3FV7

OXA-24 beta-lactamase complex with SA4-44 inhibitor

Summary for 3FV7

• Entry DOI: 10.2210/pdb3fv7/pdb
• Descriptor: Beta-lactamase OXA-24, (2S)-2-[[2-methanoyl-7-(methoxycarbonylamino)indolizin-3-yl]amino]-3-methyl-3-sulfino-butanoic acid (3 entities in total)
• Functional Keywords: b-lactamases, enzyme mechanism, carbapenem, inhibitors, hydrolase
• Biological source: Acinetobacter baumannii
• Total number of polymer chains: 1
• Total formula weight: 27984.06

Authors

Bou, G.,Santillana, E.,Sheri, A.,Beceiro, A.,Sampson, J.M.,Kalp, M.,Bethel, C.R.,Distler, A.M.,Drawz, S.M.,Pagadala, S.R.,Van den Akker, F.,Bonomo, R.A.,Romero, A.,Buynak, J.D. (deposition date: 2009-01-15, release date: 2010-02-02, Last modification date: 2023-11-22)

Primary citation

Bou, G.,Santillana, E.,Sheri, A.,Beceiro, A.,Sampson, J.M.,Kalp, M.,Bethel, C.R.,Distler, A.M.,Drawz, S.M.,Pagadala, S.R.,Van den Akker, F.,Bonomo, R.A.,Romero, A.,Buynak, J.D.
Design, synthesis, and crystal structures of 6-alkylidene-2'-substituted penicillanic acid sulfones as potent inhibitors of Acinetobacter baumannii OXA-24 carbapenemase.
J.Am.Chem.Soc., 132:13320-13331, 2010

PubMed Abstract: Class D β-lactamases represent a growing and diverse class of penicillin-inactivating enzymes that are usually resistant to commercial β-lactamase inhibitors. As many such enzymes are found in multi-drug resistant (MDR) Acinetobacter baumannii and Pseudomonas aeruginosa, novel β-lactamase inhibitors are urgently needed. Five unique 6-alkylidene-2'-substituted penicillanic acid sulfones (1-5) were synthesized and tested against OXA-24, a clinically important β-lactamase that inactivates carbapenems and is found in A. baumannii. Based upon the roles Tyr112 and Met223 play in the OXA-24 β-lactamase, we also engineered two variants (Tyr112Ala and Tyr112Ala,Met223Ala) to test the hypothesis that the hydrophobic tunnel formed by these residues influences inhibitor recognition. IC(50) values against OXA-24 and two OXA-24 β-lactamase variants ranged from 10 ± 1 (4 vs WT) to 338 ± 20 nM (5 vs Tyr112Ala, Met223Ala). Compound 4 possessed the lowest K(i) (500 ± 80 nM vs WT), and 1 possessed the highest inactivation efficiency (k(inact)/K(i) = 0.21 ± 0.02 μM(-1)  s(-1)). Electrospray ionization mass spectrometry revealed a single covalent adduct, suggesting the formation of an acyl-enzyme intermediate. X-ray structures of OXA-24 complexed to four inhibitors (2.0-2.6 Å) reveal the formation of stable bicyclic aromatic intermediates with their carbonyl oxygen in the oxyanion hole. These data provide the first structural evidence that 6-alkylidene-2'-substituted penicillin sulfones are effective mechanism-based inactivators of class D β-lactamases. Their unique chemistry makes them developmental candidates. Mechanisms for class D hydrolysis and inhibition are discussed, and a pathway for the evolution of the BlaR1 sensor of Staphylococcus aureus to the class D β-lactamases is proposed.

PubMed: 20822105
DOI: 10.1021/ja104092z

Experimental method

X-RAY DIFFRACTION (2 Å)