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Deng WH, Liao RZ. Cysteine Radical and Glutamate Collaboratively Enable C-H Bond Activation and C-N Bond Cleavage in a Glycyl Radical Enzyme HplG. J Chem Inf Model 2024; 64:4168-4179. [PMID: 38745447 DOI: 10.1021/acs.jcim.4c00122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Hydroxyprolines are abundant in nature and widely utilized by many living organisms. Isomerization of trans-4-hydroxy-d-proline (t4D-HP) to generate 2-amino-4-ketopentanoate has been found to need a glycyl radical enzyme HplG, which catalyzes the cleavage of the C-N bond, while dehydration of trans-4-hydroxy-l-proline involves a homologous enzyme of HplG. Herein, molecular dynamics simulations and quantum mechanics/molecular mechanics (QM/MM) calculations are employed to understand the reaction mechanism of HplG. Two possible reaction pathways of HplG have been explored to decipher the origin of its chemoselectivity. The QM/MM calculations reveal that the isomerization proceeds via an initial hydrogen shift from the Cγ site of t4D-HP to a catalytic cysteine radical, followed by cleavage of the Cδ-N bond in t4D-HP to form a radical intermediate that captures a hydrogen atom from the cysteine. Activation of the Cδ-H bond in t4D-HP to bring about dehydration of t4D-HP possesses an extremely high energy barrier, thus rendering the dehydration pathway implausible in HplG. On the basis of the current calculations, conserved residue Glu429 plays a pivotal role in the isomerization pathway: the hydrogen bonding between it and t4D-HP weakens the hydroxyalkyl Cγ-Hγ bond, and it acts as a proton acceptor to trigger the cleavage of the C-N bond in t4D-HP. Our current QM/MM calculations rationalize the origin of the experimentally observed chemoselectivity of HplG and propose an H-bond-assisted bond activation strategy in radical-containing enzymes. These findings have general implications on radical-mediated enzymatic catalysis and expand our understanding of how nature wisely and selectively activates the C-H bond to modulate catalytic selectivity.
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Affiliation(s)
- Wen-Hao Deng
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Rong-Zhen Liao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
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2
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Li N, Wang L, Li L, Yang MZ, Wang QX, Bai XW, Gao F, Yuan YQ, Yu ZJ, Ren ZG. The correlation between gut microbiome and atrial fibrillation: pathophysiology and therapeutic perspectives. Mil Med Res 2023; 10:51. [PMID: 37936201 PMCID: PMC10629124 DOI: 10.1186/s40779-023-00489-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 10/26/2023] [Indexed: 11/09/2023] Open
Abstract
Regulation of gut microbiota and its impact on human health is the theme of intensive research. The incidence and prevalence of atrial fibrillation (AF) are continuously escalating as the global population ages and chronic disease survival rates increase; however, the mechanisms are not entirely clarified. It is gaining awareness that alterations in the assembly, structure, and dynamics of gut microbiota are intimately engaged in the AF progression. Owing to advancements in next-generation sequencing technologies and computational strategies, researchers can explore novel linkages with the genomes, transcriptomes, proteomes, and metabolomes through parallel meta-omics approaches, rendering a panoramic view of the culture-independent microbial investigation. In this review, we summarized the evidence for a bidirectional correlation between AF and the gut microbiome. Furthermore, we proposed the concept of "gut-immune-heart" axis and addressed the direct and indirect causal roots between the gut microbiome and AF. The intricate relationship was unveiled to generate innovative microbiota-based preventive and therapeutic interventions, which shed light on a definite direction for future experiments.
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Affiliation(s)
- Na Li
- Department of Infectious Diseases, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, 250000, China
| | - Ling Wang
- Department of Cardiovascular Medicine, Henan Provincial Chest Hospital, Zhengzhou, 450008, China
| | - Lei Li
- Department of Infectious Diseases, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, 250000, China
| | - Meng-Zhao Yang
- Department of Infectious Diseases, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, 250000, China
| | - Qing-Xiang Wang
- Department of Blood Collection, Xuchang Blood Center, Xuchang, 461000, Henan, China
| | - Xi-Wen Bai
- Nanchang University Queen Marry School, Nanchang, 330036, China
| | - Feng Gao
- Department of Infectious Diseases, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, 250000, China
| | - Yi-Qiang Yuan
- Department of Cardiovascular Medicine, Henan Provincial Chest Hospital, Zhengzhou, 450008, China.
| | - Zu-Jiang Yu
- Department of Infectious Diseases, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
| | - Zhi-Gang Ren
- Department of Infectious Diseases, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, 250000, China.
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3
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Kumbhare SV, Pedroso I, Ugalde JA, Márquez-Miranda V, Sinha R, Almonacid DE. Drug and gut microbe relationships: Moving beyond antibiotics. Drug Discov Today 2023; 28:103797. [PMID: 37806386 DOI: 10.1016/j.drudis.2023.103797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 09/23/2023] [Accepted: 10/04/2023] [Indexed: 10/10/2023]
Abstract
Our understanding of drug-microbe relationships has evolved from viewing microbes as mere drug producers to a dynamic, modifiable system where they can serve as drugs or targets of precision pharmacology. This review highlights recent findings on the gut microbiome, particularly focusing on four aspects of research: (i) drugs for bugs, covering recent strategies for targeting gut pathogens; (ii) bugs as drugs, including probiotics; (iii) drugs from bugs, including postbiotics; and (iv) bugs and drugs, discussing additional types of drug-microbe interactions. This review provides a perspective on future translational research, including efficient companion diagnostics in pharmaceutical interventions.
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Affiliation(s)
| | | | - Juan A Ugalde
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Valeria Márquez-Miranda
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
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4
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Fechtner S, Allen BE, Chriswell ME, Jubair WK, Robertson CE, Kofonow JN, Frank DN, Holers VM, Kuhn KA. 3,3-dimethyl-1-butanol and its metabolite 3,3-dimethylbutyrate ameliorate collagen-induced arthritis independent of choline trimethylamine lyase activity. RESEARCH SQUARE 2023:rs.3.rs-3297018. [PMID: 37720032 PMCID: PMC10503834 DOI: 10.21203/rs.3.rs-3297018/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
Previous studies have identified significant alterations in intestinal carnitine metabolism in mice with collagen-induced arthritis (CIA), potentially linking bacterial dysbiosis with autoimmunity. Bacterial trimethylamine (TMA) lyases metabolize dietary carnitine to TMA, which is oxidized in the liver to trimethylamine-N-oxide (TMAO). TMAO is associated with inflammatory diseases, such as atherosclerosis, whose immunologic processes mirror that of rheumatoid arthritis (RA). Therefore, we investigated the possibility of ameliorating CIA by inhibiting TMA lyase activity using 3,3-dimethyl-1-butanol (DMB) or fluoromethylcholine (FMC). During CIA, mice were treated with 1% vol/vol DMB, 100mg/kg FMC, or vehicle. DMB-treated mice demonstrated significant (>50%) reduction in arthritis severity compared to FMC and vehicle-treated mice. However, in contrast to FMC, DMB treatment did not reduce cecal TMA nor circulating TMAO concentrations. Using gas chromatography, we confirmed the effect of DMB is independent of TMA lyase inhibition. Further, we identified a novel host-derived metabolite of DMB, 3,3-dimethyl-1-butyric acid (DMBut), which also significantly reduced disease and proinflammatory cytokines in CIA mice. Altogether, our study suggests that DMB the immunomodulatory activity of DMB and/or its metabolites are protective in CIA. Elucidating its target and mechanism of action may provide new directions for RA therapeutic development.
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5
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Woo AYM, Aguilar Ramos MA, Narayan R, Richards-Corke KC, Wang ML, Sandoval-Espinola WJ, Balskus EP. Targeting the human gut microbiome with small-molecule inhibitors. NATURE REVIEWS. CHEMISTRY 2023; 7:319-339. [PMID: 37117817 DOI: 10.1038/s41570-023-00471-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/20/2023] [Indexed: 04/30/2023]
Abstract
The human gut microbiome is a complex microbial community that is strongly linked to both host health and disease. However, the detailed molecular mechanisms underlying the effects of these microorganisms on host biology remain largely uncharacterized. The development of non-lethal, small-molecule inhibitors that target specific gut microbial activities enables a powerful but underutilized approach to studying the gut microbiome and a promising therapeutic strategy. In this Review, we will discuss the challenges of studying this microbial community, the historic use of small-molecule inhibitors in microbial ecology, and recent applications of this strategy. We also discuss the evidence suggesting that host-targeted drugs can affect the growth and metabolism of gut microbes. Finally, we address the issues of developing and implementing microbiome-targeted small-molecule inhibitors and define important future directions for this research.
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Affiliation(s)
- Amelia Y M Woo
- Harvard University, Department of Chemistry and Chemical Biology, Cambridge, MA, USA
| | | | - Rohan Narayan
- Harvard University, Department of Chemistry and Chemical Biology, Cambridge, MA, USA
| | | | - Michelle L Wang
- Harvard University, Department of Chemistry and Chemical Biology, Cambridge, MA, USA
| | - Walter J Sandoval-Espinola
- Harvard University, Department of Chemistry and Chemical Biology, Cambridge, MA, USA
- Universidad Nacional de Asunción, Facultad de Ciencias Exactas y Naturales, Departamento de Biotecnología, Laboratorio de Biotecnología Microbiana, San Lorenzo, Paraguay
| | - Emily P Balskus
- Harvard University, Department of Chemistry and Chemical Biology, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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6
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Constantino-Jonapa LA, Espinoza-Palacios Y, Escalona-Montaño AR, Hernández-Ruiz P, Amezcua-Guerra LM, Amedei A, Aguirre-García MM. Contribution of Trimethylamine N-Oxide (TMAO) to Chronic Inflammatory and Degenerative Diseases. Biomedicines 2023; 11:biomedicines11020431. [PMID: 36830968 PMCID: PMC9952918 DOI: 10.3390/biomedicines11020431] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/23/2023] [Accepted: 01/27/2023] [Indexed: 02/05/2023] Open
Abstract
Trimethylamine N-oxide (TMAO) is a metabolite produced by the gut microbiota and has been mainly associated with an increased incidence of cardiovascular diseases (CVDs) in humans. There are factors that affect one's TMAO level, such as diet, drugs, age, and hormones, among others. Gut dysbiosis in the host has been studied recently as a new approach to understanding chronic inflammatory and degenerative diseases, including cardiovascular diseases, metabolic diseases, and Alzheimer's disease. These disease types as well as COVID-19 are known to modulate host immunity. Diabetic and obese patients have been observed to have an increase in their level of TMAO, which has a direct correlation with CVDs. This metabolite is attributed to enhancing the inflammatory pathways through cholesterol and bile acid dysregulation, promoting foam cell formation. Additionally, TMAO activates the transcription factor NF-κB, which, in turn, triggers cytokine production. The result can be an exaggerated inflammatory response capable of inducing endoplasmic reticulum stress, which is responsible for various diseases. Due to the deleterious effects that this metabolite causes in its host, it is important to search for new therapeutic agents that allow a reduction in the TMAO levels of patients and that, thus, allow patients to be able to avoid a severe cardiovascular event. The present review discussed the synthesis of TMAO and its contribution to the pathogenesis of various inflammatory diseases.
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Affiliation(s)
- Luis A. Constantino-Jonapa
- Unidad de Investigación UNAM-INC, División de Investigación, Facultad de Medicina, UNAM, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México 14080, Mexico
| | - Yoshua Espinoza-Palacios
- Unidad de Investigación UNAM-INC, División de Investigación, Facultad de Medicina, UNAM, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México 14080, Mexico
| | - Alma R. Escalona-Montaño
- Unidad de Investigación UNAM-INC, División de Investigación, Facultad de Medicina, UNAM, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México 14080, Mexico
| | - Paulina Hernández-Ruiz
- Unidad de Investigación UNAM-INC, División de Investigación, Facultad de Medicina, UNAM, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México 14080, Mexico
| | - Luis M. Amezcua-Guerra
- Departamento de Inmunología, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México 14080, Mexico
| | - Amedeo Amedei
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy
- Interdisciplinary Internal Medicine Unit, Careggi University Hospital, 50134 Florence, Italy
| | - María M. Aguirre-García
- Unidad de Investigación UNAM-INC, División de Investigación, Facultad de Medicina, UNAM, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México 14080, Mexico
- Correspondence: ; Tel.: +52-55-5573-2911 (ext. 27316)
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7
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Sharma S, Hegde P, Panda S, Orimoloye MO, Aldrich CC. Drugging the microbiome: targeting small microbiome molecules. Curr Opin Microbiol 2023; 71:102234. [PMID: 36399893 DOI: 10.1016/j.mib.2022.102234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 10/12/2022] [Accepted: 10/17/2022] [Indexed: 11/17/2022]
Abstract
The human microbiome represents a large and diverse collection of microbes that plays an integral role in human physiology and pathophysiology through interactions with the host and within the microbial community. While early work exploring links between microbiome signatures and diseases states has been associative, emerging evidence demonstrates the metabolic products of the human microbiome have more proximal causal effects on disease phenotypes. The therapeutic implications of this shift are profound as manipulation of the microbiome by the administration of live biotherapeutics, ongoing, can now be pursued alongside research efforts toward describing inhibitors of key microbiome enzymes involved in the biosynthesis of metabolites implicated in various disease states and processing of host-derived metabolites. With growing interest in 'drugging the microbiome', we review few notable microbial metabolites for which traditional drug-development campaigns have yielded compounds with therapeutic promise.
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Affiliation(s)
- Sachin Sharma
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - Pooja Hegde
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - Subhankar Panda
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - Moyosore O Orimoloye
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA.
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8
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The Role of Gut Microbiota and Trimethylamine N-oxide in Cardiovascular Diseases. J Cardiovasc Transl Res 2022:10.1007/s12265-022-10330-0. [PMID: 36251229 DOI: 10.1007/s12265-022-10330-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 09/30/2022] [Indexed: 10/24/2022]
Abstract
Changes in the intestinal flora and its metabolites have been associated with cardiovascular disease (CVD). Short-chain fatty acids, bile acids, and especially trimethylamine N-oxide (TMAO), an endothelial toxic factor produced by gut microbiota from phosphatidylcholine in meat, have been identified to be closely related to endothelial cell dysfunction as well as tightly affiliated with CVD, the two main types being coronary artery disease (CAD) and coronary microvascular disease (CMVD). We discuss how changes in the gut flora and the metabolite TMAO contribute to the development of CAD and CMVD. The above insight might serve as a stepping stone for novel CAD and CMVD diagnostics and therapies centered on microbiota.
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9
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Simó C, Fornari T, García-Risco MR, Peña-Cearra A, Abecia L, Anguita J, Rodríguez H, García-Cañas V. Resazurin-based high-throughput screening method for the discovery of dietary phytochemicals to target microbial transformation of L-carnitine into trimethylamine, a gut metabolite associated with cardiovascular disease. Food Funct 2022; 13:5640-5653. [PMID: 35506542 DOI: 10.1039/d2fo00103a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nowadays, there is great interest in the discovery of food compounds that might inhibit gut microbial TMA production from its methylamine precursors. In this work, an innovative novel screening strategy capable of rapidly determining the differences in the metabolic response of Klebsiella pneumoniae, a bacteria producing TMA under aerobic conditions, to a library of extracts obtained from food and natural sources was developed. The proposed high-throughput screening (HTS) method combines resazurin reduction assay in 384-well plates and Gaussian Processes as a machine learning tool for data processing, allowing for a fast, cheap and highly standardized evaluation of any interfering effect of a given compound or extract on the microbial metabolism sustained by L-carnitine utilization. As a proof-of-concept of this strategy, a pilot screening of 39 extracts and 6 pure compounds was performed to search for potential candidates that could inhibit in vitro TMA formation from L-carnitine. Among all the extracts tested, three of them were selected as candidates to interfere with TMA formation. Subsequent in vitro assays confirmed the potential of oregano and red thyme hexane extracts (at 1 mg mL-1) to inhibit TMA formation in bacterial lysates. In such in vitro assay, the red thyme extract exerted comparable effects on TMA reduction (∼40%) as 7.5 mM meldonium (∼50% TMA decrease), a reported L-carnitine analogue. Our results show that metabolic activity could be used as a proxy of the capacity to produce TMA under controlled culture conditions using L-carnitine to sustain metabolism.
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Affiliation(s)
- Carolina Simó
- Molecular Nutrition and Metabolism, Institute of Food Science Research (CIAL), Spanish National Research Council (CSIC), Madrid, 28049, Spain.
| | - Tiziana Fornari
- Institute of Food Science Research (CIAL), Autonomous University of Madrid, Madrid, 28049, Spain
| | - Mónica R García-Risco
- Institute of Food Science Research (CIAL), Autonomous University of Madrid, Madrid, 28049, Spain
| | - Ainize Peña-Cearra
- CIC bioGUNE. Bizkaia Science and Technology Park, bld 801 A, 48160, Derio, Bizkaia, Spain.,Immunology, Microbiology and Parasitology Department, Medicine and Nursing Faculty, University of the Basque Country (UPV), 48940, Leioa, Spain
| | - Leticia Abecia
- CIC bioGUNE. Bizkaia Science and Technology Park, bld 801 A, 48160, Derio, Bizkaia, Spain.,Immunology, Microbiology and Parasitology Department, Medicine and Nursing Faculty, University of the Basque Country (UPV), 48940, Leioa, Spain
| | - Juan Anguita
- CIC bioGUNE. Bizkaia Science and Technology Park, bld 801 A, 48160, Derio, Bizkaia, Spain
| | - Héctor Rodríguez
- CIC bioGUNE. Bizkaia Science and Technology Park, bld 801 A, 48160, Derio, Bizkaia, Spain
| | - Virginia García-Cañas
- Molecular Nutrition and Metabolism, Institute of Food Science Research (CIAL), Spanish National Research Council (CSIC), Madrid, 28049, Spain.
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10
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Li X, Fan Z, Cui J, Li D, Lu J, Cui X, Xie L, Wu Y, Lin Q, Li Y. Trimethylamine N-Oxide in Heart Failure: A Meta-Analysis of Prognostic Value. Front Cardiovasc Med 2022; 9:817396. [PMID: 35252396 PMCID: PMC8888860 DOI: 10.3389/fcvm.2022.817396] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 01/19/2022] [Indexed: 12/19/2022] Open
Abstract
Objective The present study aimed to explore the prognostic value of trimethylamine N-oxide (TMAO) in heart failure (HF). Methods PubMed, Excerpta Medica Database (EMBASE), Cochrane Library, Web of Science, Wanfang Database, SINOMED, China Science and Technology Journal Database (VIP), and China National Knowledge Infrastructure (CNKI) were searched up to June 1, 2021. Studies recording the major adverse cardiovascular events (MACEs) or all-cause mortality in HF patients and their circulating TMAO concentrations were included. Meta-analysis was performed using Stata 13.0. Results Ten articles (12 studies) involving 13,425 participants from 2014 to 2021 were considered. Compared to low-level TMAO, elevated TMAO was correlated with MACEs and all-cause mortality in HF (RR: 1.28, 95% CI: 1.17, 1.39, P < 0.0001, random-effects model and RR: 1.35, 95% CI: 1.28, 1.42, P < 0.0001, random-effects model, respectively). Consistent results were obtained in all examined subgroups as well as in the sensitivity analysis. Conclusion Elevated TMAO may be an adverse prognostic indicator in patients with HF. Systematic Review Registration https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=267208
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Affiliation(s)
- Xingxing Li
- Second Clinical School of Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Zongjing Fan
- Department of Cardiology, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Jie Cui
- Department of Cardiology, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Dong Li
- Department of Cardiology, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Jinjin Lu
- Department of Cardiology, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Xiaoyun Cui
- Department of Cardiology, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Liandi Xie
- Department of Cardiology, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Yang Wu
- Department of Cardiology, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Qian Lin
- Department of Cardiology, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Yan Li
- Department of Cardiology, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
- *Correspondence: Yan Li
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11
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Helsley RN, Miyata T, Kadam A, Varadharajan V, Sangwan N, Huang EC, Banerjee R, Brown AL, Fung KK, Massey WJ, Neumann C, Orabi D, Osborn LJ, Schugar RC, McMullen MR, Bellar A, Poulsen KL, Kim A, Pathak V, Mrdjen M, Anderson JT, Willard B, McClain CJ, Mitchell M, McCullough AJ, Radaeva S, Barton B, Szabo G, Dasarathy S, Garcia-Garcia JC, Rotroff DM, Allende DS, Wang Z, Hazen SL, Nagy LE, Brown JM. Gut microbial trimethylamine is elevated in alcohol-associated hepatitis and contributes to ethanol-induced liver injury in mice. eLife 2022; 11:76554. [PMID: 35084335 PMCID: PMC8853661 DOI: 10.7554/elife.76554] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 12/31/2021] [Indexed: 11/13/2022] Open
Abstract
There is mounting evidence that microbes residing in the human intestine contribute to diverse alcohol-associated liver diseases (ALD) including the most deadly form known as alcohol-associated hepatitis (AH). However, mechanisms by which gut microbes synergize with excessive alcohol intake to promote liver injury are poorly understood. Furthermore, whether drugs that selectively target gut microbial metabolism can improve ALD has never been tested. We used liquid chromatography tandem mass spectrometry to quantify the levels of microbe and host choline co-metabolites in healthy controls and AH patients, finding elevated levels of the microbial metabolite trimethylamine (TMA) in AH. In subsequent studies, we treated mice with non-lethal bacterial choline TMA lyase (CutC/D) inhibitors to blunt gut microbe-dependent production of TMA in the context of chronic ethanol administration. Indices of liver injury were quantified by complementary RNA sequencing, biochemical, and histological approaches. In addition, we examined the impact of ethanol consumption and TMA lyase inhibition on gut microbiome structure via 16S rRNA sequencing. We show the gut microbial choline metabolite TMA is elevated in AH patients and correlates with reduced hepatic expression of the TMA oxygenase flavin-containing monooxygenase 3 (FMO3). Provocatively, we find that small molecule inhibition of gut microbial CutC/D activity protects mice from ethanol-induced liver injury. CutC/D inhibitor-driven improvement in ethanol-induced liver injury is associated with distinct reorganization of the gut microbiome and host liver transcriptome. The microbial metabolite TMA is elevated in patients with AH, and inhibition of TMA production from gut microbes can protect mice from ethanol-induced liver injury.
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Affiliation(s)
- Robert N Helsley
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute of the Cleveland Clinic, Cleveland, United States.,Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, United States.,Department of Pediatrics, Division of Pediatric Gastroenterology, Hepatology, and Nutrition, College of Medicine, University of Kentucky, Lexington, United States
| | - Tatsunori Miyata
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Anagha Kadam
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute of the Cleveland Clinic, Cleveland, United States.,Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Venkateshwari Varadharajan
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute of the Cleveland Clinic, Cleveland, United States.,Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Naseer Sangwan
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute of the Cleveland Clinic, Cleveland, United States.,Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Emily C Huang
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Rakhee Banerjee
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute of the Cleveland Clinic, Cleveland, United States.,Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Amanda L Brown
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute of the Cleveland Clinic, Cleveland, United States.,Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Kevin K Fung
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute of the Cleveland Clinic, Cleveland, United States.,Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - William J Massey
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute of the Cleveland Clinic, Cleveland, United States.,Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Chase Neumann
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute of the Cleveland Clinic, Cleveland, United States.,Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Danny Orabi
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute of the Cleveland Clinic, Cleveland, United States.,Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Lucas J Osborn
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute of the Cleveland Clinic, Cleveland, United States.,Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Rebecca C Schugar
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute of the Cleveland Clinic, Cleveland, United States.,Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Megan R McMullen
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Annette Bellar
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Kyle L Poulsen
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Adam Kim
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Vai Pathak
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Marko Mrdjen
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute of the Cleveland Clinic, Cleveland, United States.,Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, United States.,Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - James T Anderson
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute of the Cleveland Clinic, Cleveland, United States.,Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Belinda Willard
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute of the Cleveland Clinic, Cleveland, United States.,Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Craig J McClain
- Department of Medicine, University of Louisville, Louisville, United States
| | - Mack Mitchell
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, United States
| | - Arthur J McCullough
- Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, United States.,Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Svetlana Radaeva
- National Institute on Alcohol Abuse and Alcoholism, Bethesda, United States
| | - Bruce Barton
- Department of Population and Quantitative Health Sciences, University of Massachusetts Medical School, Worcester, United States
| | - Gyongyi Szabo
- Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, United States
| | - Srinivasan Dasarathy
- Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, United States.,Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | | | - Daniel M Rotroff
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Daniela S Allende
- Department of Anatomical Pathology, Cleveland Clinic, Cleveland, United States
| | - Zeneng Wang
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute of the Cleveland Clinic, Cleveland, United States.,Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Stanley L Hazen
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute of the Cleveland Clinic, Cleveland, United States.,Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, United States.,Department of Cardiovascular Medicine, Heart and Vascular and Thoracic Institute, Cleveland Clinic, Cleveland, United States
| | - Laura E Nagy
- Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, United States.,Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Jonathan Mark Brown
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute of the Cleveland Clinic, Cleveland, United States.,Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
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12
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Schugar RC, Gliniak CM, Osborn LJ, Massey W, Sangwan N, Horak A, Banerjee R, Orabi D, Helsley RN, Brown AL, Burrows A, Finney C, Fung KK, Allen FM, Ferguson D, Gromovsky AD, Neumann C, Cook K, McMillan A, Buffa JA, Anderson JT, Mehrabian M, Goudarzi M, Willard B, Mak TD, Armstrong AR, Swanson G, Keshavarzian A, Garcia-Garcia JC, Wang Z, Lusis AJ, Hazen SL, Brown JM. Gut microbe-targeted choline trimethylamine lyase inhibition improves obesity via rewiring of host circadian rhythms. eLife 2022; 11:63998. [PMID: 35072627 PMCID: PMC8813054 DOI: 10.7554/elife.63998] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/20/2022] [Indexed: 11/13/2022] Open
Abstract
Obesity has repeatedly been linked to reorganization of the gut microbiome, yet to this point obesity therapeutics have been targeted exclusively toward the human host. Here, we show that gut microbe-targeted inhibition of the trimethylamine N-oxide (TMAO) pathway protects mice against the metabolic disturbances associated with diet-induced obesity (DIO) or leptin deficiency (Lepob/ob). Small molecule inhibition of the gut microbial enzyme choline TMA-lyase (CutC) does not reduce food intake but is instead associated with alterations in the gut microbiome, improvement in glucose tolerance, and enhanced energy expenditure. We also show that gut microbial CutC inhibition is associated with reorganization of host circadian control of both phosphatidylcholine and energy metabolism. This study underscores the relationship between microbe and host metabolism and provides evidence that gut microbe-derived trimethylamine (TMA) is a key regulator of the host circadian clock. This work also demonstrates that gut microbe-targeted enzyme inhibitors have potential as anti-obesity therapeutics.
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Affiliation(s)
- Rebecca C Schugar
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | | | - Lucas J Osborn
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - William Massey
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Naseer Sangwan
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Anthony Horak
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Rakhee Banerjee
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Danny Orabi
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Robert N Helsley
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Amanda L Brown
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Amy Burrows
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Chelsea Finney
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Kevin K Fung
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Frederick M Allen
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Daniel Ferguson
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Anthony D Gromovsky
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Chase Neumann
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Kendall Cook
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Amy McMillan
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Jennifer A Buffa
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - James T Anderson
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | | | - Maryam Goudarzi
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Belinda Willard
- Research Core Services, Cleveland Clinic Lerner College of Medicine
| | - Tytus D Mak
- Mass Spectromety Data Center, National Institute of Standards and Technology (NIST)
| | | | - Garth Swanson
- Department of Internal Medicine, Rush University Medical Center
| | | | | | - Zeneng Wang
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Aldons J Lusis
- Department of Medicine, University of California, Los Angeles
| | - Stanley L Hazen
- Department of Cellular and Molecular Medicine, Cleveland Clinic Lerner College of Medicine
| | - Jonathan Mark Brown
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
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13
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He M, Nian B, Shi J, Sun X, Du R, Tan CP, Xu YJ, Liu Y. Influence of extraction technology on rapeseed oil functional quality: a study on rapeseed polyphenols. Food Funct 2022; 13:270-279. [PMID: 34888592 DOI: 10.1039/d1fo01507a] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Extraction technology can influence the vegetable oil functional quality. Polyphenols in rapeseed oil have been proved to be beneficial for cardiovascular health. In this study, we evaluated the effect of extraction methods on the functional quality of rapeseed oil from the perspective of phenolic compounds. The results showed that hot pressing produces the highest amount of phenolic compounds in rapeseed oil. Its most abundant phenolic compound, sinapine (9.18 μg g-1), showed the highest activity in inhibiting anaerobic choline metabolism with an EC50 value of 1.9 mM, whose downstream products are related to cardiovascular diseases. Molecular docking and molecular dynamics (MD) simulations revealed that sinapine exhibits good binding affinity toward CutC, and CutC-sinapine is a stable complex with fewer conformational fluctuations and similar tightness. Taken together, hot pressing can be considered the best extraction method for rapeseed oil from the perspective of phenolic compounds.
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Affiliation(s)
- Mengxue He
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, China.
| | - Binbin Nian
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, China.
| | - Jiachen Shi
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, China.
| | - Xian Sun
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, China.
| | - Runfeng Du
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, China.
| | - Chin Ping Tan
- Department of Food Technology, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400 Seri Kembangan, Malaysia
| | - Yong-Jiang Xu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, China.
| | - Yuanfa Liu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, China.
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14
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Gao D, Zhao H, Yin Z, Han C, Wang Y, Luo G, Gao X. Rheum tanguticum Alleviates Cognitive Impairment in APP/PS1 Mice by Regulating Drug-Responsive Bacteria and Their Corresponding Microbial Metabolites. Front Pharmacol 2021; 12:766120. [PMID: 34975476 PMCID: PMC8715007 DOI: 10.3389/fphar.2021.766120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 11/24/2021] [Indexed: 11/23/2022] Open
Abstract
Drugs targeting intestinal bacteria have shown great efficacy for alleviating symptoms of Alzheimer’s disease (AD), and microbial metabolites are important messengers. Our previous work indicated that Rheum tanguticum effectively improved cognitive function and reshaped the gut microbial homeostasis in AD rats. However, its therapeutic mechanisms remain unclear. Herein, this study aimed to elaborate the mechanisms of rhubarb for the treatment of AD by identifying effective metabolites associated with rhubarb-responsive bacteria. The results found that rhubarb reduced hippocampal inflammation and neuronal damage in APP/PS1 transgenic (Tg) mice. 16S rRNA sequencing and metabolomic analysis revealed that gut microbiota and their metabolism in Tg mice were disturbed in an age-dependent manner. Rhubarb-responsive bacteria were further identified by real-time polymerase chain reaction (RT-PCR) sequencing. Four different metabolites reversed by rhubarb were found in the position of the important nodes on rhubarb-responsive bacteria and their corresponding metabolites combined with pathological indicators co-network. Furthermore, in vitro experiments demonstrated o-tyrosine not only inhibited the viabilities of primary neurons as well as BV-2 cells, but also increased the levels of intracellular reactive oxygen species and nitric oxide. In the end, the results suggest that rhubarb ameliorates cognitive impairment in Tg mice through decreasing the abundance of o-tyrosine in the gut owing to the regulation of rhubarb-responsive bacteria. Our study provides a promising strategy for elaborating therapeutic mechanisms of bacteria-targeted drugs for AD.
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15
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Li Y, Cao H, Wang X, Guo L, Ding X, Zhao W, Zhang F. Diet-mediated metaorganismal relay biotransformation: health effects and pathways. Crit Rev Food Sci Nutr 2021:1-19. [PMID: 34802351 DOI: 10.1080/10408398.2021.2004993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
In recent years, the concept of metaorganism expands our insight into how diet-microbe-host interactions contribute to human health and diseases. We realized that many biological metabolic processes in the host can be summarized into metaorganismal relay pathways, in which metabolites such as trimethylamine-N‑oxide, short-chain fatty acids and bile acids act as double-edged swords (beneficial or harmful effects) in the initiation and progression of diseases. Pleiotropic effects of metabolites are derived from several influencing factors including dose level, targeted organ of effect, action duration and species of these metabolites. Based on the pleiotropic effects of metabolites, personalized therapeutic approaches including microecological agents, enzymatic regulators and changes in dietary habits to govern related metabolite production may provide a new insight in promoting human health. In this review, we summarize our current knowledge of metaorganismal relay pathways and elaborate on the pleiotropic effects of metabolites in these pathways, with special emphasis on related therapeutic nutritional interventions.
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Affiliation(s)
- Yanmin Li
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Hong Cao
- Department of Nutrition, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Xiaoqian Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Lichun Guo
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Xiaoying Ding
- Department of Endocrinology and Metabolism, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Zhao
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Feng Zhang
- Department of Nutrition, Affiliated Hospital of Jiangnan University, Wuxi, China
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16
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Miao L, Du J, Chen Z, Shi D, Qu H. Effects of Microbiota-Driven Therapy on Circulating Trimethylamine-N-Oxide Metabolism: A Systematic Review and Meta-Analysis. Front Cardiovasc Med 2021; 8:710567. [PMID: 34552967 PMCID: PMC8450403 DOI: 10.3389/fcvm.2021.710567] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 08/05/2021] [Indexed: 01/21/2023] Open
Abstract
Aim: This study was designed to systematically evaluate the effects of microbiota-driven therapy on decreasing TMAO and its related metabolites. Methods and Results: PubMed, EMBASE and Cochrane Library databases were searched (up to July 2021). Randomized controlled trials (RCTs), compared microbiota-driven therapy (prebiotics, probiotics, or synbiotics) with placebo on decreasing TMAO and its related metabolites, were eligible. Two researchers extracted the data independently and the disagreement was resolved by a third researcher. The risk of bias of included study was evaluated using Cochrane tool (RoB 2.0). Meta-analysis, meta-regression analysis and publication bias analysis were performed by RevMan 5.3 or Stata 12.0 software. Ten studies (12 arms) involving 342 patients (168 patients in the intervention group and 174 patients in the control group) were included. Compared with the control group, microbiota-driven therapy did not reduce circulating TMAO [SMD = −0.05, 95% CI (−0.36, 0.26), P = 0.749], choline [SMD = −0.34, 95% CI (−1.09, 0.41), P = 0.373], betaine aldehyde [SMD = −0.704, 95% CI (−1.789, 0.382), P = 0.204], and L-carnatine [SMD = −0.06, 95% CI (−0.38, 0.25), P = 0.692]. Conclusion: Current evidence does not support that microbiota-driven treatment reduce circulating levels of TMAO, choline, betaine aldehyde, and L-carnitine. However, given the small sample size, this conclusion needs to be proved in the future. Systematic Review Registration: PROSPERO:CRD42019119107.
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Affiliation(s)
- Lina Miao
- Department of Graduate School, Beijing University of Chinese Medicine, Beijing, China.,Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jianpeng Du
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Zhuhong Chen
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Dazhuo Shi
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China.,National Clinical Research Center for Chinese Medicine Cardiology, Beijing, China
| | - Hua Qu
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China.,National Clinical Research Center for Chinese Medicine Cardiology, Beijing, China.,NMPA Key Laboratory for Clinical Research and Evaluation of Traditional Chinese Medicine, Beijing, China
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17
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Goh YQ, Cheam G, Wang Y. Understanding Choline Bioavailability and Utilization: First Step Toward Personalizing Choline Nutrition. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:10774-10789. [PMID: 34392687 DOI: 10.1021/acs.jafc.1c03077] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Choline is an essential macronutrient involved in neurotransmitter synthesis, cell-membrane signaling, lipid transport, and methyl-group metabolism. Nevertheless, the vast majority are not meeting the recommended intake requirement. Choline deficiency is linked to nonalcoholic fatty liver disease, skeletal muscle atrophy, and neurodegenerative diseases. The conversion of dietary choline to trimethylamine by gut microbiota is known for its association with atherosclerosis and may contribute to choline deficiency. Choline-utilizing bacteria constitutes less than 1% of the gut community and is modulated by lifestyle interventions such as dietary patterns, antibiotics, and probiotics. In addition, choline utilization is also affected by genetic factors, further complicating the impact of choline on health. This review overviews the complex interplay between dietary intakes of choline, gut microbiota and genetic factors, and the subsequent impact on health. Understanding of gut microbiota metabolism of choline substrates and interindividual variability is warranted in the development of personalized choline nutrition.
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Affiliation(s)
- Ying Qi Goh
- Singapore Phenome Center, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 636921
| | - Guoxiang Cheam
- School of Biological Sciences, Nanyang Technological University, Singapore 639798
| | - Yulan Wang
- Singapore Phenome Center, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 636921
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18
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Shen X, Li L, Sun Z, Zang G, Zhang L, Shao C, Wang Z. Gut Microbiota and Atherosclerosis-Focusing on the Plaque Stability. Front Cardiovasc Med 2021; 8:668532. [PMID: 34414217 PMCID: PMC8368126 DOI: 10.3389/fcvm.2021.668532] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 06/30/2021] [Indexed: 12/12/2022] Open
Abstract
Cardiovascular diseases (CVDs) are major causes of mortality and morbidity in the modern society. The rupture of atherosclerotic plaque can induce thrombus formation, which is the main cause of acute cardiovascular events. Recently, many studies have demonstrated that there are some relationships between microbiota and atherosclerosis. In this review, we will focus on the effect of the microbiota and the microbe-derived metabolites, including trimethylamine-N-oxide (TMAO), short-chain fatty acids (SCFAs), and lipopolysaccharide (LPS), on the stability of atherosclerotic plaque. Finally, we will conclude with some therapies based on the microbiota and its metabolites.
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Affiliation(s)
- Xinyi Shen
- Department of Cardiology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Lihua Li
- Department of Pathology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Zhen Sun
- Department of Cardiology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Guangyao Zang
- Department of Cardiology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Lili Zhang
- Department of Cardiology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Chen Shao
- Department of Cardiology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Zhongqun Wang
- Department of Cardiology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
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19
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Su C, Li X, Yang Y, Du Y, Zhang X, Wang L, Hong B. Metformin alleviates choline diet-induced TMAO elevation in C57BL/6J mice by influencing gut-microbiota composition and functionality. Nutr Diabetes 2021; 11:27. [PMID: 34389700 PMCID: PMC8363624 DOI: 10.1038/s41387-021-00169-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 05/05/2021] [Accepted: 05/18/2021] [Indexed: 12/20/2022] Open
Abstract
Trimethylamine-N-oxide (TMAO), a gut-microbiota-dependent metabolite generated from its dietary precursors such as choline, has been identified as an independent risk factor for atherosclerosis. Metformin is the most widely used drug for the treatment of type 2 diabetes (T2D), which has therapeutic effects on hyperglycemia accelerated atherosclerosis. A growing body of evidence suggest that metformin plays a therapeutic role by regulating the structure and metabolic function of gut microbiota. However, whether metformin has an impact on gut-microbiota-mediated TMAO production from choline remains obscure. In this study, the oral administration of metformin significantly reduced choline diet-increased serum TMAO in choline diet-fed C57BL/6J mice. The diversity analysis based on 16S rRNA gene sequencing of C57BL/6J mice fecal samples indicated that metformin markedly changed the gut-microbiota composition. Metformin was positively correlated with the enrichment of different intestinal bacteria such as Bifidobacterium and Akkermansia and a lower cutC (a choline utilization gene) abundance. Furthermore, the ex vivo and in vitro inhibitory effects of metformin on choline metabolism of TMA-producing bacteria were confirmed under anaerobic condition. The results suggested that metformin suppresses serum TMAO level by remodeling gut microbiota involved in TMA generation from choline.
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Affiliation(s)
- Chunyan Su
- NHC Key Laboratory of Biotechnology of Antibiotics, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 Tiantan Xili, Beijing, 100050, China
| | - Xingxing Li
- NHC Key Laboratory of Biotechnology of Antibiotics, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 Tiantan Xili, Beijing, 100050, China.,CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 Tiantan Xili, Beijing, 100050, China
| | - Yuxin Yang
- NHC Key Laboratory of Biotechnology of Antibiotics, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 Tiantan Xili, Beijing, 100050, China
| | - Yu Du
- NHC Key Laboratory of Biotechnology of Antibiotics, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 Tiantan Xili, Beijing, 100050, China
| | - Xiumin Zhang
- NHC Key Laboratory of Biotechnology of Antibiotics, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 Tiantan Xili, Beijing, 100050, China
| | - Li Wang
- NHC Key Laboratory of Biotechnology of Antibiotics, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 Tiantan Xili, Beijing, 100050, China.
| | - Bin Hong
- NHC Key Laboratory of Biotechnology of Antibiotics, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 Tiantan Xili, Beijing, 100050, China. .,CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 Tiantan Xili, Beijing, 100050, China.
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20
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Abstract
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The genomic era has dramatically changed how we discover and investigate
microbial biochemistry. In particular, the exponential expansion in
the number of sequenced microbial genomes provides investigators with
a vast wealth of sequence data to exploit for the discovery of biochemical
functions and mechanisms, as well as novel enzymes and metabolites.
In contrast to early biochemical work, which was largely characterized
by “forward” approaches that proceed from biomass to
enzyme to gene, the availability of genome sequences enables the discovery
of new microbial metabolic activities, enzymes, and metabolites by
“reverse” approaches that originate with genetic information
or by approaches that incorporate features of both forward and reverse
methodologies. In the genomic era, the canonical organization of microbial
genomes into gene clusters presents a singular opportunity for the
utilization of genomic data. Specifically, genomic context (information
gleaned from the genes surrounding a gene of interest in the chromosome)
is a powerful tool for chemical discovery in microbial systems because
of the functional and/or physiological relationship that usually exists
between genes found within a gene cluster. This means that the investigator
can use this inferred link to generate hypotheses about the functions
of individual genes in the cluster or even the function of the entire
cluster itself. Here, we discuss how analysis of genomic context in
combination with a mechanistic understanding of enzymes can facilitate
numerous facets of microbial biochemical research including the identification
of biosynthetic gene clusters, the discovery of important and novel
enzymes, the elucidation of natural product structures, and the identification
of new metabolic pathways. We highlight work from our laboratory using
genomic context to discover and study biosynthetic pathways that produce
natural products, including the cylindrocyclophanes, nitrogen–nitrogen
bond-containing metabolites, and the gut microbial genotoxin colibactin.
Although use of genomic context is most commonly associated with studies
of natural product biosynthesis, we also show that it can be applied
to the study of primary metabolism. We illustrate this with examples
from our work studying the members of the glycyl radical enzyme superfamily
involved in choline and 4-hydroxyproline degradation in the human
gut. Looking forward, we envision increased opportunities to use such
information, with the combination of biochemical knowledge and computational
tools poised to fuel a new revolution in our ability to connect genes
and their biochemical functions. In particular, we note a need for
methods that computationally formalize the functional association
between genes when such associations are not obvious from manual gene
annotations. Such tools will drastically augment the feasibility and
scope of gene cluster analysis and accelerate the discovery of new
microbial enzymes, metabolites, and metabolic processes.
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Affiliation(s)
- Duncan J. Kountz
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Emily P. Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
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21
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Li X, Su C, Jiang Z, Yang Y, Zhang Y, Yang M, Zhang X, Du Y, Zhang J, Wang L, Jiang J, Hong B. Berberine attenuates choline-induced atherosclerosis by inhibiting trimethylamine and trimethylamine-N-oxide production via manipulating the gut microbiome. NPJ Biofilms Microbiomes 2021; 7:36. [PMID: 33863898 PMCID: PMC8052457 DOI: 10.1038/s41522-021-00205-8] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 03/16/2021] [Indexed: 12/11/2022] Open
Abstract
Trimethylamine-N-oxide (TMAO), a derivative from the gut microbiota metabolite trimethylamine (TMA), has been identified to be an independent risk factor for promoting atherosclerosis. Evidences suggest that berberine (BBR) could be used to treat obesity, diabetes and atherosclerosis, however, its mechanism is not clear mainly because of its poor oral bioavailability. Here, we show that BBR attenuated TMA/TMAO production in the C57BL/6J and ApoE KO mice fed with choline-supplemented chow diet, and mitigated atherosclerotic lesion areas in ApoE KO mice. Inhibition of TMA/TMAO production by BBR-modulated gut microbiota was proved by a single-dose administration of d9-choline in vivo. Metagenomic analysis of cecal contents demonstrated that BBR altered gut microbiota composition, microbiome functionality, and cutC/cntA gene abundance. Furthermore, BBR was shown to inhibit choline-to-TMA conversion in TMA-producing bacteria in vitro and in gut microbial consortium from fecal samples of choline-fed mice and human volunteers, and the result was confirmed by transplantation of TMA-producing bacteria in mice. These results offer new insights into the mechanisms responsible for the anti-atherosclerosis effects of BBR, which inhibits commensal microbial TMA production via gut microbiota remodeling.
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Affiliation(s)
- Xingxing Li
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Chunyan Su
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Zhibo Jiang
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yuxin Yang
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yue Zhang
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Mengxia Yang
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xiumin Zhang
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yu Du
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jin Zhang
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Li Wang
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
| | - Jiandong Jiang
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
| | - Bin Hong
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China. .,CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
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22
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Gabr MT, Machalz D, Pach S, Wolber G. A benzoxazole derivative as an inhibitor of anaerobic choline metabolism by human gut microbiota. RSC Med Chem 2020; 11:1402-1412. [PMID: 34095847 PMCID: PMC8126876 DOI: 10.1039/d0md00218f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 08/03/2020] [Indexed: 01/01/2023] Open
Abstract
Metabolic pathways mediated by human gut bacteria have emerged as potential therapeutic targets because of their association with the pathophysiology of various human diseases. The anaerobic transformation of choline into trimethylamine (TMA) by gut microbiota is directly linked to type 2 diabetes, fatty liver disease, and cardiovascular diseases. Structural analogs of choline have been developed as competitive inhibitors of choline TMA-lyase (CutC), a key enzyme for the conversion of choline to TMA. However, weak to moderate CutC inhibitory profiles of the choline analogs limit their further advancement into clinical translation. In this study, we introduce a glycomimetic-based approach for the identification of CutC inhibitors with intestinal metabolic stability. Our workflow started with screening of a small library of glycomimetics for metabolic stability in the presence of human intestinal S9 fraction. Further screening using an in vitro CutC inhibitory assay identified a benzoxazole ligand (BO-I) as a CutC inhibitor with an IC50 value of 2.4 ± 0.3 μM. Kinetic analysis revealed that BO-I functions as a non-competitive inhibitor of CutC. Interestingly, BO-I reduced the production of TMA in whole cell assays of multiple bacterial strains as well as in complex biological environments. Therefore, structural optimization of BO-I holds promise for the development of efficient gut microbiota-targeted small molecules.
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Affiliation(s)
- Moustafa T Gabr
- Department of Radiology, Stanford University School of Medicine Stanford CA 94305 USA
| | - David Machalz
- Freie Universitaet Berlin, Institute of Pharmacy, Pharmaceutical and Medicinal Chemistry (Computer-Aided Drug Design) Berlin Germany
| | - Szymon Pach
- Freie Universitaet Berlin, Institute of Pharmacy, Pharmaceutical and Medicinal Chemistry (Computer-Aided Drug Design) Berlin Germany
| | - Gerhard Wolber
- Freie Universitaet Berlin, Institute of Pharmacy, Pharmaceutical and Medicinal Chemistry (Computer-Aided Drug Design) Berlin Germany
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23
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Gabr M, Świderek K. Discovery of a Histidine-Based Scaffold as an Inhibitor of Gut Microbial Choline Trimethylamine-Lyase. ChemMedChem 2020; 15:2273-2279. [PMID: 32827245 DOI: 10.1002/cmdc.202000571] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Indexed: 01/07/2023]
Abstract
Anaerobic choline metabolism by human gut microbiota to produce trimethylamine (TMA) has recently evolved as a potential therapeutic target because of its association with chronic kidney disease and increased cardiovascular risks. Limited examples of choline analogues have been reported as inhibitors of bacterial enzyme choline TMA-lyase (CutC), a key enzyme regulating choline anaerobic metabolism. We used a new workflow to discover CutC inhibitors based on focused screening of a diversified library of small molecules for intestinal metabolic stability followed by in vitro CutC inhibitory assay. This workflow identified a histidine-based scaffold as a CutC inhibitor with an IC50 value of 1.9±0.2 μM. Remarkably, the identified CutC inhibitor was able to reduce the production of TMA in whole-cell assays using various bacterial strains as well as in complex gut microbiota environment. The improved efficiency of the new scaffold identified in this study in comparison to previously reported CutC inhibitors would enable optimization of potential leads for in vivo screening and clinical translation. Finally, docking studies and molecular-dynamic simulations were used to predict putative interactions created between inhibitor and CutC.
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Affiliation(s)
- Moustafa Gabr
- Department of Radiology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Katarzyna Świderek
- Departament de Química Física i Analítica, Universitat Jaume I, 12071, Castellón, Spain
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24
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He M, Tan CP, Xu YJ, Liu Y. Gut microbiota-derived trimethylamine-N-oxide: A bridge between dietary fatty acid and cardiovascular disease? Food Res Int 2020; 138:109812. [DOI: 10.1016/j.foodres.2020.109812] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/14/2020] [Accepted: 10/12/2020] [Indexed: 01/02/2023]
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25
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Quareshy M, Shanmugam M, Townsend E, Jameson E, Bugg TDH, Cameron AD, Chen Y. Structural basis of carnitine monooxygenase CntA substrate specificity, inhibition, and intersubunit electron transfer. J Biol Chem 2020; 296:100038. [PMID: 33158989 PMCID: PMC7948474 DOI: 10.1074/jbc.ra120.016019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/27/2020] [Accepted: 11/06/2020] [Indexed: 12/27/2022] Open
Abstract
Microbial metabolism of carnitine to trimethylamine (TMA) in the gut can accelerate atherosclerosis and heart disease, and these TMA-producing enzymes are therefore important drug targets. Here, we report the first structures of the carnitine oxygenase CntA, an enzyme of the Rieske oxygenase family. CntA exists in a head-to-tail α3 trimeric structure. The two functional domains (the Rieske and the catalytic mononuclear iron domains) are located >40 Å apart in the same monomer but adjacent in two neighboring monomers. Structural determination of CntA and subsequent electron paramagnetic resonance measurements uncover the molecular basis of the so-called bridging glutamate (E205) residue in intersubunit electron transfer. The structures of the substrate-bound CntA help to define the substrate pocket. Importantly, a tyrosine residue (Y203) is essential for ligand recognition through a π-cation interaction with the quaternary ammonium group. This interaction between an aromatic residue and quaternary amine substrates allows us to delineate a subgroup of Rieske oxygenases (group V) from the prototype ring-hydroxylating Rieske oxygenases involved in bioremediation of aromatic pollutants in the environment. Furthermore, we report the discovery of the first known CntA inhibitors and solve the structure of CntA in complex with the inhibitor, demonstrating the pivotal role of Y203 through a π-π stacking interaction with the inhibitor. Our study provides the structural and molecular basis for future discovery of drugs targeting this TMA-producing enzyme in human gut.
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Affiliation(s)
- Mussa Quareshy
- School of Life Sciences, University of Warwick, Coventry, UK.
| | - Muralidharan Shanmugam
- Manchester Institute of Biotechnology & Photon Science Institute, The University of Manchester, Manchester, UK
| | | | - Eleanor Jameson
- School of Life Sciences, University of Warwick, Coventry, UK
| | | | | | - Yin Chen
- School of Life Sciences, University of Warwick, Coventry, UK.
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26
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Bollenbach M, Ortega M, Orman M, Drennan CL, Balskus EP. Discovery of a Cyclic Choline Analog That Inhibits Anaerobic Choline Metabolism by Human Gut Bacteria. ACS Med Chem Lett 2020; 11:1980-1985. [PMID: 33062182 DOI: 10.1021/acsmedchemlett.0c00005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 03/25/2020] [Indexed: 12/24/2022] Open
Abstract
The anaerobic conversion of choline to trimethylamine (TMA) by the human gut microbiota has been linked to multiple human diseases. The potential impact of this microbial metabolic activity on host health has inspired multiple efforts to identify small molecule inhibitors. Here, we use information about the structure and mechanism of the bacterial enzyme choline TMA-lyase (CutC) to develop a cyclic choline analog that inhibits the conversion of choline to TMA in bacterial whole cells and in a complex gut microbial community. In vitro biochemical assays and a crystal structure suggest that this analog is a competitive, mechanism-based inhibitor. This work demonstrates the utility of structure-based design to access inhibitors of radical enzymes from the human gut microbiota.
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Affiliation(s)
- Maud Bollenbach
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | | | - Marina Orman
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | | | - Emily P. Balskus
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
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27
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Gabr MT, Deganutti G, Reynolds CA. Peptidomimetic-based approach toward inhibitors of microbial trimethylamine lyases. Chem Biol Drug Des 2020; 97:231-236. [PMID: 32772476 DOI: 10.1111/cbdd.13775] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/27/2020] [Accepted: 08/01/2020] [Indexed: 12/30/2022]
Abstract
The development of gut microbiota-targeted small molecules represents a promising platform for the identification of new therapeutics based on the implication of human gut bacteria with different diseases. Bacterial trimethylamine (TMA)-lyase (CutC) is expressed in gut bacteria and catalyzes the conversion of choline to TMA. The association of elevated TMA production with various disorders has directed research efforts toward identification of CutC inhibitors. Herein, we introduce peptidomimetics as a promising toolbox for the discovery of CutC inhibitors. Our approach starts with screening a library of peptidomimetics for intestinal metabolic stability followed by in vitro CutC inhibition. Compound 5 was identified from this screening platform with IC50 value of 5.9 ± 0.6 μM for CutC inhibition. Unlike previously reported CutC inhibitors, compound 5 possessed universal CutC inhibitory activity in different bacterial strains. Molecular dynamics simulations suggested a plausible binding site and inhibition mechanism for compound 5. Therefore, compound 5 is a promising lead for further structural optimization in the search for CutC-targeted small molecules.
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Affiliation(s)
- Moustafa T Gabr
- Department of Radiology, Stanford University, Stanford, CA, USA
| | - Giuseppe Deganutti
- Centre for Sport, Exercise and Life Sciences, Faculty of Health and Life Sciences, Coventry University, Coventry, United Kingdom
| | - Christopher A Reynolds
- Centre for Sport, Exercise and Life Sciences, Faculty of Health and Life Sciences, Coventry University, Coventry, United Kingdom
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28
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Simó C, García-Cañas V. Dietary bioactive ingredients to modulate the gut microbiota-derived metabolite TMAO. New opportunities for functional food development. Food Funct 2020; 11:6745-6776. [PMID: 32686802 DOI: 10.1039/d0fo01237h] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
There is a growing body of clinical evidence that supports a strong association between elevated circulating trimethylamine N-oxide (TMAO) levels with increased risk of developing adverse cardiovascular outcomes such as atherosclerosis and thrombosis. TMAO is synthesized through a meta-organismal stepwise process that involves (i) the microbial production of TMA in the gut from dietary precursors and (ii) its subsequent oxidation to TMAO by flavin-containing monooxygenases in the liver. Choline, l-carnitine, betaine, and other TMA-containing compounds are the major dietary precursors of TMA. TMAO can also be absorbed directly from the gastrointestinal tract after the intake of TMAO-rich foods such as fish and shellfish. Thus, diet is an important factor as it provides the nutritional precursors to eventually produce TMAO. A number of studies have attempted to associate circulating TMAO levels with the consumption of diets rich in these foods. On the other hand, there is growing interest for the development of novel food ingredients that reduce either the TMAO-induced damage or the endogenous TMAO levels through the interference with microbiota and host metabolic processes involved in TMAO pathway. Such novel functional food ingredients would offer great opportunities to control circulating TMAO levels or its effects, and potentially contribute to decrease cardiovascular risk. In this review we summarize and discuss current data regarding the effects of TMA precursors-enriched foods or diets on circulating TMAO levels, and recent findings regarding the circulating TMAO-lowering effects of specific foods, food constituents and phytochemicals found in herbs, individually or in extracts, and their potential beneficial effect for cardiovascular health.
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Affiliation(s)
- C Simó
- Molecular Nutrition and Metabolism, Institute of Food Science Research (CIAL, CSIC-UAM), c/Nicolás Cabrera 9, 28049 Madrid, Spain.
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29
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Altamura F, Maurice CF, Castagner B. Drugging the gut microbiota: toward rational modulation of bacterial composition in the gut. Curr Opin Chem Biol 2020; 56:10-15. [DOI: 10.1016/j.cbpa.2019.09.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 09/18/2019] [Accepted: 09/24/2019] [Indexed: 01/16/2023]
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30
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Hawkins KG, Casolaro C, Brown JA, Edwards DA, Wikswo JP. The Microbiome and the Gut-Liver-Brain Axis for Central Nervous System Clinical Pharmacology: Challenges in Specifying and Integrating In Vitro and In Silico Models. Clin Pharmacol Ther 2020; 108:929-948. [PMID: 32347548 PMCID: PMC7572575 DOI: 10.1002/cpt.1870] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 04/22/2020] [Indexed: 12/18/2022]
Abstract
The complexity of integrating microbiota into clinical pharmacology, environmental toxicology, and opioid studies arises from bidirectional and multiscale interactions between humans and their many microbiota, notably those of the gut. Hosts and each microbiota are governed by distinct central dogmas, with genetics influencing transcriptomics, proteomics, and metabolomics. Each microbiota's metabolome differentially modulates its own and the host's multi‐omics. Exogenous compounds (e.g., drugs and toxins), often affect host multi‐omics differently than microbiota multi‐omics, shifting the balance between drug efficacy and toxicity. The complexity of the host‐microbiota connection has been informed by current methods of in vitro bacterial cultures and in vivo mouse models, but they fail to elucidate mechanistic details. Together, in vitro organ‐on‐chip microphysiological models, multi‐omics, and in silico computational models have the potential to supplement the established methods to help clinical pharmacologists and environmental toxicologists unravel the myriad of connections between the gut microbiota and host health and disease.
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Affiliation(s)
- Kyle G Hawkins
- Department of Physics and Astronomy, Vanderbilt University, Nashville, Tennessee, USA
| | - Caleb Casolaro
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee, USA
| | - Jacquelyn A Brown
- Department of Physics and Astronomy, Vanderbilt University, Nashville, Tennessee, USA.,Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, Tennessee, USA
| | - David A Edwards
- Department of Anesthesiology and Department of Neurological Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - John P Wikswo
- Department of Physics and Astronomy, Vanderbilt University, Nashville, Tennessee, USA.,Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee, USA.,Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, Tennessee, USA.,Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
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31
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From Association to Causality: the Role of the Gut Microbiota and Its Functional Products on Host Metabolism. Mol Cell 2020; 78:584-596. [PMID: 32234490 DOI: 10.1016/j.molcel.2020.03.005] [Citation(s) in RCA: 156] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 01/30/2020] [Accepted: 03/02/2020] [Indexed: 12/12/2022]
Abstract
Many genomic studies have revealed associations between the gut microbiota composition and host metabolism. These observations led to the idea that a causal relationship could exist between the microbiota and metabolic diseases, a concept supported by studies showing compositional changes in the microbial community in metabolic diseases and transmissibility of host phenotype via microbiota transfer. Accumulating data suggest that the microbiota may affect host metabolic phenotypes through the production of metabolites. These bioactive microbial metabolites, sensitive fingerprints of microbial function, can act as inter-kingdom signaling messengers via penetration into host blood circulation and tissues. These fingerprints may be used for diagnostic purposes, and increased understanding of strain specificity in producing microbial metabolites can identify bacterial strains or specific metabolites that can be used for therapeutic purposes. Here, we will review data supporting the causal role of the gut microbiota in metabolism and discuss mechanisms and potential clinical implications.
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32
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Nakamura T, Okuno K, Nishiyori R, Shirakawa S. Hydrogen‐Bonding Catalysis of Alkyl‐Onium Salts. Chem Asian J 2020; 15:463-472. [DOI: 10.1002/asia.201901652] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Takumi Nakamura
- Department of Environmental ScienceGraduate School of Fisheries and Environmental SciencesNagasaki University 1-14 Bunkyo-machi Nagasaki 852-8521 Japan
| | - Ken Okuno
- Department of Environmental ScienceGraduate School of Fisheries and Environmental SciencesNagasaki University 1-14 Bunkyo-machi Nagasaki 852-8521 Japan
| | - Ryuichi Nishiyori
- Department of Environmental ScienceGraduate School of Fisheries and Environmental SciencesNagasaki University 1-14 Bunkyo-machi Nagasaki 852-8521 Japan
| | - Seiji Shirakawa
- Department of Environmental ScienceGraduate School of Fisheries and Environmental SciencesNagasaki University 1-14 Bunkyo-machi Nagasaki 852-8521 Japan
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33
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Van Treuren W, Dodd D. Microbial Contribution to the Human Metabolome: Implications for Health and Disease. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2019; 15:345-369. [PMID: 31622559 DOI: 10.1146/annurev-pathol-020117-043559] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The human gastrointestinal tract is home to an incredibly dense population of microbes. These microbes employ unique strategies to capture energy in this largely anaerobic environment. In the process of breaking down dietary- and host-derived substrates, the gut microbiota produce a broad range of metabolic products that accumulate to high levels in the gut. Increasingly, studies are revealing that these chemicals impact host biology, either by acting on cells within the gastrointestinal tract or entering circulation and exerting their effects at distal sites within the body. Given the high level of functional diversity in the gut microbiome and the varied diets that we consume, the repertoire of microbiota-derived molecules within our bodies varies dramatically across individuals. Thus, the microbes in our gut and the metabolic end products they produce represent a phenotypic lever that we can potentially control to develop new therapeutics for personalized medicine. Here, we review current understanding of how microbes in the gastrointestinal tract contribute to the molecules within our gut and those that circulate within our bodies. We also highlight examples of how these molecules affect host physiology and discuss potential strategies for controlling their production to promote human health and to treat disease.
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Affiliation(s)
- William Van Treuren
- Department of Microbiology and Immunology, Stanford University, Stanford, California 94305, USA;
| | - Dylan Dodd
- Department of Microbiology and Immunology, Stanford University, Stanford, California 94305, USA; .,Department of Pathology, Stanford University, Stanford, California 94305, USA
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34
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Du Y, Li X, Su C, Wang L, Jiang J, Hong B. The human gut microbiome - a new and exciting avenue in cardiovascular drug discovery. Expert Opin Drug Discov 2019; 14:1037-1052. [PMID: 31315489 DOI: 10.1080/17460441.2019.1638909] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Introduction: Over the past decade, numerous research efforts have identified the gut microbiota as a novel regulator of human metabolic syndrome and cardiovascular disease (CVD). With the elucidation of underlying molecular mechanisms of the gut microbiota and its metabolites, the drug-discovery process of CVD therapeutics might be expedited. Areas covered: The authors describe the evidence concerning the impact of gut microbiota on metabolic disorders and CVD and summarize the current knowledge of the gut microbial mechanisms that underlie CVD with a focus on microbial metabolites. In addition, they discuss the potential impact of the gut microbiota on the drug efficacy of available cardiometabolic therapeutic agents. Most importantly, the authors review the role of the gut microbiome as a promising source of potential drug targets and novel therapeutics for the development of new treatment modalities for CVD. This review also presents the various effective strategies to investigate the gut microbiome for CVD drug-discovery approaches. Expert opinion: With the elucidation of its causative role in cardiometabolic disease and atherosclerosis, the human gut microbiome holds promises as a reservoir of novel potential therapeutic targets as well as novel therapeutic agents, paving a new and exciting avenue in cardiovascular drug discovery.
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Affiliation(s)
- Yu Du
- NHC Key Laboratory of Biotechnology of Antibiotics , Beijing , China
| | - Xingxing Li
- NHC Key Laboratory of Biotechnology of Antibiotics , Beijing , China.,CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing , China
| | - Chunyan Su
- NHC Key Laboratory of Biotechnology of Antibiotics , Beijing , China
| | - Li Wang
- NHC Key Laboratory of Biotechnology of Antibiotics , Beijing , China
| | - Jiandong Jiang
- NHC Key Laboratory of Biotechnology of Antibiotics , Beijing , China
| | - Bin Hong
- NHC Key Laboratory of Biotechnology of Antibiotics , Beijing , China.,CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing , China
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