Virtual screening identifies broad-spectrum β-lactamase inhibitors with activity on clinically relevant serine- and metallo-carbapenemases

Abstract

Bacteria are known to evade β - lactam antibiotic action by producing β-lactamases (BLs), including carbapenemases, which are able to hydrolyze nearly all available β-lactams. The production of BLs represents one of the best known and most targeted mechanisms of resistance in bacteria. We have performed the parallel screening of commercially available compounds against a panel of clinically relevant BLs: class A CTX-M-15 and KPC-2, subclass B1 NDM-1 and VIM-2 MBLs, and the class C P. aeruginosa AmpC. The results show that all BLs prefer scaffolds having electron pair donors: KPC-2 is preferentially inhibited by sulfonamide and tetrazole-based derivatives, NDM-1 by compounds bearing a thiol, a thiosemicarbazide or thiosemicarbazone moiety, while VIM-2 by triazole-containing molecules. Few broad-spectrum BLs inhibitors were identified; among these, compound 40 potentiates imipenem activity against an NDM-1-producing E. coli clinical strain. The binary complexes of the two most promising compounds binding NDM-1 and VIM-2 were obtained at high resolution, providing strong insights to improve molecular docking simulations, especially regarding the interaction of MBLs with inhibitors.

1,2,4‐Triazole‐3‐Thione Analogues with a 2‐Ethylbenzoic Acid at Position 4 as VIM‐type Metallo‐β‐Lactamase Inhibitors

“…[35] We initiated a discovery and optimization program of MBL inhibitors based on the 1,2,4-triazole-3-thione scaffold, after the discovery by Otto Dideberg's group of its original binding mode in the active site of the di-zinc subclass B3 MBL L1, i. e. a simultaneous coordination of the two Zn ions by the N 2 (Zn1) and S 3 (Zn2) atoms of the heterocyclic moiety. [36] A similar binding mode was more recently reported in the case of the dizinc subclass B1 MBLs VIM-2 [37][38][39] and NDM-1. [39] It is also noteworthy that several studies reporting random virtual and experimental screenings for MBL inhibition retrieved compounds containing this heterocycle in the case of L1, [40] IMP-1, [41] VIM-2 [37,39] and NDM-1.…”

4-Alkyl-1,2,4-triazole-3-thione analogues as metallo-β-lactamase inhibitors

“…The compound simultaneously bound to the two Zn ions through two atoms of its heterocyclic moiety (N 2 for Zn1 and S 3 for Zn2). A similar binding was more recently established for the di-zinc subclass B1 MBLs VIM-2 [37,38] and NDM-1 [39]. It is also noticeable that several other studies, including random in silico and experimental screenings, identified this heterocycle as a potential scaffold for the inhibition of IMP-1 [40], VIM-2 [37] and NDM-1 [41].…”

“…Although less potent, the corresponding compound 39 significantly inhibited VIM-type enzymes. (38,39) was also compatible with inhibition of the same enzymes.…”

“…According to these first results and as the presence of a carboxylic group on the substituent at position 4 has already been highlighted in previous series [38,43], we kept it in a second group of 20 compounds bearing various alkanoic moieties and a phenyl ring at the 5-position (Table 2, compound 3 was added for comparison). We varied the length of the alkanoic chain (20,22,23,26,27), introduced an amide bond (21), heteroatoms (O for 24, S for 25), aromatic rings (28)(29)(30)(31), cyclohexyl moieties (32)(33)(34), or an amine group, protected (36,38,39) or not (35,37).…”

Can We Exploit β-Lactamases Intrinsic Dynamics for Designing More Effective Inhibitors?

“…In MBLs, active site inhibitors can act, disrupting the active nucleophile in the active site or, more often, contain zinc coordinating moieties that may exert off-target toxicity in host zinc enzymes and can be limitedly modulated for adjusting the ADME profile [ 54 ]. Recent studies demonstrated that common inhibition strategies can be overcome by the design of non-covalent cross-class inhibitors able to affect the catalytic efficiency of both SBLs and MBLs [ 63 , 64 ]. However, the availability of allosteric inhibitors would be highly beneficial because of the potential synergistic effect with more “traditional” inhibitors, or for the restoration of β-lactam antibiotic activity.…”