1MY8

AmpC beta-lactamase in complex with an M.carboxyphenylglycylboronic acid bearing the cephalothin R1 side chain

Summary for 1MY8

• Entry DOI: 10.2210/pdb1my8/pdb
• Related: 1FSY 1KE4 1MXO
• Descriptor: beta-lactamase, PHOSPHATE ION, (1R)-1-(2-THIENYLACETYLAMINO)-1-PHENYLMETHYLBORONIC ACID, ... (4 entities in total)
• Functional Keywords: ampc, beta-lactamase, cephalosporinase, serine hydrolase, hydrolase
• Biological source: Escherichia coli
• Cellular location: Periplasm: P00811
• Total number of polymer chains: 2
• Total formula weight: 79821.08

Authors

Morandi, F.,Caselli, E.,Morandi, S.,Focia, P.J.,Blazquez, J.,Shoichet, B.K.,Prati, F. (deposition date: 2002-10-03, release date: 2003-03-04, Last modification date: 2024-10-30)

Primary citation

Morandi, F.,Caselli, E.,Morandi, S.,Focia, P.J.,Blazquez, J.,Shoichet, B.K.,Prati, F.
Nanomolar inhibitors of AmpC beta-lactamase.
J.Am.Chem.Soc., 125:685-695, 2003

PubMed Abstract: beta-lactamases are the most widespread resistance mechanism to beta-lactam antibiotics, such as the penicillins and the cephalosporins. In an effort to combat these enzymes, a combination of stereoselective organic synthesis, enzymology, microbiology, and X-ray crystallography was used to design and evaluate new carboxyphenyl-glycylboronic acid transition-state analogue inhibitors of the class C beta-lactamase AmpC. The new compounds improve inhibition by over 2 orders of magnitude compared to analogous glycylboronic acids, with K(i) values as low as 1 nM. On the basis of the differential binding of different analogues, the introduced carboxylate alone contributes about 2.1 kcal/mol in affinity. This carboxylate corresponds to the ubiquitous C3(4)' carboxylate of beta-lactams, and this energy represents the first thermodynamic measurement of the importance of this group in molecular recognition by class C beta-lactamases. The structures of AmpC in complex with two of these inhibitors were determined by X-ray crystallography at 1.72 and 1.83 A resolution. These structures suggest a structural basis for the high affinity of the new compounds and provide templates for further design. The highest affinity inhibitor was 5 orders of magnitude more selective for AmpC than for characteristic serine proteases, such as chymotrypsin. This inhibitor reversed the resistance of clinical pathogens to the third generation cephalosporin ceftazidime; it may serve as a lead compound for drug discovery to combat bacterial resistance to beta-lactam antibiotics.

PubMed: 12526668
DOI: 10.1021/ja0288338

Experimental method

X-RAY DIFFRACTION (1.72 Å)