Simulation of chemical metabolism for fate and hazard assessment. I. Approach for simulating metabolism

Information regarding the metabolism of xenobiotic chemicals plays a central role in regulatory risk assessments. In regulatory programmes where metabolism studies are required, the studies of metabolic pathways are often incomplete and the identification of activated metabolites and important degradation products are limited by analytical methods. Because so many more new chemicals are being produced than can be assessed for potential hazards, setting assessment priorities among the thousands of untested chemicals requires methods for predictive hazard identification which can be derived directly from chemical structure and their likely metabolites. In a series of papers we are sharing our experience in the computerized management of metabolic data and the development of simulators of metabolism for predicting the environmental fate and (eco)toxicity of chemicals. The first paper of the series presents a knowledge-based formalism for the computer simulation of non-intermediary metabolism for untested chemicals, with an emphasis on qualitative and quantitative aspects of modelling metabolism.     

Studies on the metabolism and detectability of the emerging drug of abuse diphenyl‐2‐pyrrolidinemethanol (D2PM) in rat urine using GC‐MS and LC‐HR‐MS/MS

In the last years, the number of new psychoactive substances, so‐called ‘legal highs’, has enormously increased. They are sold via online shops often with inaccurate and false information about the content. The aim of this work was to study the metabolism and the detectability of the drug of abuse diphenyl‐2‐pyrrolidinemethanol (D2PM) in rat urine using gas chromatography‐mass spectrometry and liquid chromatography‐high resolution‐tandem mass spectrometry. Five phase I and two phase II metabolites were identified suggesting hydroxylation at the pyrrolidine and diphenyl part as the main metabolic steps. Assuming similar kinetics, an intake of D2PM should be detectable in human urine mainly via its metabolites. Copyright © 2013 John Wiley & Sons, Ltd.     

Voltammetry coupled to mass spectrometry in the presence of isotope O labeled water for the prediction of oxidative transformation pathways of activated aromatic ethers: Acebutolol

The coupling between an electrochemical cell (EC) and a mass spectrometer (MS) is a useful screening tool (EC-MS) to study the oxidative transformation pathways of various electroactive species. For that purpose, we showed that the EC-MS method, carried out in the presence and absence of isotope ¹⁸O labeled water leads not only to a fast identification of oxidation products but also leads to a fast elucidation of the mechanism pathway reaction. We examined herein the case of the electrochemical hydrolysis of activated aromatic ether. Acebutolol (β-blockers) was selected herein as model of activated aromatic ether, and its electrochemical oxidation was examined in both the presence and absence of isotope ¹⁸O labeled water. To elucidate electrochemical hydrolysis pathway reaction: O-dealkylation or O-dealkoxylation, our approach was used to prove its applicability. The electrochemical oxidation mechanism was then elucidated showing an O-dealkoxylation reaction. In addition, density functional theory (DFT) calculations fully support the experimental conclusions.     

Syntheses of 2‐Keto‐3‐deoxy‐D‐xylonate and 2‐Keto‐3‐deoxy‐L‐arabinonate as Stereochemical Probes for Demonstrating the Metabolic Promiscuity of Sulfolobus solfataricus Towards D‐Xylose and L‐Arabinose

Practical syntheses of 2‐keto‐3‐deoxy‐D ‐xylonate (D ‐KDX) and 2‐keto‐3‐deoxy‐L ‐arabinonate (L ‐KDA) that rely on reaction of the anion of ethyl 2‐[(tert‐butyldimethylsilyl)oxy]‐2‐(dimethoxy phosphoryl) acetate with enantiopure glyceraldehyde acetonide, followed by global deprotection of the resultant O‐silyl‐enol esters, have been developed. This has enabled us to confirm that a 2‐keto‐3‐deoxy‐D ‐gluconate aldolase from the archaeon Sulfolobus solfataricus demonstrates good activity for catalysis of the retro‐aldol cleavage of both these enantiomers to afford pyruvate and glycolaldehyde. The stereochemical promiscuity of this aldolase towards these enantiomeric aldol substrates confirms that this organism employs a metabolically promiscuous pathway to catabolise the C5‐sugars D ‐xylose and L ‐arabinose.     

水分子对α相CL-20热分解机理影响的分子动力学研究

研究六硝基六氮杂异伍兹烷(CL-20)晶体不同晶型在不同温度下的反应机理, 对于深入认识含能材料在极端条件下的冲击起爆、冲击点火和爆轰过程等具有重要意义. 基于反应力场, 研究水分子在纯α相CL-20及其水合物的晶体结构中数量随时间的变换, 分析水分子对两种体系的初始分解和第二阶段的分解路径的影响. 计算结果表明: CL-20 分子的初始分解路径与水分子无关, 第二阶段的分解反应与水分子有关. 在低温(T<1500 K)下, 水分子对两种体系没有影响, 二者的初始分解路径均为N-NO₂键生成NO₂自由基; 在1500 K≤T≤2500 K时, 水分子作为反应物或与NO₂、、OH自由基等组成催化体系, 生成O₂、H₂O₂等产物, 加速水合物体系在高温下的第二阶段反应, 使得高温下水合物体系的化学反应速率和反应生成的NO₂自由基的数量比纯CL-20体系的化学反应速率和反应生成的NO₂自由基的数量大; 在T>2500 K时, 水分子的催化反应抑制CL-20初始分解反应, 使得在3000 K时纯CL-20体系的反应速率大于水合物体系中CL-20的反应速率.     

4-Ketozeinoxanthin,a novel carotenoid produced in Escherichia coli through metabolic engineering using carotenogenic genes of bacterium and liverwort

In order to produce a novel keto-carotenoid in Escherichia coli, we introduced the marine bacterial carotenoid ketolase gene (crtW) into pathway-engineered E. coli producing carotenoids of plant origin, which carried the lycopene biosynthesis genes (crtE, crtB, and crtI) from soil bacterium Pantoea ananatis and the liverwort Marchantia polymorpha genes that encode lycopene β-cyclase (MpLCYb), lycopene ε-cyclase (MpLCYe), and β-carotenoid hydroxylase (MpBHY). A novel keto-carotenoid (1) was produced by these carotenoid biosynthesis genes in E. coli along with α-echinenone, adonirubin, and adonixanthin. The structure of 1 was determined as (3S,6′R)-3-hydroxy-β,ε-caroten-4-one based on Uv–vis, MS, ¹H NMR, and CD spectral data. This compound was named 4-ketozeinoxanthin and showed anti-tumor-promoting activity.     

Quantification of allantoin and other metabolites of the purine degradation pathway in human plasma samples using a newly developed HILIC-LC-MS/MS method

The development of a simple HILIC-LC-MS/MS method to quantify the plasma levels of allantoin, inosine, hypoxanthine, and adenosine, using stripped plasma for the bioanalytical method validation, was the purpose of this study. Chromatographic separation conducted using an XBridge BEH Amide column (2.1 × 150 mm, 3.5 μm) was achieved under gradient elution with two mobile phases: 0.1% formic acid–ACN (5:95) and 0.1% formic acid–ACN (50:50). Multiple reaction monitoring MS detection was performed using a triple quadrupole. The method validation experiments were performed according to the European Medicines Agency and the U.S. Food and Drug Administration guidelines. The lower LOQ was 50 nM, 5 nM, 20 nM, and 2 nM for allantoin, inosine, hypoxanthine, and adenosine, respectively. The recovery was repeatable and stable. The intraday precision ranged from 1.6% to 6.5%, while the interday precision ranged from 3.4% to 58.7%. Therefore, it is necessary to make a matrix-matched calibration curve each day to overcome this issue. Since the quality control samples’ stability did not always comply with the guidelines, the samples need to be analyzed soon after collection.     

Quantum Chemistry-based Molecular Dynamics Simulations as a Tool for the Assignment of ESI-MS/MS Spectra of Drug Molecules

In organic mass spectrometry, fragment ions provide important information on the analyte as a central part of its structure elucidation. With increasing molecular size and possible protonation sites, the potential energy surface (PES) of the analyte can become very complex, which results in a large number of possible fragmentation patterns. Quantum chemical (QC) calculations can help here, enabling the fast calculation of the PES and thus enhancing the mass spectrometry-based structure elucidation processes. In this work, the previously unknown fragmentation pathways of the two drug molecules Nateglinide (45 atoms) and Zopiclone (51 atoms) were investigated using a combination of generic formalisms and calculations conducted with the Quantum Chemical Mass Spectrometry (QCxMS) program. The computations of the de novo fragment spectra were conducted with the semi-empirical GFNn-xTB (n=1, 2) methods and compared against Orbitrap measured electrospray ionization (ESI) spectra in positive ion mode. It was found that the unbiased QC calculations are particularly suitable to predict non-evident fragment ion structures, sometimes contrasting the accepted generic formulation of fragment ion structures from electron migration rules, where the “true” ion fragment structures are approximated. For the first time, all fragment and intermediate structures of these large-sized molecules could be elucidated completely and routinely using this merger of methods, finding new undocumented mechanisms, that are not considered in common rules published so far. Given the importance of ESI for medicinal chemistry, pharmacokinetics, and metabolomics, this approach can significantly enhance the mass spectrometry-based structure elucidation processes and contribute to the understanding of previously unknown fragmentation pathways.     

Theoretical insights into the mechanism of photocatalytic reduction of CO2 over semiconductor catalysts

Photocatalytic reduction of CO₂ is one important approach to alleviate greenhouse gas emission and energy crisis, which has gained huge attention in the past decades. However, the lack of understanding complex reaction mechanism impedes new catalysts design. It is also very difficult to understand the mechanism by using only experimental approaches. For this concern, theoretical calculations can effectively supplement the experimental deficiency and thus play an important role. Recently theoretical calculations have been performed on adsorption, migration and reduction of CO₂ molecule on the photocatalyst surface, leading to useful information that have contributed greatly to this field. This review summarizes recent advances in first-principles calculations about CO₂ photoreduction over various semiconductor photocatalysts like metal oxides, sulfides and g-C₃N₄. The methods, models, adsorption and reaction pathways have been discussed in detail. The perspective about future investigation on the photocatalytic reduction of CO₂ using first principles calculations is also presented.     

Defect Engineering and Anisotropic Modulation of Ionic Transport in Perovskite Solid Electrolyte LixLa(1−x)/3NbO3

Solid electrolytes, such as perovskite Li_3xLa_2/1−xTiO₃, Li_xLa_(1−x)/3NbO₃ and garnet Li₇La₃Zr₂O₁₂ ceramic oxides, have attracted extensive attention in lithium-ion battery research due to their good chemical stability and the improvability of their ionic conductivity with great potential in solid electrolyte battery applications. These solid oxides eliminate safety issues and cycling instability, which are common challenges in the current commercial lithium-ion batteries based on organic liquid electrolytes. However, in practical applications, structural disorders such as point defects and grain boundaries play a dominating role in the ionic transport of these solid electrolytes, where defect engineering to tailor or improve the ionic conductive property is still seldom reported. Here, we demonstrate a defect engineering approach to alter the ionic conductive channels in Li_xLa_(1−x)/3NbO₃ (x = 0.1~0.13) electrolytes based on the rearrangements of La sites through a quenching process. The changes in the occupancy and interstitial defects of La ions lead to anisotropic modulation of ionic conductivity with the increase in quenching temperatures. Our trial in this work on the defect engineering of quenched electrolytes will offer opportunities to optimize ionic conductivity and benefit the solid electrolyte battery applications.