A focused fragment library targeting the antibiotic resistance enzyme - Oxacillinase-48: Synthesis, structural evaluation and inhibitor design

• Published in: European journal of medicinal chemistry Vol. 145; pp. 634 - 648
• Main Authors: Akhter, Sundus, Lund, Bjarte Aarmo, Ismael, Aya, Langer, Manuel, Isaksson, Johan, Christopeit, Tony, Leiros, Hanna-Kirsti S., Bayer, Annette
• Format: Journal Article
• Language: English
• Published: France Elsevier Masson SAS 10-02-2018; Elsevier
• Subjects: Benzoic acid derivatives; Chemistry: 440; Crystal structure; Fragments; Inhibition properties; Kjemi: 440; Matematikk og Naturvitenskap: 400; Mathematics and natural science: 400; Serine-β-lactamase inhibitors; Structure-guided drug design; VDP; DMSO; Fragments; Inhibition properties; Benzoic acid derivatives; NMR; Structure-guided drug design; SPR; Serine-β-lactamase inhibitors; MBL; IC50; OXA; LE; SBL; Crystal structure
• ISSN: 0223-5234; 1768-3254; 1768-3254
• DOI: 10.1016/j.ejmech.2017.12.085

β-Lactam antibiotics are of utmost importance when treating bacterial infections in the medical community. However, currently their utility is threatened by the emergence and spread of β-lactam resistance. The most prevalent resistance mechanism to β-lactam antibiotics is expression of β-lactamase enzymes. One way to overcome resistance caused by β-lactamases, is the development of β-lactamase inhibitors and today several β-lactamase inhibitors e.g. avibactam, are approved in the clinic. Our focus is the oxacillinase-48 (OXA-48), an enzyme reported to spread rapidly across the world and commonly identified in Escherichia coli and Klebsiella pneumoniae. To guide inhibitor design, we used diversely substituted 3-aryl and 3-heteroaryl benzoic acids to probe the active site of OXA-48 for useful enzyme-inhibitor interactions. In the presented study, a focused fragment library containing 49 3-substituted benzoic acid derivatives were synthesised and biochemically characterized. Based on crystallographic data from 33 fragment-enzyme complexes, the fragments could be classified into R1 or R2 binders by their overall binding conformation in relation to the binding of the R1 and R2 side groups of imipenem. Moreover, binding interactions attractive for future inhibitor design were found and their usefulness explored by the rational design and evaluation of merged inhibitors from orthogonally binding fragments. The best inhibitors among the resulting 3,5-disubstituted benzoic acids showed inhibitory potential in the low micromolar range (IC50 = 2.9 μM). For these inhibitors, the complex X-ray structures revealed non-covalent binding to Arg250, Arg214 and Tyr211 in the active site and the interactions observed with the mono-substituted fragments were also identified in the merged structures.
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•A focused fragment library was employed to explore the binding site of oxacillinase-48a.•33 fragment-enzyme complexes were structurally analyzed.•Fragment-enzyme interactions useful for future drug design were identified.•Merged inhibitors with IC50 of 2.9 µM were designed by overly of fragments-enzyme structures and structurally analyze.•A synthetic method for unsymmetrically 3,5-disubstituted benzoic acids was developed.