Structure-Based Design, Synthesis, and Biological Evaluation of Non-Acyl Sulfamate Inhibitors of the Adenylate-Forming Enzyme MenE.

N-Acyl sulfamoyladenosines (acyl-AMS) have been used extensively to inhibit adenylate-forming enzymes that are involved in a wide range of biological processes. These acyl-AMS inhibitors are nonhydrolyzable mimics of the cognate acyl adenylate intermediates that are bound tightly by adenylate-forming enzymes. However, the anionic acyl sulfamate moiety presents a pharmacological liability that may be detrimental to cell permeability and pharmacokinetic profiles. We have previously developed the acyl sulfamate OSB-AMS (1) as a potent inhibitor of the adenylate-forming enzyme MenE, an o-succinylbenzoate-CoA (OSB-CoA) synthetase that is required for bacterial menaquinone biosynthesis. Herein, we report the use of computational docking to develop novel, non-acyl sulfamate inhibitors of MenE. A m-phenyl ether-linked analogue (5) was found to be the most potent inhibitor (IC50 = 8 µM; Kd = 244 nM), and its X-ray co-crystal structure was determined to characterize its binding mode in comparison to the computational prediction. This work provides a framework for the development of potent non-acyl sulfamate inhibitors of other adenylate-forming enzymes in the future.

Mechanism of MenE inhibition by acyl-adenylate analogues and discovery of novel antibacterial agents.

MenE is an o-succinylbenzoyl-CoA (OSB-CoA) synthetase in the bacterial menaquinone biosynthesis pathway and is a promising target for the development of novel antibacterial agents. The enzyme catalyzes CoA ligation via an acyl-adenylate intermediate, and we have previously reported tight-binding inhibitors of MenE based on stable acyl-sulfonyladenosine analogues of this intermediate, including OSB-AMS (1), which has an IC50 value of ≤25 nM for Escherichia coli MenE. Herein, we show that OSB-AMS reduces menaquinone levels in Staphylococcus aureus, consistent with its proposed mechanism of action, despite the observation that the antibacterial activity of OSB-AMS is ∼1000-fold lower than the IC50 for enzyme inhibition. To inform the synthesis of MenE inhibitors with improved antibacterial activity, we have undertaken a structure-activity relationship (SAR) study stimulated by the knowledge that OSB-AMS can adopt two isomeric forms in which the OSB side chain exists either as an open-chain keto acid or a cyclic lactol. These studies revealed that negatively charged analogues of the keto acid form bind, while neutral analogues do not, consistent with the hypothesis that the negatively charged keto acid form of OSB-AMS is the active isomer. X-ray crystallography and site-directed mutagenesis confirm the importance of a conserved arginine for binding the OSB carboxylate. Although most lactol isomers tested were inactive, a novel difluoroindanediol inhibitor (11) with improved antibacterial activity was discovered, providing a pathway toward the development of optimized MenE inhibitors in the future.

Stable isotope gas chromatography-tandem mass spectrometry determination of aminoethylcysteine ketimine decarboxylated dimer in biological samples.

Aminoethylcysteine ketimine decarboxylated dimer (AECK-DD; systematic name: 1,2-3,4-5,6-7,8-octahydro-1,8a-diaza-4,6-dithiafluoren-9(8aH)-one) is a previously described metabolite of cysteamine that has been reported to be present in mammalian brain, urine, plasma, and cells in culture and vegetables and to possess potent antioxidative properties. Here, we describe a stable isotope gas chromatography-tandem mass spectrometry (GC-MS/MS) method for specific and sensitive determination of AECK-DD in biological samples. (13)C(2)-labeled AECK-DD was synthesized and used as the internal standard. Derivatization was carried out by N-pentafluorobenzylation with pentafluorobenzyl bromide in acetonitrile. Quantification was performed by selected reaction monitoring of the mass transitions m/z 328 to 268 for AECK-DD and m/z 330 to 270 for [(13)C(2)]AECK-DD in the electron capture negative ion chemical ionization mode. The procedure was systematically validated for human plasma and urine samples. AECK-DD was not detectable in human plasma above approximately 4nM but was present in urine samples of healthy humans at a maximal concentration of 46nM. AECK-DD was detectable in rat brain at very low levels of approximately 8pmol/g wet weight. Higher levels of AECK-DD were detected in mouse brain (∼1nmol/g wet weight). Among nine dietary vegetables evaluated, only shallots were found to contain trace amounts of AECK-DD (∼6.8pmol/g fresh tissue).

Porosity and pore size distribution in a sedimentary rock: Implications for the distribution of chlorinated solvents.

Characterizing properties of the rock matrix that control retention and release of chlorinated solvents is essential in evaluating the extent of contamination and the application of remediation technologies in fractured rock. Core samples from seven closely spaced boreholes in a mudstone subject to trichloroethene (TCE) contamination were analyzed using Mercury Intrusion Porosimetry to investigate porosity and pore size distribution as a function of mudstone characteristics, and depth and lateral extent in the aquifer; organic carbon content was also evaluated to identify the potential for adsorption. Porosity and retardation factor varied over two orders of magnitude, with the largest porosities and largest retardation factors associated with carbon-rich mudstone layers. Larger porosities were also measured in the shallow rock that has been subject to enhanced groundwater flow. Porosity also varied over more than an order of magnitude in spatially continuous mudstone layers. The analyses of the rock cores indicated that the largest pore diameters may be accessible to entry of the nonaqueous form of TCE. Although the porosity associated with the largest pore diameters is small (~0.1%), that volume of TCE can significantly affect the total TCE that is retained in the rock matrix. The dimensions of the largest pore diameters may also be accessible to microbes responsible for reductive dechlorination; however, the small percentage of the pore space that can accommodate microbes may limit the extent of reductive dechlorination in the rock matrix.

Stereoselective Synthesis, Docking, and Biological Evaluation of Difluoroindanediol-Based MenE Inhibitors as Antibiotics.

A stereoselective synthesis has been developed to provide all four side-chain stereoisomers of difluoroindanediol 2, the mixture of which was previously identified as an inhibitor of the o-succinylbenzoate-CoA synthetase MenE in bacterial menaquinone biosynthesis, having promising in vitro activity against methicillin-resistant Staphylococcus aureus and Mycobacterium tuberculosis. Only the (1R,3S)-diastereomer inhibited the biochemical activity of MenE, consistent with computational docking studies, and this diastereomer also exhibited in vitro antibacterial activity comparable to that of the mixture. However, mechanism-of-action studies suggest that this inhibitor and its diastereomers may act via other mechanisms beyond inhibition of menaquinone biosynthesis.

Experimental and structural testing module to analyze paralogue-specificity and affinity in the Hsp90 inhibitors series.

We here describe the first reported comprehensive analysis of Hsp90 paralogue affinity and selectivity in the clinical Hsp90 inhibitor chemotypes. This has been possible through the development of a versatile experimental assay based on a new FP-probe (16a) that we both describe here. The assay can test rapidly and accurately the binding affinity of all major Hsp90 chemotypes and has a testing range that spans low nanomolar to millimolar binding affinities. We couple this assay with a computational analysis that allows for rationalization of paralogue selectivity and defines not only the major binding modes that relay pan-paralogue binding or, conversely, paralogue selectivity, but also identifies molecular characteristics that impart such features. The methods developed here provide a blueprint for parsing out the contribution of the four Hsp90 paralogues to the perceived biological activity with the current Hsp90 chemotypes and set the ground for the development of paralogue selective inhibitors.

Iridium luminophore complexes for unimolecular oxygen sensors.

In this study, a series of novel luminescent cyclometalated Ir(III) complexes has been synthesized and evaluated for use in unimolecular oxygen-sensing materials. The complexes Ir(C6)(2)(vacac), 1, Ir(ppy)(2)(vacac), 2, fac-Ir(ppy)(2)(vppy), 3, and mer-Ir(ppy)(2)(vppy), 4, where C6 = Coumarin 6, vacac = allylacetoacetate, ppy = 2-phenylpyridine, and vppy = 2-(4-vinylphenyl)pyridine, all have pendent vinyl or allyl groups for polymer attachment via the hydrosilation reaction. These luminophore complexes were characterized by NMR, absorption, and emission spectroscopy, luminescence lifetime and quantum yield measurements, elemental analysis, and cyclic voltammetry. Complex 1 was structurally characterized using X-ray crystallography, and a series of 1-D ((1)H, (13)C) and 2-D ((1)H-(1)H, (1)H-(13)C) NMR experiments were used to resolve the solution structure of 4. Complexes 1 and 3 displayed the longest luminescence lifetimes and largest quantum efficiencies in solution (tau = 6.0 micros, phi = 0.22 for 1; tau = 0.4 micros, phi = 0.2 for 3) and, as result, are the most promising candidates for future luminescence-quenching-based oxygen-sensing studies.

Synthesis, characterization, and evaluation of [Ir(ppy)2(vpy)Cl] as a polymer-bound oxygen sensor.

This study reports new luminescent oxygen sensors in which the luminophore is covalently bound to the polymer matrix and compares their behavior to related sensors in which the luminophore is dispersed within the matrix. The cyclometalated iridium complex [Ir(ppy)(2)(vpy)Cl], 1, has been synthesized and characterized spectroscopically (absorption and emission) and by 1-D and 2-D (1)H NMR, elemental analysis, and X-ray crystallography. Complex 1 was attached via hydrosilation to hydride-terminated poly(dimethylsiloxane) (PDMS), yielding material 2. Successful luminophore attachment was determined spectroscopically from the emission properties, and through the altered physical behavior of 2 compared to a dispersion of 1 in PDMS. Hydrosilation of 1 with dimethylphenylsilane yielded [Ir(ppy)(2)(DMPSEpy)Cl], 3, which was fully characterized and used to probe the effect of hydrosilation on the spectroscopic properties of the luminophore. Evaluation of 2 as a luminescent oxygen sensor revealed significantly improved sensitivity over dispersions of 1 in PDMS. Material 2 was also blended with polystyrene (PS) to improve the physical properties of the sensor films. The blend sensors exhibited increased sensitivity relative to films of 2 alone and maintained short response times to rapid changes in air pressure. In contrast, 1 partitioned into the PS phase when dispersed in a PDMS/PS blend, resulting in longer sensor response times.