Cyclobutanone Mimics of Intermediates in Metallo‐β‐Lactamase Catalysis

Abstract

The most important resistance mechanism to β‐lactam antibiotics involves hydrolysis by two β‐lactamase categories: the nucleophilic serine and the metallo‐β‐lactamases (SBLs and MBLs, respectively). Cyclobutanones are hydrolytically stable β‐lactam analogues with potential to inhibit both SBLs and MBLs. We describe solution and crystallographic studies on the interaction of a cyclobutanone penem analogue with the clinically important MBL SPM‐1. NMR experiments using 19F‐labeled SPM‐1 imply the cyclobutanone binds to SPM‐1 with micromolar affinity. A crystal structure of the SPM‐1:cyclobutanone complex reveals binding of the hydrated cyclobutanone through interactions with one of the zinc ions, stabilisation of the hydrate by hydrogen bonding to zinc‐bound water, and hydrophobic contacts with aromatic residues. NMR analyses using a 13C‐labeled cyclobutanone support assignment of the bound species as the hydrated ketone. The results inform on how MBLs bind substrates and stabilize tetrahedral intermediates. They support further investigations on the use of transition‐state and/or intermediate analogues as inhibitors of all β‐lactamase classes.

Metallo-β-Lactamase Inhibitors Inspired on Snapshots from the Catalytic Mechanism

“…More recently, Dmitrienko et al [ 156 ] reconsidered this strategy using cyclobutanones with penem rings. Among the several studied derivatives, cyclobutanone 7 ( Figure 6 ) was identified as a good inhibitor of class A and C SBLs while displaying a weak inhibition of the B1 enzyme IMP-1 ( Table 1 ) [ 156 , 193 ]. X-ray crystallography by the Spencer and Schofield groups succeeded in trapping cyclobutanone 7 bound to the MBL SPM-1 in its hydrated form, as confirmed by Nuclear Magnetic Resonance (NMR) spectroscopy.…”

“…X-ray crystallography by the Spencer and Schofield groups succeeded in trapping cyclobutanone 7 bound to the MBL SPM-1 in its hydrated form, as confirmed by Nuclear Magnetic Resonance (NMR) spectroscopy. The bound species presents a tetrahedral C6 with two oxygen atoms, mimicking the transition state generated during β-lactam hydrolysis [ 156 , 193 ]. The C6 oxygen atoms do not form any binding interaction with Zn1 but subtend hydrogen bonds with the preserved bridging water, suggesting that this species is formed in solution and binds the metal site with a tetrahedral carbon atom.…”

“… Binding mode of the transition state mimics. Crystal complexes of ( a ) cyclobutanone:SPM-1 (PDB 5ndm) [ 193 ], ( b ) Taniborbactam:VIM-2 (PDB 6sp7) [ 183 ], ( c ) Taniborbactam:NDM-1 (chain B PDB 6rmf) [ 162 ], and ( d ) 14 :BcII (PDB 5fqb) [ 147 ]. Hydrogen bonds and metal ligands interactions are drawn with dashed lines.…”

The Development of New Small-Molecule Inhibitors Targeting Bacterial Metallo-β-lactamases

“…The intensity of the effort to discover effective MBL inhibitors is underscored by the diversity of publications that have occurred since the editorial acceptance of this review. These new efforts include complementary review [80,81] experimental studies on the structure and mechanism of the MBLs [82][83][84][85][86] ; computational study of the MBL mechanism [87,88] ; ITC as a screening method for inhibitor discovery [89] ; new inhibitor structures [90][91][92][93][94][95] ; thiol-modified NOTA inhibitor structures [96] ; and computational screening in support of new inhibitor discovery [97][98][99].…”

Both the mono- and di-anions of ellagic acid are effective inhibitors of the serine β-lactamase CTX-M-15

“…5 By contrast the class B enzymes are metallo-b-lactamases (MBLs) 6 which employ 1 or 2 Zn ions as part of their catalytic machinery and are distinct mechanistically from the SBLs. 7,8 Approved SBL inhibitors are usually paired with a b-lactam antibiotic (BLICs), 9 such as amoxicillin/clavulanate, ampicillin/ sulbactam, and piperacillin/tazobactam. 10 These combinations work well against class A b-lactamases, but are less effective against class C and D enzymes.…”