doi:10.1016/j.bmc.2007.10.075
Copyright © 2007 Elsevier Ltd All rights reserved.
Structure-based optimization of cephalothin-analogue boronic acids as β-lactamase inhibitors
Stefania Morandia, Federica Morandia, b, Emilia Casellia, Brian K. Shoichetb and Fabio Pratia,
, 
aDipartimento di Chimica, Università degli studi di Modena e Reggio Emilia, via Campi 183, 41100 Modena, Italy
bDepartment of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th Street, Byers Hall Room 508D, San Francisco, CA 94158, USA
Received 14 June 2007;
revised 11 October 2007;
accepted 23 October 2007.
Available online 27 October 2007.
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Abstract
Boronic acids have proved to be promising selective inhibitors of β-lactamases, acting as transition state analogues. Starting from a previously described nanomolar inhibitor of AmpC β-lactamase, three new inhibitors were designed to gain interactions with highly conserved residues, such as Asn343, and to bind more tightly to the enzyme. Among these, one was obtained by stereoselective synthesis and succeeded in placing its anionic group into the carboxylate binding site of the enzyme, as revealed by X-ray crystallography of the complex inhibitor/AmpC. Nevertheless, it failed at improving affinity, when compared to the lead from which it was derived. The origins of this structural and energetic discrepancy are discussed.
Keywords: β-Lactamase; Inhibition; Boronic acids; X-ray crystallography
Scheme 1. Mechanism of action of a β-lactamase (a) with a β-lactam (the antibiotic cephalothin) and (b) with a boronic acid. (c) Growing mimesis of cephalothin by boronic acids and their activity against the β-lactamase AmpC.
Scheme 2. Newly designed potential inhibitors of β-lactamases and (+)-pinanediol arylboronates, respectively, needed as their synthetic precursors.
Figure 1. Stereo view of the interactions observed between AmpC and compounds 6–8 in the modelled conformation. (A) Compound 6. (B) Compound 7. (C) Compound 8. Carbon atoms are coloured grey for the protein and orange for the ligands; oxygen atoms, red; nitrogen atoms, blue; sulfur atoms, yellow; boron atoms, magenta. Atomic interactions within hydrogen bonding distance are shown as dashed yellow lines. This figure was generated with Pymol (htpp://pymol.sourceforge.net/).
Scheme 3. Stereoselective synthesis of chiral boronic acids.
Figure 2. Stereo view of the active site region of the AmpC/8 complex determined to 2.0 Å resolution. (A) The 2Fo − Fc electron density map is shown in blue, contoured at 1.0 σ. (B) Interactions observed between AmpC and compound 8 in the crystallographic complex. Carbon atoms are coloured grey for the protein and cyan for the ligand; oxygen atoms, red; nitrogen atoms, blue; sulfur atoms, yellow; boron atoms, magenta. Dashed yellow lines represent key hydrogen bonds. Red spheres represent water molecules. (C) Overlay of the modelled and crystallographic conformations of compound 8 in the AmpC site. Carbon atoms of compound 8 in the modelled conformation, orange; carbon atoms of compound 8 in the crystal structure, cyan. This figure was generated with Pymol (htpp://pymol.sourceforge.net/).
Table 1.
Ki values of the cephalothin-analogue boronic acids versus AmpC
a These
Ki were determined in 50 mM KPi, pH 7.0.
7 The values in TRIS are typically 2-fold lower.
b Differential free energy of binding relative to compound
1, calculated at 298 K. Positive values indicate improved affinity.
Table 2.
Ki values for compounds 5 and 8 against various β-lactamases

Table 3.
Crystallographic summary for the complex AmpC
a Values in parentheses are for the highest resolution shell.
b Values cited were calculated for both molecules in the asymmetric unit.
Table 4.
Interactions in inhibitor bound and native AmpC β-lactamase
a Distances are for monomer 1 of the asymmetric unit.
b Distances are for monomer 2 of the asymmetric unit.
c For the apo structures, see
ref. 20b (PDB code: 1KE4).
d Not present.