N-Leucinyl Benzenesulfonamides as Structurally Simplified Leucyl-tRNA Synthetase Inhibitors

N-Leucinyl benzenesulfonamides have been discovered as a novel class of potent inhibitors of E. coli leucyl-tRNA synthetase. The binding of inhibitors to the enzyme was measured by using isothermal titration calorimetry. This provided information on enthalpy and entropy contributions to binding, which, together with docking studies, were used for structure-activity relationship analysis. Enzymatic assays revealed that N-leucinyl benzenesulfonamides display remarkable selectivity for E. coli leucyl-tRNA synthetase compared to S. aureus and human orthologues. The simplest analogue of the series, N-leucinyl benzenesulfonamide (R = H), showed the highest affinity against E. coli leucyl-tRNA synthetase and also exhibited antibacterial activity against Gram-negative pathogens (the best MIC = 8 μg/mL, E. coli ATCC 25922), which renders it as a promising template for antibacterial drug discovery.

Are the physicochemical properties of antibacterial compounds really different from other drugs?

Background

It is now widely recognized that there is an urgent need for new antibacterial drugs, with novel mechanisms of action, to combat the rise of multi-drug resistant bacteria. However, few new compounds are reaching the market. Antibacterial drug discovery projects often succeed in identifying potent molecules in biochemical assays but have been beset by difficulties in obtaining antibacterial activity. A commonly held view, based on analysis of marketed antibacterial compounds, is that antibacterial drugs possess very different physicochemical properties to other drugs, and that this profile is required for antibacterial activity.

Results

We have re-examined this issue by performing a cheminformatics analysis of the literature data available in the ChEMBL database. The physicochemical properties of compounds with a recorded activity in an antibacterial assay were calculated and compared to two other datasets extracted from ChEMBL, marketed antibacterials and drugs marketed for other therapeutic indications. The chemical class of the compounds and Gram-negative/Gram-positive profile were also investigated. This analysis shows that compounds with antibacterial activity have physicochemical property profiles very similar to other drug classes.

Conclusions

The observation that many current antibacterial drugs lie in regions of physicochemical property space far from conventional small molecule therapeutics is correct. However, the inference that a compound must lie in one of these “outlier” regions in order to possess antibacterial activity is not supported by our analysis.

Electronic supplementary material

The online version of this article (doi:10.1186/s13321-016-0143-5) contains supplementary material, which is available to authorized users.

Comparison of the Structure and Activity of Glycosylated and Aglycosylated Human Carboxylesterase 1

Human Carboxylesterase 1 (hCES1) is the key liver microsomal enzyme responsible for detoxification and metabolism of a variety of clinical drugs. To analyse the role of the single N-linked glycan on the structure and activity of the enzyme, authentically glycosylated and aglycosylated hCES1, generated by mutating asparagine 79 to glutamine, were produced in human embryonic kidney cells. Purified enzymes were shown to be predominantly trimeric in solution by analytical ultracentrifugation. The purified aglycosylated enzyme was found to be more active than glycosylated hCES1 and analysis of enzyme kinetics revealed that both enzymes exhibit positive cooperativity. Crystal structures of hCES1 a catalytically inactive mutant (S221A) and the aglycosylated enzyme were determined in the absence of any ligand or substrate to high resolutions (1.86 Å, 1.48 Å and 2.01 Å, respectively). Superposition of all three structures showed only minor conformational differences with a root mean square deviations of around 0.5 Å over all Cα positions. Comparison of the active sites of these un-liganded enzymes with the structures of hCES1-ligand complexes showed that side-chains of the catalytic triad were pre-disposed for substrate binding. Overall the results indicate that preventing N-glycosylation of hCES1 does not significantly affect the structure or activity of the enzyme.

Drug targeting to monocytes and macrophages using esterase-sensitive chemical motifs

The therapeutic and toxic effects of drugs are often generated through effects on distinct cell types in the body. Selective delivery of drugs to specific cells or cell lineages would, therefore, have major advantages, in particular, the potential to significantly improve the therapeutic window of an agent. Cells of the monocyte-macrophage lineage represent an important target for many therapeutic agents because of their central involvement in a wide range of diseases including inflammation, cancer, atherosclerosis, and diabetes. We have developed a versatile chemistry platform that is designed to enhance the potency and delivery of small-molecule drugs to intracellular molecular targets. One facet of the technology involves the selective delivery of drugs to cells of the monocyte-macrophage lineage, using the intracellular carboxylesterase, human carboxylesterase-1 (hCE-1), which is expressed predominantly in these cells. Here, we demonstrate selective delivery of many types of intracellularly targeted small molecules to monocytes and macrophages by attaching a small esterase-sensitive chemical motif (ESM) that is selectively hydrolyzed within these cells to a charged, pharmacologically active drug. ESM versions of histone deacetylase (HDAC) inhibitors, for example, are extremely potent anticytokine and antiarthritic agents with a wider therapeutic window than conventional HDAC inhibitors. In human blood, effects on monocytes (hCE-1-positive) are seen at concentrations 1000-fold lower than those that affect other cell types (hCE-1-negative). Chemical conjugates of this type, by limiting effects on other cells, could find widespread applicability in the treatment of human diseases where monocyte-macrophages play a key role in disease pathology.

Structure–activity relationships in 3-isothiazolones

The biological activity of a series of structurally diverse 3-isothiazolones (1) has been assessed by evaluating the minimum inhibitory concentration required to inhibit the growth of E. Coli. The structure and electronic properties of these derivatives have been calculated using both semi-empirical and ab initio molecular orbital methods. Multi-linear regression analysis shows no correlation between the experimental activity of the 3-isothiazolones and either the calculated geometries, electronic properties, or the frontier orbital energies of these derivatives, but a reasonable relationship is found with other parameters including their calculated solvation energies, suggesting that diffusion may play an important role in their mode of action.

The Selection and Design of GPCR Ligands: From Concept to the Clinic

Virtual screening methods using structure-based, pharmacophore-based and descriptor based protocols may be used to identify ligands for the G-protein coupled receptor target family. A complementary approach is the synthesis and screening of compound libraries designed using privileged motifs and/or based on validated hit molecules. A virtual screening approach based on molecular docking performed with GOLD using a templated homology model and a consensus scoring procedure can identify vasopressin 1a receptor antagonists. In a separate project a library design and synthesis approach based around validated hit GPCR ligands led to the identification of potent oxytocin antagonists. Subsequent optimisation of the initial library compounds has provided compounds that are now being evaluated in the clinic for the treatment of preterm labour.

Benefits, shortcomings, and costs of EEG monitoring

A 5-year experience with 562 carotid endarterectomies, using electroencephalogram (EEG) monitoring and selective shunting, was reviewed. EEG changes occurred in 102 patients (18%). The frequency of EEG changes, as related to cerebral vascular symptoms, was as follows: transient ischemic attacks, seven per cent (19/259); completed strokes, 37% (36/98); vertebral basilar insufficiency, 24% (32/135); asymptomatic, 21% (15/71). Patients with contralateral carotid occlusion exhibited EEG changes in 37% (28/76) of operations. Fifteen patients suffered perioperative strokes (2.6%). Nine of the 15 were associated with a technical problem of either thrombosis of the internal carotid artery (five) or emboli (four). Technical problems were more common when shunts were used (five per cent) than when they were not (0.9%). Patients who suffered strokes prior to surgery were more at risk to develop a perioperative stroke (three per cent) than those not suffering prior strokes (0.3%). The EEG did not change in three patients who had lacunar infarcts prior to surgery and who awoke with a worsened deficit. Our series does not clearly establish the advantages of EEG monitoring, which is expensive (+375/patient) and may not detect ischemia in all areas of the brain. However, the use of shunts may introduce a risk of stroke due to technical error that is equal or greater than the risk of stroke due to hemodynamic ischemia. Since the need for protection is unpredictable by angiographic or clinical criteria, the benefit of EEG monitoring may be in reducing the incidence of shunting in those patients whose tracing remains normal after clamping. The decision to shunt, however, when there is electrical dysfunction after carotid clamping should be based not only on the EEG but also on the clinical signs and computed tomography (CT) scan. Our data does not show a net benefit in selective shunting unless the patient has sustained a stroke prior to surgery.

Determining criteria for shunt placement during carotid endarterectomy. EEG versus back pressure

EEG monitoring and carotid back pressure were performed on 100 patients undergoing elective carotid endarterectomy. Shunts were inserted selectively in those patients who showed change in EEG after a trial period of carotid clamping (15%). No patient in the series awoke with a neurologic deficit. Back pressures were significantly lower in the shunted group and these pressures roughly correlated with EEG changes. Only one patient with a back pressure of greater than 40 mmHg had EEG changes and this patient had a recent mild stroke. EEG changes were most frequent in patients with contralateral carotid occlusions and in asymptomatic significant stenoses. EEG is a more discriminating indicator for shunt insertion than back pressure, although a pressure greater than 40 mmHg is safe in patients without recent stroke.