1
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Ferreira JC, Villanueva AJ, Fadl S, Al Adem K, Cinviz ZN, Nedyalkova L, Cardoso THS, Andrade ME, Saksena NK, Sensoy O, Rabeh WM. Residues in the Fructose Binding Pocket Are Required for Ketohexokinase-A Activity. J Biol Chem 2024:107538. [PMID: 38971308 DOI: 10.1016/j.jbc.2024.107538] [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: 03/06/2024] [Revised: 06/24/2024] [Accepted: 06/26/2024] [Indexed: 07/08/2024] Open
Abstract
Excessive fructose consumption is a primary contributor to the global surges in obesity, cancer, and metabolic syndrome. Fructolysis is not robustly regulated and is initiated by ketohexokinase (KHK). In this study, we determined the crystal structure of KHK-A, one of two human isozymes of KHK, in the apo-state at 1.85 Å resolution, and we investigated the roles of residues in the fructose-binding pocket by mutational analysis. Introducing alanine at D15, N42, or N45 inactivated KHK-A, whereas mutating R141 or K174 reduced activity and thermodynamic stability. Kinetic studies revealed that the R141A and K174A mutations reduced fructose affinity by 2- to 4-fold compared to WT KHK-A, without affecting ATP affinity. Molecular dynamics simulations provided mechanistic insights into the potential roles of the mutated residues in ligand coordination and the maintenance of an open state in one monomer and a closed state in the other. Protein-protein interactome analysis indicated distinct expression patterns and downregulation of partner proteins in different tumor tissues, warranting a re-evaluation of KHK's role in cancer development and progression. The connections between different cancer genes and the KHK signaling pathway suggest that KHK is a potential target for preventing cancer metastasis. This study enhances our understanding of KHK-A's structure and function and offers valuable insights into potential targets for developing treatments for obesity, cancer, and metabolic syndrome.
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Affiliation(s)
- Juliana C Ferreira
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Adrian J Villanueva
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Samar Fadl
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Kenana Al Adem
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Zeynep Nur Cinviz
- Graduate School of Engineering and Natural Sciences, Istanbul Medipol University, Istanbul, Turkey
| | - Lyudmila Nedyalkova
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Thyago H S Cardoso
- G42 Healthcare Omics Excellence Center, Masdar City, Abu Dhabi, United Arab Emirates
| | - Mario Edson Andrade
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Nitin K Saksena
- Victoria University, Footscray Park Campus, Melbourne, VIC, 3134, Australia
| | - Ozge Sensoy
- Graduate School of Engineering and Natural Sciences, Istanbul Medipol University, Istanbul, Turkey; Regenerative and Restorative Medicine Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey
| | - Wael M Rabeh
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates.
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2
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Peng C, Yang P, Zhang D, Jin C, Peng W, Wang T, Sun Q, Chen Z, Feng Y, Sun Y. KHK-A promotes fructose-dependent colorectal cancer liver metastasis by facilitating the phosphorylation and translocation of PKM2. Acta Pharm Sin B 2024; 14:2959-2976. [PMID: 39027256 PMCID: PMC11252482 DOI: 10.1016/j.apsb.2024.04.024] [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: 01/13/2024] [Revised: 03/01/2024] [Accepted: 04/15/2024] [Indexed: 07/20/2024] Open
Abstract
Excessive fructose diet is closely associated with colorectal cancer (CRC) progression. Nevertheless, fructose's specific function and precise mechanism in colorectal cancer liver metastasis (CRLM) is rarely known. Here, this study reported that the fructose absorbed by primary colorectal cancer could accelerate CRLM, and the expression of KHK-A, not KHK-C, in liver metastasis was higher than in paired primary tumors. Furthermore, KHK-A facilitated fructose-dependent CRLM in vitro and in vivo by phosphorylating PKM2 at Ser37. PKM2 phosphorylated by KHK-A inhibited its tetramer formation and pyruvic acid kinase activity but promoted the nuclear accumulation of PKM2. EMT and aerobic glycolysis activated by nuclear PKM2 enhance CRC cells' migration ability and anoikis resistance during CRLM progression. TEPP-46 treatment, targeting the phosphorylation of PKM2, inhibited the pro-metastatic effect of KHK-A. Besides, c-myc activated by nuclear PKM2 promotes alternative splicing of KHK-A, forming a positive feedback loop.
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Affiliation(s)
- Chaofan Peng
- Department of General Surgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
- Colorectal Institute of Nanjing Medical University, Nanjing 210029, China
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing 210029, China
| | - Peng Yang
- Department of General Surgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
- Colorectal Institute of Nanjing Medical University, Nanjing 210029, China
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing 210029, China
| | - Dongsheng Zhang
- Department of General Surgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
- Colorectal Institute of Nanjing Medical University, Nanjing 210029, China
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing 210029, China
| | - Chi Jin
- Department of General Surgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
- Colorectal Institute of Nanjing Medical University, Nanjing 210029, China
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing 210029, China
| | - Wen Peng
- Department of General Surgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
- Colorectal Institute of Nanjing Medical University, Nanjing 210029, China
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing 210029, China
| | - Tuo Wang
- Department of General Surgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
- Colorectal Institute of Nanjing Medical University, Nanjing 210029, China
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing 210029, China
| | - Qingyang Sun
- Department of General Surgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
- Colorectal Institute of Nanjing Medical University, Nanjing 210029, China
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing 210029, China
| | - Zhihao Chen
- Department of General Surgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
- Colorectal Institute of Nanjing Medical University, Nanjing 210029, China
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing 210029, China
| | - Yifei Feng
- Department of General Surgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
- Colorectal Institute of Nanjing Medical University, Nanjing 210029, China
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing 210029, China
- Jiangsu Province Engineering Research Center of Colorectal Cancer Precision Medicine and Translational Medicine, Nanjing 210029, China
| | - Yueming Sun
- Department of General Surgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
- Colorectal Institute of Nanjing Medical University, Nanjing 210029, China
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing 210029, China
- Jiangsu Province Engineering Research Center of Colorectal Cancer Precision Medicine and Translational Medicine, Nanjing 210029, China
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3
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Gasper WC, Gardner S, Ross A, Oppelt SA, Allen KN, Tolan DR. Michaelis-like complex of mouse ketohexokinase isoform C. Acta Crystallogr D Struct Biol 2024; 80:377-385. [PMID: 38805243 DOI: 10.1107/s2059798324003723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 04/23/2024] [Indexed: 05/29/2024] Open
Abstract
Over the past forty years there has been a drastic increase in fructose-related diseases, including obesity, heart disease and diabetes. Ketohexokinase (KHK), the first enzyme in the liver fructolysis pathway, catalyzes the ATP-dependent phosphorylation of fructose to fructose 1-phosphate. Understanding the role of KHK in disease-related processes is crucial for the management and prevention of this growing epidemic. Molecular insight into the structure-function relationship in ligand binding and catalysis by KHK is needed for the design of therapeutic inhibitory ligands. Ketohexokinase has two isoforms: ketohexokinase A (KHK-A) is produced ubiquitously at low levels, whereas ketohexokinase C (KHK-C) is found at much higher levels, specifically in the liver, kidneys and intestines. Structures of the unliganded and liganded human isoforms KHK-A and KHK-C are known, as well as structures of unliganded and inhibitor-bound mouse KHK-C (mKHK-C), which shares 90% sequence identity with human KHK-C. Here, a high-resolution X-ray crystal structure of mKHK-C refined to 1.79 Å resolution is presented. The structure was determined in a complex with both the substrate fructose and the product of catalysis, ADP, providing a view of the Michaelis-like complex of the mouse ortholog. Comparison to unliganded structures suggests that KHK undergoes a conformational change upon binding of substrates that places the enzyme in a catalytically competent form in which the β-sheet domain from one subunit rotates by 16.2°, acting as a lid for the opposing active site. Similar kinetic parameters were calculated for the mouse and human enzymes and indicate that mice may be a suitable animal model for the study of fructose-related diseases. Knowledge of the similarity between the mouse and human enzymes is important for understanding preclinical efforts towards targeting this enzyme, and this ground-state, Michaelis-like complex suggests that a conformational change plays a role in the catalytic function of KHK-C.
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Affiliation(s)
- William C Gasper
- Program in Biochemistry and Molecular Biology, Boston University, Boston, MA 02215, USA
| | - Sarah Gardner
- Department of Chemistry, Boston University, Boston, MA 02215, USA
| | - Adam Ross
- Department of Chemistry, Boston University, Boston, MA 02215, USA
| | - Sarah A Oppelt
- Program in Biochemistry and Molecular Biology, Boston University, Boston, MA 02215, USA
| | - Karen N Allen
- Program in Biochemistry and Molecular Biology, Boston University, Boston, MA 02215, USA
| | - Dean R Tolan
- Program in Biochemistry and Molecular Biology, Boston University, Boston, MA 02215, USA
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4
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Kang YL, Kim J, Kwak SB, Kim YS, Huh J, Park JW. The polyol pathway and nuclear ketohexokinase A signaling drive hyperglycemia-induced metastasis of gastric cancer. Exp Mol Med 2024; 56:220-234. [PMID: 38200154 PMCID: PMC10834943 DOI: 10.1038/s12276-023-01153-3] [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] [Received: 01/10/2023] [Revised: 10/20/2023] [Accepted: 11/07/2023] [Indexed: 01/12/2024] Open
Abstract
Diabetes might be associated with increased cancer risk, with several studies reporting hyperglycemia as a primary oncogenic stimulant. Since glucose metabolism is linked to numerous metabolic pathways, it is difficult to specify the mechanisms underlying hyperglycemia-induced cancer progression. Here, we focused on the polyol pathway, which is dramatically activated under hyperglycemia and causes diabetic complications. We investigated whether polyol pathway-derived fructose facilitates hyperglycemia-induced gastric cancer metastasis. We performed bioinformatics analysis of gastric cancer datasets and immunohistochemical analyses of gastric cancer specimens, followed by transcriptomic and proteomic analyses to evaluate phenotypic changes in gastric cancer cells. Consequently, we found a clinical association between the polyol pathway and gastric cancer progression. In gastric cancer cell lines, hyperglycemia enhanced cell migration and invasion, cytoskeletal rearrangement, and epithelial-mesenchymal transition (EMT). The hyperglycemia-induced acquisition of metastatic potential was mediated by increased fructose derived from the polyol pathway, which stimulated the nuclear ketohexokinase-A (KHK-A) signaling pathway, thereby inducing EMT by repressing the CDH1 gene. In two different xenograft models of cancer metastasis, gastric cancers overexpressing AKR1B1 were found to be highly metastatic in diabetic mice, but these effects of AKR1B1 were attenuated by KHK-A knockdown. In conclusion, hyperglycemia induces fructose formation through the polyol pathway, which in turn stimulates the KHK-A signaling pathway, driving gastric cancer metastasis by inducing EMT. Thus, the polyol and KHK-A signaling pathways could be potential therapeutic targets to decrease the metastatic risk in gastric cancer patients with diabetes.
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Affiliation(s)
- Ye-Lim Kang
- Department of Biomedical Science, BK21-Plus Education Program, Seoul National University College of Medicine, Daehak-ro, Jongno-gu, Seoul, 03080, Korea
- Department of Pharmacology, Seoul National University College of Medicine, Daehak-ro, Jongno-gu, Seoul, 03080, Korea
| | - Jiyoung Kim
- Department of Biomedical Science, BK21-Plus Education Program, Seoul National University College of Medicine, Daehak-ro, Jongno-gu, Seoul, 03080, Korea
- Department of Pharmacology, Seoul National University College of Medicine, Daehak-ro, Jongno-gu, Seoul, 03080, Korea
| | - Su-Bin Kwak
- Department of Biomedical Science, BK21-Plus Education Program, Seoul National University College of Medicine, Daehak-ro, Jongno-gu, Seoul, 03080, Korea
- Department of Pharmacology, Seoul National University College of Medicine, Daehak-ro, Jongno-gu, Seoul, 03080, Korea
| | - Yi-Sook Kim
- Department of Biomedical Science, BK21-Plus Education Program, Seoul National University College of Medicine, Daehak-ro, Jongno-gu, Seoul, 03080, Korea
- Department of Pharmacology, Seoul National University College of Medicine, Daehak-ro, Jongno-gu, Seoul, 03080, Korea
| | - June Huh
- Department of Chemical and Biological Engineering, Korea University, Anam-ro, Seongbuk-gu, Seoul, 02841, Korea
| | - Jong-Wan Park
- Department of Biomedical Science, BK21-Plus Education Program, Seoul National University College of Medicine, Daehak-ro, Jongno-gu, Seoul, 03080, Korea.
- Department of Pharmacology, Seoul National University College of Medicine, Daehak-ro, Jongno-gu, Seoul, 03080, Korea.
- Cancer Research Institute and Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Daehak-ro, Jongno-gu, Seoul, 03080, Korea.
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5
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Ortjohann M, Schönheit P. Identification and characterization of a novel type of ketohexokinase from the haloarchaeon Haloferax volcanii. FEMS Microbiol Lett 2024; 371:fnae026. [PMID: 38587824 DOI: 10.1093/femsle/fnae026] [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: 02/07/2024] [Revised: 03/18/2024] [Accepted: 04/05/2024] [Indexed: 04/09/2024] Open
Abstract
Ketohexokinase (KHK) catalyzes the ATP-dependent phosphorylation of fructose, forming fructose-1-phosphate and ADP. The enzyme is well studied in Eukarya, in particular in humans and other vertebrates, but homologs have not been identified in Bacteria and Archaea. Here we report the identification of a novel type of KHK from the haloarchaeon Haloferax volcanii (HvKHK). The encoding gene khk was identified as HVO_1812. The gene was expressed as a 90-kDa homodimeric protein, catalyzing the phosphorylation of fructose with a Vmax value of 59 U/mg and apparent KM values for ATP and fructose of 0.47 and 1.29 mM, respectively. Homologs of HvKHK were only identified in a few haloarchaea and halophilic Bacteria. The protein showed low sequence identity to characterized KHKs from Eukarya and phylogenetic analyses indicate that haloarchaeal KHKs are largely separated from eukaryal KHKs. This is the first report of the identification of KHKs in prokaryotes that form a novel cluster of sugar kinases within the ribokinase/pfkB superfamily.
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Affiliation(s)
- Marius Ortjohann
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität Kiel, Am Botanischen Garten 1-9, D-24118 Kiel, Germany
| | - Peter Schönheit
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität Kiel, Am Botanischen Garten 1-9, D-24118 Kiel, Germany
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6
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Durham TB, Hao J, Spinazze P, Stack DR, Toth JL, Massey S, Mbofana CT, Johnston RD, Lineswala JP, Wrobleski A, Mínguez JM, Perez C, Smith DL, Lamar J, Leon R, Corkins C, Durbin J, Tung F, Guo S, Linder RJ, Yumibe N, Wang W, MacKrell J, Antonellis M, Mascaro B. Identification of LY3522348: A Highly Selective and Orally Efficacious Ketohexokinase Inhibitor. J Med Chem 2023; 66:15960-15976. [PMID: 37992274 DOI: 10.1021/acs.jmedchem.3c01410] [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: 11/24/2023]
Abstract
The identification of clinical candidate LY3522348 (compound 23) is described. LY3522348 is a highly selective, oral dual inhibitor of human ketohexokinase isoforms C and A (hKHK-C, hKHK-A). Optimization began with highly efficient (S)-2-(2-methylazetidin-1-yl)-6-(1H-pyrazol-4-yl)-4-(trifluoromethyl)nicotinonitrile (3). Efforts focused on developing absorption, distribution, metabolism, potency, and in vitro safety profiles to support oral QD dosing in patients. Structure-based design leveraged vectors for substitution of the pyrazole ring, which provided an opportunity to interact with several different proximal amino acid residues in the protein. LY3522348 displayed a robust pharmacodynamic response in a mouse model of fructose metabolism and was advanced into clinical trials.
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Affiliation(s)
- Timothy B Durham
- Discovery Chemistry Research and Technology, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Junliang Hao
- Discovery Chemistry Research and Technology, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Patrick Spinazze
- Discovery Chemistry Research and Technology, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Douglas R Stack
- Discovery Chemistry Research and Technology, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - James L Toth
- Discovery Chemistry Research and Technology, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Steven Massey
- Discovery Chemistry Research and Technology, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Curren T Mbofana
- Discovery Chemistry Research and Technology, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Richard D Johnston
- Discovery Chemistry Research and Technology, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Jayana P Lineswala
- Discovery Chemistry Research and Technology, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Aaron Wrobleski
- Discovery Chemistry Research and Technology, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Jose Miguel Mínguez
- Discovery Chemistry Research and Technology, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
- Discovery Chemistry Research and Technology, Eli Lilly and Company, Lilly SA, Avenida de la Industria 30, 28108 Alcobendas, Madrid, Spain
| | - Carlos Perez
- Discovery Chemistry Research and Technology, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
- Discovery Chemistry Research and Technology, Eli Lilly and Company, Lilly SA, Avenida de la Industria 30, 28108 Alcobendas, Madrid, Spain
| | - Daryl L Smith
- Discovery Chemistry Research and Technology, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Jason Lamar
- Discovery Chemistry Research and Technology, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Rebecca Leon
- Discovery Chemistry Research and Technology, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
- Molecular Pharmacology, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Christopher Corkins
- Discovery Chemistry Research and Technology, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
- Molecular Pharmacology, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Jim Durbin
- Discovery Chemistry Research and Technology, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
- Structural Biology, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Frances Tung
- Discovery Chemistry Research and Technology, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
- Structural Biology, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Sherry Guo
- Discovery Chemistry Research and Technology, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
- Structural Biology, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Ryan J Linder
- Discovery Chemistry Research and Technology, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
- Molecular Innovation Hub, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Nathan Yumibe
- Discovery Chemistry Research and Technology, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
- ADME, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Wei Wang
- Discovery Chemistry Research and Technology, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
- Toxicology, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - James MacKrell
- Discovery Chemistry Research and Technology, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
- Diabetes and Metabolic Research, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Meghan Antonellis
- Discovery Chemistry Research and Technology, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
- Diabetes and Metabolic Research, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Bethany Mascaro
- Discovery Chemistry Research and Technology, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
- Diabetes and Metabolic Research, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
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7
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Zhu G, Li J, Lin X, Zhang Z, Hu T, Huo S, Li Y. Discovery of a Novel Ketohexokinase Inhibitor with Improved Drug Distribution in Target Tissue for the Treatment of Fructose Metabolic Disease. J Med Chem 2023; 66:13501-13515. [PMID: 37766386 DOI: 10.1021/acs.jmedchem.3c00715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2023]
Abstract
Excessive fructose absorption and its subsequent metabolisms are implicated in nonalcoholic fatty liver disease, obesity, and insulin resistance in humans. Ketohexokinase (KHK) is a primary enzyme involved in fructose metabolism via the conversion of fructose to fructose-1-phosphate. KHK inhibition might be a potential approach for the treatment of metabolic disorders. Herein, a series of novel KHK inhibitors were designed, synthesized, and evaluated. Among them, compound 14 exhibited more potent activity than PF-06835919 based on the rat KHK inhibition assay in vivo, and higher drug distribution concentration in the liver. Its good absorption, distribution, metabolism, and excretion and pharmacokinetic properties make it a promising clinical candidate.
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Affiliation(s)
- Guodong Zhu
- TuoJie Biotech (Shanghai) Co., Ltd., Shanghai 201206, P. R. China
| | - Jiao Li
- TuoJie Biotech (Shanghai) Co., Ltd., Shanghai 201206, P. R. China
| | - Xiaoyan Lin
- TuoJie Biotech (Shanghai) Co., Ltd., Shanghai 201206, P. R. China
| | - Zhen Zhang
- TuoJie Biotech (Shanghai) Co., Ltd., Shanghai 201206, P. R. China
| | - Tao Hu
- TuoJie Biotech (Shanghai) Co., Ltd., Shanghai 201206, P. R. China
| | - Shuhua Huo
- TuoJie Biotech (Shanghai) Co., Ltd., Shanghai 201206, P. R. China
| | - Yunfei Li
- TuoJie Biotech (Shanghai) Co., Ltd., Shanghai 201206, P. R. China
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8
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Ketohexokinase-A acts as a nuclear protein kinase that mediates fructose-induced metastasis in breast cancer. Nat Commun 2020; 11:5436. [PMID: 33116123 PMCID: PMC7595112 DOI: 10.1038/s41467-020-19263-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 09/29/2020] [Indexed: 02/06/2023] Open
Abstract
Harmful effects of high fructose intake on health have been widely reported. Although fructose is known to promote cancer, little is known about the underlying mechanisms. Here, we found that fructose triggers breast cancer metastasis through the ketohexokinase-A signaling pathway. Molecular experiments showed that ketohexokinase-A, rather than ketohexokinase-C, is necessary and sufficient for fructose-induced cell invasion. Ketohexokinase-A-overexpressing breast cancer was found to be highly metastatic in fructose-fed mice. Mechanistically, cytoplasmic ketohexokinase-A enters into the nucleus during fructose stimulation, which is mediated by LRRC59 and KPNB1. In the nucleus, ketohexokinase-A phosphorylates YWHAH at Ser25 and the YWHAH recruits SLUG to the CDH1 promoter, which triggers cell migration. This study provides the effect of nutrition on breast cancer metastasis. High intake of fructose should be restricted in cancer patients to reduce the risk of metastasis. From a therapeutic perspective, the ketohexokinase-A signaling pathway could be a potential target to prevent cancer metastasis.
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9
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Huddleston JP, Raushel FM. Functional Characterization of YdjH, a Sugar Kinase of Unknown Specificity in Escherichia coli K12. Biochemistry 2019; 58:3354-3364. [PMID: 31314509 DOI: 10.1021/acs.biochem.9b00327] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The ydj gene cluster is annotated to catalyze the catabolism of an unknown carbohydrate. Previously, YdjI, a class II aldolase, was shown to catalyze the retro-aldol cleavage of l-glycero-l-galacto-octuluronate-1-phosphate into DHAP and l-arabinuronate. In this report, the functional characterization of YdjH is presented. YdjH catalyzes the phosphorylation of 2-keto-monosaccharides at the C1 hydroxyl group with a substrate profile significantly more stringent than that of YdjI. Similar to YdjI, YdjH shows a strong preference for higher-order monosaccharides (seven to nine carbons) with a carboxylate terminus. The best substrate was determined to be l-glycero-l-galacto-octuluronate, yielding l-glycero-l-galacto-octuluronate-1-phosphate with a kcat of 16 s-1 and a kcat/Km of 2.1 × 104 M-1 s-1. This is apparently the first reported example of kinase activity with eight-carbon monosaccharides. Two crystal structures of YdjH were previously determined to 2.15 and 1.8 Å resolution (Protein Data Bank entries 3H49 and 3IN1 ). We present an analysis of the active site layout and use computational docking to identify potential key residues in the binding of l-glycero-l-galacto-octuluronate.
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Affiliation(s)
- Jamison P Huddleston
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Frank M Raushel
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
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10
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Large-scale conformational changes and redistribution of surface negative charge upon sugar binding dictate the fidelity of phosphorylation in Vibrio cholerae fructokinase. Sci Rep 2018; 8:16925. [PMID: 30446722 PMCID: PMC6240065 DOI: 10.1038/s41598-018-35236-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 10/25/2018] [Indexed: 11/24/2022] Open
Abstract
Fructokinase (FRK) catalyzes the first step of fructose metabolism i.e., D-fructose to D-fructose-6-phosphate (F6P), however, the mechanistic insights of this reaction are elusive yet. Here we demonstrate that the putative Vibrio cholerae fructokinase (VcFRK) exhibit strong fructose-6-kinase activity allosterically modulated by K+/Cs+. We have determined the crystal structures of apo-VcFRK and its complex with fructose, fructose-ADP-Ca2+, fructose-ADP-Ca2+-BeF3−. Collectively, we propose the catalytic mechanism and allosteric activation of VcFRK in atomistic details explaining why K+/Cs+ are better activator than Na+. Structural results suggest that apo VcFRK allows entry of fructose in the active site, sequester it through several conserved H-bonds and attains a closed form through large scale conformational changes. A double mutant (H108C/T261C-VcFRK), that arrests the closed form but unable to reopen for F6P release, is catalytically impotent highlighting the essentiality of this conformational change. Negative charge accumulation around ATP upon fructose binding, is presumed to redirect the γ-phosphate towards fructose for efficient phosphotransfer. Reduced phosphotransfer rate of the mutants E205Q and E110Q supports this view. Atomic resolution structure of VcFRK-fructose-ADP-Ca2+-BeF3−, reported first time for any sugar kinase, suggests that BeF3− moiety alongwith R176, Ca2+ and ‘anion hole’ limit the conformational space for γ-phosphate favoring in-line phospho-transfer.
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11
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Allen RJ, Musante CJ. A mathematical analysis of adaptations to the metabolic fate of fructose in essential fructosuria subjects. Am J Physiol Endocrinol Metab 2018; 315:E394-E403. [PMID: 29664676 DOI: 10.1152/ajpendo.00317.2017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Fructose is a major component of Western diets and is implicated in the pathogenesis of obesity and type 2 diabetes. In response to an oral challenge, the majority of fructose is cleared during "first-pass" liver metabolism, primarily via phosphorylation by ketohexokinase (KHK). A rare benign genetic deficiency in KHK, called essential fructosuria (EF), leads to altered fructose metabolism. The only reported symptom of EF is the appearance of fructose in the urine following either oral or intravenous fructose administration. Here we develop and use a mathematical model to investigate the adaptations to altered fructose metabolism in people with EF. First, the model is calibrated to fit available data in normal healthy subjects. Then, to mathematically represent EF subjects, we systematically implement metabolic adaptations such that model simulations match available data for this phenotype. We hypothesize that these modifications represent the major metabolic adaptations present in these subjects. This modeling approach suggests that several other aspects of fructose metabolism, beyond hepatic KHK deficiency, are altered and contribute to the etiology of this benign condition. Specifically, we predict that fructose absorption into the portal vein is altered, peripheral metabolism is slowed, renal reabsorption of fructose is mostly ablated, and alternate pathways for hepatic metabolism of fructose are upregulated. Moreover, these findings have implications for drug discovery and development, suggesting that the therapeutic targeting of fructose metabolism could lead to unexpected metabolic adaptations, potentially due to a physiological response to high-fructose conditions.
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Affiliation(s)
- Richard J Allen
- Internal Medicine Research Unit, Pfizer Inc, Cambridge, Massachusetts
| | - Cynthia J Musante
- Internal Medicine Research Unit, Pfizer Inc, Cambridge, Massachusetts
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12
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Ji T, Zhang C, Zheng L, Dunaway-Mariano D, Allen KN. Structural Basis of the Molecular Switch between Phosphatase and Mutase Functions of Human Phosphomannomutase 1 under Ischemic Conditions. Biochemistry 2018; 57:3480-3492. [PMID: 29695157 DOI: 10.1021/acs.biochem.8b00223] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The human phosphomannomutases PMM1 and PMM2 catalyze the interconversion of hexose 6-phosphates and hexose 1-phosphates. The two isoforms share 66% sequence identity and have kinetic properties similar to those of mutases in vitro but differ in their functional roles in vivo. Though the physiological role of PMM2 is catalysis of the mutase reaction that provides the mannose 1-phosphate (Man-1-P) essential for protein glycosylation, PMM1 is thought to provide a phosphohydrolase activity in the presence of inosine monophosphate (IMP), converting glucose 1,6-bisphosphate (Glu-1,6-P2) to glucose 6-phosphate (Glu-6-P), rescuing glycolysis during brain ischemia. To uncover the structural basis of how IMP binding converts PMM1 from a mutase to a phosphatase, the 1.93 Å resolution structure of PMM1 complexed with IMP was determined. The structure reveals IMP bound at the substrate recruitment site, thus inhibiting the mutase activity while simultaneously activating a phosphatase activity (IMP Kact = 1.5 μM) resulting from the hydrolysis of the phospho-enzyme. The bound structure and site-directed mutagenesis confirm that the long-range electrostatic interactions provided by Arg180 and Arg183 conserved in PMM1 are the major contributors to IMP binding, and their oblation removes phosphatase but not mutase activity. These residues are not present in the PMM2 isoform, which consequently lacks significant phosphatase activity in the presence of IMP. T2 relaxation nuclear magnetic resonance and small angle X-ray scattering together support the hypothesis that binding of IMP to PMM1 favors an enzyme conformation that is catalytically competent for water attack at the phosphoaspartyl intermediate. Such a mechanism may be generalizable to other enzymes that act through covalent intermediates.
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Affiliation(s)
- Tianyang Ji
- Department of Chemistry , Boston University , Boston , Massachusetts 02215 , United States
| | - Chunchun Zhang
- Department of Chemistry and Chemical Biology , University of New Mexico , Albuquerque , New Mexico 87131 , United States
| | - Li Zheng
- Department of Chemistry and Chemical Biology , University of New Mexico , Albuquerque , New Mexico 87131 , United States
| | - Debra Dunaway-Mariano
- Department of Chemistry and Chemical Biology , University of New Mexico , Albuquerque , New Mexico 87131 , United States
| | - Karen N Allen
- Department of Chemistry , Boston University , Boston , Massachusetts 02215 , United States
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13
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Lanaspa MA, Andres-Hernando A, Orlicky DJ, Cicerchi C, Jang C, Li N, Milagres T, Kuwabara M, Wempe MF, Rabinowitz JD, Johnson RJ, Tolan DR. Ketohexokinase C blockade ameliorates fructose-induced metabolic dysfunction in fructose-sensitive mice. J Clin Invest 2018. [PMID: 29533924 DOI: 10.1172/jci94427] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Increasing evidence suggests a role for excessive intake of fructose in the Western diet as a contributor to the current epidemics of metabolic syndrome and obesity. Hereditary fructose intolerance (HFI) is a difficult and potentially lethal orphan disease associated with impaired fructose metabolism. In HFI, the deficiency of aldolase B results in the accumulation of intracellular phosphorylated fructose, leading to phosphate sequestration and depletion, increased adenosine triphosphate (ATP) turnover, and a plethora of conditions that lead to clinical manifestations such as fatty liver, hyperuricemia, Fanconi syndrome, and severe hypoglycemia. Unfortunately, there is currently no treatment for HFI, and avoiding sugar and fructose has become challenging in our society. In this report, through use of genetically modified mice and pharmacological inhibitors, we demonstrate that the absence or inhibition of ketohexokinase (Khk), an enzyme upstream of aldolase B, is sufficient to prevent hypoglycemia and liver and intestinal injury associated with HFI. Herein we provide evidence for the first time to our knowledge of a potential therapeutic approach for HFI. Mechanistically, our studies suggest that it is the inhibition of the Khk C isoform, not the A isoform, that protects animals from HFI.
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Affiliation(s)
- Miguel A Lanaspa
- Division of Renal Diseases and Hypertension, University of Colorado, Aurora, Colorado, USA
| | - Ana Andres-Hernando
- Division of Renal Diseases and Hypertension, University of Colorado, Aurora, Colorado, USA
| | - David J Orlicky
- Division of Renal Diseases and Hypertension, University of Colorado, Aurora, Colorado, USA
| | - Christina Cicerchi
- Division of Renal Diseases and Hypertension, University of Colorado, Aurora, Colorado, USA
| | - Cholsoon Jang
- Department of Chemistry and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
| | - Nanxing Li
- Division of Renal Diseases and Hypertension, University of Colorado, Aurora, Colorado, USA
| | - Tamara Milagres
- Division of Renal Diseases and Hypertension, University of Colorado, Aurora, Colorado, USA
| | - Masanari Kuwabara
- Division of Renal Diseases and Hypertension, University of Colorado, Aurora, Colorado, USA
| | - Michael F Wempe
- Department of Pharmacology, University of Colorado, Aurora, Colorado, USA
| | - Joshua D Rabinowitz
- Department of Chemistry and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
| | - Richard J Johnson
- Division of Renal Diseases and Hypertension, University of Colorado, Aurora, Colorado, USA
| | - Dean R Tolan
- Department of Biology, Boston University, Boston, Massachusetts, USA
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14
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Gibney PA, Schieler A, Chen JC, Bacha-Hummel JM, Botstein M, Volpe M, Silverman SJ, Xu Y, Bennett BD, Rabinowitz JD, Botstein D. Common and divergent features of galactose-1-phosphate and fructose-1-phosphate toxicity in yeast. Mol Biol Cell 2018; 29:897-910. [PMID: 29444955 PMCID: PMC5896929 DOI: 10.1091/mbc.e17-11-0666] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Metabolic dysregulation leading to sugar-phosphate accumulation is toxic in organisms ranging from bacteria to humans. By comparing two models of sugar-phosphate toxicity in Saccharomyces cerevisiae, we demonstrate that toxicity occurs, at least in part, through multiple, isomer-specific mechanisms, rather than a single general mechanism.
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Affiliation(s)
- Patrick A Gibney
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.,Calico Life Sciences LLC, South San Francisco, CA 94080.,Department of Food Science, Cornell University, Ithaca, NY 14853
| | - Ariel Schieler
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | - Jonathan C Chen
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.,Department of Chemistry, Princeton University, Princeton, NJ 08544
| | | | - Maxim Botstein
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | - Matthew Volpe
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | - Sanford J Silverman
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | - Yifan Xu
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.,Department of Chemistry, Princeton University, Princeton, NJ 08544
| | | | - Joshua D Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.,Department of Chemistry, Princeton University, Princeton, NJ 08544
| | - David Botstein
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.,Calico Life Sciences LLC, South San Francisco, CA 94080.,Department of Food Science, Cornell University, Ithaca, NY 14853
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15
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Huard K, Ahn K, Amor P, Beebe DA, Borzilleri KA, Chrunyk BA, Coffey SB, Cong Y, Conn EL, Culp JS, Dowling MS, Gorgoglione MF, Gutierrez JA, Knafels JD, Lachapelle EA, Pandit J, Parris KD, Perez S, Pfefferkorn JA, Price DA, Raymer B, Ross TT, Shavnya A, Smith AC, Subashi TA, Tesz GJ, Thuma BA, Tu M, Weaver JD, Weng Y, Withka JM, Xing G, Magee TV. Discovery of Fragment-Derived Small Molecules for in Vivo Inhibition of Ketohexokinase (KHK). J Med Chem 2017; 60:7835-7849. [PMID: 28853885 DOI: 10.1021/acs.jmedchem.7b00947] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Increased fructose consumption and its subsequent metabolism have been implicated in hepatic steatosis, dyslipidemia, obesity, and insulin resistance in humans. Since ketohexokinase (KHK) is the principal enzyme responsible for fructose metabolism, identification of a selective KHK inhibitor may help to further elucidate the effect of KHK inhibition on these metabolic disorders. Until now, studies on KHK inhibition with small molecules have been limited due to the lack of viable in vivo pharmacological tools. Herein we report the discovery of 12, a selective KHK inhibitor with potency and properties suitable for evaluating KHK inhibition in rat models. Key structural features interacting with KHK were discovered through fragment-based screening and subsequent optimization using structure-based drug design, and parallel medicinal chemistry led to the identification of pyridine 12.
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Affiliation(s)
- Kim Huard
- Medicine Design, Pfizer Inc. , 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Kay Ahn
- Internal Medicine, Pfizer Inc. , 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Paul Amor
- Internal Medicine, Pfizer Inc. , 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - David A Beebe
- Internal Medicine, Pfizer Inc. , 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Kris A Borzilleri
- Structural Biology and Biophysics, Pfizer Inc. , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Boris A Chrunyk
- Structural Biology and Biophysics, Pfizer Inc. , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Steven B Coffey
- Medicine Design, Pfizer Inc. , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Yang Cong
- Medicine Design, Pfizer Inc. , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Edward L Conn
- Medicine Design, Pfizer Inc. , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Jeffrey S Culp
- Medicine Design, Pfizer Inc. , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Matthew S Dowling
- Medicine Design, Pfizer Inc. , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Matthew F Gorgoglione
- Internal Medicine, Pfizer Inc. , 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Jemy A Gutierrez
- Internal Medicine, Pfizer Inc. , 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - John D Knafels
- Structural Biology and Biophysics, Pfizer Inc. , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Erik A Lachapelle
- Medicine Design, Pfizer Inc. , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Jayvardhan Pandit
- Structural Biology and Biophysics, Pfizer Inc. , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Kevin D Parris
- Structural Biology and Biophysics, Pfizer Inc. , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Sylvie Perez
- Internal Medicine, Pfizer Inc. , 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Jeffrey A Pfefferkorn
- Internal Medicine, Pfizer Inc. , 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - David A Price
- Medicine Design, Pfizer Inc. , 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Brian Raymer
- Medicine Design, Pfizer Inc. , 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Trenton T Ross
- Internal Medicine, Pfizer Inc. , 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Andre Shavnya
- Medicine Design, Pfizer Inc. , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Aaron C Smith
- Medicine Design, Pfizer Inc. , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Timothy A Subashi
- Structural Biology and Biophysics, Pfizer Inc. , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Gregory J Tesz
- Internal Medicine, Pfizer Inc. , 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Benjamin A Thuma
- Medicine Design, Pfizer Inc. , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Meihua Tu
- Medicine Design, Pfizer Inc. , 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - John D Weaver
- Medicine Design, Pfizer Inc. , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Yan Weng
- Medicine Design, Pfizer Inc. , 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Jane M Withka
- Structural Biology and Biophysics, Pfizer Inc. , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Gang Xing
- Internal Medicine, Pfizer Inc. , 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Thomas V Magee
- Internal Medicine, Pfizer Inc. , 1 Portland Street, Cambridge, Massachusetts 02139, United States
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16
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Mirtschink P, Krek W. Hypoxia-driven glycolytic and fructolytic metabolic programs: Pivotal to hypertrophic heart disease. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:1822-8. [DOI: 10.1016/j.bbamcr.2016.02.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 01/28/2016] [Accepted: 02/13/2016] [Indexed: 01/21/2023]
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17
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A splicing switch from ketohexokinase-C to ketohexokinase-A drives hepatocellular carcinoma formation. Nat Cell Biol 2016; 18:561-71. [PMID: 27088854 DOI: 10.1038/ncb3338] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Accepted: 03/11/2016] [Indexed: 12/14/2022]
Abstract
Dietary fructose is primarily metabolized in the liver. Here we demonstrate that, compared with normal hepatocytes, hepatocellular carcinoma (HCC) cells markedly reduce the rate of fructose metabolism and the level of reactive oxygen species, as a result of a c-Myc-dependent and heterogeneous nuclear ribonucleoprotein (hnRNP) H1- and H2-mediated switch from expression of the high-activity fructokinase (KHK)-C to the low-activity KHK-A isoform. Importantly, KHK-A acts as a protein kinase, phosphorylating and activating phosphoribosyl pyrophosphate synthetase 1 (PRPS1) to promote pentose phosphate pathway-dependent de novo nucleic acid synthesis and HCC formation. Furthermore, c-Myc, hnRNPH1/2 and KHK-A expression levels and PRPS1 Thr225 phosphorylation levels correlate with each other in HCC specimens and are associated with poor prognosis for HCC. These findings reveal a pivotal mechanism underlying the distinct fructose metabolism between HCC cells and normal hepatocytes and highlight the instrumental role of KHK-A protein kinase activity in promoting de novo nucleic acid synthesis and HCC development.
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18
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Nagata R, Fujihashi M, Sato T, Atomi H, Miki K. Crystal Structure and Product Analysis of an Archaeal myo-Inositol Kinase Reveal Substrate Recognition Mode and 3-OH Phosphorylation. Biochemistry 2015; 54:3494-503. [DOI: 10.1021/acs.biochem.5b00296] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ryuhei Nagata
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Masahiro Fujihashi
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Takaaki Sato
- Department
of Synthetic Chemistry and Biological Chemistry, Graduate School of
Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- JST, CREST, 7, Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
| | - Haruyuki Atomi
- Department
of Synthetic Chemistry and Biological Chemistry, Graduate School of
Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- JST, CREST, 7, Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
| | - Kunio Miki
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
- JST, CREST, 7, Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
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19
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Carbohydrate metabolism in Archaea: current insights into unusual enzymes and pathways and their regulation. Microbiol Mol Biol Rev 2014; 78:89-175. [PMID: 24600042 DOI: 10.1128/mmbr.00041-13] [Citation(s) in RCA: 200] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The metabolism of Archaea, the third domain of life, resembles in its complexity those of Bacteria and lower Eukarya. However, this metabolic complexity in Archaea is accompanied by the absence of many "classical" pathways, particularly in central carbohydrate metabolism. Instead, Archaea are characterized by the presence of unique, modified variants of classical pathways such as the Embden-Meyerhof-Parnas (EMP) pathway and the Entner-Doudoroff (ED) pathway. The pentose phosphate pathway is only partly present (if at all), and pentose degradation also significantly differs from that known for bacterial model organisms. These modifications are accompanied by the invention of "new," unusual enzymes which cause fundamental consequences for the underlying regulatory principles, and classical allosteric regulation sites well established in Bacteria and Eukarya are lost. The aim of this review is to present the current understanding of central carbohydrate metabolic pathways and their regulation in Archaea. In order to give an overview of their complexity, pathway modifications are discussed with respect to unusual archaeal biocatalysts, their structural and mechanistic characteristics, and their regulatory properties in comparison to their classic counterparts from Bacteria and Eukarya. Furthermore, an overview focusing on hexose metabolic, i.e., glycolytic as well as gluconeogenic, pathways identified in archaeal model organisms is given. Their energy gain is discussed, and new insights into different levels of regulation that have been observed so far, including the transcript and protein levels (e.g., gene regulation, known transcription regulators, and posttranslational modification via reversible protein phosphorylation), are presented.
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20
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Endogenous fructose production and metabolism in the liver contributes to the development of metabolic syndrome. Nat Commun 2014; 4:2434. [PMID: 24022321 PMCID: PMC3833672 DOI: 10.1038/ncomms3434] [Citation(s) in RCA: 172] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2013] [Accepted: 08/13/2013] [Indexed: 12/12/2022] Open
Abstract
Carbohydrates with high glycemic index are proposed to promote the development of obesity, insulin resistance and fatty liver, but the mechanism by which this occurs remains unknown. High serum glucose concentrations glucose are known to induce the polyol pathway and increase fructose generation in the liver. Here we show that this hepatic, endogenously-produced fructose causes systemic metabolic changes. We demonstrate that mice unable to metabolize fructose are protected from an increase in energy intake and body weight, visceral obesity, fatty liver, elevated insulin levels and hyperleptinemia after exposure to 10% glucose for 14 weeks. In normal mice, glucose consumption is accompanied by aldose reductase and polyol pathway activation in steatotic areas. In this regard, we show that aldose reductase deficient mice were protected against glucose-induced fatty liver. We conclude that endogenous fructose generation and metabolism in the liver represents an important mechanism whereby glucose promotes the development of metabolic syndrome.
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21
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Birmingham WR, Starbird CA, Panosian TD, Nannemann DP, Iverson TM, Bachmann BO. Bioretrosynthetic construction of a didanosine biosynthetic pathway. Nat Chem Biol 2014; 10:392-9. [PMID: 24657930 PMCID: PMC4017637 DOI: 10.1038/nchembio.1494] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 02/24/2014] [Indexed: 01/02/2023]
Abstract
Concatenation of engineered biocatalysts into multistep pathways dramatically increases their utility, but development of generalizable assembly methods remains a significant challenge. Herein we evaluate ‘bioretrosynthesis’, which is an application of the retrograde evolution hypothesis, for biosynthetic pathway construction. To test bioretrosynthesis, we engineered a pathway for synthesis of the antiretroviral nucleoside analog didanosine (2,3-dideoxyinosine). Applying both directed evolution and structure-based approaches, we began pathway construction with a retro-extension from an engineered purine nucleoside phosphorylase and evolved 1,5-phosphopentomutase to accept the substrate 2,3-dideoxyribose 5-phosphate with a 700-fold change in substrate selectivity and 3-fold increased turnover in cell lysate. A subsequent retrograde pathway extension, via ribokinase engineering, resulted in a didanosine pathway with a 9,500-fold change in nucleoside production selectivity and 50-fold increase in didanosine production. Unexpectedly, the result of this bioretrosynthetic step was not a retro-extension from phosphopentomutase, but rather the discovery of a fortuitous pathway-shortening bypass via the engineered ribokinase.
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Affiliation(s)
- William R Birmingham
- 1] Department of Biochemistry, Vanderbilt University Medical Center, Nashville, Tennessee, USA. [2]
| | - Chrystal A Starbird
- Chemical and Physical Biology Program, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Timothy D Panosian
- 1] Department of Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee, USA. [2]
| | - David P Nannemann
- 1] Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA. [2]
| | - T M Iverson
- 1] Department of Biochemistry, Vanderbilt University Medical Center, Nashville, Tennessee, USA. [2] Department of Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Brian O Bachmann
- 1] Department of Biochemistry, Vanderbilt University Medical Center, Nashville, Tennessee, USA. [2] Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
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22
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Foley BL, Tessier MB, Woods RJ. Carbohydrate force fields. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2012; 2:652-697. [PMID: 25530813 PMCID: PMC4270206 DOI: 10.1002/wcms.89] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Carbohydrates present a special set of challenges to the generation of force fields. First, the tertiary structures of monosaccharides are complex merely by virtue of their exceptionally high number of chiral centers. In addition, their electronic characteristics lead to molecular geometries and electrostatic landscapes that can be challenging to predict and model. The monosaccharide units can also interconnect in many ways, resulting in a large number of possible oligosaccharides and polysaccharides, both linear and branched. These larger structures contain a number of rotatable bonds, meaning they potentially sample an enormous conformational space. This article briefly reviews the history of carbohydrate force fields, examining and comparing their challenges, forms, philosophies, and development strategies. Then it presents a survey of recent uses of these force fields, noting trends, strengths, deficiencies, and possible directions for future expansion.
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Affiliation(s)
- B. Lachele Foley
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Matthew B. Tessier
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Robert J. Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
- School of Chemistry, National University of Ireland, Galway, Ireland
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23
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Ezkurdia I, del Pozo A, Frankish A, Rodriguez JM, Harrow J, Ashman K, Valencia A, Tress ML. Comparative proteomics reveals a significant bias toward alternative protein isoforms with conserved structure and function. Mol Biol Evol 2012; 29:2265-83. [PMID: 22446687 PMCID: PMC3424414 DOI: 10.1093/molbev/mss100] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Advances in high-throughput mass spectrometry are making proteomics an increasingly important tool in genome annotation projects. Peptides detected in mass spectrometry experiments can be used to validate gene models and verify the translation of putative coding sequences (CDSs). Here, we have identified peptides that cover 35% of the genes annotated by the GENCODE consortium for the human genome as part of a comprehensive analysis of experimental spectra from two large publicly available mass spectrometry databases. We detected the translation to protein of “novel” and “putative” protein-coding transcripts as well as transcripts annotated as pseudogenes and nonsense-mediated decay targets. We provide a detailed overview of the population of alternatively spliced protein isoforms that are detectable by peptide identification methods. We found that 150 genes expressed multiple alternative protein isoforms. This constitutes the largest set of reliably confirmed alternatively spliced proteins yet discovered. Three groups of genes were highly overrepresented. We detected alternative isoforms for 10 of the 25 possible heterogeneous nuclear ribonucleoproteins, proteins with a key role in the splicing process. Alternative isoforms generated from interchangeable homologous exons and from short indels were also significantly enriched, both in human experiments and in parallel analyses of mouse and Drosophila proteomics experiments. Our results show that a surprisingly high proportion (almost 25%) of the detected alternative isoforms are only subtly different from their constitutive counterparts. Many of the alternative splicing events that give rise to these alternative isoforms are conserved in mouse. It was striking that very few of these conserved splicing events broke Pfam functional domains or would damage globular protein structures. This evidence of a strong bias toward subtle differences in CDS and likely conserved cellular function and structure is remarkable and strongly suggests that the translation of alternative transcripts may be subject to selective constraints.
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Affiliation(s)
- Iakes Ezkurdia
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre, Madrid, Spain
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Maryanoff BE, O'Neill JC, McComsey DF, Yabut SC, Luci DK, Jordan AD, Masucci JA, Jones WJ, Abad MC, Gibbs AC, Petrounia I. Inhibitors of Ketohexokinase: Discovery of Pyrimidinopyrimidines with Specific Substitution that Complements the ATP-Binding Site. ACS Med Chem Lett 2011; 2:538-43. [PMID: 24900346 DOI: 10.1021/ml200070g] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Accepted: 04/18/2011] [Indexed: 12/21/2022] Open
Abstract
Attenuation of fructose metabolism by the inhibition of ketohexokinase (KHK; fructokinase) should reduce body weight, free fatty acids, and triglycerides, thereby offering a novel approach to treat diabetes and obesity in response to modern diets. We have identified potent, selective inhibitors of human hepatic KHK within a series of pyrimidinopyrimidines (1). For example, 8, 38, and 47 exhibited KHK IC50 values of 12, 7, and 8 nM, respectively, and also showed potent cellular KHK inhibition (IC50 < 500 nM), which relates to their intrinsic potency vs KHK and their ability to penetrate cells. X-ray cocrystal structures of KHK complexes of 3, 8, and 47 revealed the important interactions within the enzyme's adenosine 5'-triphosphate (ATP)-binding pocket.
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Affiliation(s)
- Bruce E. Maryanoff
- Johnson & Johnson Pharmaceutical Research & Development, Spring House, Pennsylvania 19477-0776, United States
| | - John C. O'Neill
- Johnson & Johnson Pharmaceutical Research & Development, Spring House, Pennsylvania 19477-0776, United States
| | - David F. McComsey
- Johnson & Johnson Pharmaceutical Research & Development, Spring House, Pennsylvania 19477-0776, United States
| | - Stephen C. Yabut
- Johnson & Johnson Pharmaceutical Research & Development, Spring House, Pennsylvania 19477-0776, United States
| | - Diane K. Luci
- Johnson & Johnson Pharmaceutical Research & Development, Spring House, Pennsylvania 19477-0776, United States
| | - Alfonzo D. Jordan
- Johnson & Johnson Pharmaceutical Research & Development, Spring House, Pennsylvania 19477-0776, United States
| | - John A. Masucci
- Johnson & Johnson Pharmaceutical Research & Development, Spring House, Pennsylvania 19477-0776, United States
| | - William J. Jones
- Johnson & Johnson Pharmaceutical Research & Development, Spring House, Pennsylvania 19477-0776, United States
| | - Marta C. Abad
- Johnson & Johnson Pharmaceutical Research & Development, Spring House, Pennsylvania 19477-0776, United States
| | - Alan C. Gibbs
- Johnson & Johnson Pharmaceutical Research & Development, Spring House, Pennsylvania 19477-0776, United States
| | - Ioanna Petrounia
- Johnson & Johnson Pharmaceutical Research & Development, Spring House, Pennsylvania 19477-0776, United States
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25
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Gibbs AC, Abad MC, Zhang X, Tounge BA, Lewandowski FA, Struble GT, Sun W, Sui Z, Kuo LC. Electron density guided fragment-based lead discovery of ketohexokinase inhibitors. J Med Chem 2010; 53:7979-91. [PMID: 21033679 DOI: 10.1021/jm100677s] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A fragment-based drug design paradigm has been successfully applied in the discovery of lead series of ketohexokinase inhibitors. The paradigm consists of three iterations of design, synthesis, and X-ray crystallographic screening to progress low molecular weight fragments to leadlike compounds. Applying electron density of fragments within the protein binding site as defined by X-ray crystallography, one can generate target specific leads without the use of affinity data. Our approach contrasts with most fragment-based drug design methodology where solution activity is a main design guide. Herein we describe the discovery of submicromolar ketohexokinase inhibitors with promising druglike properties.
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Affiliation(s)
- Alan C Gibbs
- Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477, USA
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26
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Hegyi H, Kalmar L, Horvath T, Tompa P. Verification of alternative splicing variants based on domain integrity, truncation length and intrinsic protein disorder. Nucleic Acids Res 2010; 39:1208-19. [PMID: 20972208 PMCID: PMC3045584 DOI: 10.1093/nar/gkq843] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
According to current estimations ∼95% of multi-exonic human protein-coding genes undergo alternative splicing (AS). However, for 4000 human proteins in PDB, only 14 human proteins have structures of at least two alternative isoforms. Surveying these structural isoforms revealed that the maximum insertion accommodated by an isoform of a fully ordered protein domain was 5 amino acids, other instances of domain changes involved intrinsic structural disorder. After collecting 505 minor isoforms of human proteins with evidence for their existence we analyzed their length, protein disorder and exposed hydrophobic surface. We found that strict rules govern the selection of alternative splice variants aimed to preserve the integrity of globular domains: alternative splice sites (i) tend to avoid globular domains or (ii) affect them only marginally or (iii) tend to coincide with a location where the exposed hydrophobic surface is minimal or (iv) the protein is disordered. We also observed an inverse correlation between the domain fraction lost and the full length of the minor isoform containing the domain, possibly indicating a buffering effect for the isoform protein counteracting the domain truncation effect. These observations provide the basis for a prediction method (currently under development) to predict the viability of splice variants.
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Affiliation(s)
- Hedi Hegyi
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, PO Box 7, 1518 Budapest, Hungary.
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27
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Cabrera R, Babul J, Guixé V. Ribokinase family evolution and the role of conserved residues at the active site of the PfkB subfamily representative, Pfk-2 from Escherichia coli. Arch Biochem Biophys 2010; 502:23-30. [DOI: 10.1016/j.abb.2010.06.024] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2010] [Revised: 06/18/2010] [Accepted: 06/20/2010] [Indexed: 11/25/2022]
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28
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Diggle CP, Shires M, Leitch D, Brooke D, Carr IM, Markham AF, Hayward BE, Asipu A, Bonthron DT. Ketohexokinase: expression and localization of the principal fructose-metabolizing enzyme. J Histochem Cytochem 2009; 57:763-74. [PMID: 19365088 DOI: 10.1369/jhc.2009.953190] [Citation(s) in RCA: 128] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Ketohexokinase (KHK, also known as fructokinase) initiates the pathway through which most dietary fructose is metabolized. Very little is known about the cellular localization of this enzyme. Alternatively spliced KHK-C and KHK-A mRNAs are known, but the existence of the KHK-A protein isoform has not been demonstrated in vivo. Using antibodies to KHK for immunohistochemistry and Western blotting of rodent tissues, including those from mouse knockouts, coupled with RT-PCR assays, we determined the distribution of the splice variants. The highly expressed KHK-C isoform localized to hepatocytes in the liver and to the straight segment of the proximal renal tubule. In both tissues, cytoplasmic and nuclear staining was observed. The KHK-A mRNA isoform was observed exclusively in a range of other tissues, and by Western blotting, the presence of endogenous immunoreactive KHK-A protein was shown for the first time, proving that the KHK-A mRNA is translated into KHK-A protein in vivo, and supporting the suggestion that this evolutionarily conserved isoform is physiologically functional. However, the low levels of KHK-A expression prevented its immunohistochemical localization within these tissues. Our results highlight that the use of in vivo biological controls (tissues from knockout animals) is required to distinguish genuine KHK immunoreactivity from experimental artifact.
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Affiliation(s)
- Christine P Diggle
- Leeds Institute of Molecular Medicine, University of Leeds, St James's University Hospital, Beckett Street, Leeds LS9 7TF, United Kingdom
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