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Commey KL, Enaka A, Nakamura R, Yamamoto A, Tsukigawa K, Nishi K, Otagiri M, Yamasaki K. 7-Phenylheptanoic Acid-Hydroxypropyl β-Cyclodextrin Complex Slows the Progression of Renal Failure in Adenine-Induced Chronic Kidney Disease Mice. Toxins (Basel) 2024; 16:316. [PMID: 39057956 PMCID: PMC11281668 DOI: 10.3390/toxins16070316] [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: 05/22/2024] [Revised: 06/27/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
The characteristic accumulation of circulating uremic toxins, such as indoxyl sulfate (IS), in chronic kidney disease (CKD) further exacerbates the disease progression. The gut microbiota, particularly gut bacterial-specific enzymes, represents a selective and attractive target for suppressing uremic toxin production and slowing the progression of renal failure. This study investigates the role of 4-phenylbutyrate (PB) and structurally related compounds, which are speculated to possess renoprotective properties in suppressing IS production and slowing or reversing renal failure in CKD. In vitro enzyme kinetic studies showed that 7-phenylheptanoic acid (PH), a PB homologue, suppresses the tryptophan indole lyase (TIL)-catalyzed decomposition of tryptophan to indole, the precursor of IS. A hydroxypropyl β-cyclodextrin (HPβCD) inclusion complex formulation of PH was prepared to enhance its biopharmaceutical properties and to facilitate in vivo evaluation. Prophylactic oral administration of the PH-HPβCD complex formulation reduced circulating IS and attenuated the deterioration of renal function and tubulointerstitial fibrosis in adenine-induced CKD mice. Additionally, treatment of moderately advanced adenine-induced CKD mice with the formulation ameliorated renal failure, although tissue fibrosis was not improved. These findings suggest that PH-HPβCD can slow the progression of renal failure and may have implications for preventing or managing CKD, particularly in early-stage disease.
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Affiliation(s)
- Kindness Lomotey Commey
- Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda, Kumamoto 860-0082, Japan; (K.L.C.); (A.E.); (R.N.); (A.Y.); (K.T.); (K.N.); (M.O.)
- DDS Research Institute, Sojo University, 4-22-1 Ikeda, Kumamoto 860-0082, Japan
| | - Airi Enaka
- Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda, Kumamoto 860-0082, Japan; (K.L.C.); (A.E.); (R.N.); (A.Y.); (K.T.); (K.N.); (M.O.)
| | - Ryota Nakamura
- Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda, Kumamoto 860-0082, Japan; (K.L.C.); (A.E.); (R.N.); (A.Y.); (K.T.); (K.N.); (M.O.)
| | - Asami Yamamoto
- Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda, Kumamoto 860-0082, Japan; (K.L.C.); (A.E.); (R.N.); (A.Y.); (K.T.); (K.N.); (M.O.)
| | - Kenji Tsukigawa
- Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda, Kumamoto 860-0082, Japan; (K.L.C.); (A.E.); (R.N.); (A.Y.); (K.T.); (K.N.); (M.O.)
- DDS Research Institute, Sojo University, 4-22-1 Ikeda, Kumamoto 860-0082, Japan
| | - Koji Nishi
- Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda, Kumamoto 860-0082, Japan; (K.L.C.); (A.E.); (R.N.); (A.Y.); (K.T.); (K.N.); (M.O.)
- DDS Research Institute, Sojo University, 4-22-1 Ikeda, Kumamoto 860-0082, Japan
| | - Masaki Otagiri
- Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda, Kumamoto 860-0082, Japan; (K.L.C.); (A.E.); (R.N.); (A.Y.); (K.T.); (K.N.); (M.O.)
- DDS Research Institute, Sojo University, 4-22-1 Ikeda, Kumamoto 860-0082, Japan
| | - Keishi Yamasaki
- Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda, Kumamoto 860-0082, Japan; (K.L.C.); (A.E.); (R.N.); (A.Y.); (K.T.); (K.N.); (M.O.)
- DDS Research Institute, Sojo University, 4-22-1 Ikeda, Kumamoto 860-0082, Japan
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Yang X, Mao Z, Huang J, Wang R, Dong H, Zhang Y, Ma H. Improving pathway prediction accuracy of constraints-based metabolic network models by treating enzymes as microcompartments. Synth Syst Biotechnol 2023; 8:597-605. [PMID: 37743907 PMCID: PMC10514394 DOI: 10.1016/j.synbio.2023.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/12/2023] [Accepted: 09/06/2023] [Indexed: 09/26/2023] Open
Abstract
Metabolic network models have become increasingly precise and accurate as the most widespread and practical digital representations of living cells. The prediction functions were significantly expanded by integrating cellular resources and abiotic constraints in recent years. However, if unreasonable modeling methods were adopted due to a lack of consideration of biological knowledge, the conflicts between stoichiometric and other constraints, such as thermodynamic feasibility and enzyme resource availability, would lead to distorted predictions. In this work, we investigated a prediction anomaly of EcoETM, a constraints-based metabolic network model, and introduced the idea of enzyme compartmentalization into the analysis process. Through rational combination of reactions, we avoid the false prediction of pathway feasibility caused by the unrealistic assumption of free intermediate metabolites. This allowed us to correct the pathway structures of l-serine and l-tryptophan. A specific analysis explains the application method of the EcoETM-like model and demonstrates its potential and value in correcting the prediction results in pathway structure by resolving the conflict between different constraints and incorporating the evolved roles of enzymes as reaction compartments. Notably, this work also reveals the trade-off between product yield and thermodynamic feasibility. Our work is of great value for the structural improvement of constraints-based models.
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Affiliation(s)
- Xue Yang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Zhitao Mao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Jianfeng Huang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Ruoyu Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Huaming Dong
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
- School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430205, China
| | - Yanfei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Hongwu Ma
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
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Graboski AL, Kowalewski ME, Simpson JB, Cao X, Ha M, Zhang J, Walton WG, Flaherty DP, Redinbo MR. Mechanism-based inhibition of gut microbial tryptophanases reduces serum indoxyl sulfate. Cell Chem Biol 2023; 30:1402-1413.e7. [PMID: 37633277 DOI: 10.1016/j.chembiol.2023.07.015] [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: 05/02/2023] [Revised: 06/27/2023] [Accepted: 07/31/2023] [Indexed: 08/28/2023]
Abstract
Indoxyl sulfate is a microbially derived uremic toxin that accumulates in late-stage chronic kidney disease and contributes to both renal and cardiovascular toxicity. Indoxyl sulfate is generated by the metabolism of indole, a compound created solely by gut microbial tryptophanases. Here, we characterize the landscape of tryptophanase enzymes in the human gut microbiome and find remarkable structural and functional similarities across diverse taxa. We leverage this homology through a medicinal chemistry campaign to create a potent pan-inhibitor, (3S) ALG-05, and validate its action as a transition-state analog. (3S) ALG-05 successfully reduces indole production in microbial culture and displays minimal toxicity against microbial and mammalian cells. Mice treated with (3S) ALG-05 show reduced cecal indole and serum indoxyl sulfate levels with minimal changes in other tryptophan-metabolizing pathways. These studies present a non-bactericidal pan-inhibitor of gut microbial tryptophanases with potential promise for reducing indoxyl sulfate in chronic kidney disease.
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Affiliation(s)
- Amanda L Graboski
- Department of Pharmacology, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mark E Kowalewski
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA
| | - Joshua B Simpson
- Department of Chemistry, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA
| | - Xufeng Cao
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
| | - Mary Ha
- Department of Chemistry, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jianan Zhang
- Department of Chemistry, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA
| | - William G Walton
- Department of Chemistry, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA
| | - Daniel P Flaherty
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
| | - Matthew R Redinbo
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA; Department of Chemistry, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA.
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Oikawa D, Yamashita S, Takahashi S, Waki T, Kikuchi K, Abe T, Katayama T, Nakayama T. (+)-Sesamin, a sesame lignan, is a potent inhibitor of gut bacterial tryptophan indole-lyase that is a key enzyme in chronic kidney disease pathogenesis. Biochem Biophys Res Commun 2022; 590:158-162. [PMID: 34974305 DOI: 10.1016/j.bbrc.2021.12.088] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/23/2021] [Indexed: 01/04/2023]
Abstract
The progression of chronic kidney disease (CKD) increases the risks of cardiovascular morbidity and end-stage kidney disease. Indoxyl sulfate (IS), which is derived from dietary l-tryptophan by the action of bacterial l-tryptophan indole-lyase (TIL) in the gut, serves as a uremic toxin that exacerbates CKD-related kidney disorder. A mouse model previously showed that inhibition of TIL by 2-aza-l-tyrosine effectively reduced the plasma IS level, causing the recovery of renal damage. In this study, we found that (+)-sesamin and related lignans, which occur abundantly in sesame seeds, inhibit intestinal bacteria TILs. Kinetic studies revealed that (+)-sesamin and sesamol competitively inhibited Escherichia coli TIL (EcTIL) with Ki values of 7 μM and 14 μM, respectively. These Ki values were smaller than that of 2-aza-l-tyrosine (143 μM). Molecular docking simulation of (+)-sesamin- (or sesamol-)binding to EcTIL predicted that these inhibitors potentially bind near the active site of EcTIL, where the cofactor pyridoxal 5'-phosphate is bound, consistent with the kinetic results. (+)-Sesamin is a phytochemical with a long history of consumption and is generally regarded as safe. Hence, dietary supplementation of (+)-sesamin encapsulated in enteric capsules could be a promising mechanism-based strategy to prevent CKD progression. Moreover, the present findings would provide a new structural basis for designing more potent TIL inhibitors for the development of mechanism-based therapeutic drugs to treat CKD.
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Affiliation(s)
- Daiki Oikawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Satoshi Yamashita
- Department of Material Chemistry, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Japan
| | - Seiji Takahashi
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Toshiyuki Waki
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Koichi Kikuchi
- Division of Nephrology, Endocrinology and Vascular Medicine, Tohoku University Graduate School of Medicine, Sendai, 980-8574, Japan; Department of Medical Megabank Tohoku University, Sendai, 980-8574, Japan
| | - Takaaki Abe
- Division of Nephrology, Endocrinology and Vascular Medicine, Tohoku University Graduate School of Medicine, Sendai, 980-8574, Japan; Department of Medical Science, Tohoku University Graduate School of Biomedical Engineering, Sendai, 980-8574, Japan; Department of Clinical Biology and Hormonal Regulation, Tohoku University Graduate School of Medicine, Sendai, 980-8574, Japan
| | - Takane Katayama
- Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Toru Nakayama
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan.
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5
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Ali R, Ahamad MZ, Singh S, Haq W. Regioselective Synthesis of Symmetrical and Unsymmetrical Bis(heteroaryl)methane (BHM)-Containing Amino Acids. European J Org Chem 2019. [DOI: 10.1002/ejoc.201900043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Rafat Ali
- Medicinal and Process Chemistry Division; CSIR-Central Drug Research Institute; -226031 Lucknow India
| | - Mohd. Zisan Ahamad
- Medicinal and Process Chemistry Division; CSIR-Central Drug Research Institute; -226031 Lucknow India
| | - Shalini Singh
- Medicinal and Process Chemistry Division; CSIR-Central Drug Research Institute; -226031 Lucknow India
| | - Wahajul Haq
- Medicinal and Process Chemistry Division; CSIR-Central Drug Research Institute; -226031 Lucknow India
- Academy of Scientific and Innovative Research; -11000 New Delhi India
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Han FS, Ling G, Zhang J, Zhang RZ. A Convenient Synthesis of Indole and 1,4-Dihydropyridine Hybrid Macromolecules by Dimerization of [2-(1H-Indol-3-yl)ethyl]pyridinium Salts. HETEROCYCLES 2018. [DOI: 10.3987/com-17-13822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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7
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Do Q, Nguyen GT, Phillips RS. Inhibition of tyrosine phenol-lyase by tyrosine homologues. Amino Acids 2016; 48:2243-51. [DOI: 10.1007/s00726-016-2263-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Accepted: 05/20/2016] [Indexed: 11/28/2022]
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8
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LaGuerre A, Löhr F, Bernhard F, Dötsch V. Labeling of membrane proteins by cell-free expression. Methods Enzymol 2015; 565:367-88. [PMID: 26577739 DOI: 10.1016/bs.mie.2015.06.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The particular advantage of the cell-free reaction is that it allows a plethora of supplementation during protein expression and offers complete control over the available amino acid pool in view of concentration and composition. In combination with the fast and reliable production efficiencies of cell-free systems, the labeling and subsequent structural evaluation of very challenging targets, such as membrane proteins, comes into focus. We describe current methods for the isotopic labeling of cell-free synthesized membrane proteins and we review techniques available to the practitioner pursuing structural studies by nuclear magnetic resonance spectroscopy. Though isotopic labeling of individual amino acid types appears to be relatively straightforward, an ongoing critical issue in most labeling schemes for structural approaches is the selective substitution of deuterons for protons. While few options are available, the continuous refinement of labeling schemes in combination with improved pulse sequences and optimized instrumentation gives promising perspectives for extended applications in the structural evaluation of cell-free synthesized membrane.
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Affiliation(s)
- Aisha LaGuerre
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt-am-Main, Germany.
| | - Frank Löhr
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt-am-Main, Germany
| | - Frank Bernhard
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt-am-Main, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt-am-Main, Germany
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