4MBF

Crystal structure of Penam sulfone PSR-4-157 bound to SHV-1 beta-lactamase

Summary for 4MBF

• Entry DOI: 10.2210/pdb4mbf/pdb
• Related: 2H5S 4MBH 4MBK
• Descriptor: Beta-lactamase SHV-1, CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE, 6-({(2R,3S)-3-carboxy-2-methyl-3-[(3-oxopropyl)amino]-2-sulfinopropyl}oxy)-6-oxohexanoic acid, ... (4 entities in total)
• Functional Keywords: class a beta-lactamase, hydrolase, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• Biological source: Klebsiella pneumoniae
• Total number of polymer chains: 1
• Total formula weight: 30687.02

Authors

Rodkey, E.A.,van den Akker, F. (deposition date: 2013-08-19, release date: 2014-07-30)

Primary citation

Rodkey, E.A.,Winkler, M.L.,Bethel, C.R.,Pagadala, S.R.,Buynak, J.D.,Bonomo, R.A.,van den Akker, F.
Penam sulfones and beta-lactamase inhibition: SA2-13 and the importance of the C2 side chain length and composition.
Plos One, 9:e85892-e85892, 2014

PubMed Abstract: β-Lactamases are the major reason β-lactam resistance is seen in Gram-negative bacteria. To combat this resistance mechanism, β-lactamase inhibitors are currently being developed. Presently, there are only three that are in clinical use (clavulanate, sulbactam and tazobactam). In order to address this important medical need, we explored a new inhibition strategy that takes advantage of a long-lived inhibitory trans-enamine intermediate. SA2-13 was previously synthesized and shown to have a lower k(react) than tazobactam. We investigated here the importance of the carboxyl linker length and composition by synthesizing three analogs of SA2-13 (PSR-4-157, PSR-4-155, and PSR-3-226). All SA2-13 analogs yielded higher turnover numbers and k(react) compared to SA2-13. We next demonstrated using protein crystallography that increasing the linker length by one carbon allowed for better capture of a trans-enamine intermediate; in contrast, this trans-enamine intermediate did not occur when the C2 linker length was decreased by one carbon. If the linker was altered by both shortening it and changing the carboxyl moiety into a neutral amide moiety, the stable trans-enamine intermediate in wt SHV-1 did not form; this intermediate could only be observed when a deacylation deficient E166A variant was studied. We subsequently studied SA2-13 against a relatively recently discovered inhibitor-resistant (IR) variant of SHV-1, SHV K234R. Despite the alteration in the mechanism of resistance due to the K→R change in this variant, SA2-13 was effective at inhibiting this IR enzyme and formed a trans-enamine inhibitory intermediate similar to the intermediate seen in the wt SHV-1 structure. Taken together, our data reveals that the C2 side chain linker length and composition profoundly affect the formation of the trans-enamine intermediate of penam sulfones. We also show that the design of SA2-13 derivatives offers promise against IR SHV β-lactamases that possess the K234R substitution.

PubMed: 24454944
DOI: 10.1371/journal.pone.0085892

Experimental method

X-RAY DIFFRACTION (1.54 Å)