9V4A

Crystal Structure of Xeruborbactam (QPX7728) in complex with SME-1 class A carbapenemase

Summary for 9V4A

• Entry DOI: 10.2210/pdb9v4a/pdb
• Descriptor: Beta-lactamase SME-1, 1,2-ETHANEDIOL, (1aR,7bS)-5-fluoro-2-hydroxy-1,1a,2,7b-tetrahydrocyclopropa[c][1,2]benzoxaborinine-4-carboxylic acid, ... (5 entities in total)
• Functional Keywords: boronic acid, complex, carbapenemase, hydrolase
• Biological source: Serratia marcescens
• Total number of polymer chains: 1
• Total formula weight: 30758.25

Authors

Dhankhar, K.,Baidya, S.,Hazra, S. (deposition date: 2025-05-23, release date: 2025-10-08, Last modification date: 2025-10-22)

Primary citation

Dhankhar, K.,S R Nair, A.,Hazra, M.,Alhmeidi Alkhatib, A.E.,Baidya, S.,Mishra, N.C.,Hazra, S.
Structural Insights into the Role of the Stereochemistry of the Cyclopropyl Ring in the Inhibitory Activity of Xeruborbactam against SME-1 Class A Carbapenemase.
Biochemistry, 64:4217-4231, 2025

PubMed Abstract: Xeruborbactam is a boronic acid-based transition-state analogue that has exhibited great potential as a clinically relevant inhibitor of carbapenemase enzymes, including class A carbapenemases. In this work, we have investigated the mechanism of inhibition of xeruborbactam against SME-1 carbapenemase using kinetic, structural, and thermodynamic approaches. With a (app) of 4 nM, xeruborbactam shows more potent inhibitory activity than any other beta-lactamase inhibitor available until now. Structural data from crystal complexes revealed that xeruborbactam covalently engages Ser70 at the active site and forms stabilizing interactions; in particular, the cyclopropyl group forms hydrophobic interactions with His105, further stabilizing the adduct, which correlates with a high rate of borylation and minimal deborylation. We investigated xeruborbactam with its 2,3-cyclopropyl isomer to grasp the influence of the stereochemistry of the cyclopropyl ring. Although both inhibitors bind covalently to Ser70 in SME-1, the 2,3-isomer adopts a different conformation of the cyclopropyl ring, which makes the C3 carbon much farther from His105, Asn132, and Lys73, thereby decreasing the binding affinity and (app) of the isomer. Furthermore, the fluorine-12 atom takes different conformations in the two structures, changing the terrain of interaction with the protein. Consistent with its lowered inhibition efficiency, the 2,3-isomer shows a lower borylation rate and weaker enzyme-inhibitor binding. In the molecular dynamics, xeruborbactam stabilized SME-1 more than its isomer, which is consistent with our experimental findings. These results together show the strong inhibitory profile of xeruborbactam and highlight the importance of stereochemistry in the design of next-generation β-lactamase inhibitors and diagnostics for AMR.

PubMed: 41002159
DOI: 10.1021/acs.biochem.5c00336

Experimental method

X-RAY DIFFRACTION (2.4 Å)