1
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Simpson JB, Walker ME, Sekela JJ, Ivey SM, Jariwala PB, Storch CM, Kowalewski ME, Graboski AL, Lietzan AD, Walton WG, Davis KA, Cloer EW, Borlandelli V, Hsiao YC, Roberts LR, Perlman DH, Liang X, Overkleeft HS, Bhatt AP, Lu K, Redinbo MR. Gut microbial β-glucuronidases influence endobiotic homeostasis and are modulated by diverse therapeutics. Cell Host Microbe 2024; 32:925-944.e10. [PMID: 38754417 PMCID: PMC11176022 DOI: 10.1016/j.chom.2024.04.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 03/18/2024] [Accepted: 04/24/2024] [Indexed: 05/18/2024]
Abstract
Hormones and neurotransmitters are essential to homeostasis, and their disruptions are connected to diseases ranging from cancer to anxiety. The differential reactivation of endobiotic glucuronides by gut microbial β-glucuronidase (GUS) enzymes may influence interindividual differences in the onset and treatment of disease. Using multi-omic, in vitro, and in vivo approaches, we show that germ-free mice have reduced levels of active endobiotics and that distinct gut microbial Loop 1 and FMN GUS enzymes drive hormone and neurotransmitter reactivation. We demonstrate that a range of FDA-approved drugs prevent this reactivation by intercepting the catalytic cycle of the enzymes in a conserved fashion. Finally, we find that inhibiting GUS in conventional mice reduces free serotonin and increases its inactive glucuronide in the serum and intestines. Our results illuminate the indispensability of gut microbial enzymes in sustaining endobiotic homeostasis and indicate that therapeutic disruptions of this metabolism promote interindividual response variabilities.
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Affiliation(s)
- Joshua B Simpson
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
| | - Morgan E Walker
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
| | - Joshua J Sekela
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
| | - Samantha M Ivey
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
| | - Parth B Jariwala
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
| | - Cameron M Storch
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
| | - Mark E Kowalewski
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, USA
| | - Amanda L Graboski
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA
| | - Adam D Lietzan
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - William G Walton
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
| | - Kacey A Davis
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, USA
| | - Erica W Cloer
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Valentina Borlandelli
- Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Yun-Chung Hsiao
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lee R Roberts
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA 02141, USA
| | - David H Perlman
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA 02141, USA
| | - Xue Liang
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA 02141, USA
| | - Hermen S Overkleeft
- Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Aadra P Bhatt
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Division of Gastroenterology and Hepatology, Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kun Lu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Matthew R Redinbo
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA; Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, USA.
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2
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Lietzan AD, Simpson JB, Walton WG, Jariwala PB, Xu Y, Boynton MH, Liu J, Redinbo MR. Microbial β-glucuronidases drive human periodontal disease etiology. SCIENCE ADVANCES 2023; 9:eadg3390. [PMID: 37146137 PMCID: PMC10162664 DOI: 10.1126/sciadv.adg3390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 03/29/2023] [Indexed: 05/07/2023]
Abstract
Periodontitis is a chronic inflammatory disease associated with persistent oral microbial dysbiosis. The human β-glucuronidase (GUS) degrades constituents of the periodontium and is used as a biomarker for periodontitis severity. However, the human microbiome also encodes GUS enzymes, and the role of these factors in periodontal disease is poorly understood. Here, we define the 53 unique GUSs in the human oral microbiome and examine diverse GUS orthologs from periodontitis-associated pathogens. Oral bacterial GUS enzymes are more efficient polysaccharide degraders and processers of biomarker substrates than the human enzyme, particularly at pHs associated with disease progression. Using a microbial GUS-selective inhibitor, we show that GUS activity is reduced in clinical samples obtained from individuals with untreated periodontitis and that the degree of inhibition correlates with disease severity. Together, these results establish oral GUS activity as a biomarker that captures both host and microbial contributions to periodontitis, facilitating more efficient clinical monitoring and treatment paradigms for this common inflammatory disease.
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Affiliation(s)
- Adam D. Lietzan
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Joshua B. Simpson
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - William G. Walton
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Parth B. Jariwala
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Yongmei Xu
- Department of Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Marcella H. Boynton
- Division of General Medicine and Clinical Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- North Carolina Translational and Clinical Sciences Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jian Liu
- Department of Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Matthew R. Redinbo
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Integrated Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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3
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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: 9] [Impact Index Per Article: 9.0] [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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4
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Beliaeva MA, Wilmanns M, Zimmermann M. Decipher enzymes from human microbiota for drug discovery and development. Curr Opin Struct Biol 2023; 80:102567. [PMID: 36963164 DOI: 10.1016/j.sbi.2023.102567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 02/03/2023] [Accepted: 02/13/2023] [Indexed: 03/26/2023]
Abstract
The human microbiota plays an important role in human health and contributes to the metabolism of therapeutic drugs affecting their potency. However, the current knowledge on human gut bacterial metabolism is limited and lacks an understanding of the underlying mechanisms of observed drug biotransformations. Despite the complexity of the gut microbial community, genomic and metagenomic sequencing provides insights into the diversity of chemical reactions that can be carried out by the microbiota and poses new challenges to functionally annotate thousands of bacterial enzymes. Here, we outline methods to systematically address the structural and functional space of the human microbiome, highlighting a combination of in silico and in vitro approaches. Systematic knowledge about microbial enzymes could eventually be applied for personalized therapy, the development of prodrugs and modulators of unwanted bacterial activity, and the further discovery of new antibiotics.
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Affiliation(s)
- Mariia A Beliaeva
- European Molecular Biology Laboratory, Heidelberg, Germany; European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany. https://twitter.com/@MariiaABeliaeva
| | - Matthias Wilmanns
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany. https://twitter.com/@WilmannsGroup
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5
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Simpson JB, Sekela JJ, Carry BS, Beaty V, Patel S, Redinbo MR. Diverse but desolate landscape of gut microbial azoreductases: A rationale for idiopathic IBD drug response. Gut Microbes 2023; 15:2203963. [PMID: 37122075 PMCID: PMC10132220 DOI: 10.1080/19490976.2023.2203963] [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: 12/08/2022] [Revised: 02/01/2023] [Accepted: 04/04/2023] [Indexed: 05/02/2023] Open
Abstract
Prodrugs reliant on microbial activation are widely used but exhibit a range of efficacies that remain poorly understood. The anti-inflammatory compound 5-aminosalicylic acid (5-ASA), which is packaged in a variety of azo-linked prodrugs provided to most Ulcerative Colitis (UC) patients, shows confounding inter-individual variabilities in response. Such prodrugs must be activated by azo-bond reduction to form 5-ASA, a process that has been attributed to both enzymatic and non-enzymatic catalysis. Gut microbial azoreductases (AzoRs) are the first catalysts shown to activate azo-linked drugs and to metabolize toxic azo-chemicals. Here, we chart the scope of the structural and functional diversity of AzoRs in health and in patients with the inflammatory bowel diseases (IBDs) UC and Crohn's Disease (CD). Using structural metagenomics, we define the landscape of gut microbial AzoRs in 413 healthy donor and 1059 IBD patient fecal samples. Firmicutes encode a significantly higher number of unique AzoRs compared to other phyla. However, structural and biochemical analyses of distinct AzoRs from the human microbiome reveal significant differences between prevalent orthologs in the processing of toxic azo-dyes, and their generally poor activation of IBD prodrugs. Furthermore, while individuals with IBD show higher abundances of AzoR-encoding gut microbial taxa than healthy controls, the overall abundance of AzoR-encoding microbes is markedly low in both disease and health. Together, these results establish that gut microbial AzoRs are functionally diverse but sparse in both health and disease, factors that may contribute to non-optimal processing of azo-linked prodrugs and idiopathic IBD drug responses.
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Affiliation(s)
- Joshua B. Simpson
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Josh J. Sekela
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Benjamin S. Carry
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Violet Beaty
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Shakshi Patel
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Matthew. R. Redinbo
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics, Department of Microbiology and Immunology, and the Integrated Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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6
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Letertre MPM, Bhatt AP, Harvey M, Nicholson JK, Wilson ID, Redinbo MR, Swann JR. Characterizing the metabolic effects of the selective inhibition of gut microbial β-glucuronidases in mice. Sci Rep 2022; 12:17435. [PMID: 36261446 PMCID: PMC9581996 DOI: 10.1038/s41598-022-21518-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 09/28/2022] [Indexed: 01/13/2023] Open
Abstract
The hydrolysis of xenobiotic glucuronides by gut bacterial glucuronidases reactivates previously detoxified compounds resulting in severe gut toxicity for the host. Selective bacterial β-glucuronidase inhibitors can mitigate this toxicity but their impact on wider host metabolic processes has not been studied. To investigate this the inhibitor 4-(8-(piperazin-1-yl)-1,2,3,4-tetrahydro-[1,2,3]triazino[4',5':4,5]thieno[2,3-c]isoquinolin-5-yl)morpholine (UNC10201652, Inh 9) was administered to mice to selectively inhibit a narrow range of bacterial β-glucuronidases in the gut. The metabolomic profiles of the intestinal contents, biofluids, and several tissues involved in the enterohepatic circulation were measured and compared to control animals. No biochemical perturbations were observed in the plasma, liver or gall bladder. In contrast, the metabolite profiles of urine, colon contents, feces and gut wall were altered compared to the controls. Changes were largely restricted to compounds derived from gut microbial metabolism. This work establishes that inhibitors targeted towards bacterial β-glucuronidases modulate the functionality of the intestinal microbiota without adversely impacting the host metabolic system.
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Affiliation(s)
- Marine P M Letertre
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- CNRS, CEISAM, UMR 6230, Nantes Université, 44000, Nantes, France
| | - Aadra P Bhatt
- Department of Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Michael Harvey
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Jeremy K Nicholson
- The Australian National Phenome Centre, Health Futures Institute, Murdoch University, Perth, Australia
- Institute of Global Health Innovation, Faculty of Medicine, Imperial College London, London, UK
| | - Ian D Wilson
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Matthew R Redinbo
- Departments of Chemistry, Biocemistry, Microbiology and Genomics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Jonathan R Swann
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK.
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7
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Walker ME, Simpson JB, Redinbo MR. A structural metagenomics pipeline for examining the gut microbiome. Curr Opin Struct Biol 2022; 75:102416. [PMID: 35841748 PMCID: PMC10039758 DOI: 10.1016/j.sbi.2022.102416] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 04/25/2022] [Accepted: 05/18/2022] [Indexed: 12/13/2022]
Abstract
Metagenomic sequencing data provide a rich resource from which to expand our understanding of differential protein functions involved in human health. Here, we outline a pipeline that combines microbial whole genome sequencing with protein structure data to yield a structural metagenomics-informed atlas of microbial enzyme families of interest. Visualizing metagenomics data through a structural lens facilitates downstream studies including targeted inhibition and probe-based proteomics to define at the molecular level how different enzyme orthologs impact in vivo function. Application of this pipeline to gut microbial enzymes like glucuronidases, TMA lyases, and bile salt hydrolases is expected to pinpoint their involvement in health and disease and may aid in the development of therapeutics that target specific enzymes within the microbiome.
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Affiliation(s)
- Morgan E Walker
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Joshua B Simpson
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Matthew R Redinbo
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Integrated Program for Biological and Genome Sciences, And Departments of Biochemistry and Microbiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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8
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Dikeocha IJ, Al-Kabsi AM, Miftahussurur M, Alshawsh MA. Pharmacomicrobiomics: Influence of gut microbiota on drug and xenobiotic metabolism. FASEB J 2022; 36:e22350. [PMID: 35579628 DOI: 10.1096/fj.202101986r] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 04/28/2022] [Accepted: 05/02/2022] [Indexed: 11/11/2022]
Abstract
Gut microbiota is the most diverse and complex biological ecosystem, which is estimated to consist of greater than 5 million distinct genes and 100 trillion cells which are in constant communication with the host environment. The interaction between the gut microbiota and drugs and other xenobiotic compounds is bidirectional, quite complicated, and not fully understood yet. The impact of xenobiotics from pollution, manufacturing processes or from the environment is harmful to human health at varying degrees and this needs to be recognized and addressed. The gut microbiota is capable of biotransforming/metabolizing of various drugs and xenobiotic compounds as well as altering the activity and toxicity of these substances, thereby influencing how a host responds to drugs and xenobiotics and this emerging field is known as pharmacomicrobiomics. In this review, we discussed different mechanisms of drug-gut microbiota interaction and highlighted the influence of drug-gut microbiome interactions on the clinical response in humans.
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Affiliation(s)
| | | | - Muhammad Miftahussurur
- Helicobacter Pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia.,Division of Gastroentero-Hepatology, Department of Internal Medicine, Faculty of Medicine, Dr. Soetomo Teaching Hospital, Universitas Airlangga, Surabaya, Indonesia
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9
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Zhang J, Walker ME, Sanidad KZ, Zhang H, Liang Y, Zhao E, Chacon-Vargas K, Yeliseyev V, Parsonnet J, Haggerty TD, Wang G, Simpson JB, Jariwala PB, Beaty VV, Yang J, Yang H, Panigrahy A, Minter LM, Kim D, Gibbons JG, Liu L, Li Z, Xiao H, Borlandelli V, Overkleeft HS, Cloer EW, Major MB, Goldfarb D, Cai Z, Redinbo MR, Zhang G. Microbial enzymes induce colitis by reactivating triclosan in the mouse gastrointestinal tract. Nat Commun 2022; 13:136. [PMID: 35013263 PMCID: PMC8748916 DOI: 10.1038/s41467-021-27762-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 11/24/2021] [Indexed: 12/24/2022] Open
Abstract
Emerging research supports that triclosan (TCS), an antimicrobial agent found in thousands of consumer products, exacerbates colitis and colitis-associated colorectal tumorigenesis in animal models. While the intestinal toxicities of TCS require the presence of gut microbiota, the molecular mechanisms involved have not been defined. Here we show that intestinal commensal microbes mediate metabolic activation of TCS in the colon and drive its gut toxicology. Using a range of in vitro, ex vivo, and in vivo approaches, we identify specific microbial β-glucuronidase (GUS) enzymes involved and pinpoint molecular motifs required to metabolically activate TCS in the gut. Finally, we show that targeted inhibition of bacterial GUS enzymes abolishes the colitis-promoting effects of TCS, supporting an essential role of specific microbial proteins in TCS toxicity. Together, our results define a mechanism by which intestinal microbes contribute to the metabolic activation and gut toxicity of TCS, and highlight the importance of considering the contributions of the gut microbiota in evaluating the toxic potential of environmental chemicals.
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Affiliation(s)
- Jianan Zhang
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
| | - Morgan E Walker
- Departments of Chemistry, Biochemistry, Microbiology and Genomics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Hongna Zhang
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, SAR, China
- Department of Occupational and Environmental Health, School of Public Health, Qingdao University, Qingdao, China
| | - Yanshan Liang
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, SAR, China
| | - Ermin Zhao
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
| | | | - Vladimir Yeliseyev
- Massachusetts Host-Microbiota Center, Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Julie Parsonnet
- Department of Medicine and Department of Health Research and Policy, Stanford University, Stanford, CA, USA
| | - Thomas D Haggerty
- Department of Medicine and Department of Health Research and Policy, Stanford University, Stanford, CA, USA
| | - Guangqiang Wang
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Joshua B Simpson
- Departments of Chemistry, Biochemistry, Microbiology and Genomics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Parth B Jariwala
- Departments of Chemistry, Biochemistry, Microbiology and Genomics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Violet V Beaty
- Departments of Chemistry, Biochemistry, Microbiology and Genomics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jun Yang
- Department of Entomology and Nematology, University of California, Davis, CA, USA
| | - Haixia Yang
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
| | - Anand Panigrahy
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
| | - Lisa M Minter
- Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Daeyoung Kim
- Department of Mathematics and Statistics, University of Massachusetts, Amherst, MA, USA
| | - John G Gibbons
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
| | - LinShu Liu
- Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA, USA
| | - Zhengze Li
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
| | - Hang Xiao
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
| | - Valentina Borlandelli
- Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Hermen S Overkleeft
- Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Erica W Cloer
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael B Major
- Department of Cell Biology and Physiology, and Department of Otolaryngology, Washington University, St. Louis, MO, USA
| | - Dennis Goldfarb
- Department of Cell Biology and Physiology, Institute for Informatics, Washington University, St. Louis, MO, USA
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, SAR, China.
| | - Matthew R Redinbo
- Departments of Chemistry, Biochemistry, Microbiology and Genomics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Guodong Zhang
- Department of Food Science, University of Massachusetts, Amherst, MA, USA.
- Department of Food Science and Technology, National University of Singapore, Singapore, Singapore.
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10
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Simpson JB, Sekela JJ, Graboski AL, Borlandelli VB, Bivins MM, Barker NK, Sorgen AA, Mordant AL, Johnson RL, Bhatt AP, Fodor AA, Herring LE, Overkleeft H, Lee JR, Redinbo MR. Metagenomics combined with activity-based proteomics point to gut bacterial enzymes that reactivate mycophenolate. Gut Microbes 2022; 14:2107289. [PMID: 35953888 PMCID: PMC9377255 DOI: 10.1080/19490976.2022.2107289] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/19/2022] [Indexed: 02/04/2023] Open
Abstract
Mycophenolate mofetil (MMF) is an important immunosuppressant prodrug prescribed to prevent organ transplant rejection and to treat autoimmune diseases. MMF usage, however, is limited by severe gastrointestinal toxicity that is observed in approximately 45% of MMF recipients. The active form of the drug, mycophenolic acid (MPA), undergoes extensive enterohepatic recirculation by bacterial β-glucuronidase (GUS) enzymes, which reactivate MPA from mycophenolate glucuronide (MPAG) within the gastrointestinal tract. GUS enzymes demonstrate distinct substrate preferences based on their structural features, and gut microbial GUS enzymes that reactivate MPA have not been identified. Here, we compare the fecal microbiomes of transplant recipients receiving MMF to healthy individuals using shotgun metagenomic sequencing. We find that neither microbial composition nor the presence of specific structural classes of GUS genes are sufficient to explain the differences in MPA reactivation measured between fecal samples from the two cohorts. We next employed a GUS-specific activity-based chemical probe and targeted metaproteomics to identify and quantify the GUS proteins present in the human fecal samples. The identification of specific GUS enzymes was improved by using the metagenomics data collected from the fecal samples. We found that the presence of GUS enzymes that bind the flavin mononucleotide (FMN) is significantly correlated with efficient MPA reactivation. Furthermore, structural analysis identified motifs unique to these FMN-binding GUS enzymes that provide molecular support for their ability to process this drug glucuronide. These results indicate that FMN-binding GUS enzymes may be responsible for reactivation of MPA and could be a driving force behind MPA-induced GI toxicity.
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Affiliation(s)
- Joshua B. Simpson
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Josh J. Sekela
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Amanda L. Graboski
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Valentina B. Borlandelli
- Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Marissa M. Bivins
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Natalie K. Barker
- UNC Proteomics Core Facility, Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alicia A. Sorgen
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Angie L. Mordant
- UNC Proteomics Core Facility, Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rebecca L. Johnson
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Aadra P. Bhatt
- Division of Gastroenterology and Hepatology, Department of Medicine, Center for Gastrointestinal Biology and Disease, and the Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Anthony A. Fodor
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Laura E. Herring
- UNC Proteomics Core Facility, Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Hermen Overkleeft
- Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - John R. Lee
- Department of Medicine, Division of Nephrology and Hypertension, New York, New York, USA
| | - Matthew. R. Redinbo
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics, Department of Microbiology and Immunology, and the Institute for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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11
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Sui Y, Wu J, Chen J. The Role of Gut Microbial β-Glucuronidase in Estrogen Reactivation and Breast Cancer. Front Cell Dev Biol 2021; 9:631552. [PMID: 34458248 PMCID: PMC8388929 DOI: 10.3389/fcell.2021.631552] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 07/09/2021] [Indexed: 12/15/2022] Open
Abstract
Over the past decade, the gut microbiota has received considerable attention for its interactions with the host. Microbial β-glucuronidase generated by this community has hence aroused concern for its biotransformation activity to a wide range of exogenous (foreign) and endogenous compounds. Lately, the role of gut microbial β-glucuronidase in the pathogenesis of breast cancer has been proposed for its estrogen reactivation activity. This is plausible considering that estrogen glucuronides are the primary products of estrogens' hepatic phase II metabolism and are subject to β-glucuronidase-catalyzed hydrolysis in the gut via bile excretion. However, research in this field is still at its very preliminary stage. This review outlines the biology of microbial β-glucuronidase in the gastrointestinal tract and elaborates on the clues to the existence of microbial β-glucuronidase-estrogen metabolism-breast cancer axis. The research gaps in this field will be discussed and possible strategies to address these challenges are suggested.
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Affiliation(s)
- Yue Sui
- School of Chinese Medicine, The University of Hong Kong, Hong Kong, China
| | - Jianming Wu
- Sichuan Key Medical Laboratory of New Drug Discovery and Druggability Evaluation, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Jianping Chen
- School of Chinese Medicine, The University of Hong Kong, Hong Kong, China
- Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen, China
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12
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Glucuronides Hydrolysis by Intestinal Microbial β-Glucuronidases (GUS) Is Affected by Sampling, Enzyme Preparation, Buffer pH, and Species. Pharmaceutics 2021; 13:pharmaceutics13071043. [PMID: 34371734 PMCID: PMC8309147 DOI: 10.3390/pharmaceutics13071043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/03/2021] [Accepted: 07/06/2021] [Indexed: 01/02/2023] Open
Abstract
Glucuronides hydrolysis by intestinal microbial β-Glucuronidases (GUS) is an important procedure for many endogenous and exogenous compounds. The purpose of this study is to determine the impact of experimental conditions on glucuronide hydrolysis by intestinal microbial GUS. Standard probe 4-Nitrophenyl β-D-glucopyranoside (pNPG) and a natural glucuronide wogonoside were used as the model compounds. Feces collection time, buffer conditions, interindividual, and species variations were evaluated by incubating the substrates with enzymes. The relative reaction activity of pNPG, reaction rates, and reaction kinetics for wogonoside were calculated. Fresh feces showed the highest hydrolysis activities. Sonication increased total protein yield during enzyme preparation. The pH of the reaction system increased the activity in 0.69–1.32-fold, 2.9–12.9-fold, and 0.28–1.56-fold for mouse, rat, and human at three different concentrations of wogonoside, respectively. The Vmax for wogonoside hydrolysis was 2.37 ± 0.06, 4.48 ± 0.11, and 5.17 ± 0.16 μmol/min/mg and Km was 6.51 ± 0.71, 3.04 ± 0.34, and 0.34 ± 0.047 μM for mouse, rat, and human, respectively. The inter-individual difference was significant (4–6-fold) using inbred rats as the model animal. Fresh feces should be used to avoid activity loss and sonication should be utilized in enzyme preparation to increase hydrolysis activity. The buffer pH should be appropriate according to the species. Inter-individual and species variations were significant.
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13
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Jiang J, Liu LP, Hassoun S. Learning graph representations of biochemical networks and its application to enzymatic link prediction. Bioinformatics 2021; 37:793-799. [PMID: 33051674 PMCID: PMC8097755 DOI: 10.1093/bioinformatics/btaa881] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 08/01/2020] [Accepted: 09/29/2020] [Indexed: 11/20/2022] Open
Abstract
Motivation The complete characterization of enzymatic activities between molecules remains incomplete, hindering biological engineering and limiting biological discovery. We develop in this work a technique, enzymatic link prediction (ELP), for predicting the likelihood of an enzymatic transformation between two molecules. ELP models enzymatic reactions cataloged in the KEGG database as a graph. ELP is innovative over prior works in using graph embedding to learn molecular representations that capture not only molecular and enzymatic attributes but also graph connectivity. Results We explore transductive (test nodes included in the training graph) and inductive (test nodes not part of the training graph) learning models. We show that ELP achieves high AUC when learning node embeddings using both graph connectivity and node attributes. Further, we show that graph embedding improves link prediction by 30% in area under curve over fingerprint-based similarity approaches and by 8% over support vector machines. We compare ELP against rule-based methods. We also evaluate ELP for predicting links in pathway maps and for reconstruction of edges in reaction networks of four common gut microbiota phyla: actinobacteria, bacteroidetes, firmicutes and proteobacteria. To emphasize the importance of graph embedding in the context of biochemical networks, we illustrate how graph embedding can guide visualization. Availability and implementation The code and datasets are available through https://github.com/HassounLab/ELP.
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Affiliation(s)
- Julie Jiang
- Department of Computer Science, Tufts University, Medford 02155, USA
| | - Li-Ping Liu
- Department of Computer Science, Tufts University, Medford 02155, USA
| | - Soha Hassoun
- Department of Computer Science, Tufts University, Medford 02155, USA.,Department of Chemical and Biological Engineering, Tufts University, Medford 02155, USA
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14
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Wang P, Jia Y, Wu R, Chen Z, Yan R. Human gut bacterial β-glucuronidase inhibition: An emerging approach to manage medication therapy. Biochem Pharmacol 2021; 190:114566. [PMID: 33865833 DOI: 10.1016/j.bcp.2021.114566] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/09/2021] [Accepted: 04/12/2021] [Indexed: 10/21/2022]
Abstract
Bacterial β-glucuronidase enzymes (BGUSs) are at the interface of host-microbial metabolic symbiosis, playing an important role in health and disease as well as medication outcomes (efficacy or toxicity) by deconjugating a large number of endogenous and exogenous glucuronides. In recent years, BGUSs inhibition has emerged as a new approach to manage diseases and medication therapy and attracted an increasing research interest. However, a growing body of evidence underlines great genetic diversity, functional promiscuity and varied inhibition propensity of BGUSs, which have posed big challenges to identifying BGUSs involved in a specific pathophysiological or pharmacological process and developing effective inhibition. In this article, we offered a general introduction of the function, in particular the physiological, pathological and pharmacological roles, of BGUSs and their taxonomic distribution in human gut microbiota, highlighting the structural features (active sites and adjacent loop structures) that affecting the protein-substrate (inhibitor) interactions. Recent advances in BGUSs-mediated deconjugation of drugs and carcinogens and the discovery and applications of BGUS inhibitors in management of medication therapy, typically, irinotecan-induced diarrhea and non-steroidal anti-inflammatory drugs (NSAIDs)-induced enteropathy, were also reviewed. At the end, we discussed the perspectives and the challenges of tailoring BGUS inhibition towards precision medicine.
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Affiliation(s)
- Panpan Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao, China
| | - Yifei Jia
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao, China
| | - Rongrong Wu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao, China
| | - Zhiqiang Chen
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao, China
| | - Ru Yan
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao, China.
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15
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Abdelsalam NA, Ramadan AT, ElRakaiby MT, Aziz RK. Toxicomicrobiomics: The Human Microbiome vs. Pharmaceutical, Dietary, and Environmental Xenobiotics. Front Pharmacol 2020; 11:390. [PMID: 32372951 PMCID: PMC7179069 DOI: 10.3389/fphar.2020.00390] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 03/16/2020] [Indexed: 12/13/2022] Open
Abstract
The harmful impact of xenobiotics on the environment and human health is being more widely recognized; yet, inter- and intraindividual genetic variations among humans modulate the extent of harm, mostly through modulating the outcome of xenobiotic metabolism and detoxification. As the Human Genome Project revealed that host genetic, epigenetic, and regulatory variations could not sufficiently explain the complexity of interindividual variability in xenobiotics metabolism, its sequel, the Human Microbiome Project, is investigating how this variability may be influenced by human-associated microbial communities. Xenobiotic-microbiome relationships are mutual and dynamic. Not only does the human microbiome have a direct metabolizing potential on xenobiotics, but it can also influence the expression of the host metabolizing genes and the activity of host enzymes. On the other hand, xenobiotics may alter the microbiome composition, leading to a state of dysbiosis, which is linked to multiple diseases and adverse health outcomes, including increased toxicity of some xenobiotics. Toxicomicrobiomics studies these mutual influences between the ever-changing microbiome cloud and xenobiotics of various origins, with emphasis on their fate and toxicity, as well the various classes of microbial xenobiotic-modifying enzymes. This review article discusses classic and recent findings in toxicomicrobiomics, with examples of interactions between gut, skin, urogenital, and oral microbiomes with pharmaceutical, food-derived, and environmental xenobiotics. The current state and future prospects of toxicomicrobiomic research are discussed, and the tools and strategies for performing such studies are thoroughly and critically compared.
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Affiliation(s)
| | - Ahmed Tarek Ramadan
- The Center for Genome and Microbiome Research, Cairo University, Cairo, Egypt
| | - Marwa Tarek ElRakaiby
- The Center for Genome and Microbiome Research, Cairo University, Cairo, Egypt.,Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Ramy Karam Aziz
- The Center for Genome and Microbiome Research, Cairo University, Cairo, Egypt.,Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
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16
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Bhatt AP, Pellock SJ, Biernat KA, Walton WG, Wallace BD, Creekmore BC, Letertre MM, Swann JR, Wilson ID, Roques JR, Darr DB, Bailey ST, Montgomery SA, Roach JM, Azcarate-Peril MA, Sartor RB, Gharaibeh RZ, Bultman SJ, Redinbo MR. Targeted inhibition of gut bacterial β-glucuronidase activity enhances anticancer drug efficacy. Proc Natl Acad Sci U S A 2020; 117:7374-7381. [PMID: 32170007 PMCID: PMC7132129 DOI: 10.1073/pnas.1918095117] [Citation(s) in RCA: 116] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Irinotecan treats a range of solid tumors, but its effectiveness is severely limited by gastrointestinal (GI) tract toxicity caused by gut bacterial β-glucuronidase (GUS) enzymes. Targeted bacterial GUS inhibitors have been shown to partially alleviate irinotecan-induced GI tract damage and resultant diarrhea in mice. Here, we unravel the mechanistic basis for GI protection by gut microbial GUS inhibitors using in vivo models. We use in vitro, in fimo, and in vivo models to determine whether GUS inhibition alters the anticancer efficacy of irinotecan. We demonstrate that a single dose of irinotecan increases GI bacterial GUS activity in 1 d and reduces intestinal epithelial cell proliferation in 5 d, both blocked by a single dose of a GUS inhibitor. In a tumor xenograft model, GUS inhibition prevents intestinal toxicity and maintains the antitumor efficacy of irinotecan. Remarkably, GUS inhibitor also effectively blocks the striking irinotecan-induced bloom of Enterobacteriaceae in immune-deficient mice. In a genetically engineered mouse model of cancer, GUS inhibition alleviates gut damage, improves survival, and does not alter gut microbial composition; however, by allowing dose intensification, it dramatically improves irinotecan's effectiveness, reducing tumors to a fraction of that achieved by irinotecan alone, while simultaneously promoting epithelial regeneration. These results indicate that targeted gut microbial enzyme inhibitors can improve cancer chemotherapeutic outcomes by protecting the gut epithelium from microbial dysbiosis and proliferative crypt damage.
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Affiliation(s)
- Aadra P Bhatt
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290
- Department of Medicine, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7555
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7555
| | - Samuel J Pellock
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290
| | - Kristen A Biernat
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290
| | - William G Walton
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290
| | - Bret D Wallace
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290
| | - Benjamin C Creekmore
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290
| | - Marine M Letertre
- Computational and Systems Medicine, Department of Surgery & Cancer, Imperial College London, SW7 2AZ London, United Kingdom
| | - Jonathan R Swann
- Computational and Systems Medicine, Department of Surgery & Cancer, Imperial College London, SW7 2AZ London, United Kingdom
| | - Ian D Wilson
- Computational and Systems Medicine, Department of Surgery & Cancer, Imperial College London, SW7 2AZ London, United Kingdom
| | - Jose R Roques
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - David B Darr
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Sean T Bailey
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Stephanie A Montgomery
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7525
| | - Jeffrey M Roach
- Department of Medicine, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7555
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7555
| | - M Andrea Azcarate-Peril
- Department of Medicine, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7555
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7555
| | - R Balfour Sartor
- Department of Medicine, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7555
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7555
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Raad Z Gharaibeh
- Department of Medicine, Division of Gastroenterology, University of Florida, Gainesville, FL 32610
| | - Scott J Bultman
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7264
| | - Matthew R Redinbo
- Department of Biochemistry, Integrated Program for Biological and Genome Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290;
- Department of Biophysics, Integrated Program for Biological and Genome Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290
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17
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Ervin SM, Hanley RP, Lim L, Walton WG, Pearce KH, Bhatt AP, James LI, Redinbo MR. Targeting Regorafenib-Induced Toxicity through Inhibition of Gut Microbial β-Glucuronidases. ACS Chem Biol 2019; 14:2737-2744. [PMID: 31663730 DOI: 10.1021/acschembio.9b00663] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Regorafenib (Stivarga) is an oral small molecule kinase inhibitor used to treat metastatic colorectal cancer, hepatocellular carcinomas, and gastrointestinal stromal tumors. Diarrhea is one of the most frequently observed adverse reactions associated with regorafenib. This toxicity may arise from the reactivation of the inactive regorafenib-glucuronide to regorafenib by gut microbial β-glucuronidase (GUS) enzymes in the gastrointestinal tract. We sought to unravel the molecular basis of regorafenib-glucuronide processing by human intestinal GUS enzymes and to examine the potential inhibition of these enzymes. Using a panel of 31 unique gut microbial GUS enzymes derived from the 279 mapped from the human gut microbiome, we found that only four were capable of regorafenib-glucuronide processing. Using crystal structures as a guide, we pinpointed the molecular features unique to these enzymes that confer regorafenib-glucuronide processing activity. Furthermore, a pilot screen identified the FDA-approved drug raloxifene as an inhibitor of regorafenib reactivation by the GUS proteins discovered. Novel synthetic raloxifene analogs exhibited improved potency in both in vitro and ex vivo studies. Taken together, these data establish that regorafenib reactivation is exclusively catalyzed by gut microbial enzymes and that these enzymes are amenable to targeted inhibition. Our results unravel key molecular details of regorafenib reactivation in the GI tract and provide a potential pathway to improve clinical outcomes with regorafenib.
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Affiliation(s)
- Samantha M. Ervin
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Ronan P. Hanley
- Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Lauren Lim
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - William G. Walton
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Kenneth H. Pearce
- Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Aadra P. Bhatt
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Lindsey I. James
- Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Matthew R. Redinbo
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Integrated Program for Biological and Genome Sciences and Departments of Biochemistry and Microbiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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18
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Ervin SM, Li H, Lim L, Roberts LR, Liang X, Mani S, Redinbo MR. Gut microbial β-glucuronidases reactivate estrogens as components of the estrobolome that reactivate estrogens. J Biol Chem 2019; 294:18586-18599. [PMID: 31636122 DOI: 10.1074/jbc.ra119.010950] [Citation(s) in RCA: 153] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 10/17/2019] [Indexed: 02/06/2023] Open
Abstract
Gut microbial β-glucuronidase (GUS) enzymes have been suggested to be involved in the estrobolome, the collection of microbial reactions involving estrogens. Furthermore, bacterial GUS enzymes within the gastrointestinal tract have been postulated to be a contributing factor in hormone-driven cancers. However, to date, there has been no experimental evidence to support these hypotheses. Here we provide the first in vitro analysis of the ability of 35 human gut microbial GUS enzymes to reactivate two distinct estrogen glucuronides, estrone-3-glucuronide and estradiol-17-glucuronide, to estrone and estradiol, respectively. We show that certain members within the Loop 1, mini-Loop 1, and FMN-binding classes of gut microbial GUS enzymes can reactivate estrogens from their inactive glucuronides. We provide molecular details of key interactions that facilitate these catalytic processes and present the structures of two novel human gut microbial GUS enzymes related to the estrobolome. Further, we demonstrate that estrogen reactivation by Loop 1 bacterial GUS enzymes can be inhibited both in purified enzymes and in fecal preparations of mixed murine fecal microbiota. Finally, however, despite these in vitro and ex vivo data, we show that a Loop 1 GUS-specific inhibitor is not capable of reducing the development of tumors in the PyMT mouse model of breast cancer. These findings validate that gut microbial GUS enzymes participate in the estrobolome but also suggest that the estrobolome is a multidimensional set of processes on-going within the mammalian gastrointestinal tract that likely involves many enzymes, including several distinct types of GUS proteins.
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Affiliation(s)
- Samantha M Ervin
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Hao Li
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Lauren Lim
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Lee R Roberts
- Exploratory Science Center, Merck & Co., Inc., Cambridge, Massachusetts 02141
| | - Xue Liang
- Exploratory Science Center, Merck & Co., Inc., Cambridge, Massachusetts 02141
| | - Sridhar Mani
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Matthew R Redinbo
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599; Integrated Program for Biological and Genome Sciences and Departments of Biochemistry and Microbiology, University of North Carolina, Chapel Hill, North Carolina 27599.
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