summary for 8V9H

• Entry DOI: 10.2210/pdb8v9h/pdb
• Related: 8V9G
• Descriptor: beta-lactamase, (5R)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-5-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid, 1,2-ETHANEDIOL, ... (7 entities in total)
• Functional Keywords: class a beta-lactamase, carbapenemase, meropenem, antibiotic resistance, hydrolase
• Biological source: Klebsiella pneumoniae
• Total number of polymer chains: 2
• Total formula weight: 64165.12

Authors

Smith, C.A.,Stewart, N.K.,Vakulenko, S.B. (deposition date: 2023-12-08, release date: 2024-04-03, Last modification date: 2024-10-16)

Primary citation

Stewart, N.K.,Toth, M.,Quan, P.,Beer, M.,Buynak, J.D.,Smith, C.A.,Vakulenko, S.B.
Restricted Rotational Flexibility of the C5 alpha-Methyl-Substituted Carbapenem NA-1-157 Leads to Potent Inhibition of the GES-5 Carbapenemase.
Acs Infect Dis., 10:1232-1249, 2024

PubMed Abstract: Carbapenem antibiotics are used as a last-resort treatment for infections caused by multidrug-resistant bacteria. The wide spread of carbapenemases in Gram-negative bacteria has severely compromised the utility of these drugs and represents a serious public health threat. To combat carbapenemase-mediated resistance, new antimicrobials and inhibitors of these enzymes are urgently needed. Here, we describe the interaction of the atypically C5α-methyl-substituted carbapenem, NA-1-157, with the GES-5 carbapenemase. MICs of this compound against , , and producing the enzyme were reduced 4-16-fold when compared to MICs of the commercial carbapenems, reaching clinically sensitive breakpoints. When NA-1-157 was combined with meropenem, a strong synergistic effect was observed. Kinetic and ESI-LC/MS studies demonstrated that NA-1-157 is a potent inhibitor of GES-5, with a high inactivation efficiency of (2.9 ± 0.9) × 10 M s. Acylation of GES-5 by NA-1-157 was biphasic, with the fast phase completing within seconds, and the slow phase taking several hours and likely proceeding through a reversible tetrahedral intermediate. Deacylation was extremely slow ( = (2.4 ± 0.3) × 10 s), resulting in a residence time of 48 ± 6 days. MD simulation of the GES-5-meropenem and GES-5-NA-1-157 acyl-enzyme complexes revealed that the C5α-methyl group in NA-1-157 sterically restricts rotation of the 6α-hydroxyethyl group preventing ingress of the deacylating water into the vicinity of the scissile bond of the acyl-enzyme intermediate. These data demonstrate that NA-1-157 is a potent irreversible inhibitor of the GES-5 carbapenemase.

PubMed: 38511828
DOI: 10.1021/acsinfecdis.3c00683

Experimental method

X-RAY DIFFRACTION (1.5 Å)