Bicyclic Boronate VNRX-5133 Inhibits Metallo- and Serine-β-Lactamases

The bicyclic boronate VNRX-5133 (taniborbactam) is a new type of β-lactamase inhibitor in clinical development. We report that VNRX-5133 inhibits serine-β-lactamases (SBLs) and some clinically important metallo-β-lactamases (MBLs), including NDM-1 and VIM-1/2. VNRX-5133 activity against IMP-1 and tested B2/B3 MBLs was lower/not observed. Crystallography reveals how VNRX-5133 binds to the class D SBL OXA-10 and MBL NDM-1. The crystallographic results highlight the ability of bicyclic boronates to inhibit SBLs and MBLs via binding of a tetrahedral (sp3) boron species. The structures imply conserved binding of the bicyclic core with SBLs/MBLs. With NDM-1, by crystallography, we observed an unanticipated VNRX-5133 binding mode involving cyclization of its acylamino oxygen onto the boron of the bicyclic core. Different side-chain binding modes for bicyclic boronates for SBLs and MBLs imply scope for side-chain optimization. The results further support the "high-energy-intermediate" analogue approach for broad-spectrum β-lactamase inhibitor development and highlight the ability of boron inhibitors to interchange between different hybridization states/binding modes

Non-Hydrolytic β-Lactam Antibiotic Fragmentation by l,d-Transpeptidases and Serine β-Lactamase Cysteine Variants

Enzymes often use nucleophilic serine, threonine, and cysteine residues to achieve the same type of reaction; the underlying reasons for this are not understood. While bacterial d,d‐transpeptidases (penicillin‐binding proteins) employ a nucleophilic serine, l,d‐transpeptidases use a nucleophilic cysteine. The covalent complexes formed by l,d‐transpeptidases with some β‐lactam antibiotics undergo non‐hydrolytic fragmentation. This is not usually observed for penicillin‐binding proteins, or for the related serine β‐lactamases. Replacement of the nucleophilic serine of serine β‐lactamases with cysteine yields enzymes which fragment β‐lactams via a similar mechanism as the l,d‐transpeptidases, implying the different reaction outcomes are principally due to the formation of thioester versus ester intermediates. The results highlight fundamental differences in the reactivity of nucleophilic serine and cysteine enzymes, and imply new possibilities for the inhibition of nucleophilic enzymes

Hydroxylamine as an oxygen nucleophile: substitution of sulfonamide by a hydroxyl group in benzothiazole-2-sulfonamides

Item does not contain fulltextBenzothiazole-2-sulfonamides react with an excess of hydroxylamine in aqueous solutions to form 2-hydroxybenzothiazole, sulfur dioxide, and the corresponding amine. Mechanistic studies that employ a combination of structure-reactivity relationships, oxygen labeling experiments, and (in)direct detection of intermediates and products reveal that the reaction proceeds via oxygen attack, and that oxygen incorporated in the 2-hydroxybenzothiazole product derives from hydroxylamine. The reaction, which is performed under mild conditions, can be used as a deprotection method for cleavage of benzothiazole-2-sulfonyl-protected amino acids

Mechanism of biomolecular recognition of trimethyllysine by the fluorinated aromatic cage of KDM5A PHD3 finger

Contains fulltext : 220109.pdf (publisher's version ) (Open Access

Cation-pi Interactions Contribute to Substrate Recognition in gamma-Butyrobetaine Hydroxylase Catalysis

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Chemical basis for the recognition of trimethyllysine by epigenetic reader proteins

A large number of structurally diverse epigenetic reader proteins specifically recognize methylated lysine residues on histone proteins. Here we describe comparative thermodynamic, structural and computational studies on recognition of the positively charged natural trimethyllysine and its neutral analogues by reader proteins. This work provides experimental and theoretical evidence that reader proteins predominantly recognize trimethyllysine via a combination of favourable cation–π interactions and the release of the high-energy water molecules that occupy the aromatic cage of reader proteins on the association with the trimethyllysine side chain. These results have implications in rational drug design by specifically targeting the aromatic cage of readers of trimethyllysine

Reading and erasing of the phosphonium analogue of trimethyllysine by epigenetic proteins

Nε-Methylation of lysine residues in histones plays an essential role in the regulation of eukaryotic transcription. The ‘highest’ methylation mark, Nε-trimethyllysine, is specifically recognised by Nε-trimethyllysine binding ‘reader’ domains, and undergoes demethylation, as catalysed by 2-oxoglutarate dependent JmjC oxygenases. We report studies on the recognition of the closest positively charged Nε-trimethyllysine analogue, i.e. its trimethylphosphonium derivative (KPme3), by Nε-trimethyllysine histone binding proteins and Nε-trimethyllysine demethylases. Calorimetric and computational studies with histone binding proteins reveal that H3KP4me3 binds more tightly than the natural H3K4me3 substrate, though the relative differences in binding affinity vary. Studies with JmjC demethylases show that some, but not all, of them can accept the phosphonium analogue of their natural substrates and that the methylation state selectivity can be changed by substitution of nitrogen for phosphorus. The combined results reveal that very subtle changes, e.g. substitution of nitrogen for phosphorus, can substantially affect interactions between ligand and reader domains / demethylases, knowledge that we hope will inspire the development of highly selective small molecules modulating their activity

Gender-Related Differences in Presentation, Treatment, and Outcome of Patients With Atrial Fibrillation in Europe. A Report From the Euro Heart Survey on Atrial Fibrillation

Objectives: This study sought to investigate gender-related differences in patients with atrial fibrillation (AF) in Europe. Background: Gender-related differences may play a significant role in AF. Methods: We analyzed the data of 5,333 patients (42% female) enrolled in the Euro Heart Survey on Atrial Fibrillation. Results: Compared with men, the women were older, had a lower quality of life (QoL), had more comorbidities, more often had heart failure (HF) with preserved left ventricular systolic function (18% vs. 7%, p < 0.001), and less often had HF with systolic dysfunction (17% vs. 26%, p < 0.001). Among patients with typical AF symptoms (56% of women, 49% of men), there was no gender-related difference in the choice of rate or rhythm control. Among patients with atypical or no symptoms (44% of women, 51% of men), women less frequently underwent rhythm control (39% vs. 51%, p < 0.001) than did men. Women underwent less electrical cardioversion (22% vs. 28%, p < 0.001). Prescription of oral anticoagulants was identical (65%) in both genders. One-year outcome was similar except that women had a higher chance for stroke (odds ratio 1.83 in multivariable regression analysis, p = 0.019). Conclusions: Women with AF had more comorbidities, more HF with preserved systolic function, and a lower QoL than men. In the large group with atypical or no symptoms, women were treated appropriately more conservatively with less rhythm control than men. Women had a higher chance for stroke. Long-term QoL changes and other morbidities and mortality were similar. © 2007 American College of Cardiology Foundation