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Wang H, Zhu W, Hong Y, Wei W, Zheng N, He X, Bao Y, Gao X, Huang W, Sheng L, Li M, Li H. Astragalus polysaccharides attenuate chemotherapy-induced immune injury by modulating gut microbiota and polyunsaturated fatty acid metabolism. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 128:155492. [PMID: 38479258 DOI: 10.1016/j.phymed.2024.155492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 02/02/2024] [Accepted: 02/26/2024] [Indexed: 05/01/2024]
Abstract
BACKGROUND The damage of chemotherapy drugs to immune function and intestinal mucosa is a common side effect during chemotherapy. Astragalus polysaccharides (APS) exhibit immunomodulatory properties and are recognized for preserving the integrity of the human intestinal barrier. Nevertheless, their application and mechanisms of action in chemotherapy-induced immune damage and intestinal barrier disruption remain insufficiently explored. PURPOSE This study delved into investigating how APS mitigates chemotherapy-induced immune dysfunction and intestinal mucosal injury, while also providing deeper insights into the underlying mechanisms. METHODS In a chemotherapy mice model induced by 5-fluorouracil (5-Fu), the assessment of APS's efficacy encompassed evaluations of immune organ weight, body weight, colon length, and histopathology. The regulation of different immune cells in spleen was detected by flow cytometry. 16S rRNA gene sequencings, ex vivo microbiome assay, fecal microbiota transplantation (FMT), and targeted metabolomics analysis were applied to explore the mechanisms of APS effected on chemotherapy-induced mice. RESULTS APS ameliorated chemotherapy-induced damage to immune organs and regulated immune cell differentiation disorders, including CD4+T, CD8+T, CD19+B, F4/80+CD11B+ macrophages. APS also alleviated colon shortening and upregulated the expression of intestinal barrier proteins. Furthermore, APS significantly restored structure of gut microbiota following chemotherapy intervention. Ex vivo microbiome assays further demonstrated the capacity of APS to improve 5-Fu-induced microbiota growth inhibition and compositional change. FMT demonstrated that the regulation of gut microbiota by APS could promote the recovery of immune functions and alleviate shortening of the colon length. Remarkably, APS significantly ameliorated the imbalance of linoleic acid (LA) and α-linolenic acid in polyunsaturated fatty acid (PUFA) metabolism. Further in vitro experiments showed that LA could promote splenic lymphocyte proliferation. In addition, both LA and DGLA down-regulated the secretion of NO and partially up-regulated the percentage of F4/80+CD11B+CD206+ cells. CONCLUSION APS can effectively ameliorate chemotherapy-induced immune damage and intestinal mucosal disruption by regulating the composition of the gut microbiota and further restoring PUFA metabolism. These findings indicate that APS can serve as an adjuvant to improve the side effects such as intestinal and immune damage caused by chemotherapy.
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Affiliation(s)
- Hao Wang
- Functional Metabolomics and Gut Microbiome Laboratory, School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Weize Zhu
- Functional Metabolomics and Gut Microbiome Laboratory, School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Ying Hong
- Functional Metabolomics and Gut Microbiome Laboratory, School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Wenjing Wei
- Functional Metabolomics and Gut Microbiome Laboratory, School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Ningning Zheng
- Functional Metabolomics and Gut Microbiome Laboratory, School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Xiaofang He
- Functional Metabolomics and Gut Microbiome Laboratory, School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Yiyang Bao
- Functional Metabolomics and Gut Microbiome Laboratory, School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Xinxin Gao
- Functional Metabolomics and Gut Microbiome Laboratory, School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Wenjin Huang
- Functional Metabolomics and Gut Microbiome Laboratory, School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Lili Sheng
- Functional Metabolomics and Gut Microbiome Laboratory, School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Mingxiao Li
- Functional Metabolomics and Gut Microbiome Laboratory, School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
| | - Houkai Li
- Functional Metabolomics and Gut Microbiome Laboratory, School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
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Tan J, Fu B, Zhao X, Ye L. Novel Techniques and Models for Studying the Role of the Gut Microbiota in Drug Metabolism. Eur J Drug Metab Pharmacokinet 2024; 49:131-147. [PMID: 38123834 DOI: 10.1007/s13318-023-00874-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/27/2023] [Indexed: 12/23/2023]
Abstract
The gut microbiota, known as the second human genome, plays a vital role in modulating drug metabolism, significantly impacting therapeutic outcomes and adverse effects. Emerging research has elucidated that the microbiota mediates a range of modifications of drugs, leading to their activation, inactivation, or even toxication. In diverse individuals, variations in the gut microbiota can result in differences in microbe-drug interactions, underscoring the importance of personalized approaches in pharmacotherapy. However, previous studies on drug metabolism in the gut microbiota have been hampered by technical limitations. Nowadays, advances in biotechnological tools, such as microbially derived metabolism screening and microbial gene editing, have provided a deeper insight into the mechanism of drug metabolism by gut microbiota, moving us toward personalized therapeutic interventions. Given this situation, our review summarizes recent advances in the study of gut-microbiota-mediated drug metabolism and showcases techniques and models developed to navigate the challenges posed by the microbial involvement in drug action. Therefore, we not only aim at understanding the complex interaction between the gut microbiota and drugs and outline the development of research techniques and models, but we also summarize the specific applications of new techniques and models in researching gut-microbiota-mediated drug metabolism, with the expectation of providing new insights on how to study drug metabolism by gut microbiota.
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Affiliation(s)
- Jianling Tan
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Bingxuan Fu
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Xiaojie Zhao
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Ling Ye
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China.
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Liu B, Liu C, Chai X, Fan X, Huang T, Zhan J, Zhu Q, Zeng D, Gong Z, He L, Yang Y, Zhou X, Jiang B, Zhang X, Liu M. Real-Time NMR-Based Drug Discovery to Identify Inhibitors against Fatty Acid Synthesis in Living Cancer Cells. Anal Chem 2024. [PMID: 38334355 DOI: 10.1021/acs.analchem.3c04954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
Abnormal fatty acid metabolism is recognized as a key driver of tumor development and progression. Although numerous inhibitors have been developed to target this pathway, finding drugs with high specificity that do not disrupt normal cellular metabolism remains a formidable challenge. In this paper, we introduced a novel real-time NMR-based drug screening technique that operates within living cells. This technique provides a direct way to putatively identify molecular targets involved in specific metabolic processes, making it a powerful tool for cell-based drug screening. Using 2-13C acetate as a tracer, combined with 3D cell clusters and a bioreactor system, our approach enables real-time detection of inhibitors that target fatty acid metabolism within living cells. As a result, we successfully demonstrated the initial application of this method in the discovery of traditional Chinese medicines that specifically target fatty acid metabolism. Elucidating the mechanisms behind herbal medicines remains challenging due to the complex nature of their compounds and the presence of multiple targets. Remarkably, our findings demonstrate the significant inhibitory effect of P. cocos on fatty acid synthesis within cells, illustrating the potential of this approach in analyzing fatty acid metabolism events and identifying drug candidates that selectively inhibit fatty acid synthesis at the cellular level. Moreover, this systematic approach represents a valuable strategy for discovering the intricate effects of herbal medicine.
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Affiliation(s)
- Biao Liu
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Caixiang Liu
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Chai
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Xinyu Fan
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Tao Huang
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Jianhua Zhan
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Qinjun Zhu
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Danyun Zeng
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhou Gong
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lichun He
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunhuang Yang
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Zhou
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bin Jiang
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Optics Valley Laboratory, Wuhan 430074, China
| | - Xu Zhang
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Optics Valley Laboratory, Wuhan 430074, China
| | - Maili Liu
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Optics Valley Laboratory, Wuhan 430074, China
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Nagana Gowda GA, Pascua V, Lusk JA, Hong NN, Guo L, Dong J, Sweet IR, Raftery D. Monitoring live mitochondrial metabolism in real-time using NMR spectroscopy. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2023; 61:718-727. [PMID: 36882950 PMCID: PMC10483017 DOI: 10.1002/mrc.5341] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/03/2023] [Accepted: 03/03/2023] [Indexed: 06/18/2023]
Abstract
Investigation of mitochondrial metabolism is gaining increased interest owing to the growing recognition of the role of mitochondria in health and numerous diseases. Studies of isolated mitochondria promise novel insights into the metabolism devoid of confounding effects from other cellular organelles such as cytoplasm. This study describes the isolation of mitochondria from mouse skeletal myoblast cells (C2C12) and the investigation of live mitochondrial metabolism in real-time using isotope tracer-based NMR spectroscopy. [3-13 C1 ]pyruvate was used as the substrate to monitor the dynamic changes of the downstream metabolites in mitochondria. The results demonstrate an intriguing phenomenon, in which lactate is produced from pyruvate inside the mitochondria and the results were confirmed by treating mitochondria with an inhibitor of mitochondrial pyruvate carrier (UK5099). Lactate is associated with health and numerous diseases including cancer and, to date, it is known to occur only in the cytoplasm. The insight that lactate is also produced inside mitochondria opens avenues for exploring new pathways of lactate metabolism. Further, experiments performed using inhibitors of the mitochondrial respiratory chain, FCCP and rotenone, show that [2-13 C1 ]acetyl coenzyme A, which is produced from [3-13 C1 ]pyruvate and acts as a primary substrate for the tricarboxylic acid cycle in mitochondria, exhibits a remarkable sensitivity to the inhibitors. These results offer a direct approach to visualize mitochondrial respiration through altered levels of the associated metabolites.
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Affiliation(s)
- G. A. Nagana Gowda
- Northwest Metabolomics Research Center, Anesthesiology and Pain Medicine, University of Washington, Seattle, Washington 98109, USA
- Mitochondria and Metabolism Center, Anesthesiology and Pain Medicine, University of Washington, Seattle, Washington 98109, USA
| | - Vadim Pascua
- Northwest Metabolomics Research Center, Anesthesiology and Pain Medicine, University of Washington, Seattle, Washington 98109, USA
- Mitochondria and Metabolism Center, Anesthesiology and Pain Medicine, University of Washington, Seattle, Washington 98109, USA
| | - John A. Lusk
- Northwest Metabolomics Research Center, Anesthesiology and Pain Medicine, University of Washington, Seattle, Washington 98109, USA
- Mitochondria and Metabolism Center, Anesthesiology and Pain Medicine, University of Washington, Seattle, Washington 98109, USA
| | - Natalie N. Hong
- Northwest Metabolomics Research Center, Anesthesiology and Pain Medicine, University of Washington, Seattle, Washington 98109, USA
- Mitochondria and Metabolism Center, Anesthesiology and Pain Medicine, University of Washington, Seattle, Washington 98109, USA
| | - Lin Guo
- Northwest Metabolomics Research Center, Anesthesiology and Pain Medicine, University of Washington, Seattle, Washington 98109, USA
| | - Jiyang Dong
- Northwest Metabolomics Research Center, Anesthesiology and Pain Medicine, University of Washington, Seattle, Washington 98109, USA
- Department of Electronic Science, Xiamen University, Xiamen 361005, China
| | - Ian R. Sweet
- Department of Medicine, University of Washington, Seattle, Washington 98109, USA
| | - Daniel Raftery
- Northwest Metabolomics Research Center, Anesthesiology and Pain Medicine, University of Washington, Seattle, Washington 98109, USA
- Mitochondria and Metabolism Center, Anesthesiology and Pain Medicine, University of Washington, Seattle, Washington 98109, USA
- Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
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5
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Leigh SJ, Uhlig F, Wilmes L, Sanchez-Diaz P, Gheorghe CE, Goodson MS, Kelley-Loughnane N, Hyland NP, Cryan JF, Clarke G. The impact of acute and chronic stress on gastrointestinal physiology and function: a microbiota-gut-brain axis perspective. J Physiol 2023; 601:4491-4538. [PMID: 37756251 DOI: 10.1113/jp281951] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
The physiological consequences of stress often manifest in the gastrointestinal tract. Traumatic or chronic stress is associated with widespread maladaptive changes throughout the gut, although comparatively little is known about the effects of acute stress. Furthermore, these stress-induced changes in the gut may increase susceptibility to gastrointestinal disorders and infection, and impact critical features of the neural and behavioural consequences of the stress response by impairing gut-brain axis communication. Understanding the mechanisms behind changes in enteric nervous system circuitry, visceral sensitivity, gut barrier function, permeability, and the gut microbiota following stress is an important research objective with pathophysiological implications in both neurogastroenterology and psychiatry. Moreover, the gut microbiota has emerged as a key aspect of physiology sensitive to the effects of stress. In this review, we focus on different aspects of the gastrointestinal tract including gut barrier function as well as the immune, humoral and neuronal elements involved in gut-brain communication. Furthermore, we discuss the evidence for a role of stress in gastrointestinal disorders. Existing gaps in the current literature are highlighted, and possible avenues for future research with an integrated physiological perspective have been suggested. A more complete understanding of the spatial and temporal dynamics of the integrated host and microbial response to different kinds of stressors in the gastrointestinal tract will enable full exploitation of the diagnostic and therapeutic potential in the fast-evolving field of host-microbiome interactions.
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Affiliation(s)
- Sarah-Jane Leigh
- APC Microbiome Ireland, Cork, Ireland
- Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland
| | - Friederike Uhlig
- APC Microbiome Ireland, Cork, Ireland
- Department of Physiology, University College Cork, Cork, Ireland
| | - Lars Wilmes
- APC Microbiome Ireland, Cork, Ireland
- Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - Paula Sanchez-Diaz
- APC Microbiome Ireland, Cork, Ireland
- Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland
| | - Cassandra E Gheorghe
- APC Microbiome Ireland, Cork, Ireland
- Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland
| | - Michael S Goodson
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, Ohio, USA
| | - Nancy Kelley-Loughnane
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, Ohio, USA
| | - Niall P Hyland
- APC Microbiome Ireland, Cork, Ireland
- Department of Physiology, University College Cork, Cork, Ireland
| | - John F Cryan
- APC Microbiome Ireland, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - Gerard Clarke
- APC Microbiome Ireland, Cork, Ireland
- Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland
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6
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Wang X, Li C, Li Z, Qi Y, Zhang X, Zhao X, Zhao C, Lin X, Lu X, Xu G. A Structure-Guided Molecular Network Strategy for Global Untargeted Metabolomics Data Annotation. Anal Chem 2023; 95:11603-11612. [PMID: 37493263 DOI: 10.1021/acs.analchem.3c00849] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
Large-scale metabolite annotation is a bottleneck in untargeted metabolomics. Here, we present a structure-guided molecular network strategy (SGMNS) for deep annotation of untargeted ultra-performance liquid chromatography-high resolution mass spectrometry (MS) metabolomics data. Different from the current network-based metabolite annotation method, SGMNS is based on a global connectivity molecular network (GCMN), which was constructed by molecular fingerprint similarity of chemical structures in metabolome databases. Neighbor metabolites with similar structures in GCMN are expected to produce similar spectra. Network annotation propagation of SGMNS is performed using known metabolites as seeds. The experimental MS/MS spectra of seeds are assigned to corresponding neighbor metabolites in GCMN as their "pseudo" spectra; the propagation is done by searching predicted retention times, MS1, and "pseudo" spectra against metabolite features in untargeted metabolomics data. Then, the annotated metabolite features were used as new seeds for annotation propagation again. Performance evaluation of SGMNS showed its unique advantages for metabolome annotation. The developed method was applied to annotate six typical biological samples; a total of 701, 1557, 1147, 1095, 1237, and 2041 metabolites were annotated from the cell, feces, plasma (NIST SRM 1950), tissue, urine, and their pooled sample, respectively, and the annotation accuracy was >83% with RSD <2%. The results show that SGMNS fully exploits the chemical space of the existing metabolomes for metabolite deep annotation and overcomes the shortcoming of insufficient reference MS/MS spectra.
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Affiliation(s)
- Xinxin Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, P.R. China
| | - Chao Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P.R. China
- School of Computer Science & Technology, Dalian University of Technology, Dalian 116024, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, P.R. China
| | - Zaifang Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, P.R. China
| | - Yanpeng Qi
- School of Computer Science & Technology, Dalian University of Technology, Dalian 116024, P.R. China
| | - Xiuqiong Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, P.R. China
| | - Xinjie Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, P.R. China
| | - Chunxia Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, P.R. China
| | - Xiaohui Lin
- School of Computer Science & Technology, Dalian University of Technology, Dalian 116024, P.R. China
| | - Xin Lu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, P.R. China
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, P.R. China
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7
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Sugiki T, Ito A, Hatanaka Y, Tsukamoto M, Murata T, Miyanishi K, Kagawa A, Fujiwara T, Kitagawa M, Morita Y, Negoro M. Real-time monitoring of enzyme-catalyzed phosphoribosylation of anti-influenza prodrug favipiravir by time-lapse nuclear magnetic resonance spectroscopy. NMR IN BIOMEDICINE 2023; 36:e4888. [PMID: 36468685 DOI: 10.1002/nbm.4888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
Favipiravir (brand name Avigan), a widely known anti-influenza prodrug, is metabolized by endogenous enzymes of host cells to generate the active form, which exerts inhibition of viral RNA-dependent RNA polymerase activity; first, favipiravir is converted to its phosphoribosylated form, favipiravir-ribofuranosyl-5'-monophosphate (favipiravir-RMP), by hypoxanthine-guanine phosphoribosyltransferase (HGPRT). Because this phosphoribosylation reaction is the rate-determining step in the generation of the active metabolite, quantitative and real-time monitoring of the HGPRT-catalyzed reaction is essential to understanding the pharmacokinetics of favipiravir. However, assay methods enabling such monitoring have not been established. 19 F- or 31 P-based nuclear magnetic resonance (NMR) are powerful techniques for observation of intermolecular interactions, chemical reactions, and metabolism of molecules of interest, given that NMR signals of the heteronuclei sensitively reflect changes in the chemical environment of these moieties. Here, we demonstrated direct, sensitive, target-selective, nondestructive, and real-time observation of HGPRT-catalyzed conversion of favipiravir to favipiravir-RMP by performing time-lapse 19 F-NMR monitoring of the fluorine atom of favipiravir. In addition, we showed that 31 P-NMR can be used for real-time observation of the identical reaction by monitoring phosphorus atoms of the phosphoribosyl group of favipiravir-RMP and of the pyrophosphate product of that reaction. Furthermore, we demonstrated that NMR approaches permit the determination of general parameters of enzymatic activity such as Vmax and Km . This method not only can be widely employed in enzyme assays, but also may be of use in the screening and development of new favipiravir-analog antiviral prodrugs that can be phosphoribosylated more efficiently by HGPRT, which would increase the intracellular concentration of the drug's active form. The techniques demonstrated in this study would allow more detailed investigation of the pharmacokinetics of fluorinated drugs, and might significantly contribute to opening new avenues for widespread pharmaceutical studies.
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Affiliation(s)
| | - Akihiro Ito
- Analytical Instrument Facility, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
| | - Yuko Hatanaka
- Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, Japan
- Center for Quantum Information and Quantum Biology (QIQB), Osaka University, Toyonaka, Osaka, Japan
| | - Masaki Tsukamoto
- Graduate School of Informatics, Nagoya University, Nagoya, Aichi, Japan
| | - Tsuyoshi Murata
- Faculty of Engineering, Aichi Institute of Technology, Yakusa, Toyota, Aichi, Japan
| | - Koichiro Miyanishi
- Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, Japan
- Center for Quantum Information and Quantum Biology (QIQB), Osaka University, Toyonaka, Osaka, Japan
| | - Akinori Kagawa
- Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, Japan
- Center for Quantum Information and Quantum Biology (QIQB), Osaka University, Toyonaka, Osaka, Japan
| | - Toshimichi Fujiwara
- Institute for Protein Research, Osaka University, Osaka, Japan
- Center for Quantum Information and Quantum Biology (QIQB), Osaka University, Toyonaka, Osaka, Japan
| | - Masahiro Kitagawa
- Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, Japan
- Center for Quantum Information and Quantum Biology (QIQB), Osaka University, Toyonaka, Osaka, Japan
| | - Yasushi Morita
- Faculty of Engineering, Aichi Institute of Technology, Yakusa, Toyota, Aichi, Japan
| | - Makoto Negoro
- Center for Quantum Information and Quantum Biology (QIQB), Osaka University, Toyonaka, Osaka, Japan
- Institute for Quantum Life Science, National Institute for Quantum and Radiological Science and Technology, Chiba, Japan
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Affiliation(s)
- G. A. Nagana Gowda
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington
- Mitochondria and Metabolism Center, Department of Anesthesiology and Pain Medicine, University of Washington
| | - Daniel Raftery
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington
- Mitochondria and Metabolism Center, Department of Anesthesiology and Pain Medicine, University of Washington
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109
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9
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Hafsa, Shah HUR, Ahmad K, Ashfaq M, Oku H. Free radical scavenging, antibacterial potentials and spectroscopic characterizations of benzoyl thiourea derivatives and their metal complexes. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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