Strategies for metabolite profiling based on liquid chromatography

A mass defect filtering combined background subtraction strategy for rapid screening and identification of metabolites in rat plasma after oral administration of Yindan Xinnaotong soft capsule

The absorbed prototypes and metabolites of traditional Chinese medicines (TCMs) serves an important part in pharmacological action and clinical effects. However, the comprehensive characterization of which is facing actual or possible rigorous challenges due to the lack of data mining methods and the complexity of metabolite samples. Yindan Xinnaotong soft capsule (YDXNT), a typical traditional Chinese medicine prescription consisting of extracts from 8 herbal medicines, is widely used for the treatment of angina pectoris and ischemic stroke in the clinic. This study established a systematic data mining strategy based on ultra-high performance liquid chromatography tandem quadrupole-time-of-fight mass spectrometry (UHPLC-Q-TOF MS) for comprehensive metabolite profiling of YDXNT in rat plasma after oral administration. The multi-level feature ion filtration strategy was primarily conducted through the full scan MS data of plasma samples. All potential metabolites were rapidly fileted out from the endogenous background interference based on the background subtract and the chemical type specifically mass defect filter (MDF) windows including flavonoids, ginkgolides, phenolic acids, saponins, and tanshinones. As the MDF windows of certain types were overlapped, the screened-out potential metabolites were deeply characterized and identified according to their retention times (RT), integrating neutral loss filtering (NLF), diagnostic fragment ions filtering (DFIF), and further confirmed by reference standards. Thus, a total of 122 compounds, consisting of 29 prototype components (16 confirmed with reference standards) and 93 metabolites had been identified. This study provides a rapid and robust metabolite profiling method for researching complicated traditional Chinese medicine prescriptions.

Major benznidazole metabolites in patients treated for Chagas disease: Mass spectrometry-based identification, structural analysis and detoxification pathways

Benznidazole is the drug of choice for the treatment of Chagas disease, but its metabolism in humans is unclear. Here, we identified and characterized the major benznidazole metabolites and their biosynthetic mechanisms in humans by analyzing the ionic profiles of urine samples from patients and untreated donors through reversed-phase UHPLC-ESI-QTOF-MS and UHPLC-ESI-QqLIT-MS. A strategy for simultaneous detection and fragmentation of characteristic positive and negative ions was employed using information-dependent acquisitions (IDA). Selected precursor ions, neutral losses, and MS³ experiments complemented the study. A total of six phase-I and ten phase-II metabolites were identified and structurally characterized in urine of benznidazole-treated patients. Based on creatinine-corrected ion intensities, nitroreduction to amino-benznidazole (M1) and its subsequent N-glucuronidation to M5 were the main metabolic pathways, followed by imidazole-ring cleavage, oxidations, and cysteine conjugations. This extensive exploration of benznidazole metabolites revealed potentially toxic structures in the form of glucuronides and glutathione derivatives, which may be associated with recurrent treatment adverse events; this possibility warrants further exploration in future clinical trials. Incorporation of this knowledge of the benznidazole metabolic profile into clinical pharmacology trials could lead to improved treatments, facilitate the study of possible drug-drug interactions, and even mitigation of adverse drug reactions.

UHPLC-Q-TOF-MS/MS based metabolite profiling of duvelisib and establishment of its metabolism mechanisms

Duvelisib is a dual inhibitor of phosphoinositide 3 kinase that received global approval by USFDA in 2018 to treat follicular lymphoma after at least two prior systemic therapies. An extensive literature search revealed that till date, metabolites of duvelisib are not characterized and information on the same is not available in any literature. Moreover, its metabolism pathway is yet to be established. This study aimed to investigate and characterize the metabolites of duvelisib generated in microsomes and S9 fractions. In this study, five duvelisib metabolites have been identified using UHPLC-Q-TOF-MS/MS technique of analysis. The structural characterisation of the metabolites was performed by comparing the fragmentation pattern of duvelisib and its metabolites through an accurate mass measurement technique. Three metabolites were found to be generated through phase I hydroxylation and dechlorination reaction. The other two metabolites were generated through a phase II glucuronidation reaction. The metabolism mechanism established through this study can be useful to improve the safety profile of the drug of its similar category in the future after establishment their toxicity profile of the identified metabolites.

Liquid Chromatography-Mass Spectrometry for Clinical Metabolomics: An Overview

Metabolomics is a discipline that offers a comprehensive analysis of metabolites in biological samples. In the last decades, the notable evolution in liquid chromatography and mass spectrometry technologies has driven an exponential progress in LC-MS-based metabolomics. Targeted and untargeted metabolomics strategies are important tools in health and medical science, especially in the study of disease-related biomarkers, drug discovery and development, toxicology, diet, physical exercise, and precision medicine. Clinical and biological problems can now be understood in terms of metabolic phenotyping. This overview highlights the current approaches to LC-MS-based metabolomics analysis and its applications in the clinical research.

Integrative metabolic profile of myelodysplastic syndrome based on UHPLC-MS

Myelodysplastic syndrome (MDS) is a neoplastic disease originating from hematopoietic stem cells. Currently, hematopoietic stem cell transplantation (HSCT) is the most effective cure, although lenalidomide, azacytidine, and decitabine have been applied to relieve symptoms of MDS. The purpose of this study was to evaluate the changes in endogenous metabolites by applying a UHPLC-MS (ultra-high-performance liquid chromatography-MS) metabolomics approach and to investigate metabolic pathways related to MDS. An untargeted metabolomics approach based on UHPLC-MS in combination with multivariate data analysis, including partial least squares discrimination analysis and orthogonal partial least squares discriminant analysis, was established to investigate potential biomarkers in the plasma of MDS patients. As a result, 29 biomarkers were identified to distinguish between MDS patients, HSCT patients, and healthy controls, which were mainly related to inflammation regulation, amino acid metabolism, fatty acid metabolism, and energy metabolism. To our knowledge, this is the first time where plasma metabolomics was combined with HSCT to study the pathogenesis and therapeutic target of MDS. The identification of biomarkers and analysis of metabolic pathways could offer the possibility of discovering new therapeutic targets for MDS in the future.

Advancements in practical and scientific bioanalytical approaches to metabolism studies in drug development

Advancement in metabolism profiling approaches and bioanalytical techniques has been revolutionized over the last two decades. Different in vitro and in vivo approaches along with advanced bioanalytical techniques are enabling the accurate qualitative and quantitative analysis of metabolites. This review summarizes various modern in vitro and in vivo approaches for executing metabolism studies with special emphasis on the recent advancement in the field. Advanced bioanalytical techniques, which can be employed in metabolism studies, have been discussed suggesting their particular application based on specific study objectives. This article can efficiently guide the researchers to scientifically plan metabolism studies and their bioanalysis during drug development programs taking advantage of a detailed understanding of instances of failure in the past.

Ion Mobility–Mass Spectrometry for Bioanalysis

This paper aims to cover the main strategies based on ion mobility spectrometry (IMS) for the analysis of biological samples. The determination of endogenous and exogenous compounds in such samples is important for the understanding of the health status of individuals. For this reason, the development of new approaches that can be complementary to the ones already established (mainly based on liquid chromatography coupled to mass spectrometry) is welcomed. In this regard, ion mobility spectrometry has appeared in the analytical scenario as a powerful technique for the separation and characterization of compounds based on their mobility. IMS has been used in several areas taking advantage of its orthogonality with other analytical separation techniques, such as liquid chromatography, gas chromatography, capillary electrophoresis, or supercritical fluid chromatography. Bioanalysis is not one of the areas where IMS has been more extensively applied. However, over the last years, the interest in using this approach for the analysis of biological samples has clearly increased. This paper introduces the reader to the principles controlling the separation in IMS and reviews recent applications using this technique in the field of bioanalysis.

A systematic strategy integrating solid-phase extraction, full scan range splitting, mass defect filter and precursor ion list for comprehensive metabolite profiling of Danqi Tongmai tablet in rats

In vivo metabolite profiling of herbal medicines remains a challenge due to the complex chemical composition and drastic interference from biological matrix. In this study, a systematic strategy was established for comprehensive metabolite profiling of Danqi Tongmai (DQTM) tablet, a combination of salvianolic acids and notoginsenosides, in rats after oral administration. This strategy was composed of six steps. Firstly, the rat plasma and tissue samples were collected at multiple time points to increase the representativeness of samples. Secondly, different sample preparation methods were systematically investigated including protein precipitation, liquid-liquid extraction and solid-phase extraction to obtain superior extraction efficiency for both salvianolic acids and notoginsenosides. Thirdly, the MS acquisition method was optimized by splitting the full scan range into two separate segments to improve the detection capability for minor components. Fourthly, an extended polygonal mass defect filter (EP-MDF) model was constructed to filter potential metabolites of salvianolic acids and notoginsenosides, and remove large amounts of interference ions. Fifthly, ion intensity-based time point-staggered precursor ion list (IITPS-PIL) was generated to trigger more targeted MS/MS acquisition for potential metabolites at the highest concentration. Finally, the absorbed prototypes and metabolites were comprehensively characterized by reference standards and MS/MS fragmentation. The proposed strategy significantly improved the detection ability for trace prototypes and metabolites in vivo. A total of 370 components, including 94 prototypes (38 confirmed with reference standards) and 276 metabolites, were tentatively characterized in rat plasma and tissue samples after oral administration of DQTM. Collectively, this paper provided an applicable reference for comprehensive metabolite profiling of herbal medicines in complex biological samples.

Scaffold-hopping as a strategy to address metabolic liabilities of aromatic compounds

Understanding and minimizing oxidative metabolism of aromatic compounds is a key hurdle in lead optimization. Metabolic processes not only clear compounds from the body, but they can also transform parent compounds into reactive metabolites. One particularly useful strategy when addressing metabolically labile or oxidation-prone structures is scaffold-hopping. Replacement of an aromatic system with a more electron-deficient ring system can often increase robustness towards cytochrome P450-mediated oxidation while conserving the structural requirements of the pharmacophore. The most common example of this substitution strategy, replacement of a phenyl ring with a pyridyl substituent, is prevalent throughout the literature; however scaffold-hopping encompasses a much wider scope of heterocycle replacement. This review will showcase recent examples where different scaffold-hopping approaches were used to reduce metabolic clearance or block the formation of reactive metabolites. Additionally, we will highlight considerations that should be made to garner the most benefit from a scaffold-hopping strategy for lead optimization.

LC-MS Untargeted Analysis

LC-MS untargeted analysis is a valuable tool in the field of metabolic profiling (metabonomics/metabolomics), and the applications of this technology have grown rapidly over the past decade. LC-MS offers advantages over other analytical platforms such as speed, sensitivity, relative ease of sample preparation, and large dynamic range. As with any analytical approach, there are still drawbacks and challenges to overcome, but advances are constantly being made regarding both column chemistries and instrumentation. There are numerous untargeted LC-MS approaches which can be used in this ever-growing research field; these can be optimized depending on sample type and the nature of the study or biological question. Some of the main LC-MS approaches for the untargeted analysis of biological samples will be described in detail in the following protocol.