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LC-MS in Bioactive Molecules Study

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A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Analytical Chemistry".

Deadline for manuscript submissions: closed (31 October 2023) | Viewed by 7871

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Prof. Dr. Wenzhi Yang

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State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China
Interests: TCM; polysaccharide characterization method; multidimensional chromatography; ion mobility mass spectrometry

Dr. Yuelin Song

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Guest Editor

Modern Research Center for Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100029, China
Interests: traditional chinese medicine; analytical chemistry; effective substance; mechanism; new analytical method

Dr. Heshui Yu

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Guest Editor

College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
Interests: traditional chinese medicine; preparation technology; analytical chemistry; volatile components analysis; ion mobility mass spectrometry

Special Issue Information

Dear Colleagues,

Discovery of novel bioactive molecules of a natural source trends to be increasingly difficult mainly because of their low abundance. LC-MS offers a practical solution due to the high sensitivity of detection and universality to most natural components, which greatly drives novel bioactive compounds discovery by feat of the astonishing advance both in the chromatography and MS. Multidimensional chromatography (MDC) can greatly expand the peak capacity and selectivity of separation, thus exhibiting remarkable superiority in resolving the co-eluting components and enhanced analysis of the trace level bioactive molecules from both the qualitative and quantitative aspects. Modern MS instruments are endowed with more options to establish the fit-for-purpose strategies in addressing the chemical complexity of natural products either in the untargeted or the targeted mode. In particular, application of versatile data-dependent acquisition (DDA) or data-independent acquisition (DIA) or their combination to herbal components analysis has been an attractive topic in analytical chemistry. Recent years have witnessed the rapid development of ion mobility mass spectrometry (IM-MS) in natural product research, which provides an additional dimension of separation thus enabling the acquisition of high-definition MS spectra. More importantly, collision cross section (CCS) determination and prediction have shown great potential in database creation supporting the more reliable metabolites identification and especially the isomers discrimination. Aside from these emerging trends, LC-MS analysis combined with online bioactivity evaluation or the computational approaches also largely promotes the discovery of novel bioactive natural compounds beneficial to the development of new drugs or the other healthcare products.

Prof. Dr. Wenzhi Yang
Dr. Yuelin Song
Dr. Heshui Yu
Guest Editors

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Keywords

liquid chromatography-mass spectrometry
multidimensional chromatography
mass spectrometry scan method
Ion-mobility mass spectrometry
computational data processing
isomers differentiation
collision cross section prediction
online bioactivity screening

Published Papers (4 papers)

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Research

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13 pages, 2899 KiB

Open AccessArticle

Identification of Xanthine Oxidase Inhibitors from Celery Seeds Using Affinity Ultrafiltration–Liquid Chromatography–Mass Spectrometry

by Xiaona Gan, Bo Peng, Liang Chen, Yanjun Jiang, Tingzhao Li, Bo Li and Xiaodong Liu

Molecules 2023, 28(16), 6048; https://doi.org/10.3390/molecules28166048 - 14 Aug 2023

Cited by 1 | Viewed by 1506

Abstract

Celery seeds have been used as an effective dietary supplement to manage hyperuricemia and diminish gout recurrence. Xanthine oxidase (XOD), the critical enzyme responsible for uric acid production, represents the most promising target for anti-hyperuricemia in clinical practice. In this study, we aimed to establish a method based on affinity ultrafiltration–liquid chromatography–mass spectrometry (UF–LC–MS) to directly and rapidly identify the bioactive compounds contributing to the XOD-inhibitory effects of celery seed crude extracts. Chemical profiling of celery seed extracts was performed using UPLC-TOF/MS. The structure was elucidated by matching the multistage fragment ion data to the database and publications of high-resolution natural product mass spectrometry. Thirty-two compounds, including fourteen flavonoids and six phenylpeptides, were identified from celery seed extracts. UF–LC–MS showed that luteolin-7-O-apinosyl glucoside, luteolin-7-O-glucoside, luteolin-7-O-malonyl apinoside, luteolin-7-O-6′-malonyl glucoside, luteolin, apigenin, and chrysoeriol were potential binding compounds of XOD. A further enzyme activity assay demonstrated that celery seed extract (IC₅₀ = 1.98 mg/mL), luteolin-7-O-apinosyl glucoside (IC₅₀ = 3140.51 μmol/L), luteolin-7-O-glucoside (IC₅₀ = 975.83 μmol/L), luteolin-7-O-6′-malonyl glucoside (IC₅₀ = 2018.37 μmol/L), luteolin (IC₅₀ = 69.23 μmol/L), apigenin (IC₅₀ = 92.56 μmol/L), and chrysoeriol (IC₅₀ = 40.52 μmol/L) could dose-dependently inhibit XOD activities. This study highlighted UF–LC–MS as a useful platform for screening novel XOD inhibitors and revealed the chemical basis of celery seed as an anti-gout dietary supplement. Full article

(This article belongs to the Special Issue LC-MS in Bioactive Molecules Study)

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13 pages, 2421 KiB

Open AccessArticle

Characterization of Metabolic Correlations of Ursodeoxycholic Acid with Other Bile Acid Species through In Vitro Sequential Metabolism and Isomer-Focused Identification

by Wei Li, Wei Chen, Xiaoya Niu, Chen Zhao, Pengfei Tu, Jun Li, Wenjing Liu and Yuelin Song

Molecules 2023, 28(12), 4801; https://doi.org/10.3390/molecules28124801 - 16 Jun 2023

Cited by 1 | Viewed by 1246

Abstract

As a first-line agent for cholestasis treatment in a clinic, ursodeoxycholic acid rectifies the perturbed bile acids (BAs) submetabolome in a holistic manner. Considering the endogenous distribution of ursodeoxycholic acid and extensive occurrences of isomeric metabolites, it is challenging to point out whether a given bile acid species is impacted by ursodeoxycholic acid in a direct or indirect manner, thus hindering the therapeutic mechanism clarification. Here, an in-depth exploration of the metabolism pattern of ursodeoxycholic acid was attempted. Sequential metabolism in vitro with enzyme-enriched liver microsomes was implemented to simulate the step-wise metabolism and to capture the metabolically labile intermediates in the absence of endogenous BAs. Squared energy-resolved mass spectrometry (ER²-MS) was utilized to achieve isomeric identification of the conjugated metabolites. As a result, 20 metabolites (M1–M20) in total were observed and confirmatively identified. Of those, eight metabolites were generated by hydroxylation, oxidation, and epimerization, which were further metabolized to nine glucuronides and three sulfates by uridine diphosphate-glycosyltransferases and sulfotransferases, respectively. Regarding a given phase II metabolite, the conjugation sites were correlated with first-generation breakdown graphs corresponding to the linkage fission mediated by collision-induced dissociation, and the structural nuclei were identified by matching second-generation breakdown graphs with the known structures. Together, except for intestinal-bacteria-involved biotransformation, the current study characterized BA species directly influenced by ursodeoxycholic acid administration. Moreover, sequential metabolism in vitro should be a meaningful way of characterizing the metabolic pathways of endogenous substances, and squared energy-resolved mass spectrometry is a legitimate tool for structurally identifying phase II metabolites. Full article

(This article belongs to the Special Issue LC-MS in Bioactive Molecules Study)

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15 pages, 2689 KiB

Open AccessArticle

Characterization and Biological Activities of Four Biotransformation Products of Diosgenin from Rhodococcus erythropolis

by Yanjie Li, Chengyu Zhang, Kexin Kong and Xiaohui Yan

Molecules 2023, 28(7), 3093; https://doi.org/10.3390/molecules28073093 - 30 Mar 2023

Viewed by 1373

Abstract

Diosgenin (DSG), a steroidal sapogenin derived from the tuberous roots of yam, possesses multiple biological properties. DSG has been widely used as a starting material for the industrial production of steroid drugs. Despite its significant pharmacological activities, moderate potency and low solubility hinder the medicinal application of DSG. Biotransformation is an efficient method to produce valuable derivatives of natural products. In this work, we performed the biotransformation of DSG using five Rhodococcus strains. Compounds 1–4 were isolated and identified from Rhodococcus erythropolis. Compounds 1 and 2 showed potent cytotoxicity against the A549, MCF-7, and HepG2 cell lines. Compounds 3 and 4 are novel entities, and each possesses a terminal carboxyl group attached to the spiroacetal ring. Remarkably, 4 exhibited significant cell protective effects for kidney, liver, and vascular endothelial cells, suggesting the therapeutic potential of this compound in chronic renal diseases, atherosclerosis, and hypertension. We further optimized the fermentation conditions aiming to increase the titer of compound 4. Finally, the yield of compound 4 was improved by 2.9-fold and reached 32.4 mg/L in the optimized conditions. Our study lays the foundation for further developing compound 4 as a cell protective agent. Full article

(This article belongs to the Special Issue LC-MS in Bioactive Molecules Study)

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Review

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27 pages, 2110 KiB

Open AccessReview

Collision Cross Section Prediction Based on Machine Learning

by Xiaohang Li, Hongda Wang, Meiting Jiang, Mengxiang Ding, Xiaoyan Xu, Bei Xu, Yadan Zou, Yuetong Yu and Wenzhi Yang

Molecules 2023, 28(10), 4050; https://doi.org/10.3390/molecules28104050 - 12 May 2023

Cited by 7 | Viewed by 3053

Abstract

Ion mobility-mass spectrometry (IM-MS) is a powerful separation technique providing an additional dimension of separation to support the enhanced separation and characterization of complex components from the tissue metabolome and medicinal herbs. The integration of machine learning (ML) with IM-MS can overcome the barrier to the lack of reference standards, promoting the creation of a large number of proprietary collision cross section (CCS) databases, which help to achieve the rapid, comprehensive, and accurate characterization of the contained chemical components. In this review, advances in CCS prediction using ML in the past 2 decades are summarized. The advantages of ion mobility-mass spectrometers and the commercially available ion mobility technologies with different principles (e.g., time dispersive, confinement and selective release, and space dispersive) are introduced and compared. The general procedures involved in CCS prediction based on ML (acquisition and optimization of the independent and dependent variables, model construction and evaluation, etc.) are highlighted. In addition, quantum chemistry, molecular dynamics, and CCS theoretical calculations are also described. Finally, the applications of CCS prediction in metabolomics, natural products, foods, and the other research fields are reflected. Full article

(This article belongs to the Special Issue LC-MS in Bioactive Molecules Study)

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