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Wang Y, Qian D, Wang X, Zhang X, Li Z, Meng X, Yu L, Yan X, He Z. Biomimetic Trypsin-Responsive Structure-Bridged Mesoporous Organosilica Nanomedicine for Precise Treatment of Acute Pancreatitis. ACS NANO 2024; 18:19283-19302. [PMID: 38990194 DOI: 10.1021/acsnano.4c05369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
Developing strategies to target injured pancreatic acinar cells (PACs) in conjunction with primary pathophysiology-specific pharmacological therapy presents a challenge in the management of acute pancreatitis (AP). We designed and synthesized a trypsin-cleavable organosilica precursor bridged by arginine-based amide bonds, leveraging trypsin's ability to selectively identify guanidino groups on arginine via Asp189 at the active S1 pocket and cleave the carboxy-terminal (C-terminal) amide bond via catalytic triads. The precursors were incorporated into the framework of mesoporous silica nanoparticles (MSNs) for encapsulating the membrane-permeable Ca2+ chelator BAPTA-AM with a high loading content (∼43.9%). Mesenchymal stem cell membrane coating and surface modification with PAC-targeting ligands endow MSNs with inflammation recruitment and precise PAC-targeting abilities, resulting in the highest distribution at 3 h in the pancreas with 4.7-fold more accumulation than that of naked MSNs. The outcomes transpired as follows: After bioinspired MSNs' skeleton biodegradation by prematurely and massively activated trypsin, BAPTA-AM was on-demand released in injured PACs, thereby effectively eliminating intracellular calcium overload (reduced Ca2+ level by 81.3%), restoring cellular redox status, blocking inflammatory cascades, and inhibiting cell necrosis by impeding the IκBα/NF-κB/TNF-α/IL-6 and CaMK-II/p-RIP3/p-MLKL/caspase-8,9 signaling pathways. In AP mice, a single dose of the formulation significantly restored pancreatic function (lipase and amylase reduced more by 60%) and improved the survival rate from 50 to 91.6%. The formulation offers a potentially effective strategy for clinical translation in AP treatment.
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Affiliation(s)
- Yanan Wang
- Frontiers Science Center for Deep Ocean Multispheres and Earth Systems, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education/Sanya Oceanographic Institution, Ocean University of China, Qingdao/Sanya 266100/572024, China
- Sanya Oceanographic Institution, Sanya 572024, China
- College of Chemistry and Chemical Engineering, Ocean University of China, 266100 Qingdao, China
| | - Deyao Qian
- Frontiers Science Center for Deep Ocean Multispheres and Earth Systems, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education/Sanya Oceanographic Institution, Ocean University of China, Qingdao/Sanya 266100/572024, China
- College of Chemistry and Chemical Engineering, Ocean University of China, 266100 Qingdao, China
| | - Xinyuan Wang
- Frontiers Science Center for Deep Ocean Multispheres and Earth Systems, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education/Sanya Oceanographic Institution, Ocean University of China, Qingdao/Sanya 266100/572024, China
- College of Chemistry and Chemical Engineering, Ocean University of China, 266100 Qingdao, China
| | - Xue Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth Systems, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education/Sanya Oceanographic Institution, Ocean University of China, Qingdao/Sanya 266100/572024, China
- College of Chemistry and Chemical Engineering, Ocean University of China, 266100 Qingdao, China
| | - Zerui Li
- Frontiers Science Center for Deep Ocean Multispheres and Earth Systems, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education/Sanya Oceanographic Institution, Ocean University of China, Qingdao/Sanya 266100/572024, China
- College of Chemistry and Chemical Engineering, Ocean University of China, 266100 Qingdao, China
| | - Xinlei Meng
- Frontiers Science Center for Deep Ocean Multispheres and Earth Systems, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education/Sanya Oceanographic Institution, Ocean University of China, Qingdao/Sanya 266100/572024, China
- College of Chemistry and Chemical Engineering, Ocean University of China, 266100 Qingdao, China
| | - Liangmin Yu
- Frontiers Science Center for Deep Ocean Multispheres and Earth Systems, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education/Sanya Oceanographic Institution, Ocean University of China, Qingdao/Sanya 266100/572024, China
- Sanya Oceanographic Institution, Sanya 572024, China
- College of Chemistry and Chemical Engineering, Ocean University of China, 266100 Qingdao, China
| | - Xuefeng Yan
- Frontiers Science Center for Deep Ocean Multispheres and Earth Systems, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education/Sanya Oceanographic Institution, Ocean University of China, Qingdao/Sanya 266100/572024, China
- College of Chemistry and Chemical Engineering, Ocean University of China, 266100 Qingdao, China
| | - Zhiyu He
- Frontiers Science Center for Deep Ocean Multispheres and Earth Systems, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education/Sanya Oceanographic Institution, Ocean University of China, Qingdao/Sanya 266100/572024, China
- Sanya Oceanographic Institution, Sanya 572024, China
- College of Chemistry and Chemical Engineering, Ocean University of China, 266100 Qingdao, China
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2
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Dehhaghi M, Heydari M, Panahi HKS, Lewin SR, Heng B, Brew BJ, Guillemin GJ. The roles of the kynurenine pathway in COVID-19 neuropathogenesis. Infection 2024:10.1007/s15010-024-02293-y. [PMID: 38802702 DOI: 10.1007/s15010-024-02293-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 05/07/2024] [Indexed: 05/29/2024]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the highly contagious respiratory disease Corona Virus Disease 2019 (COVID-19) that may lead to various neurological and psychological disorders that can be acute, lasting days to weeks or months and possibly longer. The latter is known as long-COVID or more recently post-acute sequelae of COVID (PASC). During acute COVID-19 infection, a strong inflammatory response, known as the cytokine storm, occurs in some patients. The levels of interferon-γ (IFN-γ), interferon-β (IFN-β), interleukin-6 (IL-6) and tumour necrosis factor-alpha (TNF-α) are particularly increased. These cytokines are known to activate the enzyme indoleamine 2,3-dioxygenase 1 (IDO-1), catalysing the first step of tryptophan (Trp) catabolism through the kynurenine pathway (KP) leading to the production of several neurotoxic and immunosuppressive metabolites. There is already data showing elevation in KP metabolites both acutely and in PASC, especially regarding cognitive impairment. Thus, it is likely that KP involvement is significant in SARS-CoV-2 pathogenesis especially neurologically.
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Affiliation(s)
- Mona Dehhaghi
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
| | - Mostafa Heydari
- Department of Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tehran University of Medical Science, Tehran, Iran
| | - Hamed Kazemi Shariat Panahi
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
| | - Sharon R Lewin
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Department of Infectious Diseases, The Alfred Hospital and Monash University, Melbourne, VIC, Australia
| | - Benjamin Heng
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia.
| | - Bruce J Brew
- Peter Duncan Neurosciences Unit, St. Vincent's Centre for Applied Medical Research, Sydney, NSW, Australia.
- Faculty of Medicine and Health, School of Clinical Medicine, UNSW Sydney, NSW, Australia.
- Departments of Neurology and Immunology, St. Vincent's Hospital, Sydney, NSW, Australia.
- University of Notre Dame, Darlinghurst, Sydney, NSW, Australia.
| | - Gilles J Guillemin
- Peter Duncan Neurosciences Unit, St. Vincent's Centre for Applied Medical Research, Sydney, NSW, Australia
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Institut Pertanian Bogor University, Bogor, Indonesia
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3
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Rebai R, Carmena-Bargueño M, Toumi ME, Derardja I, Jasmin L, Pérez-Sánchez H, Boudah A. Identification of potent inhibitors of kynurenine-3-monooxygenase from natural products: In silico and in vitro approaches. Heliyon 2024; 10:e30287. [PMID: 38726174 PMCID: PMC11079110 DOI: 10.1016/j.heliyon.2024.e30287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 03/31/2024] [Accepted: 04/23/2024] [Indexed: 05/12/2024] Open
Abstract
Existing inhibitors of kynurenine-3-monooxygenase (KMO) have side effects and poorly cross the blood-brain barrier. Therefore, the discovery of new molecules targeting KMO isnecessary.This study aims to develop a novel therapeutic drug targeting KMO using computational methods and experimental validation of natural compounds.The results of our study show that the top four compounds, namely, 3'-Hydroxy-alpha-naphthoflavone exhibited the best docking scores with KMO (-10.0 kcal/mol), followed by 3'-Hydroxy-ss-naphthoflavone (-9.9 kcal/mol), genkwanin (-9.2 kcal/mol) and apigenin(-9.1 kcal/mol) respectively. Molecular dynamics was used to assess the stability of the primary target, KMO, and inhibitor complexes. We found stable interactions of 3'-Hydroxy-ss-naphthoflavone and apigenin with KMO up to 100 ns. Further, kinetic measurements showed that 3'-Hydroxy-alpha-naphthoflavone and 3'-Hydroxy-ss-naphthoflavone induce competitive inhibition with a good IC50 activity (15.85 ± 0.98 μM and 18.71 ± 0.78, respectively), while Genkwanin and Apigenin exhibit non-competitive inhibition mechanism (21.61 ± 0.97 μM and 24.14 ± 1.00 μM, respectively).Drug-likeness features and ADME analysis features also showed that the top four compounds could be used as potential candidates to replace the synthetic KMO inhibitor drugs with known side effects and poor brain-blood barrier penetration.
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Affiliation(s)
- Redouane Rebai
- Department of Natural and Life Sciences, University Mohamed Khider of Biskra, BP 145 RP, 07000, Biskra, Algeria
- Laboratory of biotechnology, National Higher School of Biotechnology, Ville universitaire (university of Constantine 3) Ali Mendjeli, BP E66 25100, Constantine, Algeria
| | - Miguel Carmena-Bargueño
- Structural Bioinformatics and High-Performance Computing Research Group (BIO-HPC), Computer Engineering Department, Universidad Católica de Murcia (UCAM), Campus de los Jerónimos 135, 30107, Guadalupe, Spain
| | - Mohammed Esseddik Toumi
- Laboratory of Microbiological Engineering and Application, Biochemistry and Molecular and Cellular Biology Department, Faculty of Nature and Life Sciences, University of Mentouri Brothers Constantine 1, Constantine, 25017, Algeria
| | - Imene Derardja
- Department of Natural and Life Sciences, University Mohamed Khider of Biskra, BP 145 RP, 07000, Biskra, Algeria
| | - Luc Jasmin
- Department of Oral and Maxillofacial Surgery, University of California, San Francisco, 707 Parnassus Ave Suite D-1201, San Francisco, CA, 94143, USA
| | - Horacio Pérez-Sánchez
- Structural Bioinformatics and High-Performance Computing Research Group (BIO-HPC), Computer Engineering Department, Universidad Católica de Murcia (UCAM), Campus de los Jerónimos 135, 30107, Guadalupe, Spain
| | - Abdennacer Boudah
- Laboratory of biotechnology, National Higher School of Biotechnology, Ville universitaire (university of Constantine 3) Ali Mendjeli, BP E66 25100, Constantine, Algeria
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4
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Özkiliç Y. DFT modeling of water-assisted hydrogen peroxide formation from a C(4a)-(hydro)peroxyflavin. Turk J Chem 2024; 48:470-483. [PMID: 39050937 PMCID: PMC11265908 DOI: 10.55730/1300-0527.3673] [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: 07/07/2023] [Revised: 06/14/2024] [Accepted: 04/18/2024] [Indexed: 07/27/2024] Open
Abstract
The cofactor of a class A monooxygenase is reduced at an external location of the enzyme and is subsequently pulled back into the active site after the reduction. This observation brings the question; is there any defense mechanism of the active site of a monooxygenase against the formation of the harmful hydrogen peroxide from the reactive C(4a)-(hydro)peroxide intermediate? In this study, the barrier energies of one to three water molecule-mediated uncoupling reaction mechanisms in water exposed reaction conditions were determined. These were found to be facile barriers. Secondly, uncoupling was modeled in the active site of kynurenine 3-monooxygenase complex which was represented with 258 atoms utilizing cluster approach. Comparison of the barrier energy of the cluster model to the models that represent the water exposed conditions revealed that the enzyme does not have an inhibitory reaction site architecture as the compared barrier energies are roughly the same. The main defense mechanism of KMO against the formation of the hydrogen peroxide is deduced to be the insulation, and without this insulation, the monooxygenation would not take place as the barrier height of the hydrogen peroxide formation within the active site is almost half of that of the monooxygenation.
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Affiliation(s)
- Yılmaz Özkiliç
- Department of Chemistry, Faculty of Science and Letters, İstanbul Technical University, İstanbul, Turkiye
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5
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León-Letelier RA, Dou R, Vykoukal J, Sater AHA, Ostrin E, Hanash S, Fahrmann JF. The kynurenine pathway presents multi-faceted metabolic vulnerabilities in cancer. Front Oncol 2023; 13:1256769. [PMID: 37876966 PMCID: PMC10591110 DOI: 10.3389/fonc.2023.1256769] [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: 07/11/2023] [Accepted: 09/22/2023] [Indexed: 10/26/2023] Open
Abstract
The kynurenine pathway (KP) and associated catabolites play key roles in promoting tumor progression and modulating the host anti-tumor immune response. To date, considerable focus has been on the role of indoleamine 2,3-dioxygenase 1 (IDO1) and its catabolite, kynurenine (Kyn). However, increasing evidence has demonstrated that downstream KP enzymes and their associated metabolite products can also elicit tumor-microenvironment immune suppression. These advancements in our understanding of the tumor promotive role of the KP have led to the conception of novel therapeutic strategies to target the KP pathway for anti-cancer effects and reversal of immune escape. This review aims to 1) highlight the known biological functions of key enzymes in the KP, and 2) provide a comprehensive overview of existing and emerging therapies aimed at targeting discrete enzymes in the KP for anti-cancer treatment.
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Affiliation(s)
- Ricardo A. León-Letelier
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Rongzhang Dou
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Jody Vykoukal
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Ali Hussein Abdel Sater
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Edwin Ostrin
- Department of General Internal Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Samir Hanash
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Johannes F. Fahrmann
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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6
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Hayes AJ, Zheng X, O'Kelly J, Neyton LPA, Bochkina NA, Uings I, Liddle J, Baillie JK, Just G, Binnie M, Homer NZM, Murray TBJ, Baily J, McGuire K, Skouras C, Garden OJ, Webster SP, Iredale JP, Howie SEM, Mole DJ. Kynurenine monooxygenase regulates inflammation during critical illness and recovery in experimental acute pancreatitis. Cell Rep 2023; 42:112763. [PMID: 37478012 DOI: 10.1016/j.celrep.2023.112763] [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: 08/10/2020] [Revised: 12/14/2022] [Accepted: 06/21/2023] [Indexed: 07/23/2023] Open
Abstract
Kynurenine monooxygenase (KMO) blockade protects against multiple organ failure caused by acute pancreatitis (AP), but the link between KMO and systemic inflammation has eluded discovery until now. Here, we show that the KMO product 3-hydroxykynurenine primes innate immune signaling to exacerbate systemic inflammation during experimental AP. We find a tissue-specific role for KMO, where mice lacking Kmo solely in hepatocytes have elevated plasma 3-hydroxykynurenine levels that prime inflammatory gene transcription. 3-Hydroxykynurenine synergizes with interleukin-1β to cause cellular apoptosis. Critically, mice with elevated 3-hydroxykynurenine succumb fatally earlier and more readily to experimental AP. Therapeutically, blockade with the highly selective KMO inhibitor GSK898 rescues the phenotype, reducing 3-hydroxykynurenine and protecting against critical illness and death. Together, our findings establish KMO and 3-hydroxykynurenine as regulators of inflammation and the innate immune response to sterile inflammation. During critical illness, excess morbidity and death from multiple organ failure can be rescued by systemic KMO blockade.
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Affiliation(s)
- Alastair J Hayes
- University of Edinburgh Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK; Clinical Surgery, University of Edinburgh, Edinburgh, UK
| | - Xiaozhong Zheng
- University of Edinburgh Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - James O'Kelly
- University of Edinburgh Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK; Clinical Surgery, University of Edinburgh, Edinburgh, UK
| | - Lucile P A Neyton
- University of Edinburgh Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK; The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Natalia A Bochkina
- School of Mathematics and Maxwell Institute, University of Edinburgh, Edinburgh, UK
| | - Iain Uings
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, UK
| | - John Liddle
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, UK
| | | | - George Just
- Mass Spectrometry Core, Edinburgh Clinical Research Facility, University of Edinburgh, Edinburgh, UK
| | - Margaret Binnie
- Mass Spectrometry Core, Edinburgh Clinical Research Facility, University of Edinburgh, Edinburgh, UK
| | - Natalie Z M Homer
- Mass Spectrometry Core, Edinburgh Clinical Research Facility, University of Edinburgh, Edinburgh, UK
| | | | - James Baily
- Charles River Laboratories, East Lothian, UK
| | - Kris McGuire
- University of Edinburgh Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | | | - O James Garden
- Clinical Surgery, University of Edinburgh, Edinburgh, UK
| | - Scott P Webster
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, UK
| | | | - Sarah E M Howie
- University of Edinburgh Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - Damian J Mole
- University of Edinburgh Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK; Clinical Surgery, University of Edinburgh, Edinburgh, UK.
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7
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Williford EE, DeAngelo CM, Blake KS, Kumar H, Lam KK, Jones KV, Tolia NH, Dantas G, Wencewicz TA. Structure-Based Design of Bisubstrate Tetracycline Destructase Inhibitors That Block Flavin Redox Cycling. J Med Chem 2023; 66:3917-3933. [PMID: 36877173 PMCID: PMC10099279 DOI: 10.1021/acs.jmedchem.2c01629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Tetracyclines (TCs) are an important class of antibiotics threatened by an emerging new resistance mechanism─enzymatic inactivation. These TC-inactivating enzymes, also known as tetracycline destructases (TDases), inactivate all known TC antibiotics, including drugs of last resort. Combination therapies consisting of a TDase inhibitor and a TC antibiotic represent an attractive strategy for overcoming this type of antibiotic resistance. Here, we report the structure-based design, synthesis, and evaluation of bifunctional TDase inhibitors derived from anhydrotetracycline (aTC). By appending a nicotinamide isostere to the C9 position of the aTC D-ring, we generated bisubstrate TDase inhibitors. The bisubstrate inhibitors have extended interactions with TDases by spanning both the TC and presumed NADPH binding pockets. This simultaneously blocks TC binding and the reduction of FAD by NADPH while "locking" TDases in an unproductive FAD "out" conformation.
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Affiliation(s)
- Emily E. Williford
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, USA
| | - Caitlin M. DeAngelo
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, USA
| | - Kevin S. Blake
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, 4513 Clayton Ave., St. Louis, MO, 63108, USA
| | - Hirdesh Kumar
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institute of Health, 9000 Rockville Pike, BG 29B Rm 4NN08, Bethesda, MD, 20814, USA
| | - Kendrick K. Lam
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, USA
| | - Katherine V. Jones
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, USA
| | - Niraj H. Tolia
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institute of Health, 9000 Rockville Pike, BG 29B Rm 4NN08, Bethesda, MD, 20814, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, 4513 Clayton Ave., St. Louis, MO, 63108, USA
- Department of Pathology and Immunology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO, 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, 4515 McKinley Ave., St. Louis, MO, 63110, USA
- Department of Biomedical Engineering, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, USA
| | - Timothy A. Wencewicz
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, USA
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8
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Shen H, Xu X, Bai Y, Wang X, Wu Y, Zhong J, Wu Q, Luo Y, Shang T, Shen R, Xi M, Sun H. Therapeutic potential of targeting kynurenine pathway in neurodegenerative diseases. Eur J Med Chem 2023; 251:115258. [PMID: 36917881 DOI: 10.1016/j.ejmech.2023.115258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/17/2023] [Accepted: 03/07/2023] [Indexed: 03/11/2023]
Abstract
Kynurenine pathway (KP), the primary pathway of L-tryptophan (Trp) metabolism in mammals, contains several neuroactive metabolites such as kynurenic acid (KA) and quinolinic acid (QA). Its imbalance involved in aging and neurodegenerative diseases (NDs) has attracted much interest in therapeutically targeting KP enzymes and KP metabolite-associated receptors, especially kynurenine monooxygenase (KMO). Currently, many agents have been discovered with significant improvement in animal models but only one aryl hydrocarbon receptor (AHR) agonist 30 (laquinimod) has entered clinical trials for treating Huntington's disease (HD). In this review, we describe neuroactive KP metabolites, discuss the dysregulation of KP in aging and NDs and summarize the development of KP regulators in preclinical and clinical studies, offering an outlook of targeting KP for NDs treatment in future.
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Affiliation(s)
- Hualiang Shen
- Zhejiang Engineering Research Center of Fat-soluble Vitamin, Shaoxing University, Shaoxing, 312000, China; College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Xinde Xu
- Zhejiang Medicine Co. Ltd., Shaoxing, 312500, China
| | - Yalong Bai
- Zhejiang Medicine Co. Ltd., Shaoxing, 312500, China
| | | | - Yibin Wu
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Jia Zhong
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Qiyi Wu
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Yanjuan Luo
- Zhejiang Engineering Research Center of Fat-soluble Vitamin, Shaoxing University, Shaoxing, 312000, China; College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Tianbo Shang
- Zhejiang Engineering Research Center of Fat-soluble Vitamin, Shaoxing University, Shaoxing, 312000, China; College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Runpu Shen
- Zhejiang Engineering Research Center of Fat-soluble Vitamin, Shaoxing University, Shaoxing, 312000, China; College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Meiyang Xi
- Zhejiang Engineering Research Center of Fat-soluble Vitamin, Shaoxing University, Shaoxing, 312000, China; College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China.
| | - Haopeng Sun
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, 210009, China.
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9
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Gao J, Cui Y, Bao W, Hao Y, Piao X, Gu X. Ubiquitylome study reveals the regulatory effect of α-lipoic acid on ubiquitination of key proteins in tryptophan metabolism pathway of pig liver. Int J Biol Macromol 2023; 236:123795. [PMID: 36828089 DOI: 10.1016/j.ijbiomac.2023.123795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023]
Abstract
The decline in antioxidant defenses make it easily for human and animals to suffer from liver damage and diseases induced by oxidative stress, causing enormous losses to human health and livestock production. As one of the canonical protein post-translational modifications (PTMs), ubiquitination is widely involved in cell proliferation, apoptosis and damage/repair response, and is proven to be involved in the ability of mammals to resist oxidative stress. To explore whether α-lipoic acid (LA), a safe and efficient antioxidant, plays a role in regulating liver antioxidant status by PTMs, proteins in livers of pigs fed with LA were analyzed at the level of proteome and ubiquitylome. Based on proteome-wide enrichment of ubiquitination, a total of 7274 proteins were identified and 5326 were quantified, we also identified 1564 ubiquitination sites in 580 ubiquitinated proteins, among which there were 136 differentially ubiquitinated sites in 103 differentially ubiquitinated proteins upon LA. Further bioinformatics analysis showed that these differential proteins were mainly enriched in tryptophan metabolic pathway, and accompanied by significantly improvement of liver antioxidant capacity. We revealed the regulatory effect of LA on ubiquitination of kynurenine 3-monooxygenase (KMO) and other key proteins in tryptophan metabolism pathway of pig liver for the first time.
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Affiliation(s)
- Jie Gao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yanjun Cui
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Weiguang Bao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yue Hao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiangshu Piao
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xianhong Gu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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10
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Ferroptosis in Rat Lung Tissue during Severe Acute Pancreatitis-Associated Acute Lung Injury: Protection of Qingyi Decoction. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2023; 2023:5827613. [PMID: 36820405 PMCID: PMC9938780 DOI: 10.1155/2023/5827613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/06/2022] [Accepted: 11/25/2022] [Indexed: 02/13/2023]
Abstract
Qingyi decoction (QYD) has anti-inflammatory pharmacological properties and substantial therapeutic benefits on severe acute pancreatitis (SAP) in clinical practice. However, its protective mechanism against SAP-associated acute lung injury (ALI) remains unclear. In this study, we screened the active ingredients of QYD from the perspective of network pharmacology to identify its core targets and signaling pathways against SAP-associated ALI. Rescue experiments were used to determine the relationship between QYD and ferroptosis. Then, metabolomics and 16s rDNA sequencing were used to identify differential metabolites and microbes in lung tissue. Correlation analysis was utilized to explore the relationship between core targets, signaling pathways, metabolic phenotypes, and microbial flora, sorting out the potential molecular network of QYD against SAP-associated lung ALI. Inflammatory damage was caused by SAP in the rat lung. QYD could effectively alleviate lung injury, improve respiratory function, and significantly reduce serum inflammatory factor levels in SAP rats. Network pharmacology and molecular docking identified three key targets: ALDH2, AnxA1, and ICAM-1. Mechanistically, QYD may inhibit ferroptosis by promoting the ALDH2 expression and suppress neutrophil infiltration by blocking the cleavage of intact AnxA1 and downregulating ICAM-1 expression. Ferroptosis activator counteracts the pulmonary protective effect of QYD in SAP rats. In addition, seven significant differential metabolites were identified in lung tissues. QYD relatively improved the lung microbiome's abundance in SAP rats. Further correlation analysis determined the correlation between ferroptosis, differential metabolites, and differential microbes. In this work, the network pharmacology, metabolomics, and 16s rDNA sequencing were integrated to uncover the mechanism of QYD against SAP-associated ALI. This novel integrated method may play an important role in future research on traditional Chinese medicine.
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Chen Y, Zhang J, Yang Y, Xiang K, Li H, Sun D, Chen L. Kynurenine‐3‐monooxygenase (KMO): From its biological functions to therapeutic effect in diseases progression. J Cell Physiol 2022; 237:4339-4355. [DOI: 10.1002/jcp.30876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/21/2022] [Accepted: 09/01/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Yanmei Chen
- Key Laboratory of Structure‐Based Drug Design & Discovery, Wuya College of Innovation, School of Traditional Chinese Materia Medica, Ministry of Education Shenyang Pharmaceutical University Shenyang China
| | - Jiahui Zhang
- Key Laboratory of Structure‐Based Drug Design & Discovery, Wuya College of Innovation, School of Traditional Chinese Materia Medica, Ministry of Education Shenyang Pharmaceutical University Shenyang China
| | - Yueying Yang
- Key Laboratory of Structure‐Based Drug Design & Discovery, Wuya College of Innovation, School of Traditional Chinese Materia Medica, Ministry of Education Shenyang Pharmaceutical University Shenyang China
| | - Ke Xiang
- Key Laboratory of Structure‐Based Drug Design & Discovery, Wuya College of Innovation, School of Traditional Chinese Materia Medica, Ministry of Education Shenyang Pharmaceutical University Shenyang China
| | - Hua Li
- Key Laboratory of Structure‐Based Drug Design & Discovery, Wuya College of Innovation, School of Traditional Chinese Materia Medica, Ministry of Education Shenyang Pharmaceutical University Shenyang China
- College of Pharmacy Fujian University of Traditional Chinese Medicine Fuzhou China
| | - Dejuan Sun
- Key Laboratory of Structure‐Based Drug Design & Discovery, Wuya College of Innovation, School of Traditional Chinese Materia Medica, Ministry of Education Shenyang Pharmaceutical University Shenyang China
| | - Lixia Chen
- Key Laboratory of Structure‐Based Drug Design & Discovery, Wuya College of Innovation, School of Traditional Chinese Materia Medica, Ministry of Education Shenyang Pharmaceutical University Shenyang China
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12
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Simplified quality assessment for small-molecule ligands in the Protein Data Bank. Structure 2022; 30:252-262.e4. [PMID: 35026162 PMCID: PMC8849442 DOI: 10.1016/j.str.2021.10.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 09/14/2021] [Accepted: 10/06/2021] [Indexed: 02/05/2023]
Abstract
More than 70% of the experimentally determined macromolecular structures in the Protein Data Bank (PDB) contain small-molecule ligands. Quality indicators of ∼643,000 ligands present in ∼106,000 PDB X-ray crystal structures have been analyzed. Ligand quality varies greatly with regard to goodness of fit between ligand structure and experimental data, deviations in bond lengths and angles from known chemical structures, and inappropriate interatomic clashes between the ligand and its surroundings. Based on principal component analysis, correlated quality indicators of ligand structure have been aggregated into two largely orthogonal composite indicators measuring goodness of fit to experimental data and deviation from ideal chemical structure. Ranking of the composite quality indicators across the PDB archive enabled construction of uniformly distributed composite ranking score. This score is implemented at RCSB.org to compare chemically identical ligands in distinct PDB structures with easy-to-interpret two-dimensional ligand quality plots, allowing PDB users to quickly assess ligand structure quality and select the best exemplars.
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13
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Curry A, White D, Cen Y. Small Molecule Regulators Targeting NAD + Biosynthetic Enzymes. Curr Med Chem 2022; 29:1718-1738. [PMID: 34060996 PMCID: PMC8630097 DOI: 10.2174/0929867328666210531144629] [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: 01/23/2021] [Revised: 04/02/2021] [Accepted: 04/07/2021] [Indexed: 01/03/2023]
Abstract
Nicotinamide adenine dinucleotide (NAD+) is a key player in many metabolic pathways as an activated carrier of electrons. In addition to being the cofactor for redox reactions, NAD+ also serves as the substrate for various enzymatic transformations such as adenylation and ADP-ribosylation. Maintaining cellular NAD+ homeostasis has been suggested as an effective anti-aging strategy. Given the importance of NAD+ in regulating a broad spectrum of cellular events, small molecules targeting NAD+ metabolism have been pursued as therapeutic interventions for the treatment of mitochondrial disorders and agerelated diseases. In this article, small molecule regulators of NAD+ biosynthetic enzymes will be reviewed. The focus will be given to the discovery and development of these molecules, the mechanism of action as well as their therapeutic potentials.
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Affiliation(s)
- Alyson Curry
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Dawanna White
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Yana Cen
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA;,Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA,Address correspondence to this author at the Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA; Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA; Tel: 804-828-7405;
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14
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Özkılıç Y, Tüzün NŞ. Computational Survey of Recent Experimental Developments in the Hydroxylation Mechanism of Kynurenine 3-Monooxygenase. J Phys Chem A 2021; 125:9459-9477. [PMID: 34676771 DOI: 10.1021/acs.jpca.1c05397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recently, two new mechanistic proposals for the kynurenine 3-monooxygenase (KMO) catalyzed hydroxylation reaction of l-Kynurenine (l-Kyn) have been proposed. According to the first proposal, instead of the distal oxygen, the proximal oxygen of the hydroperoxide intermediate of flavin adenine dinucleotide (FAD) is transferred to the substrate ring. The second study proposes that l-Kyn participates in its base form in the reaction. To address these proposals, the reaction was reconsidered with a 386 atom quantum cluster model that is based on a recent X-ray structure (PDB id: 6FOX). The computations were carried out at the UB3LYP/6-311+G(2d,2p)//UB3LYP/6-31G(d,p) level with solvation (polarizable continuum model) and dispersion (DFT-D3(BJ)) corrections. To supplement the results of the density functional theory (DFT) calculations, molecular dynamics (MD) simulations of the protein-substrate complex were employed. The comparison of a proximal oxygen transfer mechanism to the distal oxygen transfer mechanism revealed that the former requires too high of a barrier energy while the latter validated our previous results. According to the MD simulations, the hydroperoxy moiety does not favor an alignment that might promote the proximal oxygen transfer mechanism. In the second part of the study, hydroxylation reaction with the base form of l-Kyn was sought. Although DFT calculations confirmed a much more facile reaction with the base form of l-Kyn, a mechanism which would allow the deprotonation of the l-Kyn before the oxygen transfer could not be determined with the X-ray-based positions. A concerted mechanism with both the oxygen transfer and the deprotonation required a high barrier energy. A stepwise mechanism involving the deprotonation of l-Kyn was found, starting from an MD frame. The overall barrier of the oxygen transfer step of this model was found to be in the range of that of with neutral l-Kyn. MD simulations supported the idea of ineffectiveness of the nearby shell surrounding the utilized active site core on the deprotonation of l-Kyn.
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Affiliation(s)
- Yılmaz Özkılıç
- Department of Chemistry, Faculty of Science and Letters, Istanbul Technical University, Maslak, Istanbul 34469, Turkey
| | - Nurcan Ş Tüzün
- Department of Chemistry, Faculty of Science and Letters, Istanbul Technical University, Maslak, Istanbul 34469, Turkey
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15
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Pharmacophore-Based Virtual Screening of Novel Competitive Inhibitors of the Neurodegenerative Disease Target Kynurenine-3-Monooxygenase. Molecules 2021; 26:molecules26113314. [PMID: 34073016 PMCID: PMC8199213 DOI: 10.3390/molecules26113314] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/26/2021] [Accepted: 05/26/2021] [Indexed: 11/27/2022] Open
Abstract
The pathogenesis of several neurodegenerative diseases such as Alzheimer’s or Huntington’s disease has been associated with metabolic dysfunctions caused by imbalances in the brain and cerebral spinal fluid levels of neuroactive metabolites. Kynurenine monooxygenase (KMO) is considered an ideal therapeutic target for the regulation of neuroactive tryptophan metabolites. Despite significant efforts, the known KMO inhibitors lack blood–brain barrier (BBB) permeability and upon the mimicking of the substrate binding mode, are subject to produce reactive oxygen species as a side reaction. The computational drug design is further complicated by the absence of complete crystal structure information for human KMO (hKMO). In the current work, we performed virtual screening of readily available compounds using several protein–ligand complex pharmacophores. Each of the pharmacophores accounts for one of three distinct reported KMO protein-inhibitor binding conformations. As a result, six novel KMO inhibitors were discovered based on an in vitro fluorescence assay. Compounds VS1 and VS6 were predicted to be BBB permeable and avoid the hydrogen peroxide production dilemma, making them valuable, novel hit compounds for further drug property optimization and advancement in the drug design pipeline.
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16
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Tryptophan Metabolism via Kynurenine Pathway: Role in Solid Organ Transplantation. Int J Mol Sci 2021; 22:ijms22041921. [PMID: 33671985 PMCID: PMC7919278 DOI: 10.3390/ijms22041921] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 01/01/2023] Open
Abstract
Solid organ transplantation is a gold standard treatment for patients suffering from an end-stage organ disease. Patient and graft survival have vastly improved during the last couple of decades; however, the field of transplantation still encounters several unique challenges, such as a shortage of transplantable organs and increasing pool of extended criteria donor (ECD) organs, which are extremely prone to ischemia-reperfusion injury (IRI), risk of graft rejection and challenges in immune regulation. Moreover, accurate and specific biomarkers, which can timely predict allograft dysfunction and/or rejection, are lacking. The essential amino acid tryptophan and, especially, its metabolites via the kynurenine pathway has been widely studied as a contributor and a therapeutic target in various diseases, such as neuropsychiatric, autoimmune disorders, allergies, infections and malignancies. The tryptophan-kynurenine pathway has also gained interest in solid organ transplantation and a variety of experimental studies investigating its role both in IRI and immune regulation after allograft implantation was first published. In this review, the current evidence regarding the role of tryptophan and its metabolites in solid organ transplantation is presented, giving insights into molecular mechanisms and into therapeutic and diagnostic/prognostic possibilities.
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17
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Full-length in meso structure and mechanism of rat kynurenine 3-monooxygenase inhibition. Commun Biol 2021; 4:159. [PMID: 33542467 PMCID: PMC7862291 DOI: 10.1038/s42003-021-01666-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 01/05/2021] [Indexed: 01/30/2023] Open
Abstract
The structural mechanisms of single-pass transmembrane enzymes remain elusive. Kynurenine 3-monooxygenase (KMO) is a mitochondrial protein involved in the eukaryotic tryptophan catabolic pathway and is linked to various diseases. Here, we report the mammalian full-length structure of KMO in its membrane-embedded form, complexed with compound 3 (identified internally) and compound 4 (identified via DNA-encoded chemical library screening) at 3.0 Å resolution. Despite predictions suggesting that KMO has two transmembrane domains, we show that KMO is actually a single-pass transmembrane protein, with the other transmembrane domain lying laterally along the membrane, where it forms part of the ligand-binding pocket. Further exploration of compound 3 led to identification of the brain-penetrant compound, 5. We show that KMO is dimeric, and that mutations at the dimeric interface abolish its activity. These results will provide insight for the drug discovery of additional blood-brain-barrier molecules, and help illuminate the complex biology behind single-pass transmembrane enzymes.
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18
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Reis RAG, Li H, Johnson M, Sobrado P. New frontiers in flavin-dependent monooxygenases. Arch Biochem Biophys 2021; 699:108765. [PMID: 33460580 DOI: 10.1016/j.abb.2021.108765] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 01/08/2021] [Accepted: 01/11/2021] [Indexed: 12/15/2022]
Abstract
Flavin-dependent monooxygenases catalyze a wide variety of redox reactions in important biological processes and are responsible for the synthesis of highly complex natural products. Although much has been learned about FMO chemistry in the last ~80 years of research, several aspects of the reactions catalyzed by these enzymes remain unknown. In this review, we summarize recent advancements in the flavin-dependent monooxygenase field including aspects of flavin dynamics, formation and stabilization of reactive species, and the hydroxylation mechanism. Novel catalysis of flavin-dependent N-oxidases involving consecutive oxidations of amines to generate oximes or nitrones is presented and the biological relevance of the products is discussed. In addition, the activity of some FMOs have been shown to be essential for the virulence of several human pathogens. We also discuss the biomedical relevance of FMOs in antibiotic resistance and the efforts to identify inhibitors against some members of this important and growing family enzymes.
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Affiliation(s)
| | - Hao Li
- Department of Biochemistry, Blacksburg, VA, 24061, USA
| | - Maxim Johnson
- Department of Biochemistry, Blacksburg, VA, 24061, USA
| | - Pablo Sobrado
- Department of Biochemistry, Blacksburg, VA, 24061, USA; Center for Drug Discovery, Virginia Tech, Blacksburg, VA, 24061, USA.
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19
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Zhang S, Collier MEW, Heyes DJ, Giorgini F, Scrutton NS. Advantages of brain penetrating inhibitors of kynurenine-3-monooxygenase for treatment of neurodegenerative diseases. Arch Biochem Biophys 2020; 697:108702. [PMID: 33275878 DOI: 10.1016/j.abb.2020.108702] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/18/2020] [Accepted: 11/24/2020] [Indexed: 01/16/2023]
Abstract
Kynurenine-3-monooxygenase (KMO) is an important therapeutic target for several brain disorders that has been extensively studied in recent years. Potent inhibitors towards KMO have been developed and tested within different disease models, showing great therapeutic potential, especially in models of neurodegenerative disease. The inhibition of KMO reduces the production of downstream toxic kynurenine pathway metabolites and shifts the flux to the formation of the neuroprotectant kynurenic acid. However, the efficacy of KMO inhibitors in neurodegenerative disease has been limited by their poor brain permeability. Combined with virtual screening and prodrug strategies, a novel brain penetrating KMO inhibitor has been developed which dramatically decreases neurotoxic metabolites. This review highlights the importance of KMO as a drug target in neurological disease and the benefits of brain permeable inhibitors in modulating kynurenine pathway metabolites in the central nervous system.
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Affiliation(s)
- Shaowei Zhang
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Mary E W Collier
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Derren J Heyes
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Flaviano Giorgini
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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20
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Tryptophan Metabolism as a Pharmacological Target. Trends Pharmacol Sci 2020; 42:60-73. [PMID: 33256987 DOI: 10.1016/j.tips.2020.11.006] [Citation(s) in RCA: 131] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 02/07/2023]
Abstract
L-Tryptophan is an essential amino acid required for protein synthesis. It undergoes an extensive and complex metabolism along several pathways, resulting in many bioactive molecules acting in various organs through different action mechanisms. Enzymes involved in its metabolism, metabolites themselves, or their receptors, represent potential therapeutic targets, which are the subject of dynamic research. Disruptions in L-tryptophan metabolism are reported in several neurological, metabolic, psychiatric, and intestinal disorders, paving the way to develop drugs to target it. This review will briefly describe L-tryptophan metabolism and present and discuss the most recent pharmacological developments targeting it.
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21
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In silico methods predict new blood-brain barrier permeable structure for the inhibition of kynurenine 3-monooxygenase. J Mol Graph Model 2020; 100:107701. [PMID: 32805560 DOI: 10.1016/j.jmgm.2020.107701] [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: 12/06/2019] [Revised: 06/14/2020] [Accepted: 07/10/2020] [Indexed: 11/23/2022]
Abstract
Kynurenine 3-monooxygenase (KMO) regulates the levels of bioactive substances in the kynurenine pathway of tryptophan catabolism and its activity is tied to so many diseases that finding an appropriate inhibitor for KMO has become an urgent task. This especially proved to be difficult for the central nervous system related diseases due to the requirement that the supposed inhibitor should be both blood brain barrier permeable and should not cause hydrogen peroxide as a harmful side product. In this in silico study, we present our step-wise approach, whose starting point is based on the important experimental observations. To tackle the problem, a library of 7561938 structures was obtained from Zinc15 database utilizing the tranche browser. From this library, a subset of 501777 structures was determined with the considerations of their functional groups that constrain their applicability. Then, the binding affinity ranking of this set of structures was determined via virtual screening. Starting from the structures whose affinities are the highest among this subset, the ADMET properties were checked through in silico methods and the binding properties of the selected inhibitor candidates were further investigated via molecular dynamics simulations and MM/GBSA calculations. According to the computational results of this study, ZINC_71915355 has passed all the evaluations and is a potentially BBB permeable structure that can inhibit KMO. Additionally, ZINC_19827377 was identified as a new potential KMO inhibitor which may be more suitable for peripheral administration. From the in silico study presented herein, ZINC_71915355 and ZINC_19827377 structures, which showed high binding affinity without harmful H2O2 production, along with the tailored properties can now serve as powerful candidates for KMO inhibition and these hits are worth of further experimental validation.
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22
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Martin KS, Azzolini M, Lira Ruas J. The kynurenine connection: how exercise shifts muscle tryptophan metabolism and affects energy homeostasis, the immune system, and the brain. Am J Physiol Cell Physiol 2020; 318:C818-C830. [DOI: 10.1152/ajpcell.00580.2019] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Tryptophan catabolism through the kynurenine pathway generates a variety of bioactive metabolites. Physical exercise can modulate kynurenine pathway metabolism in skeletal muscle and thus change the concentrations of select compounds in peripheral tissues and in the central nervous system. Here we review recent advances in our understanding of how exercise alters tryptophan-kynurenine metabolism in muscle and its subsequent local and distal effects. We propose that the effects of kynurenine pathway metabolites on skeletal muscle, adipose tissue, immune system, and the brain suggest that some of these compounds could qualify as exercise-induced myokines. Indeed, some of the more recently discovered biological activities for kynurenines include many of the best-known benefits of exercise: improved energy homeostasis, promotion of an anti-inflammatory environment, and neuroprotection. Finally, by considering the tissue expression of the different membrane and cytosolic receptors for kynurenines, we discuss known and potential biological activities for these tryptophan metabolites.
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Affiliation(s)
- Kyle S. Martin
- Molecular and Cellular Exercise Physiology, Department of Physiology and Pharmacology, Karolinska Institutet, Biomedicum, Stockholm, Sweden
| | - Michele Azzolini
- Molecular and Cellular Exercise Physiology, Department of Physiology and Pharmacology, Karolinska Institutet, Biomedicum, Stockholm, Sweden
| | - Jorge Lira Ruas
- Molecular and Cellular Exercise Physiology, Department of Physiology and Pharmacology, Karolinska Institutet, Biomedicum, Stockholm, Sweden
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23
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Huang YS, Ogbechi J, Clanchy FI, Williams RO, Stone TW. IDO and Kynurenine Metabolites in Peripheral and CNS Disorders. Front Immunol 2020; 11:388. [PMID: 32194572 PMCID: PMC7066259 DOI: 10.3389/fimmu.2020.00388] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 02/18/2020] [Indexed: 12/12/2022] Open
Abstract
The importance of the kynurenine pathway in normal immune system function has led to an appreciation of its possible contribution to autoimmune disorders such as rheumatoid arthritis. Indoleamine-2,3-dioxygenase (IDO) activity exerts a protective function, limiting the severity of experimental arthritis, whereas deletion or inhibition exacerbates the symptoms. Other chronic disorder with an inflammatory component, such as atherosclerosis, are also suppressed by IDO activity. It is suggested that this overall anti-inflammatory activity is mediated by a change in the relative production or activity of Th17 and regulatory T cell populations. Kynurenines may play an anti-inflammatory role also in CNS disorders such as Huntington's disease, Alzheimer's disease and multiple sclerosis, in which signs of inflammation and neurodegeneration are involved. The possibility is discussed that in Huntington's disease kynurenines interact with other anti-inflammatory molecules such as Human Lymphocyte Antigen-G which may be relevant in other disorders. Kynurenine involvement may account for the protection afforded to animals with cerebral malaria and trypanosomiasis when they are treated with an inhibitor of kynurenine-3-monoxygenase (KMO). There is some evidence that changes in IL-10 may contribute to this protection and the relationship between kynurenines and IL-10 in arthritis and other inflammatory conditions should be explored. In addition, metabolites of kynurenine downstream of KMO, such as anthranilic acid and 3-hydroxy-anthranilic acid can influence inflammation, and the ratio of these compounds is a valuable biomarker of inflammatory status although the underlying molecular mechanisms of the changes require clarification. Hence it is essential that more effort be expended to identify their sites of action as potential targets for drug development. Finally, we discuss increasing awareness of the epigenetic regulation of IDO, for example by DNA methylation, a phenomenon which may explain differences between individuals in their susceptibility to arthritis and other inflammatory disorders.
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Affiliation(s)
- Yi-Shu Huang
- The Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, United Kingdom
| | - Joy Ogbechi
- The Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, United Kingdom
| | - Felix I Clanchy
- The Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, United Kingdom
| | - Richard O Williams
- The Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, United Kingdom
| | - Trevor W Stone
- The Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, United Kingdom
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24
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A urinary metabolomic study from subjects after long-term occupational exposure to low concentration acrylamide using UPLC-QTOF/MS. Arch Biochem Biophys 2020; 681:108279. [DOI: 10.1016/j.abb.2020.108279] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 01/09/2020] [Accepted: 01/20/2020] [Indexed: 02/08/2023]
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25
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Manenda MS, Picard MÈ, Zhang L, Cyr N, Zhu X, Barma J, Pascal JM, Couture M, Zhang C, Shi R. Structural analyses of the Group A flavin-dependent monooxygenase PieE reveal a sliding FAD cofactor conformation bridging OUT and IN conformations. J Biol Chem 2020; 295:4709-4722. [PMID: 32111738 DOI: 10.1074/jbc.ra119.011212] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 02/26/2020] [Indexed: 02/02/2023] Open
Abstract
Group A flavin-dependent monooxygenases catalyze the cleavage of the oxygen-oxygen bond of dioxygen, followed by the incorporation of one oxygen atom into the substrate molecule with the aid of NADPH and FAD. These flavoenzymes play an important role in many biological processes, and their most distinct structural feature is the choreographed motions of flavin, which typically adopts two distinct conformations (OUT and IN) to fulfill its function. Notably, these enzymes seem to have evolved a delicate control system to avoid the futile cycle of NADPH oxidation and FAD reduction in the absence of substrate, but the molecular basis of this system remains elusive. Using protein crystallography, size-exclusion chromatography coupled to multi-angle light scattering (SEC-MALS), and small-angle X-ray scattering (SEC-SAXS) and activity assay, we report here a structural and biochemical characterization of PieE, a member of the Group A flavin-dependent monooxygenases involved in the biosynthesis of the antibiotic piericidin A1. This analysis revealed that PieE forms a unique hexamer. Moreover, we found, to the best of our knowledge for the first time, that in addition to the classical OUT and IN conformations, FAD possesses a "sliding" conformation that exists in between the OUT and IN conformations. This observation sheds light on the underlying mechanism of how the signal of substrate binding is transmitted to the FAD-binding site to efficiently initiate NADPH binding and FAD reduction. Our findings bridge a gap currently missing in the orchestrated order of chemical events catalyzed by this important class of enzymes.
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Affiliation(s)
- Mahder S Manenda
- Département de Biochimie, de Microbiologie, et de Bio-informatique, PROTEO, Université Laval, Québec G1V 0A6, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
| | - Marie-Ève Picard
- Département de Biochimie, de Microbiologie, et de Bio-informatique, PROTEO, Université Laval, Québec G1V 0A6, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
| | - Liping Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Normand Cyr
- Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Xiaojun Zhu
- Département de Biochimie, de Microbiologie, et de Bio-informatique, PROTEO, Université Laval, Québec G1V 0A6, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
| | - Julie Barma
- Département de Biochimie, de Microbiologie, et de Bio-informatique, PROTEO, Université Laval, Québec G1V 0A6, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
| | - John M Pascal
- Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Manon Couture
- Département de Biochimie, de Microbiologie, et de Bio-informatique, PROTEO, Université Laval, Québec G1V 0A6, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
| | - Changsheng Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Rong Shi
- Département de Biochimie, de Microbiologie, et de Bio-informatique, PROTEO, Université Laval, Québec G1V 0A6, Canada .,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
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26
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Lu Y, Shao M, Wu T. Kynurenine-3-monooxygenase: A new direction for the treatment in different diseases. Food Sci Nutr 2020; 8:711-719. [PMID: 32148781 PMCID: PMC7020307 DOI: 10.1002/fsn3.1418] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 11/24/2019] [Accepted: 12/21/2019] [Indexed: 12/14/2022] Open
Abstract
Kynurenine-3-monooxygenase (KMO) is an enzyme that relies on nicotinamide adenine dinucleotide phosphate (NADP), a key site in the kynurenine pathway (KP), which has great effects on neurological diseases, cancer, and peripheral inflammation. This review mainly pay attention to the research of KMO mechanism for the treatment of different diseases, and hopes to provide assistance for clinical and drug use. KMO controlling the chief division of the KP, which directly controls downstream product quinolinic acid (QUIN) and indirectly controls kynurenic acid (KYNA), plays an important role in many diseases, especially neurological diseases.
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Affiliation(s)
- Yifei Lu
- Institute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Mingmei Shao
- Institute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Tao Wu
- Institute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
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27
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Tryptophan metabolism as a common therapeutic target in cancer, neurodegeneration and beyond. Nat Rev Drug Discov 2019; 18:379-401. [PMID: 30760888 DOI: 10.1038/s41573-019-0016-5] [Citation(s) in RCA: 762] [Impact Index Per Article: 152.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
L-Tryptophan (Trp) metabolism through the kynurenine pathway (KP) is involved in the regulation of immunity, neuronal function and intestinal homeostasis. Imbalances in Trp metabolism in disorders ranging from cancer to neurodegenerative disease have stimulated interest in therapeutically targeting the KP, particularly the main rate-limiting enzymes indoleamine-2,3-dioxygenase 1 (IDO1), IDO2 and tryptophan-2,3-dioxygenase (TDO) as well as kynurenine monooxygenase (KMO). However, although small-molecule IDO1 inhibitors showed promise in early-stage cancer immunotherapy clinical trials, a phase III trial was negative. This Review summarizes the physiological and pathophysiological roles of Trp metabolism, highlighting the vast opportunities and challenges for drug development in multiple diseases.
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28
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Zhang S, Sakuma M, Deora GS, Levy CW, Klausing A, Breda C, Read KD, Edlin CD, Ross BP, Wright Muelas M, Day PJ, O’Hagan S, Kell DB, Schwarcz R, Leys D, Heyes DJ, Giorgini F, Scrutton NS. A brain-permeable inhibitor of the neurodegenerative disease target kynurenine 3-monooxygenase prevents accumulation of neurotoxic metabolites. Commun Biol 2019; 2:271. [PMID: 31372510 PMCID: PMC6656724 DOI: 10.1038/s42003-019-0520-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 06/28/2019] [Indexed: 12/16/2022] Open
Abstract
Dysregulation of the kynurenine pathway (KP) leads to imbalances in neuroactive metabolites associated with the pathogenesis of several neurodegenerative disorders, including Huntington's disease (HD). Inhibition of the enzyme kynurenine 3-monooxygenase (KMO) in the KP normalises these metabolic imbalances and ameliorates neurodegeneration and related phenotypes in several neurodegenerative disease models. KMO is thus a promising candidate drug target for these disorders, but known inhibitors are not brain permeable. Here, 19 new KMO inhibitors have been identified. One of these (1) is neuroprotective in a Drosophila HD model but is minimally brain penetrant in mice. The prodrug variant (1b) crosses the blood-brain barrier, releases 1 in the brain, thereby lowering levels of 3-hydroxykynurenine, a toxic KP metabolite linked to neurodegeneration. Prodrug 1b will advance development of targeted therapies against multiple neurodegenerative and neuroinflammatory diseases in which KP likely plays a role, including HD, Alzheimer's disease, and Parkinson's disease.
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Affiliation(s)
- Shaowei Zhang
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, M1 7DN UK
| | - Michiyo Sakuma
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, M1 7DN UK
| | - Girdhar S. Deora
- School of Pharmacy, The University of Queensland, Brisbane, Queensland 4072 Australia
| | - Colin W. Levy
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, M1 7DN UK
| | - Alex Klausing
- Maryland Psychiatric Research Center, University of Maryland School of Medicine, Baltimore, MD 21228 USA
| | - Carlo Breda
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH UK
| | - Kevin D. Read
- Drug Discovery Unit, School of Life Sciences, University of Dundee, Dundee, Scotland DD1 5EH UK
| | | | - Benjamin P. Ross
- School of Pharmacy, The University of Queensland, Brisbane, Queensland 4072 Australia
| | - Marina Wright Muelas
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, M1 7DN UK
| | - Philip J. Day
- Manchester Institute of Biotechnology and Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PL UK
| | - Stephen O’Hagan
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, M1 7DN UK
| | - Douglas B. Kell
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, M1 7DN UK
| | - Robert Schwarcz
- Maryland Psychiatric Research Center, University of Maryland School of Medicine, Baltimore, MD 21228 USA
| | - David Leys
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, M1 7DN UK
| | - Derren J. Heyes
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, M1 7DN UK
| | - Flaviano Giorgini
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH UK
| | - Nigel S. Scrutton
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, M1 7DN UK
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29
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Özkılıç Y, Tüzün NŞ. Mechanism of Kynurenine 3-Monooxygenase-Catalyzed Hydroxylation Reaction: A Quantum Cluster Approach. J Phys Chem A 2019; 123:3149-3159. [PMID: 30888816 DOI: 10.1021/acs.jpca.8b11831] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The mechanism of the hydroxylation reaction between l-Kyn and model flavin adenine dinucleotide (FAD)-hydroperoxide was investigated via density functional theory (DFT) calculations in the absence and in the presence of the kynurenine 3-monooxygenase (KMO) enzyme by considering possible pathways that can lead to the product 3-hydroxykynurenine (3-HK). Crystal structure (pdb code: 5NAK )-based calculations involved a quantum cluster model in which the active site of the enzyme with the substrate l-Kyn was represented with 348 atoms. According to the deduced mechanism, KMO-catalyzed hydroxylation reaction takes place with four transformations. In the initial transition state, FAD delivers its peroxy hydroxyl to the l-Kyn ring, creating an sp3-hybridized carbon center. Then, the hydrogen on the hydroxyl moiety is immediately transferred back to the proximal oxygen that remained on FAD. These consequent transformations are in line with the somersault rearrangement previously described for similar enzymatic systems. The second step corresponds to a hydride shift from the sp3-hybridized carbon of the substrate ring to its adjacent carbon, producing the keto form of 3-HK. Then, keto-3-HK is transformed into its enol form (3-HK) with a water-assisted tautomerization. Lastly, FAD is oxidized with a water-assisted dehydration, which also involves 3-HK as a catalyst. In the proposed pathway, Asn54, Pro318, and a crystal water molecule were seen to play significant roles in the proton relays. The energies obtained via the cluster approach were calculated at the B3LYP/6-311+G(2d,2p)//B3LYP/6-31G(d,p) level with solvation (polarizable continuum model) and dispersion (DFT-D3(BJ)) corrections.
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Affiliation(s)
- Yılmaz Özkılıç
- Department of Chemistry, Faculty of Science and Letters , Istanbul Technical University , Maslak, Istanbul 34469 , Turkey
| | - Nurcan Ş Tüzün
- Department of Chemistry, Faculty of Science and Letters , Istanbul Technical University , Maslak, Istanbul 34469 , Turkey
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30
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Zheng X, Zhang A, Binnie M, McGuire K, Webster SP, Hughes J, Howie SEM, Mole DJ. Kynurenine 3-monooxygenase is a critical regulator of renal ischemia-reperfusion injury. Exp Mol Med 2019; 51:1-14. [PMID: 30760699 PMCID: PMC6374422 DOI: 10.1038/s12276-019-0210-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 10/18/2018] [Accepted: 11/13/2018] [Indexed: 02/07/2023] Open
Abstract
Acute kidney injury (AKI) following ischemia–reperfusion injury (IRI) has a high mortality and lacks specific therapies. Here, we report that mice lacking kynurenine 3-monooxygenase (KMO) activity (Kmonull mice) are protected against AKI after renal IRI. We show that KMO is highly expressed in the kidney and exerts major metabolic control over the biologically active kynurenine metabolites 3-hydroxykynurenine, kynurenic acid, and downstream metabolites. In experimental AKI induced by kidney IRI, Kmonull mice had preserved renal function, reduced renal tubular cell injury, and fewer infiltrating neutrophils compared with wild-type (Kmowt) control mice. Together, these data confirm that flux through KMO contributes to AKI after IRI, and supports the rationale for KMO inhibition as a therapeutic strategy to protect against AKI during critical illness. Inhibition of a metabolic enzyme linked to inflammation could be a novel treatment approach for sudden kidney failure following a “reperfusion” injury caused by blood flow returning to the organ after a period of insufficient blood supply. Damian Mole and colleagues from the University of Edinburgh, UK, temporarily blocked blood vessels leading to the kidneys of mice to induce organ damage. Mice that lacked a working copy of kynurenine 3-monooxygenase (KMO), a gene that encodes an enzyme involved in metabolizing an essential amino acid linked to immune activation, were protected from injury. These KMO-mutant mice experienced less damage to the kidney’s tubular cells and had fewer pro-inflammatory cells than genetically normal animals. The findings support the idea that blocking KMO and its associated metabolic pathway could help mitigate kidney damage following reperfusion injury in humans.
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Affiliation(s)
- Xiaozhong Zheng
- Centre for Inflammation Research, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Ailiang Zhang
- Centre for Inflammation Research, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Margaret Binnie
- Centre for Cardiovascular Science, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Kris McGuire
- Centre for Cardiovascular Science, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Scott P Webster
- Centre for Cardiovascular Science, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Jeremy Hughes
- Centre for Inflammation Research, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Sarah E M Howie
- Centre for Inflammation Research, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Damian J Mole
- Centre for Inflammation Research, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK.
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31
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Phillips RS, Iradukunda EC, Hughes T, Bowen JP. Modulation of Enzyme Activity in the Kynurenine Pathway by Kynurenine Monooxygenase Inhibition. Front Mol Biosci 2019; 6:3. [PMID: 30800661 PMCID: PMC6376250 DOI: 10.3389/fmolb.2019.00003] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 01/21/2019] [Indexed: 11/13/2022] Open
Abstract
The kynurenine pathway is the major route for tryptophan metabolism in mammals. Several of the metabolites in the kynurenine pathway, however, are potentially toxic, particularly 3-hydroxykynurenine, 3-hydroxyanthranilic acid, and quinolinic acid. Quinolinic acid (QUIN) is an excitotoxic agonist at the NMDA receptor, and has been shown to be elevated in neurodegenerative diseases such as Alzheimer's Disease and Huntington's Disease. Thus, inhibitors of enzymes in the kynurenine pathway may be valuable to treat these diseases. Kynurenine monooxygenase (KMO) is the ideal target for an inhibitor, since inhibition of it would be expected to decrease the toxic metabolites and increase kynurenic acid (KynA), which is neuroprotective. The first generation of KMO inhibitors was based on structural analogs of the substrate, L-kynurenine. These compounds showed reduction of QUIN and increased KynA in vivo in rats. After the determination of the x-ray crystal structure of yeast KMO, inhibitor design has been facilitated. Benzisoxazoles with sub-nM binding to KMO have been developed recently. Some KMO ligands promote the reaction of NADPH with O2 without hydroxylation, resulting in uncoupled formation of H2O2. This potentially toxic side reaction should be avoided in the design of drugs targeting the kynurenine pathway for treatment of neurodegenerative disorders.
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Affiliation(s)
- Robert S Phillips
- Department of Chemistry, University of Georgia, Athens, GA, United States.,Department of Biochemistry, University of Georgia, Athens, GA, United States
| | | | - Tamera Hughes
- Department of Pharmaceutical Sciences, College of Pharmacy, Mercer University, Atlanta, GA, United States
| | - J Phillip Bowen
- Department of Pharmaceutical Sciences, College of Pharmacy, Mercer University, Atlanta, GA, United States
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32
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Shave S, McGuire K, Pham NT, Mole DJ, Webster SP, Auer M. Diclofenac Identified as a Kynurenine 3-Monooxygenase Binder and Inhibitor by Molecular Similarity Techniques. ACS OMEGA 2018; 3:2564-2568. [PMID: 30023839 PMCID: PMC6044753 DOI: 10.1021/acsomega.7b02091] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 02/07/2018] [Indexed: 06/08/2023]
Abstract
In this study, we apply a battery of molecular similarity techniques to known inhibitors of kynurenine 3-monooxygenase (KMO), querying each against a repository of approved, experimental, nutraceutical, and illicit drugs. Four compounds are assayed against KMO. Subsequently, diclofenac (also known by the trade names Voltaren, Voltarol, Aclonac, and Cataflam) has been confirmed as a human KMO protein binder and inhibitor in cell lysate with low micromolar KD and IC50, respectively, and low millimolar cellular IC50. Hit to drug hopping, as exemplified here for one of the most successful anti-inflammatory medicines ever invented, holds great promise for expansion into new disease areas and highlights the not-yet-fully-exploited potential of drug repurposing.
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Affiliation(s)
- Steven Shave
- School
of Biological Sciences, University of Edinburgh, The King’s Buildings, Max
Born Crescent, CH Waddington Building, Edinburgh, Scotland EH9 3BF, U.K.
| | - Kris McGuire
- MRC Centre for Inflammation Research, Queen’s
Medical Research
Institute, and Centre for Cardiovascular Science, Queen’s Medical Research
Institute, The University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, U.K.
| | - Nhan T. Pham
- School
of Biological Sciences, University of Edinburgh, The King’s Buildings, Max
Born Crescent, CH Waddington Building, Edinburgh, Scotland EH9 3BF, U.K.
| | - Damian J. Mole
- MRC Centre for Inflammation Research, Queen’s
Medical Research
Institute, and Centre for Cardiovascular Science, Queen’s Medical Research
Institute, The University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, U.K.
| | - Scott P. Webster
- MRC Centre for Inflammation Research, Queen’s
Medical Research
Institute, and Centre for Cardiovascular Science, Queen’s Medical Research
Institute, The University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, U.K.
| | - Manfred Auer
- School
of Biological Sciences, University of Edinburgh, The King’s Buildings, Max
Born Crescent, CH Waddington Building, Edinburgh, Scotland EH9 3BF, U.K.
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33
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Kim HT, Na BK, Chung J, Kim S, Kwon SK, Cha H, Son J, Cho JM, Hwang KY. Structural Basis for Inhibitor-Induced Hydrogen Peroxide Production by Kynurenine 3-Monooxygenase. Cell Chem Biol 2018; 25:426-438.e4. [PMID: 29429898 DOI: 10.1016/j.chembiol.2018.01.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 10/17/2017] [Accepted: 01/08/2018] [Indexed: 11/18/2022]
Abstract
Kynurenine 3-monooxygenase (KMO) inhibitors have been developed for the treatment of neurodegenerative disorders. The mechanisms of flavin reduction and hydrogen peroxide production by KMO inhibitors are unknown. Herein, we report the structure of human KMO and crystal structures of Saccharomyces cerevisiae (sc) and Pseudomonas fluorescens (pf) KMO with Ro 61-8048. Proton transfer in the hydrogen bond network triggers flavin reduction in p-hydroxybenzoate hydroxylase, but the mechanism triggering flavin reduction in KMO is different. Conformational changes via π-π interactions between the loop above the flavin and substrate or non-substrate effectors lead to disorder of the C-terminal α helix in scKMO and shifts of domain III in pfKMO, stimulating flavin reduction. Interestingly, Ro 61-8048 has two different binding modes. It acts as a competitive inhibitor in scKMO and as a non-substrate effector in pfKMO. These findings provide understanding of the catalytic cycle of KMO and insight for structure-based drug design of KMO inhibitors.
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Affiliation(s)
- Hyun Tae Kim
- Crystalgenomics, Inc., 5F, Tower A, Korea Bio Park 700, Daewangpangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13524, Korea; Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Korea
| | - Byeong Kwan Na
- Crystalgenomics, Inc., 5F, Tower A, Korea Bio Park 700, Daewangpangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13524, Korea
| | - Jiwoung Chung
- Crystalgenomics, Inc., 5F, Tower A, Korea Bio Park 700, Daewangpangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13524, Korea
| | - Sulhee Kim
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Korea
| | - Sool Ki Kwon
- Crystalgenomics, Inc., 5F, Tower A, Korea Bio Park 700, Daewangpangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13524, Korea
| | - Hyunju Cha
- Crystalgenomics, Inc., 5F, Tower A, Korea Bio Park 700, Daewangpangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13524, Korea
| | - Jonghyeon Son
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Korea
| | - Joong Myung Cho
- Crystalgenomics, Inc., 5F, Tower A, Korea Bio Park 700, Daewangpangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13524, Korea.
| | - Kwang Yeon Hwang
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Korea.
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34
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Gao J, Yao L, Xia T, Liao X, Zhu D, Xiang Y. Biochemistry and structural studies of kynurenine 3-monooxygenase reveal allosteric inhibition by Ro 61-8048. FASEB J 2018; 32:2036-2045. [PMID: 29208702 DOI: 10.1096/fj.201700397rr] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The human kynurenine 3-monooxygenase (hKMO) is a potential therapeutic target for neurodegenerative and neurologic disorders. Inhibition of KMO by Ro 61-8048, a potent, selective, and the most widely used inhibitor of KMO, was shown effective in various models of neurodegenerative or neurologic disorders. However, the molecular basis of hKMO inhibition by Ro 61-8048 is not clearly understood. Here, we report biochemistry studies on hKMO and crystal structures of an hKMO homolog, pfKMO from Pseudomonas fluorescens, in complex with the substrate l-kynurenine and Ro 61-8048. We found that the C-terminal ∼110 aa are essential for the enzymatic activity of hKMO and the homologous C-terminal region of pfKMO folds into a distinct, all-α-helical domain, which associates with the N-terminal catalytic domain to form a unique tunnel in proximity to the substrate-binding pocket. The tunnel binds the Ro 61-8048 molecule, which fills most of the tunnel, and Ro 61-8048 is hydrogen bonded with several completely conserved residues, including an essential catalytic residue. Modification of Ro 61-8048 and biochemical studies of the modified Ro 61-8048 derivatives suggested that Ro 61-8048 inhibits the enzyme in an allosteric manner by affecting the conformation of the essential catalytic residue and by blocking entry of the substrate or product release. The unique binding sites distinguish Ro 61-8048 as a noncompetitive and highly selective inhibitor from other competitive inhibitors, which should facilitate further optimization of Ro 61-8048 and the development of new inhibitory drugs to hKMO.-Gao, J., Yao, L., Xia, T., Liao, X., Zhu, D., Xiang, Y. Biochemistry and structural studies of kynurenine 3-monooxygenase reveal allosteric inhibition by Ro 61-8048.
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Affiliation(s)
- Jingjing Gao
- School of Medicine, Center for Infectious Disease Research, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing Advanced Innovation Center for Structural Biology
| | - Licheng Yao
- School of Pharmaceutical Sciences, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing, China; and
| | - Tingting Xia
- School of Pharmaceutical Sciences, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing, China; and
| | - Xuebin Liao
- School of Pharmaceutical Sciences, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing, China; and
| | - Deyu Zhu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Ye Xiang
- School of Medicine, Center for Infectious Disease Research, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing Advanced Innovation Center for Structural Biology
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35
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Walker AL, Ancellin N, Beaufils B, Bergeal M, Binnie M, Bouillot A, Clapham D, Denis A, Haslam CP, Holmes DS, Hutchinson JP, Liddle J, McBride A, Mirguet O, Mowat CG, Rowland P, Tiberghien N, Trottet L, Uings I, Webster SP, Zheng X, Mole DJ. Development of a Series of Kynurenine 3-Monooxygenase Inhibitors Leading to a Clinical Candidate for the Treatment of Acute Pancreatitis. J Med Chem 2017; 60:3383-3404. [PMID: 28398044 DOI: 10.1021/acs.jmedchem.7b00055] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Recently, we reported a novel role for KMO in the pathogenesis of acute pancreatitis (AP). A number of inhibitors of kynurenine 3-monooxygenase (KMO) have previously been described as potential treatments for neurodegenerative conditions and particularly for Huntington's disease. However, the inhibitors reported to date have insufficient aqueous solubility relative to their cellular potency to be compatible with the intravenous (iv) dosing route required in AP. We have identified and optimized a novel series of high affinity KMO inhibitors with favorable physicochemical properties. The leading example is exquisitely selective, has low clearance in two species, prevents lung and kidney damage in a rat model of acute pancreatitis, and is progressing into preclinical development.
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Affiliation(s)
- Ann L Walker
- Discovery Partnerships with Academia, GlaxoSmithKline , Gunnels Wood Road, Stevenage SG1 2NY, UK
| | | | | | - Marylise Bergeal
- Platform Technology Sciences, GlaxoSmithKline Stevenage SG1 2NY, UK
| | - Margaret Binnie
- Centre for Cardiovascular Science, University of Edinburgh , Edinburgh EH16 4TJ, UK
| | - Anne Bouillot
- Flexible Discovery Unit, GlaxoSmithKline , Paris, France
| | - David Clapham
- Platform Technology Sciences, GlaxoSmithKline Stevenage SG1 2NY, UK
| | - Alexis Denis
- Flexible Discovery Unit, GlaxoSmithKline , Paris, France
| | - Carl P Haslam
- Platform Technology Sciences, GlaxoSmithKline Stevenage SG1 2NY, UK
| | - Duncan S Holmes
- Discovery Partnerships with Academia, GlaxoSmithKline , Gunnels Wood Road, Stevenage SG1 2NY, UK
| | | | - John Liddle
- Discovery Partnerships with Academia, GlaxoSmithKline , Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Andrew McBride
- Centre for Cardiovascular Science, University of Edinburgh , Edinburgh EH16 4TJ, UK
| | | | - Christopher G Mowat
- EastChem School of Chemistry, University of Edinburgh , Edinburgh EH9 3FJ, UK
| | - Paul Rowland
- Platform Technology Sciences, GlaxoSmithKline Stevenage SG1 2NY, UK
| | | | - Lionel Trottet
- Flexible Discovery Unit, GlaxoSmithKline , Paris, France
| | - Iain Uings
- Discovery Partnerships with Academia, GlaxoSmithKline , Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Scott P Webster
- Centre for Cardiovascular Science, University of Edinburgh , Edinburgh EH16 4TJ, UK
| | - Xiaozhong Zheng
- MRC Centre for Inflammation Research, University of Edinburgh , Edinburgh EH16 4TJ, UK
| | - Damian J Mole
- MRC Centre for Inflammation Research, University of Edinburgh , Edinburgh EH16 4TJ, UK
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