Rhodanine hydrolysis leads to potent thioenolate mediated metallo-β-lactamase inhibition

Abstract

The use of β-lactam antibiotics is compromised by resistance, which is provided by β-lactamases belonging to both metallo (MBL)- and serine (SBL)-β-lactamase subfamilies. The rhodanines are one of very few compound classes that inhibit penicillin-binding proteins (PBPs), SBLs and, as recently reported, MBLs. Here, we describe crystallographic analyses of the mechanism of inhibition of the clinically relevant VIM-2 MBL by a rhodanine, which reveal that the rhodanine ring undergoes hydrolysis to give a thioenolate. The thioenolate is found to bind via di-zinc chelation, mimicking the binding of intermediates in β-lactam hydrolysis. Crystallization of VIM-2 in the presence of the intact rhodanine led to observation of a ternary complex of MBL, a thioenolate fragment and rhodanine. The crystallographic observations are supported by kinetic and biophysical studies, including (19)F NMR analyses, which reveal the rhodanine-derived thioenolate to be a potent broad-spectrum MBL inhibitor and a lead structure for the development of new types of clinically useful MBL inhibitors.

19F‐NMR Reveals the Role of Mobile Loops in Product and Inhibitor Binding by the São Paulo Metallo‐β‐Lactamase

“…Thus, binding of 1 influences both the α3 and L3 regions (Figures S22–24). Interestingly, however, the results imply that 1 binds to SPM‐1 in the presence of ML302F, which is known to bind to the active site zinc ions 17. Together with the observation that 1 binds to apo ‐Y58C* as evidenced by line broadening (Figure 2 C), the results imply that 1 binds to SPM‐1 in an unprecedented manner that does not involve coordination to the zinc ions.…”

“…Significant line broadening, which is typical of a system in intermediate exchange, was observed when isoquinoline ( 1 )13, 14 was titrated with Y58C*. Addition of ML302F17 to a sample containing Y58C* and 1 led to the appearance of the peak characteristic of the ML302F‐bound complex and a new peak deshielded by 1.1 ppm relative to that of the Y58C* peak (Figure 2 C). With F151C*, 1 induced broadening and chemical‐shift changes (Figure 2 D).…”

Cross-class metallo-β-lactamase inhibition by bisthiazolidines reveals multiple binding modes

“…For comparison, we have also solved, to 1.98 Å resolution, the structure of uncomplexed dizinc IMP-1, also in the space group P2 1 2 1 2 1 (SI Results). BcII crystallized in the previously described space group C2 (30), with one molecule in the ASU and one molecule of 1b identified in the active site (B-factor 1.6 times greater than the main chain). Sfh-I crystallized in space group P2 1 (14), with 1a clearly defined in both monomers of the ASU (B-factors 1.2 times greater than the protein main chain).…”

Isatin derivatives with activity against apoptosis-resistant cancer cells

“…21 Rhodanine ( 8 ) derivatives are well known beta-lactamase inhibitors. 22,23 Analogues of thiazolidinedione ( 9 ) are peroxisome proliferator-activated receptor (PPAR) agonists and have been used as antidiabetic drugs. 24 Condensation of isatins with the above mentioned heterocycles was found to work best with sodium acetate in acetic acid, providing the desired isatin derivatives 10a–f in satisfactory yields (Scheme 2).…”