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Chapter 10 : Crystal Structures of Class C β-Lactamases: Mechanistic Implications and Perspectives in Drug Design
Category: Bacterial Pathogenesis
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The class C enzymes are considered to be the most homogeneous and least effective among the different groups of β-lactamases. The design of novel inhibitors is discussed in this chapter. Besides the “classical” AmpC class C β-lactamases, two related enzymes can be mentioned. The first is an ES class C β-lactamase (Enterobacter cloacae GC1) that deserves special attention from a structural point of view, to understand both its activity and inhibition potential. The second is a cold-adapted enzyme from a psychrophilic microorganism (Psychrobacter immobilis A5) that could lead to a better understanding of bacterial adaptation to temperature. Structures of complexes with class C β-lactamases were used to approach the mechanism of these enzymes. Several consensus binding sites were identified from the crystal structures, and predictions by the computational programs showed some correlation with the experimentally observed binding sites. To investigate the structural bases of these energies, X-ray crystal structures of N289A/13 and N289A/14 were determined to 1.49 and 1.39 Å, respectively. Crystallographic structures of a large number of class C β-lactamases have been reported and studied. As was presented in “Structural Features of the Active Sites of Class C β-Lactamases and Mechanistic Considerations” above, those structures produced a clear picture of different intermediates along the catalytic route of class C β- lactamases. The section entitled “Complexes with Class C β-Lactamases and Drug Design” selected a number of examples where structure-based drug design approaches were successful in identifying and optimizing original inhibitors.
(Top) Overall fold of class C β-lactamases composed of two distinct domains: an all-α domain (left) and an α/β domain (right). (Middle) Views of the active site showing the conserved sequence motifs: S64XXK, Y150(A/S)N, and K315TG. (Bottom) Views of the active site of Ampc C in complex with m-aminophenylboronic acid. Coordinates are taken from PDB entries 2BLS and 3BLS.
Chemical diagrams of compounds 1 to 4 and 6 to 9.
Comparison of the active site of E. coli AmpC in complex with imipenem 2 (left) and moxalactam 3(right). Coordinates are taken from crystallographic structures 1LL5 and 1FCO, respectively.
Views of the active sites of E. coli AmpC inactive mutant (S64G) in complex with cephalothin ( 4 ) showing snapshots along the catalytic pathway of hydrolysis by the β-lactamase: ES (enzyme-substrate complex), EI (acyl-enzyme intermediate), and EP (enzyme product complex). Coordinates are taken from crystallographic structures 1KVL and 1KVM.
Chemical diagrams of compounds 5 and 5*.
Active site of E. cloacae GC1 ES β-lactamase inhibited by cephem 5, leading to intermediate 5* after acylation by reactive serine Ser64 and intramolecular rearrangement. Coordinates are taken from crystallographic structure 1GA0.
Comparison of the active sites of E. cloacae 908R (left) and ES CG1 (right) class C β-lactamases after reaction with methylidene penems 7 and 8, respectively. Coordinates were taken from PDB files 1Y54 and 1ONH.
Possible mechanism of inhibition of class C β-lactamases by methylidene penems leading to a seven-membered dihydrothiazepine ring system after acylation and intramolecular rearrangement.
Chemical diagrams of compounds 10 to 13*.
Chemical diagrams of compounds 14 to 17.
Comparison of the crystal structures of complexes between E. coli AmpC and thiophene-sulfonamide derivatives designed as original non-β-lactam inhibitors. Coordinates of those complexes between AmpC and compounds 15 (top), 16 (middle), and 17 (bottom) were obtained from PDB files 1L2S, 1XGI, and 1XGJ.
Selected structures of class C β-lactamases that were obtained by crystallography a