Addressing the metabolic activation potential of new leads in drug discovery: a case study using ion trap mass spectrometry and tritium labeling techniques

Metabolic activation of drug candidates to electrophilic reactive metabolites that can covalently modify cellular macromolecules may result in acute and/or idiosyncratic immune system-mediated toxicities in humans. This presents a significant potential liability for the future development of these compounds as safe therapeutic agents. We present here an example of an approach where sites of metabolic activation within a new drug candidate series were rapidly identified using online liquid chromatography/multi-stage mass spectrometry on an ion trap mass spectrometer. This was accomplished by trapping the reactive intermediates formed upon incubation of compounds with rat and human liver microsomes as their corresponding glutathione conjugates and mass spectral characterization of these thiol adducts. Based on the structures of the GSH adducts identified, potential sites and mechanisms of bioactivation within the chemical structure were proposed. These metabolism studies were interfaced with iterative structural modifications of the chemical series in order to block these bioactivation sites within the molecule. This strategy led to a significant reduction in the propensity of the compounds to undergo metabolic activation as evidenced by reductions in the irreversible binding of radioactivity to liver microsomal material upon incubation of tritium-labeled compounds with this in vitro system. With the efficiency and throughput achievable with such an approach, it appears feasible to identify and address the metabolic activation potential of new drug leads during routine metabolite identification studies in an early drug discovery setting.     

Enzyme inhibitors as chemical tools to study enzyme catalysis: rational design, synthesis, and applications

Carefully designed molecules that are intimately related to the reaction mechanism of enzymes are often highly selective and potent inhibitors that serve as extremely useful chemical probes for understanding the reaction mechanism and structure of enzymes. This article describes the design, synthesis, and applications of specific inhibitors of two mechanistically distinct groups of enzymes, ATP-dependent amide ligases and Ser- and Thr-hydrolases. Our strategy is based on the premise that stable analogues of the transition state (transition-state analogues) are highly potent inhibitors that serve as good mechanistic probes, and that a key structure of a good inhibitor of one enzyme is also utilized for the inhibitors of other enzymes that share the same chemistry in their catalyzed reactions, irrespective of the degree of structural similarity and evolutionary link between the enzymes. According to these principles, we designed and synthesized a series of phosphinate- and sulfoximine-based transition-state analogue inhibitors of glutathione synthetase, gamma-glutamylcysteine synthetase and asparagine synthetase. For the second group of enzymes, we synthesized a gamma-monofluorophosphono glutamate analogue for mechanism-based affinity labeling of gamma-glutamyltranspeptidase and fluorescent phosphonic acid esters for the active-site titration of lipase. These inhibitors were used successfully as ligands for detailed kinetic analyses, X-ray crystallography, and mass analysis of the enzymes to identify the key amino acid residues responsible for catalysis and substrate recognition in the transition state.     

Ab initio through‐space/bond interaction analysis of the long C–C bonds in Bi(anthracene‐9,10‐dimethylene) photoisomers

The bi(anthracene‐9,10‐dimethylene) photoisomer has remarkably long C–C single bonds. To examine the lengthening of the C–C bond, we propose a novel procedure for quantitatively analyzing orbital interactions in a molecule at the level of the ab initio molecular orbital method. In this procedure, we can cut off the specific through‐space/bond interactions in a molecule by artificially increasing the absolute magnitude of the exponents in a Gaussian function. Then, the spatial orbital interactions were perfectly cut off, and, each term that makes up the total energy, that is, the nuclear–electron attractions, the electron–electron repulsions, and the nuclear–nuclear repulsions cancel each other. Several model molecules of the photoisomer were analyzed by this procedure. It was found that the orbital interaction between the p orbital on the benzene ring and the σ* orbital on the C–C bond in question, σ→σ* electron transfer through π orbital, weakens the C–C bond efficiently when these orbitals were located in the “periplanar” conformation. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

Cp/mas 13c nmr and Electron Diffraction Study of Bacterial Cellulose Structure Affected by Cell Wall Polysaccharides

Acetobacter xylinum was cultured in Schramm–Hestrin medium containing pectin (pectin medium), xylan (xylan medium), or glucomannan (mannan medium). X-ray diffractometry revealed that xylan and glucomannan affected the size of the cellulose crystals and their d-spacing values. Solid-state cross polarization magic angle spinning carbon-13 nuclear magnetic resonance spectroscopy indicated that the ratio of cellulose I was reduced by the addition of polysaccharides. These effects were more remarkable on the cellulose in the mannan medium than that in the xylan medium, and were scarcely observed in the pectin medium. Electron diffraction analysis revealed that these effects on hemicelluloses along cellulose microfibrils are continuous in the mannan medium and discontinuous in the xylan medium. These findings suggest that the uronic acid in the polysaccharides prevents interactions with cellulose leading to alterations of the structure of the cellulose crystal.     

神经生长因子的化学发光标记与检测

以辣根过氧化物酶（ＨＲＰ）和吖啶酯（ＡＥ）为化学发光标记试剂分别标记神经生长因子（ＮＧＦ）单克隆抗体，经分离纯化制成标记抗体（ＨＲＰ－Ａｂ，ＡＥ－Ａｂ），采用化学发光免疫分析法（ＣＬＩＡ）对ＮＧＦ进行检测，其检出限为０．５ｎｇ／ｍＬ，线性范围为２～１２８ｎｇ／ｍＬ．１０例样本分别用ＣＬＩＡ和ＲＩＡ进行检测，其结果无显著性差异．     

影响双(2-丁氧羰基-3,4,6-三氯苯基)草酸酯化学发光体系的因素

过氧草酸酯类化学发光是一类以多氯代水杨酸酯与草酰氯反应生成的草酸酯、过氧化氢和荧光剂为主要组成的化学发光体［１，２］．它除了具有发光效率高，强度大，寿命长的特点外，还可以通过选择荧光剂调节发光的颜色．采用这类发光体系可制成多种化学光源．在草酸酯和荧光...     

Using the diphosphanyl radical as a potential spin label: effect of motion on the EPR spectrum of an R1(R2)P--PR1 radical

The EPR spectrum of the novel radical Mes*(CH3)P--PMes* (Mes*=2,4,6-(tBu)3C6H2) was measured in the temperature range 100-300 K, and was found to be drastically temperature dependent as a result of the large anisotropy of the 31P hyperfine tensors. Below 180 K, a spectrum of the liquid solution is accurately simulated by calculating the spectral modifications due to slow tumbling of the radical. To achieve this simulation, an algorithm was developed by extending the well-known nitroxide slow-motion simulation technique for the coupling of one electron spin to two nuclear spins. An additional dynamic process responsible for the observed line broadening was found to occur between 180 K and room temperature; this broadening is consistent with an exchange between two conformations. The differences between the isotropic 31P couplings associated with the two conformers are shown to be probably due to an internal rotation about the P--P bond.     

Synthesis of [18,19,21,22‐13C4]‐Labeled Tautomycin as an NMR Probe of Protein Phosphatase Inhibitor

We have accomplished the synthesis of ¹³C‐labeled tautomycin at the C18, C19, C21, and C22 positions starting from 100 % [¹³C]triethylphosphonoacetate for the purpose of elucidating the dynamics and conformation of the C17–C26 moiety. NMR spectroscopy of ¹³C‐labeled tautomycin revealed strong binding with protein phosphatase type 1 and new features in the ¹³C NMR spectrum, such as the very small three‐bond coupling constants (²J).     

Chemoenzymatic synthesis of [3,9-C]-labeled NeuAc and KDN

The chemoenzymatic synthesis of ¹³C-labeled sialic acid (NeuAc) and 3-deoxy-d-glycero-d-galacto-2-nonulosonic acid (KDN) as useful molecular probes for studying the conformation of sialyl or KDN oligosaccharides attached to proteins was performed by using [6-¹³C]-ManNAc, [6-¹³C]-Man and [3-¹³C]-pyruvic acid sodium salt. In the synthesis of the compounds, 5,6-anhydro intermediates were found to easily provide not only 6-¹³C-labeled but also 5-, and 6-modified NeuAc and KDN analogs. Furthermore, it was demonstrated that identical results are obtained by NMR for both [3,9-¹³C]-NeuAc and 1:1 mixtures of [3-¹³C]- and [9-¹³C]-NeuAc.     

High throughput drug screening by direct RNA profiling on DNA sensors

The feasibility of DNA microarray sensor technology as a routine technique of molecular pharmacology to perform high throughput drug screening and the advantages of directly labeled RNA for a high throughput experiment are presented in this paper. A novel, single-step direct chemical labeling method for DNA microarray target samples has been developed to reduce the sample amount, cost, time and error of the experiment by eliminating the need for enzyme mediated labeling. Reproducibility of the data for high throughput drug screening is demonstrated by monitoring differential gene expression of a set of 45 gene targets involved in the genotoxic stress response pathways.