1
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Gunn K, Losman JA. Isocitrate Dehydrogenase Mutations in Cancer: Mechanisms of Transformation and Metabolic Liability. Cold Spring Harb Perspect Med 2024; 14:a041537. [PMID: 38191174 PMCID: PMC11065172 DOI: 10.1101/cshperspect.a041537] [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: 01/10/2024]
Abstract
Isocitrate dehydrogenase 1 and 2 (IDH1 and IDH2) are metabolic enzymes that interconvert isocitrate and 2-oxoglutarate (2OG). Gain-of-function mutations in IDH1 and IDH2 occur in a number of cancers, including acute myeloid leukemia, glioma, cholangiocarcinoma, and chondrosarcoma. These mutations cripple the wild-type activity of IDH and cause the enzymes to catalyze a partial reverse reaction in which 2OG is reduced but not carboxylated, resulting in production of the (R)-enantiomer of 2-hydroxyglutarate ((R)-2HG). (R)-2HG accumulation in IDH-mutant tumors results in profound dysregulation of cellular metabolism. The most well-characterized oncogenic effects of (R)-2HG involve the dysregulation of 2OG-dependent epigenetic tumor-suppressor enzymes. However, (R)-2HG has many other effects in IDH-mutant cells, some that promote transformation and others that induce metabolic dependencies. Herein, we review how cancer-associated IDH mutations impact epigenetic regulation and cellular metabolism and discuss how these effects can potentially be leveraged to therapeutically target IDH-mutant tumors.
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Affiliation(s)
- Kathryn Gunn
- Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Julie-Aurore Losman
- Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
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2
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Herold RA, Schofield CJ, Armstrong FA. Electrochemical Nanoreactor Provides a Comprehensive View of Isocitrate Dehydrogenase Cancer-drug Kinetics. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 135:e202309149. [PMID: 38529044 PMCID: PMC10962547 DOI: 10.1002/ange.202309149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Indexed: 03/27/2024]
Abstract
The ability to control enzyme cascades entrapped in a nanoporous electrode material (the "Electrochemical Leaf", e-Leaf) has been exploited to gain detailed kinetic insight into the mechanism of an anti-cancer drug. Ivosidenib, used to treat acute myeloid leukemia, acts on a common cancer-linked variant of isocitrate dehydrogenase 1 (IDH1 R132H) inhibiting its "gain-of-function" activity-the undesired reduction of 2-oxoglutarate (2OG) to the oncometabolite 2-hydroxyglutarate (2HG). The e-Leaf quantifies the kinetics of IDH1 R132H inhibition across a wide and continuous range of conditions, efficiently revealing factors underlying the inhibitor residence time. Selective inhibition of IDH1 R132H by Ivosidenib and another inhibitor, Novartis 224, is readily resolved as a two-stage process whereby initial rapid non-inhibitory binding is followed by a slower step to give the inhibitory complex. These kinetic features are likely present in other allosteric inhibitors of IDH1/2. Such details, essential for understanding inhibition mechanisms, are not readily resolved in conventional steady-state kinetics or by techniques that rely only on measuring binding. Extending the new method and analytical framework presented here to other enzyme systems will be straightforward and should rapidly reveal insight that is difficult or often impossible to obtain using other methods.
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Affiliation(s)
- Ryan A. Herold
- Inorganic Chemistry LaboratoryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QRUK
| | - Christopher J. Schofield
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of OxfordMansfield RoadOxfordOX1 3QYUK
| | - Fraser A. Armstrong
- Inorganic Chemistry LaboratoryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QRUK
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3
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Herold RA, Schofield CJ, Armstrong FA. Electrochemical Nanoreactor Provides a Comprehensive View of Isocitrate Dehydrogenase Cancer-drug Kinetics. Angew Chem Int Ed Engl 2023; 62:e202309149. [PMID: 37607127 PMCID: PMC10962598 DOI: 10.1002/anie.202309149] [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: 06/29/2023] [Revised: 08/11/2023] [Accepted: 08/18/2023] [Indexed: 08/24/2023]
Abstract
The ability to control enzyme cascades entrapped in a nanoporous electrode material (the "Electrochemical Leaf", e-Leaf) has been exploited to gain detailed kinetic insight into the mechanism of an anti-cancer drug. Ivosidenib, used to treat acute myeloid leukemia, acts on a common cancer-linked variant of isocitrate dehydrogenase 1 (IDH1 R132H) inhibiting its "gain-of-function" activity-the undesired reduction of 2-oxoglutarate (2OG) to the oncometabolite 2-hydroxyglutarate (2HG). The e-Leaf quantifies the kinetics of IDH1 R132H inhibition across a wide and continuous range of conditions, efficiently revealing factors underlying the inhibitor residence time. Selective inhibition of IDH1 R132H by Ivosidenib and another inhibitor, Novartis 224, is readily resolved as a two-stage process whereby initial rapid non-inhibitory binding is followed by a slower step to give the inhibitory complex. These kinetic features are likely present in other allosteric inhibitors of IDH1/2. Such details, essential for understanding inhibition mechanisms, are not readily resolved in conventional steady-state kinetics or by techniques that rely only on measuring binding. Extending the new method and analytical framework presented here to other enzyme systems will be straightforward and should rapidly reveal insight that is difficult or often impossible to obtain using other methods.
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Affiliation(s)
- Ryan A. Herold
- Inorganic Chemistry LaboratoryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QRUK
| | - Christopher J. Schofield
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of OxfordMansfield RoadOxfordOX1 3QYUK
| | - Fraser A. Armstrong
- Inorganic Chemistry LaboratoryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QRUK
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4
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Gunn K, Myllykoski M, Cao JZ, Ahmed M, Huang B, Rouaisnel B, Diplas BH, Levitt MM, Looper R, Doench JG, Ligon KL, Kornblum HI, McBrayer SK, Yan H, Duy C, Godley LA, Koivunen P, Losman JA. (R)-2-Hydroxyglutarate Inhibits KDM5 Histone Lysine Demethylases to Drive Transformation in IDH-Mutant Cancers. Cancer Discov 2023; 13:1478-1497. [PMID: 36847506 PMCID: PMC10238656 DOI: 10.1158/2159-8290.cd-22-0825] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 12/21/2022] [Accepted: 02/22/2023] [Indexed: 03/01/2023]
Abstract
Oncogenic mutations in isocitrate dehydrogenase 1 (IDH1) and IDH2 occur in a wide range of cancers, including acute myeloid leukemia (AML) and glioma. Mutant IDH enzymes convert 2-oxoglutarate (2OG) to (R)-2-hydroxyglutarate [(R)-2HG], an oncometabolite that is hypothesized to promote cellular transformation by dysregulating 2OG-dependent enzymes. The only (R)-2HG target that has been convincingly shown to contribute to transformation by mutant IDH is the myeloid tumor suppressor TET2. However, there is ample evidence to suggest that (R)-2HG has other functionally relevant targets in IDH-mutant cancers. Here, we show that (R)-2HG inhibits KDM5 histone lysine demethylases and that this inhibition contributes to cellular transformation in IDH-mutant AML and IDH-mutant glioma. These studies provide the first evidence of a functional link between dysregulation of histone lysine methylation and transformation in IDH-mutant cancers. SIGNIFICANCE Mutant IDH is known to induce histone hypermethylation. However, it is not known if this hypermethylation is functionally significant or is a bystander effect of (R)-2HG accumulation in IDH-mutant cells. Here, we provide evidence that KDM5 inhibition by (R)-2HG contributes to mutant IDH-mediated transformation in AML and glioma. This article is highlighted in the In This Issue feature, p. 1275.
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Affiliation(s)
- Kathryn Gunn
- Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Matti Myllykoski
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, FI-90220, Oulu, Finland; Oulu Center for Cell-Matrix Research, University of Oulu, FI-90220, Oulu, Finland
| | - John Z. Cao
- Committee on Cancer Biology, Biological Sciences Division, University of Chicago, Chicago, IL 60637, USA
| | - Manna Ahmed
- Cancer Signaling and Epigenetics Program, Cancer Epigenetic Institute, Fox Chase Cancer Center, Philadelphia, PA 19111
| | - Bofu Huang
- Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Betty Rouaisnel
- Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Bill H. Diplas
- Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA
| | - Michael M. Levitt
- Children’s Medical Center Research Institute and Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ryan Looper
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
| | - John G. Doench
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Keith L. Ligon
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Pathology, Boston Children’s Hospital and Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Harley I. Kornblum
- Intellectual and Developmental Disabilities Research Center, David Geffen School of Medicine at UCLA, Los Angeles, California 90095, USA
| | - Samuel K. McBrayer
- Children’s Medical Center Research Institute and Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hai Yan
- Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA
| | - Cihangir Duy
- Cancer Signaling and Epigenetics Program, Cancer Epigenetic Institute, Fox Chase Cancer Center, Philadelphia, PA 19111
| | - Lucy A. Godley
- Committee on Cancer Biology, Biological Sciences Division, University of Chicago, Chicago, IL 60637, USA
- Section of Hematology/Oncology, Departments of Medicine and Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Peppi Koivunen
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, FI-90220, Oulu, Finland; Oulu Center for Cell-Matrix Research, University of Oulu, FI-90220, Oulu, Finland
| | - Julie-Aurore Losman
- Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Division of Hematology, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
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5
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Wang QX, Zhang PY, Li QQ, Tong ZJ, Wu JZ, Yu SP, Yu YC, Ding N, Leng XJ, Chang L, Xu JG, Sun SL, Yang Y, Li NG, Shi ZH. Challenges for the development of mutant isocitrate dehydrogenases 1 inhibitors to treat glioma. Eur J Med Chem 2023; 257:115464. [PMID: 37235998 DOI: 10.1016/j.ejmech.2023.115464] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023]
Abstract
Glioma is one of the most common types of brain tumors, and its high recurrence and mortality rates threaten human health. In 2008, the frequent isocitrate dehydrogenase 1 (IDH1) mutations in glioma were reported, which brought a new strategy in the treatment of this challenging disease. In this perspective, we first discuss the possible gliomagenesis after IDH1 mutations (mIDH1). Subsequently, we systematically investigate the reported mIDH1 inhibitors and present a comparative analysis of the ligand-binding pocket in mIDH1. Additionally, we also discuss the binding features and physicochemical properties of different mIDH1 inhibitors to facilitate the future development of mIDH1 inhibitors. Finally, we discuss the possible selectivity features of mIDH1 inhibitors against WT-IDH1 and IDH2 by combining protein-based and ligand-based information. We hope that this perspective can inspire the development of mIDH1 inhibitors and bring potent mIDH1 inhibitors for the treatment of glioma.
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Affiliation(s)
- Qing-Xin Wang
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Peng-Yu Zhang
- School of Computer Science and Engineering, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Qing-Qing Li
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Zhen-Jiang Tong
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Jia-Zhen Wu
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Shao-Peng Yu
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Yan-Cheng Yu
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Ning Ding
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Xue-Jiao Leng
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Liang Chang
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Jin-Guo Xu
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Shan-Liang Sun
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China.
| | - Ye Yang
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, China.
| | - Nian-Guang Li
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China.
| | - Zhi-Hao Shi
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu, 211198, China.
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6
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Liu S, Abboud M, Mikhailov V, Liu X, Reinbold R, Schofield CJ. Differentiating Inhibition Selectivity and Binding Affinity of Isocitrate Dehydrogenase 1 Variant Inhibitors. J Med Chem 2023; 66:5279-5288. [PMID: 36952395 PMCID: PMC10108345 DOI: 10.1021/acs.jmedchem.3c00203] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Indexed: 03/25/2023]
Abstract
Isocitrate dehydrogenase (IDH) 1/2 gain-of-function variants catalyze the production of the oncometabolite 2-hydroxyglutarate and are validated targets for leukemia treatment. We report binding and inhibition studies on 13 IDH1/2 variant inhibitors, including clinical candidates and drugs, with wild-type (wt) IDH1 and its cancer-associated variant, IDH1 R132H. Interestingly, all the variant inhibitors bind wt IDH1 despite not, or only weakly, inhibiting it. Selective inhibition of the IDH1 R132H variant over wt IDH1 does not principally relate to the affinities of the inhibitors for the resting forms of the enzymes. Rather, the independent binding of Mg2+ and 2-oxoglutarate to the IDH1 variant makes the variant more susceptible to allosteric inhibition, compared to the tighter binding of the isocitrate-Mg2+ complex substrate to wt IDH1. The results highlight that binding affinity need not correlate with inhibition selectivity and have implications for interpretation of inhibitor screening results with IDH and related enzymes using turnover versus binding assays.
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Affiliation(s)
| | | | - Victor Mikhailov
- Chemistry Research Laboratory, Department
of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Xiao Liu
- Chemistry Research Laboratory, Department
of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Raphael Reinbold
- Chemistry Research Laboratory, Department
of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Christopher J. Schofield
- Chemistry Research Laboratory, Department
of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
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7
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Neumaier F, Zlatopolskiy BD, Neumaier B. Mutated Isocitrate Dehydrogenase (mIDH) as Target for PET Imaging in Gliomas. Molecules 2023; 28:molecules28072890. [PMID: 37049661 PMCID: PMC10096429 DOI: 10.3390/molecules28072890] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/21/2023] [Accepted: 03/21/2023] [Indexed: 04/14/2023] Open
Abstract
Gliomas are the most common primary brain tumors in adults. A diffuse infiltrative growth pattern and high resistance to therapy make them largely incurable, but there are significant differences in the prognosis of patients with different subtypes of glioma. Mutations in isocitrate dehydrogenase (IDH) have been recognized as an important biomarker for glioma classification and a potential therapeutic target. However, current clinical methods for detecting mutated IDH (mIDH) require invasive tissue sampling and cannot be used for follow-up examinations or longitudinal studies. PET imaging could be a promising approach for non-invasive assessment of the IDH status in gliomas, owing to the availability of various mIDH-selective inhibitors as potential leads for the development of PET tracers. In the present review, we summarize the rationale for the development of mIDH-selective PET probes, describe their potential applications beyond the assessment of the IDH status and highlight potential challenges that may complicate tracer development. In addition, we compile the major chemical classes of mIDH-selective inhibitors that have been described to date and briefly consider possible strategies for radiolabeling of the most promising candidates. Where available, we also summarize previous studies with radiolabeled analogs of mIDH inhibitors and assess their suitability for PET imaging in gliomas.
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Affiliation(s)
- Felix Neumaier
- Forschungszentrum Jülich GmbH, Institute of Neuroscience and Medicine, Nuclear Chemistry (INM-5), Wilhelm-Johnen-Str., 52428 Jülich, Germany
- Institute of Radiochemistry and Experimental Molecular Imaging, Faculty of Medicine and University Hospital Cologne, University of Cologne, Kerpener Str. 62, 50937 Cologne, Germany
| | - Boris D Zlatopolskiy
- Forschungszentrum Jülich GmbH, Institute of Neuroscience and Medicine, Nuclear Chemistry (INM-5), Wilhelm-Johnen-Str., 52428 Jülich, Germany
- Institute of Radiochemistry and Experimental Molecular Imaging, Faculty of Medicine and University Hospital Cologne, University of Cologne, Kerpener Str. 62, 50937 Cologne, Germany
| | - Bernd Neumaier
- Forschungszentrum Jülich GmbH, Institute of Neuroscience and Medicine, Nuclear Chemistry (INM-5), Wilhelm-Johnen-Str., 52428 Jülich, Germany
- Institute of Radiochemistry and Experimental Molecular Imaging, Faculty of Medicine and University Hospital Cologne, University of Cologne, Kerpener Str. 62, 50937 Cologne, Germany
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8
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Montella L, Cuomo M, Del Gaudio N, Buonaiuto M, Costabile D, Visconti R, Di Risi T, Vinciguerra R, Trio F, Ferraro S, Bove G, Facchini G, Altucci L, Chiariotti L, Della Monica R. Epigenetic alterations in glioblastomas: Diagnostic, prognostic and therapeutic relevance. Int J Cancer 2022. [PMID: 36479695 DOI: 10.1002/ijc.34381] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/17/2022] [Accepted: 11/08/2022] [Indexed: 12/12/2022]
Abstract
Glioblastoma, the most common and heterogeneous tumor affecting brain parenchyma, is dismally characterized by a very poor prognosis. Thus, the search of new, more effective treatments is a vital need. Here, we will review the druggable epigenetic features of glioblastomas that are, indeed, currently explored in preclinical studies and in clinical trials for the development of more effective, personalized treatments. In detail, we will review the studies that have led to the identification of epigenetic signatures, IDH mutations, MGMT gene methylation, histone modification alterations, H3K27 mutations and epitranscriptome landscapes of glioblastomas, in each case discussing the corresponding targeted therapies and their potential efficacy. Finally, we will emphasize how recent technological improvements permit to routinely investigate many glioblastoma epigenetic biomarkers in clinical practice, further enforcing the hope that personalized drugs, targeting specific epigenetic features, could be in future a therapeutic option for selected patients.
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Affiliation(s)
- Liliana Montella
- ASL NA2 NORD, Oncology Operative Unit, "Santa Maria delle Grazie" Hospital, Pozzuoli, Italy
| | - Mariella Cuomo
- CEINGE Biotecnologie Avanzate scarl, Naples, Italy.,Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", Naples, Italy
| | - Nunzio Del Gaudio
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Michela Buonaiuto
- CEINGE Biotecnologie Avanzate scarl, Naples, Italy.,Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", Naples, Italy
| | - Davide Costabile
- CEINGE Biotecnologie Avanzate scarl, Naples, Italy.,SEMM-European School of Molecular Medicine, University of Naples "Federico II", Naples, Italy
| | - Roberta Visconti
- CEINGE Biotecnologie Avanzate scarl, Naples, Italy.,Institute for the Experimental Endocrinology and Oncology, Italian National Council of Research, Naples, Italy
| | - Teodolinda Di Risi
- CEINGE Biotecnologie Avanzate scarl, Naples, Italy.,Department of Public Health, University of Naples "Federico II", Naples, Italy
| | | | | | - Sara Ferraro
- CEINGE Biotecnologie Avanzate scarl, Naples, Italy
| | - Guglielmo Bove
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Gaetano Facchini
- ASL NA2 NORD, Oncology Operative Unit, "Santa Maria delle Grazie" Hospital, Pozzuoli, Italy
| | - Lucia Altucci
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy.,BIOGEM, Ariano Irpino, Italy
| | - Lorenzo Chiariotti
- CEINGE Biotecnologie Avanzate scarl, Naples, Italy.,Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", Naples, Italy
| | - Rosa Della Monica
- CEINGE Biotecnologie Avanzate scarl, Naples, Italy.,Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", Naples, Italy
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9
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Tian W, Zhang W, Wang Y, Jin R, Wang Y, Guo H, Tang Y, Yao X. Recent advances of IDH1 mutant inhibitor in cancer therapy. Front Pharmacol 2022; 13:982424. [PMID: 36091829 PMCID: PMC9449373 DOI: 10.3389/fphar.2022.982424] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/02/2022] [Indexed: 11/23/2022] Open
Abstract
Isocitrate dehydrogenase (IDH) is the key metabolic enzyme that catalyzes the conversion of isocitrate to α-ketoglutarate (α-KG). Two main types of IDH1 and IDH2 are present in humans. In recent years, mutations in IDH have been observed in several tumors, including glioma, acute myeloid leukemia, and chondrosarcoma. Among them, the frequency of IDH1 mutations is higher than IDH2. IDH1 mutations have been shown to increase the conversion of α-KG to 2-hydroxyglutarate (2-HG). IDH1 mutation-mediated accumulation of 2-HG leads to epigenetic dysregulation, altering gene expression, and impairing cell differentiation. A rapidly emerging therapeutic approach is through the development of small molecule inhibitors targeting mutant IDH1 (mIDH1), as evidenced by the recently approved of the first selective IDH1 mutant inhibitor AG-120 (ivosidenib) for the treatment of IDH1-mutated AML. This review will focus on mIDH1 as a therapeutic target and provide an update on IDH1 mutant inhibitors in development and clinical trials.
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Affiliation(s)
- Wangqi Tian
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi, China
| | - Weitong Zhang
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi, China
| | - Yifan Wang
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi, China
| | - Ruyi Jin
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi, China
| | - Yuwei Wang
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi, China
- *Correspondence: Yuwei Wang,
| | - Hui Guo
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi, China
| | - Yuping Tang
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi, China
| | - Xiaojun Yao
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, China
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10
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Chen C, Wang Z, Qin Y. Connections between metabolism and epigenetics: mechanisms and novel anti-cancer strategy. Front Pharmacol 2022; 13:935536. [PMID: 35935878 PMCID: PMC9354823 DOI: 10.3389/fphar.2022.935536] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 06/29/2022] [Indexed: 12/26/2022] Open
Abstract
Cancer cells undergo metabolic adaptations to sustain their growth and proliferation under several stress conditions thereby displaying metabolic plasticity. Epigenetic modification is known to occur at the DNA, histone, and RNA level, which can alter chromatin state. For almost a century, our focus in cancer biology is dominated by oncogenic mutations. Until recently, the connection between metabolism and epigenetics in a reciprocal manner was spotlighted. Explicitly, several metabolites serve as substrates and co-factors of epigenetic enzymes to carry out post-translational modifications of DNA and histone. Genetic mutations in metabolic enzymes facilitate the production of oncometabolites that ultimately impact epigenetics. Numerous evidences also indicate epigenome is sensitive to cancer metabolism. Conversely, epigenetic dysfunction is certified to alter metabolic enzymes leading to tumorigenesis. Further, the bidirectional relationship between epigenetics and metabolism can impact directly and indirectly on immune microenvironment, which might create a new avenue for drug discovery. Here we summarize the effects of metabolism reprogramming on epigenetic modification, and vice versa; and the latest advances in targeting metabolism-epigenetic crosstalk. We also discuss the principles linking cancer metabolism, epigenetics and immunity, and seek optimal immunotherapy-based combinations.
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11
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Das D, Karthik N, Taneja R. Epigenetic Small-Molecule Modulators Targeting Metabolic Pathways in Cancer. Subcell Biochem 2022; 100:523-555. [PMID: 36301505 DOI: 10.1007/978-3-031-07634-3_16] [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] [Indexed: 06/16/2023]
Abstract
Metabolic deregulation is a key factor in cancer progression. Epigenetic changes and metabolic rewiring are intertwined in cancer. Deregulated epigenetic modifiers cause metabolic aberrations by targeting the expression of metabolic enzymes. Conversely, metabolites and cofactors affect the expression and activity of epigenetic regulators. Small molecules are promising therapeutic approaches to target the epigenetic-metabolomic crosstalk in cancer. Here, we focus on the interplay between metabolic rewiring and epigenetic landscape in the context of tumourigenesis and highlight recent advances in the use of small-molecule drug targets for therapy.
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Affiliation(s)
- Dipanwita Das
- Department of Physiology and Healthy Longevity Translational Research Program Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Nandini Karthik
- Department of Physiology and Healthy Longevity Translational Research Program Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Reshma Taneja
- Department of Physiology and Healthy Longevity Translational Research Program Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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12
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Zhou X, Zheng M, Zhao N, Hu Y, Yang K, Huo J, Liu G, Huang J, Chen L, Zhou Y, Li H. Discovery of linear unnatural peptides as potent mutant isocitrate dehydrogenase 1 inhibitors by Ugi reaction. Bioorg Chem 2021; 119:105569. [PMID: 34954572 DOI: 10.1016/j.bioorg.2021.105569] [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: 10/04/2021] [Revised: 12/10/2021] [Accepted: 12/14/2021] [Indexed: 11/02/2022]
Abstract
Isocitrate dehydrogenases 1 (IDH1) catalyzes the oxidative decarboxylation of isocitrate to ɑ-ketoglutaric acid (α-KG). It is the most frequently mutated metabolic gene in human cancer and its mutations interfere with cell metabolism and epigenetic regulation, thus promoting tumorigenesis. In order to discover potent new mutant IDH1 inhibitors, based on the structure of marketed inhibitor AG-120 (Ivosidenib), we designed, synthesized and evaluated a series of linear unnatural peptide analogues via Ugi reaction, as potential mutant IDH1 inhibitors. All these compounds were evaluated for their inhibition on mutant IDH1 enzyme activity. The structure-activity relationship was discussed on the basis of experimental data, with an attempt to pave the way for future studies. Among them, 43 exhibited potent and selective enzyme inhibitory activity, and showed strong binding affinity with mutant IDH1. It can decrease the cellular concentration of 2-HG, and suppress the proliferation of HT1080 and IDH1 mutant-U-87 cells by selectively inhibiting the activity of mutant IDH1.
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Affiliation(s)
- Xuechen Zhou
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji-Rongcheng Center for Biomedicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Mengzhu Zheng
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji-Rongcheng Center for Biomedicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Na Zhao
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization, Ministry of Education, School of Pharmacy, Shihezi University, Shihezi 832002, China
| | - Yixin Hu
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji-Rongcheng Center for Biomedicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Kaiyin Yang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji-Rongcheng Center for Biomedicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Junfeng Huo
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji-Rongcheng Center for Biomedicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Guangyuan Liu
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji-Rongcheng Center for Biomedicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jiangeng Huang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji-Rongcheng Center for Biomedicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Lixia Chen
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China.
| | - Yirong Zhou
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji-Rongcheng Center for Biomedicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Hua Li
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji-Rongcheng Center for Biomedicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China.
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13
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Bhattacharjee D, Balabhaskararao K, Jain N. Mutant IDH1 inhibitors activate pSTAT3-Y705 leading to an increase in BCAT1 and YKL-40 levels in mutant IDH1-expressing cells. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1868:119114. [PMID: 34329662 DOI: 10.1016/j.bbamcr.2021.119114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 07/01/2021] [Accepted: 07/23/2021] [Indexed: 12/11/2022]
Abstract
IDH1 mutations are frequent and early events in gliomas. Mutant IDH1 produces D-2HG that causes epigenetic changes by increasing histone and DNA methylations, thereby contributing to tumor growth. Mutant IDH1 rewires metabolism and endows a few therapeutic vulnerabilities in cells. But, mutant IDH1 inhibitor(s) treatments reverse these therapeutic vulnerabilities by increasing cell growth. Nevertheless, it is unclear how mutant IDH1 inhibitor(s) increases cell growth. As mutant IDH1 inhibitor(s) increase cell growth, therefore we asked whether mutant IDH1 inhibitor(s) activate oncogenes in mutant IDH1-expressing cells. To answer this question, we used allosteric mutant IDH1 inhibitors to treat mutant IDH1-expressing HT1080 cells, and examined for activation of oncogenes by assessing the levels of our read-outs: BCAT1 and YKL-40. We found that mutant IDH1 inhibitors' treatments increased BCAT1 and YKL-40 levels in HT1080 cells. Next, we observed that mutant IDH1 inhibitors activated STAT3 by phosphorylation at Tyr-705 position (pSTAT3-Y705) and its nuclear translocation. Upon examining the molecular mechanism of pSTAT3-Y705 activation in mutant IDH1 inhibitor-treated cells, we found that mutant IDH1 strongly bound STAT3, but mutant IDH1 inhibitor treatment decreased mutant IDH1-STAT3 binding. Furthermore, we observed that STAT3-knockdown and pharmacological inhibition of STAT3 attenuated the mutant IDH1 inhibitor-mediated increase in BCAT1 and YKL-40 levels, whereas STAT3 overexpression and Interleukin-6 (STAT3 activator) treatments increased BCAT1 and YKL-40 levels. We conclude that mutant IDH1 inhibitors activate the oncogenic transcription factor-STAT3 leading to an increase in BCAT1 and YKL-40 levels in mutant IDH1-expressing cells.
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Affiliation(s)
- Debanjan Bhattacharjee
- Department of Applied Biology, CSIR-Indian Institute of Chemical Technology, Uppal Road, Hyderabad 500007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Kancharana Balabhaskararao
- Department of Applied Biology, CSIR-Indian Institute of Chemical Technology, Uppal Road, Hyderabad 500007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Nishant Jain
- Department of Applied Biology, CSIR-Indian Institute of Chemical Technology, Uppal Road, Hyderabad 500007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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14
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Rohde JM, Karavadhi S, Pragani R, Liu L, Fang Y, Zhang W, McIver A, Zheng H, Liu Q, Davis MI, Urban DJ, Lee TD, Cheff DM, Hollingshead M, Henderson MJ, Martinez NJ, Brimacombe KR, Yasgar A, Zhao W, Klumpp-Thomas C, Michael S, Covey J, Moore WJ, Stott GM, Li Z, Simeonov A, Jadhav A, Frye S, Hall MD, Shen M, Wang X, Patnaik S, Boxer MB. Discovery and Optimization of 2 H-1λ 2-Pyridin-2-one Inhibitors of Mutant Isocitrate Dehydrogenase 1 for the Treatment of Cancer. J Med Chem 2021; 64:4913-4946. [PMID: 33822623 PMCID: PMC8968748 DOI: 10.1021/acs.jmedchem.1c00019] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Neomorphic mutations in isocitrate dehydrogenase 1 (IDH1) are oncogenic for a number of malignancies, primarily low-grade gliomas and acute myeloid leukemia. We report a medicinal chemistry campaign around a 7,7-dimethyl-7,8-dihydro-2H-1λ2-quinoline-2,5(6H)-dione screening hit against the R132H and R132C mutant forms of isocitrate dehydrogenase (IDH1). Systematic SAR efforts produced a series of potent pyrid-2-one mIDH1 inhibitors, including the atropisomer (+)-119 (NCATS-SM5637, NSC 791985). In an engineered mIDH1-U87-xenograft mouse model, after a single oral dose of 30 mg/kg, 16 h post dose, between 16 and 48 h, (+)-119 showed higher tumoral concentrations that corresponded to lower 2-HG concentrations, when compared with the approved drug AG-120 (ivosidenib).
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Affiliation(s)
- Jason M. Rohde
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD, 20850, USA
- Current address: Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, MD 20910
| | - Surendra Karavadhi
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Rajan Pragani
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Li Liu
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Yuhong Fang
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Weihe Zhang
- Center for Integrative Chemical Biology and Drug Discovery, Division for Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514
| | - Andrew McIver
- Center for Integrative Chemical Biology and Drug Discovery, Division for Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514
| | - Hongchao Zheng
- Center for Integrative Chemical Biology and Drug Discovery, Division for Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514
| | - Qingyang Liu
- Center for Integrative Chemical Biology and Drug Discovery, Division for Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514
| | - Mindy I. Davis
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Daniel J. Urban
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Tobie D. Lee
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Dorian M. Cheff
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Melinda Hollingshead
- Biological Testing Branch, Developmental therapeutics Program, National Cancer Institute, Frederick, MD 21702
| | - Mark J. Henderson
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Natalia J. Martinez
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Kyle R. Brimacombe
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Adam Yasgar
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Wei Zhao
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Carleen Klumpp-Thomas
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Sam Michael
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Joseph Covey
- Developmental Therapeutics Program Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD 20850
| | - William J. Moore
- NExT Program Support, Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, 21702
| | - Gordon M. Stott
- NExT Program Support, Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, 21702
| | - Zhuyin Li
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Ajit Jadhav
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Stephen Frye
- Center for Integrative Chemical Biology and Drug Discovery, Division for Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514
| | - Matthew D. Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Min Shen
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Xiaodong Wang
- Center for Integrative Chemical Biology and Drug Discovery, Division for Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514
| | - Samarjit Patnaik
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Matthew B. Boxer
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD, 20850, USA
- Current address: Veralox Therapeutics Inc., 4539 Metropolitan Ct., Frederick, MD 21704
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15
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An acidic residue buried in the dimer interface of isocitrate dehydrogenase 1 (IDH1) helps regulate catalysis and pH sensitivity. Biochem J 2021; 477:2999-3018. [PMID: 32729927 DOI: 10.1042/bcj20200311] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 07/28/2020] [Accepted: 07/29/2020] [Indexed: 12/19/2022]
Abstract
Isocitrate dehydrogenase 1 (IDH1) catalyzes the reversible NADP+-dependent conversion of isocitrate to α-ketoglutarate (αKG) to provide critical cytosolic substrates and drive NADPH-dependent reactions like lipid biosynthesis and glutathione regeneration. In biochemical studies, the forward reaction is studied at neutral pH, while the reverse reaction is typically characterized in more acidic buffers. This led us to question whether IDH1 catalysis is pH-regulated, which would have functional implications under conditions that alter cellular pH, like apoptosis, hypoxia, cancer, and neurodegenerative diseases. Here, we show evidence of catalytic regulation of IDH1 by pH, identifying a trend of increasing kcat values for αKG production upon increasing pH in the buffers we tested. To understand the molecular determinants of IDH1 pH sensitivity, we used the pHinder algorithm to identify buried ionizable residues predicted to have shifted pKa values. Such residues can serve as pH sensors, with changes in protonation states leading to conformational changes that regulate catalysis. We identified an acidic residue buried at the IDH1 dimer interface, D273, with a predicted pKa value upshifted into the physiological range. D273 point mutations had decreased catalytic efficiency and, importantly, loss of pH-regulated catalysis. Based on these findings, we conclude that IDH1 activity is regulated, at least in part, by pH. We show this regulation is mediated by at least one buried acidic residue ∼12 Å from the IDH1 active site. By establishing mechanisms of regulation of this well-conserved enzyme, we highlight catalytic features that may be susceptible to pH changes caused by cell stress and disease.
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16
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Davies G, Semple H, McCandless M, Cairns J, Holdgate GA. High-Throughput Mechanism of Inhibition. SLAS DISCOVERY 2021; 26:248-256. [PMID: 33482076 DOI: 10.1177/2472555220983809] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Enzymes represent a significant proportion of the druggable genome and constitute a rich source of drug targets. Delivery of a successful program for developing a modulator of enzyme activity requires an understanding of the enzyme's mechanism and the mode of interaction of compounds. This allows an understanding of how physiological conditions in disease-relevant cells will affect inhibitor potency. As a result, there is increasing interest in evaluating hit compounds from high-throughput screens to determine their mode of interaction with the target. This work revisits the common inhibition modalities and illustrates the impact of substrate concentration relative to Km upon the pattern of changes in IC50 that are expected for increasing substrate concentration. It proposes a new, high-throughput approach for assessing mode of inhibition, incorporating analyses based on a minimal descriptive model, to deliver a workflow that allows rapid and earlier compound classification immediately after high-throughput screening.
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Affiliation(s)
- Gareth Davies
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park UK
| | - Hannah Semple
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park UK
| | - Megan McCandless
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park UK
| | - Jonathan Cairns
- Data Sciences and Quantitative Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
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17
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Wang Y, Tang S, Lai H, Jin R, Long X, Li N, Tang Y, Guo H, Yao X, Leung ELH. Discovery of Novel IDH1 Inhibitor Through Comparative Structure-Based Virtual Screening. Front Pharmacol 2020; 11:579768. [PMID: 33262701 PMCID: PMC7686577 DOI: 10.3389/fphar.2020.579768] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 09/14/2020] [Indexed: 12/30/2022] Open
Abstract
IDH1 mutations occur in about 20–30% of gliomas and are a promising target for the treatment of cancer. In the present study, the performance of aIDH1R132H was verified via glide-docking-based virtual screening. On the basis of the two crystal structures (5TQH and 6B0Z) with the best discriminating ability to identify IDH1R132H inhibitors from a decoy set, a docking-based virtual screening strategy was employed for identifying new IDH1R132H inhibitors. In the end, 57 structurally diverse compounds were reserved and evaluated through experimental tests, and 10 of them showed substantial activity in targeting IDH1R132H (IC50 < 50 μM). Molecular docking technology showed that L806-0255, V015-1671, and AQ-714/41674992 could bind to the binding pocket composed of hydrophobic residues. These findings indicate that L806-0255, V015-1671, and AQ-714/41674992 have the potential as lead compounds for the treatment of IDH1-mutated gliomas through further optimization.
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Affiliation(s)
- Yuwei Wang
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xi'an, China.,State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Shuai Tang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academic of Sciences, Shanghai, China
| | - Huanling Lai
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Ruyi Jin
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xi'an, China
| | - Xu Long
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xi'an, China
| | - Na Li
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xi'an, China
| | - Yuping Tang
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xi'an, China
| | - Hui Guo
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xi'an, China
| | - Xiaojun Yao
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Elaine Lai-Han Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
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18
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Isocitrate dehydrogenase variants in cancer - Cellular consequences and therapeutic opportunities. Curr Opin Chem Biol 2020; 57:122-134. [PMID: 32777735 PMCID: PMC7487778 DOI: 10.1016/j.cbpa.2020.06.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 06/25/2020] [Accepted: 06/30/2020] [Indexed: 12/20/2022]
Abstract
Abnormal metabolism is common in cancer cells and often correlates with mutations in genes encoding for enzymes involved in small-molecule metabolism. Isocitrate dehydrogenase 1 (IDH1) is the most frequently mutated metabolic gene in cancer. Cancer-associated substitutions in IDH1 and IDH2 impair wild-type production of 2-oxoglutarate and reduced nicotinamide adenine dinucleotide phosphate (NADPH) from isocitrate and oxidised nicotinamide adenine dinucleotide phosphate (NADP+ ), and substantially promote the IDH variant catalysed conversion of 2-oxoglutarate to d-2-hydroxyglutarate (d-2HG). Elevated d-2HG is a biomarker for some cancers, and inhibition of IDH1 and IDH2 variants is being pursued as a medicinal chemistry target. We provide an overview of the types of cancer-associated IDH variants, discuss some of the proposed consequences of altered metabolism as a result of elevated d-2HG, summarise therapeutic efforts targeting IDH variants and identify areas for future research.
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19
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Kanellopoulos AK, Mariano V, Spinazzi M, Woo YJ, McLean C, Pech U, Li KW, Armstrong JD, Giangrande A, Callaerts P, Smit AB, Abrahams BS, Fiala A, Achsel T, Bagni C. Aralar Sequesters GABA into Hyperactive Mitochondria, Causing Social Behavior Deficits. Cell 2020; 180:1178-1197.e20. [DOI: 10.1016/j.cell.2020.02.044] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 01/01/2020] [Accepted: 02/18/2020] [Indexed: 12/21/2022]
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20
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Chambers JM, Miller W, Quichocho G, Upadhye V, Matteo DA, Bobkov AA, Sohl CD, Schiffer JM. Water Networks and Correlated Motions in Mutant Isocitrate Dehydrogenase 1 (IDH1) Are Critical for Allosteric Inhibitor Binding and Activity. Biochemistry 2020; 59:479-490. [PMID: 31869219 DOI: 10.1021/acs.biochem.9b01023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Point mutations in human isocitrate dehydrogenase 1 (IDH1) can drive malignancies, including lower-grade gliomas and secondary glioblastomas, chondrosarcomas, and acute myeloid leukemias. These mutations, which usually affect residue R132, ablate the normal activity of catalyzing the NADP+-dependent oxidation of isocitrate to α-ketoglutarate (αKG) while also acquiring a neomorphic activity of reducing αKG to d-2-hydroxyglutarate (D2HG). Mutant IDH1 can be selectively therapeutically targeted due to structural differences that occur in the wild type (WT) versus mutant form of the enzyme, though the full mechanisms of this selectivity are still under investigation. Here we probe the mechanistic features of the neomorphic activity and selective small molecule inhibition through a new lens, employing WaterMap and molecular dynamics simulations. These tools identified a high-energy path of water molecules connecting the inhibitor binding site with the αKG and NADP+ binding sites in mutant IDH1. This water path aligns spatially with the α10 helix from WT IDH1 crystal structures. Mutating residues at the termini of this water path specifically disrupted inhibitor binding and/or D2HG production, revealing additional key residues to consider in optimizing druglike molecules against mutant IDH1. Taken together, our findings from molecular simulations and mutant enzyme kinetic assays provide insight into how disrupting water paths through enzyme active sites can impact not only inhibitor potency but also substrate recognition and activity.
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Affiliation(s)
- Jennifer M Chambers
- Schrödinger , 120 West 45th Street , New York , New York 10036 , United States
| | - Wade Miller
- Schrödinger , 222 Third Street, Suite 2230 , Cambridge , Massachusetts 02142 , United States
| | - Giovanni Quichocho
- Department of Chemistry and Biochemistry , San Diego State University , San Diego , California 92182 , United States
| | - Viraj Upadhye
- Department of Chemistry and Biochemistry , San Diego State University , San Diego , California 92182 , United States
| | - Diego Avellaneda Matteo
- Department of Chemistry and Biochemistry , San Diego State University , San Diego , California 92182 , United States
| | - Andrey A Bobkov
- Sanford Burnham Prebys Medical Discovery Institute , La Jolla , California 92037 , United States
| | - Christal D Sohl
- Department of Chemistry and Biochemistry , San Diego State University , San Diego , California 92182 , United States
| | - Jamie M Schiffer
- Janssen Research and Development , 3210 Merryfield Row , San Diego , California 92121 , United States
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21
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Verdura S, Cuyàs E, Lozano-Sánchez J, Bastidas-Velez C, Llorach-Parés L, Fernández-Arroyo S, Hernández-Aguilera A, Joven J, Nonell-Canals A, Bosch-Barrera J, Martin-Castillo B, Vellon L, Sanchez-Martinez M, Segura-Carretero A, Menendez JA. An olive oil phenolic is a new chemotype of mutant isocitrate dehydrogenase 1 (IDH1) inhibitors. Carcinogenesis 2019; 40:27-40. [PMID: 30428017 DOI: 10.1093/carcin/bgy159] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 10/09/2018] [Accepted: 11/13/2018] [Indexed: 01/02/2023] Open
Abstract
Mutations in the isocitrate dehydrogenase 1 (IDH1) gene confer an oncogenic gain-of-function activity that allows the conversion of α-ketoglutarate (α-KG) to the oncometabolite R-2-hydroxyglutarate (2HG). The accumulation of 2HG inhibits α-KG-dependent histone and DNA demethylases, thereby generating genome-wide hypermethylation phenotypes with cancer-initiating properties. Several chemotypes of mutant IDH1/2-targeted inhibitors have been reported, and some of them are under evaluation in clinical trials. However, the recognition of acquired resistance to such inhibitors within a few years of clinical use raises an urgent need to discover new mutant IDH1 antagonists. Here, we report that a naturally occurring phenolic compound in extra-virgin olive oil (EVOO) selectively inhibits the production of 2HG by neomorphic IDH1 mutations. In silico docking, molecular dynamics, including steered simulations, predicted the ability of the oleoside decarboxymethyl oleuropein aglycone (DOA) to preferentially occupy the allosteric pocket of mutant IDH1. DOA inhibited the enzymatic activity of recombinant mutant IDH1 (R132H) protein in the low micromolar range, whereas >10-fold higher concentrations were required to inhibit the activity of wild-type (WT) IDH1. DOA suppressed 2HG overproduction in engineered human cells expressing a heterozygous IDH1-R132H mutation. DOA restored the 2HG-suppressed activity of histone demethylases as it fully reversed the hypermethylation of H3K9me3 in IDH1-mutant cells. DOA epigenetically restored the expression of PD-L1, an immunosuppressive gene silenced in IDH1 mutant cells via 2HG-driven DNA hypermethylation. DOA selectively blocked colony formation of IDH1 mutant cells while sparing WT IDH1 isogenic counterparts. In sum, the EVOO-derived oleoside DOA is a new, naturally occurring chemotype of mutant IDH1 inhibitors.
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Affiliation(s)
- Sara Verdura
- Program Against Cancer Therapeutic Resistance (ProCURE), Metabolism and Cancer Group, Catalan Institute of Oncology, Girona, Spain.,Girona Biomedical Research Institute (IDIBGI), Edifici M2, Parc Hospitalari Martí i Julià, Salt, Girona, Spain
| | - Elisabet Cuyàs
- Program Against Cancer Therapeutic Resistance (ProCURE), Metabolism and Cancer Group, Catalan Institute of Oncology, Girona, Spain.,Girona Biomedical Research Institute (IDIBGI), Edifici M2, Parc Hospitalari Martí i Julià, Salt, Girona, Spain
| | - Jesús Lozano-Sánchez
- Department of Analytical Chemistry, Faculty of Sciences, University of Granada, Granada, Spain.,Research and Development Functional Food Centre (CIDAF), PTS Granada, Granada, Spain
| | - Cristian Bastidas-Velez
- Girona Biomedical Research Institute (IDIBGI), Edifici M2, Parc Hospitalari Martí i Julià, Salt, Girona, Spain
| | | | - Salvador Fernández-Arroyo
- Unitat de Recerca Biomèdica, Hospital Universitari de Sant Joan, IISPV, Rovira i Virgili University, Reus, Spain
| | - Anna Hernández-Aguilera
- Unitat de Recerca Biomèdica, Hospital Universitari de Sant Joan, IISPV, Rovira i Virgili University, Reus, Spain
| | - Jorge Joven
- Unitat de Recerca Biomèdica, Hospital Universitari de Sant Joan, IISPV, Rovira i Virgili University, Reus, Spain
| | | | - Joaquim Bosch-Barrera
- Girona Biomedical Research Institute (IDIBGI), Edifici M2, Parc Hospitalari Martí i Julià, Salt, Girona, Spain.,Department of Medical Sciences, Medical School, University of Girona, Girona, Spain.,Medical Oncology, Girona, Spain
| | - Begoña Martin-Castillo
- Girona Biomedical Research Institute (IDIBGI), Edifici M2, Parc Hospitalari Martí i Julià, Salt, Girona, Spain.,Unit of Clinical Research, Catalan Institute of Oncology, Girona, Spain
| | - Luciano Vellon
- Stem Cells Laboratory, Institute of Biology and Experimental Medicine (IBYME-CONICET), Buenos Aires, Argentina
| | | | - Antonio Segura-Carretero
- Department of Analytical Chemistry, Faculty of Sciences, University of Granada, Granada, Spain.,Research and Development Functional Food Centre (CIDAF), PTS Granada, Granada, Spain
| | - Javier A Menendez
- Program Against Cancer Therapeutic Resistance (ProCURE), Metabolism and Cancer Group, Catalan Institute of Oncology, Girona, Spain.,Girona Biomedical Research Institute (IDIBGI), Edifici M2, Parc Hospitalari Martí i Julià, Salt, Girona, Spain
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22
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Chen D, Xia S, Wang M, Lin R, Li Y, Mao H, Aguiar M, Famulare CA, Shih AH, Brennan CW, Gao X, Pan Y, Liu S, Fan J, Jin L, Song L, Zhou A, Mukherjee J, Pieper RO, Mishra A, Peng J, Arellano M, Blum WG, Lonial S, Boggon TJ, Levine RL, Chen J. Mutant and Wild-Type Isocitrate Dehydrogenase 1 Share Enhancing Mechanisms Involving Distinct Tyrosine Kinase Cascades in Cancer. Cancer Discov 2019; 9:756-777. [PMID: 30862724 DOI: 10.1158/2159-8290.cd-18-1040] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 02/10/2019] [Accepted: 03/07/2019] [Indexed: 01/03/2023]
Abstract
Isocitrate dehydrogenase 1 (IDH1) is important for reductive carboxylation in cancer cells, and the IDH1 R132H mutation plays a pathogenic role in cancers including acute myeloid leukemia (AML). However, the regulatory mechanisms modulating mutant and/or wild-type (WT) IDH1 function remain unknown. Here, we show that two groups of tyrosine kinases (TK) enhance the activation of mutant and WT IDH1 through preferential Y42 or Y391 phosphorylation. Mechanistically, Y42 phosphorylation occurs in IDH1 monomers, which promotes dimer formation with enhanced substrate (isocitrate or α-ketoglutarate) binding, whereas Y42-phosphorylated dimers show attenuated disruption to monomers. Y391 phosphorylation occurs in both monomeric and dimeric IDH1, which enhances cofactor (NADP+ or NADPH) binding. Diverse oncogenic TKs phosphorylate IDH1 WT at Y42 and activate Src to phosphorylate IDH1 at Y391, which contributes to reductive carboxylation and tumor growth, whereas FLT3 or the FLT3-ITD mutation activates JAK2 to enhance mutant IDH1 activity through phosphorylation of Y391 and Y42, respectively, in AML cells. SIGNIFICANCE: We demonstrated an intrinsic connection between oncogenic TKs and activation of WT and mutant IDH1, which involves distinct TK cascades in related cancers. In particular, these results provide an additional rationale supporting the combination of FLT3 and mutant IDH1 inhibitors as a promising clinical treatment of mutant IDH1-positive AML.See related commentary by Horton and Huntly, p. 699.This article is highlighted in the In This Issue feature, p. 681.
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Affiliation(s)
- Dong Chen
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia.,Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia
| | - Siyuan Xia
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia.,Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia
| | - Mei Wang
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia.,Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia.,Department of Pharmacy, Children's Hospital of Soochow University, Suzhou, China
| | - Ruiting Lin
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia.,Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia
| | - Yuancheng Li
- Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia.,Department of Radiology and Imaging Sciences, Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia
| | - Hui Mao
- Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia.,Department of Radiology and Imaging Sciences, Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia
| | - Mike Aguiar
- Cell Signaling Technology, Inc., Danvers, Massachusetts
| | | | - Alan H Shih
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Xue Gao
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia.,Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia
| | - Yaozhu Pan
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia.,General Hospital of Lanzhou Military Region, Lanzhou, China
| | - Shuangping Liu
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia.,Department of Pathology, Medical College, Dalian University, Dalian, China
| | - Jun Fan
- Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia.,Department of Radiation Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia
| | - Lingtao Jin
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia.,Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia
| | - Lina Song
- Department of Neurobiology, Morehouse School of Medicine, Atlanta, Georgia
| | - An Zhou
- Department of Neurobiology, Morehouse School of Medicine, Atlanta, Georgia
| | - Joydeep Mukherjee
- Department of Neurological Surgery, University of California, San Francisco, California
| | - Russell O Pieper
- Department of Neurological Surgery, University of California, San Francisco, California
| | - Ashutosh Mishra
- Department of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Junmin Peng
- Department of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Martha Arellano
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia.,Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia
| | - William G Blum
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia.,Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia
| | - Sagar Lonial
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia.,Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia
| | - Titus J Boggon
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut
| | - Ross L Levine
- Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Jing Chen
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia. .,Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia
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23
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Inhibitor potency varies widely among tumor-relevant human isocitrate dehydrogenase 1 mutants. Biochem J 2018; 475:3221-3238. [PMID: 30249606 DOI: 10.1042/bcj20180424] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 09/14/2018] [Accepted: 09/18/2018] [Indexed: 01/15/2023]
Abstract
Mutations in isocitrate dehydrogenase 1 (IDH1) drive most low-grade gliomas and secondary glioblastomas and many chondrosarcomas and acute myeloid leukemia cases. Most tumor-relevant IDH1 mutations are deficient in the normal oxidization of isocitrate to α-ketoglutarate (αKG), but gain the neomorphic activity of reducing αKG to D-2-hydroxyglutarate (D2HG), which drives tumorigenesis. We found previously that IDH1 mutants exhibit one of two reactivities: deficient αKG and moderate D2HG production (including commonly observed R132H and R132C) or moderate αKG and high D2HG production (R132Q). Here, we identify a third type of reactivity, deficient αKG and high D2HG production (R132L). We show that R132Q IDH1 has unique structural features and distinct reactivities towards mutant IDH1 inhibitors. Biochemical and cell-based assays demonstrate that while most tumor-relevant mutations were effectively inhibited by mutant IDH1 inhibitors, R132Q IDH1 had up to a 16 300-fold increase in IC50 versus R132H IDH1. Only compounds that inhibited wild-type (WT) IDH1 were effective against R132Q. This suggests that patients with a R132Q mutation may have a poor response to mutant IDH1 therapies. Molecular dynamics simulations revealed that near the NADP+/NADPH-binding site in R132Q IDH1, a pair of α-helices switches between conformations that are more wild-type-like or more mutant-like, highlighting mechanisms for preserved WT activity. Dihedral angle changes in the dimer interface and buried surface area charges highlight possible mechanisms for loss of inhibitor affinity against R132Q. This work provides a platform for predicting a patient's therapeutic response and identifies a potential resistance mutation that may arise upon treatment with mutant IDH inhibitors.
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24
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Chitneni SK, Yan H, Zalutsky MR. Synthesis and Evaluation of a 18F-Labeled Triazinediamine Analogue for Imaging Mutant IDH1 Expression in Gliomas by PET. ACS Med Chem Lett 2018; 9:606-611. [PMID: 30034587 DOI: 10.1021/acsmedchemlett.7b00478] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 05/01/2018] [Indexed: 11/28/2022] Open
Abstract
Mutations in the isocitrate dehydrogenase gene 1 (IDH1) are common in gliomas. Studies suggest that IDH1 mutations are early events in glioma formation and are important drivers of malignant progression. Herein, we report the synthesis and evaluation of a 18F-labeled triazinediamine analogue, [18F]1, as a candidate radiotracer for noninvasive imaging of IDH1 mutations in gliomas by positron emission tomography (PET). In vitro studies revealed good binding inhibition potency and binding affinity for [18F]1 in IDH1 mutant glioma cell lines, with a half-maximal inhibitory concentration value (IC50) of 54 nM and an equilibrium dissociation constant (Kd) of 40 nM. In vivo studies using mutant IDH1 glioma xenografts showed good tumor uptake of [18F]1 and specific inhibition by the unlabeled 1, but also elevated radioactivity uptake in the bone, suggesting significant defluorination. The results support further optimization of the triazinediamine scaffold to develop a more stable and potent 18F-labeled analogue for PET imaging of IDH1 mutations in gliomas.
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Affiliation(s)
- Satish K. Chitneni
- Department of Radiology and ‡Department of Pathology, Duke University Medical Center, Durham, North Carolina 27710, United States
| | | | - Michael R. Zalutsky
- Department of Radiology and ‡Department of Pathology, Duke University Medical Center, Durham, North Carolina 27710, United States
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25
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Abstract
T-cell lymphomas (TCL) are a rare, heterogeneous group of non-Hodgkin lymphomas associated with very poor prognosis with standard cytotoxic chemotherapy. Epigenetic-based therapy, such as with histone deacetylase inhibitors, was initially discovered to be efficacious in TCL. In recent years, our understanding of the mechanisms driving T-cell lymphomagenesis has validated the use of epigenetic-based drugs and has also led to the development of novel agents with promising efficacy in pre-clinical and early clinical trials. These new treatments play upon the prominent existence of epigenetic and immune dysfunction present in T-cell lymphomas. With these advances, novel therapeutic regimens combining traditional chemotherapy as well as epigenetic and/or immunotherapy serve as promising future treatment options for TCL. In this review, we discuss the traditional methods of treatment for TCL as well as novel agents and combinations that will likely change the treatment paradigms resulting in better clinical outcomes.
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26
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A widely-applicable high-throughput cellular thermal shift assay (CETSA) using split Nano Luciferase. Sci Rep 2018; 8:9472. [PMID: 29930256 PMCID: PMC6013488 DOI: 10.1038/s41598-018-27834-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 06/08/2018] [Indexed: 11/15/2022] Open
Abstract
Assessment of the interactions between a drug and its protein target in a physiologically relevant cellular environment constitutes a major challenge in the pre-clinical drug discovery space. The Cellular Thermal Shift Assay (CETSA) enables such an assessment by quantifying the changes in the thermal stability of proteins upon ligand binding in intact cells. Here, we present the development and validation of a homogeneous, standardized, target-independent, and high-throughput (384- and 1536-well formats) CETSA platform that uses a split Nano Luciferase approach (SplitLuc CETSA). The broad applicability of the assay was demonstrated for diverse targets, and its performance was compared with independent biochemical and cell-based readouts using a set of well-characterized inhibitors. Moreover, we investigated the utility of the platform as a primary assay for high-throughput screening. The SplitLuc CETSA presented here enables target engagement studies for medium and high-throughput applications. Additionally, it provides a rapid assay development and screening platform for targets where phenotypic or other cell-based assays are not readily available.
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27
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Ma T, Zou F, Pusch S, Xu Y, von Deimling A, Zha X. Inhibitors of Mutant Isocitrate Dehydrogenases 1 and 2 (mIDH1/2): An Update and Perspective. J Med Chem 2018; 61:8981-9003. [DOI: 10.1021/acs.jmedchem.8b00159] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Tianfang Ma
- Department of Pharmaceutical Engineering and Department of Biochemical Engineering, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, P. R. China
- Department of Medicinal Chemistry, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, P. R. China
| | - Fangxia Zou
- Department of Pharmaceutical Engineering and Department of Biochemical Engineering, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, P. R. China
- Department of Medicinal Chemistry, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, P. R. China
| | - Stefan Pusch
- German Consortium
of Translational Cancer Research (DKTK), Clinical Cooperation Unit
Neuropathology, German Cancer Research Center (DKFZ), INF 280, Heidelberg D-69120, Germany
- Department of Neuropathology, Institute of Pathology, Ruprecht-Karls-Universität Heidelberg, INF 224, Heidelberg D-69120, Germany
| | - Yungen Xu
- Department of Medicinal Chemistry, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, P. R. China
| | - Andreas von Deimling
- German Consortium
of Translational Cancer Research (DKTK), Clinical Cooperation Unit
Neuropathology, German Cancer Research Center (DKFZ), INF 280, Heidelberg D-69120, Germany
- Department of Neuropathology, Institute of Pathology, Ruprecht-Karls-Universität Heidelberg, INF 224, Heidelberg D-69120, Germany
| | - Xiaoming Zha
- Department of Pharmaceutical Engineering and Department of Biochemical Engineering, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, P. R. China
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28
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Wang F, Li Z, Zhang T, Yan G, Hu M, Zhao L, Zhao Y, Chen Y. Discovery of a novel class of pyridine derivatives that selectively inhibits mutant isocitrate dehydrogenase 2. Chem Biol Drug Des 2018; 91:1087-1093. [PMID: 29120536 DOI: 10.1111/cbdd.13139] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 08/12/2017] [Accepted: 09/23/2017] [Indexed: 02/05/2023]
Affiliation(s)
- Fangying Wang
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center of Biotherapy; West China Hospital; West China Medical School of Sichuan University; Chengdu China
| | - Zhuoling Li
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center of Biotherapy; West China Hospital; West China Medical School of Sichuan University; Chengdu China
| | - Tao Zhang
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center of Biotherapy; West China Hospital; West China Medical School of Sichuan University; Chengdu China
| | - Guoyi Yan
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center of Biotherapy; West China Hospital; West China Medical School of Sichuan University; Chengdu China
| | - Mingxing Hu
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center of Biotherapy; West China Hospital; West China Medical School of Sichuan University; Chengdu China
| | - Lifeng Zhao
- Sichuan Industrial Institute of Antibiotics; Chengdu University; Chengdu China
| | - Yinglan Zhao
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center of Biotherapy; West China Hospital; West China Medical School of Sichuan University; Chengdu China
| | - Yuanwei Chen
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center of Biotherapy; West China Hospital; West China Medical School of Sichuan University; Chengdu China
- Hinova Pharmaceuticals Inc.; Chengdu China
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29
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Beyond Brooding on Oncometabolic Havoc in IDH-Mutant Gliomas and AML: Current and Future Therapeutic Strategies. Cancers (Basel) 2018; 10:cancers10020049. [PMID: 29439493 PMCID: PMC5836081 DOI: 10.3390/cancers10020049] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 02/03/2018] [Accepted: 02/06/2018] [Indexed: 12/21/2022] Open
Abstract
Isocitrate dehydrogenases 1 and 2 (IDH1,2), the key Krebs cycle enzymes that generate NADPH reducing equivalents, undergo heterozygous mutations in >70% of low- to mid-grade gliomas and ~20% of acute myeloid leukemias (AMLs) and gain an unusual new activity of reducing the α-ketoglutarate (α-KG) to D-2 hydroxyglutarate (D-2HG) in a NADPH-consuming reaction. The oncometabolite D-2HG, which accumulates >35 mM, is widely accepted to drive a progressive oncogenesis besides exacerbating the already increased oxidative stress in these cancers. More importantly, D-2HG competes with α-KG and inhibits a large number of α-KG-dependent dioxygenases such as TET (Ten-eleven translocation), JmjC domain-containing KDMs (histone lysine demethylases), and the ALKBH DNA repair proteins that ultimately lead to hypermethylation of the CpG islands in the genome. The resulting CpG Island Methylator Phenotype (CIMP) accounts for major gene expression changes including the silencing of the MGMT (O6-methylguanine DNA methyltransferase) repair protein in gliomas. Glioma patients with IDH1 mutations also show better therapeutic responses and longer survival, the reasons for which are yet unclear. There has been a great surge in drug discovery for curtailing the mutant IDH activities, and arresting tumor proliferation; however, given the unique and chronic metabolic effects of D-2HG, the promise of these compounds for glioma treatment is uncertain. This comprehensive review discusses the biology, current drug design and opportunities for improved therapies through exploitable synthetic lethality pathways, and an intriguing oncometabolite-inspired strategy for primary glioblastoma.
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30
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Ye D, Guan KL, Xiong Y. Metabolism, Activity, and Targeting of D- and L-2-Hydroxyglutarates. Trends Cancer 2018; 4:151-165. [PMID: 29458964 PMCID: PMC5884165 DOI: 10.1016/j.trecan.2017.12.005] [Citation(s) in RCA: 148] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 12/11/2017] [Accepted: 12/12/2017] [Indexed: 12/30/2022]
Abstract
Isocitrate dehydrogenases (IDH1/2) are frequently mutated in multiple types of human cancer, resulting in neomorphic enzymes that convert α-ketoglutarate (α-KG) to 2-hydroxyglutarate (2-HG). The current view on the mechanism of IDH mutation holds that 2-HG acts as an antagonist of α-KG to competitively inhibit the activity of α-KG-dependent dioxygenases, including those involved in histone and DNA demethylation. Recent studies have implicated 2-HG in activities beyond epigenetic modification. Multiple enzymes have been discovered that lack mutations but that can nevertheless produce 2-HG promiscuously under hypoxic or acidic conditions. Therapies are being developed to treat IDH-mutant cancers by targeting either the mutant IDH enzymes directly or the pathways sensitized by 2-HG.
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Affiliation(s)
- Dan Ye
- Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of General Surgery, Huashan Hospital, Fudan University, Shanghai 200040, China.
| | - Kun-Liang Guan
- Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of Pharmacology and Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yue Xiong
- Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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31
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Synthesis and evaluation of radiolabeled AGI-5198 analogues as candidate radiotracers for imaging mutant IDH1 expression in tumors. Bioorg Med Chem Lett 2018; 28:694-699. [PMID: 29366652 DOI: 10.1016/j.bmcl.2018.01.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 01/09/2018] [Accepted: 01/11/2018] [Indexed: 11/23/2022]
Abstract
Mutations in the metabolic enzyme isocitrate dehydrogenase 1 (IDH1) are commonly found in gliomas. AGI-5198, a potent and selective inhibitor of the mutant IDH1 enzyme, was radiolabeled with radioiodine and fluorine-18. These radiotracers were evaluated as potential probes for imaging mutant IDH1 expression in tumors with positron emission tomography (PET). Radioiodination of AGI-5198 was achieved using a tin precursor in 79 ± 6% yield (n = 9), and 18F-labeling was accomplished by the Ugi reaction in a decay-corrected radiochemical yield of 2.6 ± 1.6% (n = 5). The inhibitory potency of the analogous nonradioactive compounds against mutant IDH1 (IDH1-R132H) was determined in enzymatic assays. Cell uptake studies using radiolabeled AGI-5198 analogues revealed somewhat higher uptake in IDH1-mutated cells than that in wild-type IDH1 cells. The radiolabeled compounds displayed favorable tissue distribution characteristics in vivo, and good initial uptake in IDH1-mutated tumor xenografts; however, tumor uptake decreased with time. Radioiodinated AGI-5198 exhibited higher tumor-to-background ratios compared with 18F-labeled AGI-5198; unfortunately, similar results were observed in wild-type IDH1 tumor xenografts as well, indicating lack of selectivity for mutant IDH1 for this tracer. These results suggest that AGI-5198 analogues are not a promising platform for radiotracer development. Nonetheless, insights gained from this study may help in design and optimization of novel chemical scaffolds for developing radiotracers for imaging the mutant IDH1 enzyme.
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32
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Coussens NP, Braisted JC, Peryea T, Sittampalam GS, Simeonov A, Hall MD. Small-Molecule Screens: A Gateway to Cancer Therapeutic Agents with Case Studies of Food and Drug Administration-Approved Drugs. Pharmacol Rev 2017; 69:479-496. [PMID: 28931623 DOI: 10.1124/pr.117.013755] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
High-throughput screening (HTS) of small-molecule libraries accelerates the discovery of chemical leads to serve as starting points for probe or therapeutic development. With this approach, thousands of unique small molecules, representing a diverse chemical space, can be rapidly evaluated by biologically and physiologically relevant assays. The origins of numerous United States Food and Drug Administration-approved cancer drugs are linked to HTS, which emphasizes the value in this methodology. The National Institutes of Health Molecular Libraries Program made HTS accessible to the public sector, enabling the development of chemical probes and drug-repurposing initiatives. In this work, the impact of HTS in the field of oncology is considered among both private and public sectors. Examples are given for the discovery and development of approved cancer drugs. The importance of target validation is discussed, and common assay approaches for screening are reviewed. A rigorous examination of the PubChem database demonstrates that public screening centers are contributing to early-stage drug discovery in oncology by focusing on new targets and developing chemical probes. Several case studies highlight the value of different screening strategies and the potential for drug repurposing.
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Affiliation(s)
- Nathan P Coussens
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland
| | - John C Braisted
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland
| | - Tyler Peryea
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland
| | - G Sitta Sittampalam
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland
| | - Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland
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Holdgate GA, Meek TD, Grimley RL. Mechanistic enzymology in drug discovery: a fresh perspective. Nat Rev Drug Discov 2017; 17:115-132. [PMID: 29192286 DOI: 10.1038/nrd.2017.219] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Given the therapeutic and commercial success of small-molecule enzyme inhibitors, as exemplified by kinase inhibitors in oncology, a major focus of current drug-discovery and development efforts is on enzyme targets. Understanding the course of an enzyme-catalysed reaction can help to conceptualize different types of inhibitor and to inform the design of screens to identify desired mechanisms. Exploiting this information allows the thorough evaluation of diverse compounds, providing the knowledge required to efficiently optimize leads towards differentiated candidate drugs. This review highlights the rationale for conducting high-quality mechanistic enzymology studies and considers the added value in combining such studies with orthogonal biophysical methods.
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Affiliation(s)
- Geoffrey A Holdgate
- Discovery Sciences, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, Milton Road, Cambridge, CB4 0WG, UK
| | - Thomas D Meek
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, USA
| | - Rachel L Grimley
- Discovery Sciences, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, Milton Road, Cambridge, CB4 0WG, UK
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Assessing inhibitors of mutant isocitrate dehydrogenase using a suite of pre-clinical discovery assays. Sci Rep 2017; 7:12758. [PMID: 28986582 PMCID: PMC5630632 DOI: 10.1038/s41598-017-12630-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 09/08/2017] [Indexed: 12/15/2022] Open
Abstract
Isocitrate dehydrogenase 1 and 2 (IDH1 and IDH2) are key metabolic enzymes that are mutated in a variety of cancers to confer a gain-of-function activity resulting in the accumulation of an oncometabolite, D-2-hydroxyglutarate (2-HG). Accumulation of 2-HG can result in epigenetic dysregulation and a block in cellular differentiation, suggesting these mutations play a role in neoplasia. Based on its potential as a cancer target, a number of small molecule inhibitors have been developed to specifically inhibit mutant forms of IDH (mIDH1 and mIDH2). We present a comprehensive suite of in vitro preclinical drug development assays that can be used as a tool-box to identify lead compounds for mIDH drug discovery programs, as well as what we believe is the most comprehensive publically available dataset on the top mIDH inhibitors. This involved biochemical, cell-based, and tier-one ADME techniques.
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M Gagné L, Boulay K, Topisirovic I, Huot MÉ, Mallette FA. Oncogenic Activities of IDH1/2 Mutations: From Epigenetics to Cellular Signaling. Trends Cell Biol 2017; 27:738-752. [PMID: 28711227 DOI: 10.1016/j.tcb.2017.06.002] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 06/11/2017] [Accepted: 06/13/2017] [Indexed: 01/03/2023]
Abstract
Gliomas and leukemias remain highly refractory to treatment, thus highlighting the need for new and improved therapeutic strategies. Mutations in genes encoding enzymes involved in the tricarboxylic acid (TCA) cycle, such as the isocitrate dehydrogenases 1 and 2 (IDH1/2), are frequently encountered in astrocytomas and secondary glioblastomas, as well as in acute myeloid leukemias; however, the precise molecular mechanisms by which these mutations promote tumorigenesis remain to be fully characterized. Gain-of-function mutations in IDH1/2 have been shown to stimulate production of the oncogenic metabolite R-2-hydroxyglutarate (R-2HG), which inhibits α-ketoglutarate (αKG)-dependent enzymes. We review recent advances on the elucidation of oncogenic functions of IDH1/2 mutations, and of the associated oncometabolite R-2HG, which link altered metabolism of cancer cells to epigenetics, RNA methylation, cellular signaling, hypoxic response, and DNA repair.
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Affiliation(s)
- Laurence M Gagné
- Centre de Recherche sur le Cancer de l'Université Laval, Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Université Laval Québec, QC, G1V 0A6, Canada; Centre Hospitalier Universitaire (CHU) de Québec - Axe Oncologie (Hôtel-Dieu de Québec), Québec City, QC, G1R 3S3, Canada
| | - Karine Boulay
- Département de Biochimie et Médecine Moléculaire, CP 6128, Succursale Centre-Ville, Montréal, QC, H3C 3J7, Canada; Chromatin Structure and Cellular Senescence Research Unit, Maisonneuve-Rosemont Hospital Research Centre, Montréal, QC, H1T 2M4, Canada; Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC, H3T 1E2, Canada
| | - Ivan Topisirovic
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC, H3T 1E2, Canada; Gerald Bronfman Department of Oncology, and Departments of Experimental Medicine, and Biochemistry, McGill University, Montreal, QC, H4A 3T2, Canada
| | - Marc-Étienne Huot
- Centre de Recherche sur le Cancer de l'Université Laval, Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Université Laval Québec, QC, G1V 0A6, Canada; Centre Hospitalier Universitaire (CHU) de Québec - Axe Oncologie (Hôtel-Dieu de Québec), Québec City, QC, G1R 3S3, Canada.
| | - Frédérick A Mallette
- Département de Biochimie et Médecine Moléculaire, CP 6128, Succursale Centre-Ville, Montréal, QC, H3C 3J7, Canada; Chromatin Structure and Cellular Senescence Research Unit, Maisonneuve-Rosemont Hospital Research Centre, Montréal, QC, H1T 2M4, Canada; Département de Médecine, Université de Montréal, CP 6128, Succursale Centre-Ville, Montréal, QC, H3C 3J7, Canada.
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Dang L, Su SSM. Isocitrate Dehydrogenase Mutation and (R)-2-Hydroxyglutarate: From Basic Discovery to Therapeutics Development. Annu Rev Biochem 2017; 86:305-331. [DOI: 10.1146/annurev-biochem-061516-044732] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Lenny Dang
- Agios Pharmaceuticals Inc., Cambridge, Massachusetts 02139;,
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Pan-mutant-IDH1 inhibitor BAY1436032 is highly effective against human IDH1 mutant acute myeloid leukemia in vivo. Leukemia 2017; 31:2020-2028. [PMID: 28232670 PMCID: PMC5629366 DOI: 10.1038/leu.2017.46] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 01/07/2017] [Accepted: 01/13/2017] [Indexed: 01/15/2023]
Abstract
Neomorphic mutations in isocitrate dehydrogenase 1 (IDH1) are frequently found in several human cancer types including acute myeloid leukemia (AML) and lead to the production of high levels of the oncometabolite (R)-2-hydroxyglutarate (R-2HG). Here we report the characterization of BAY1436032, a novel pan-mutant IDH1 inhibitor, both in vitro and in vivo. BAY1436032 specifically inhibits R-2HG production and colony growth, and induces myeloid differentiation of AML cells carrying IDH1R132H, IDH1R132C, IDH1R132G, IDH1R132L and IDH1R132S mutations. In addition, the compound impacts on DNA methylation and attenuates histone hypermethylation. Oral administration of BAY1436032 led to leukemic blast clearance, myeloid differentiation, depletion of leukemic stem cells and prolonged survival in two independent patient-derived xenograft IDH1 mutant AML mouse models. Together, BAY1436032 is highly effective against all major types of IDH1 mutant AML.
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Interplay between epigenetics and metabolism in oncogenesis: mechanisms and therapeutic approaches. Oncogene 2017; 36:3359-3374. [PMID: 28092669 PMCID: PMC5485177 DOI: 10.1038/onc.2016.485] [Citation(s) in RCA: 181] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 11/07/2016] [Accepted: 11/07/2016] [Indexed: 02/06/2023]
Abstract
Epigenetic and metabolic alterations in cancer cells are highly intertwined. Oncogene-driven metabolic rewiring modifies the epigenetic landscape via modulating the activities of DNA and histone modification enzymes at the metabolite level. Conversely, epigenetic mechanisms regulate the expression of metabolic genes, thereby altering the metabolome. Epigenetic-metabolomic interplay has a critical role in tumourigenesis by coordinately sustaining cell proliferation, metastasis and pluripotency. Understanding the link between epigenetics and metabolism could unravel novel molecular targets, whose intervention may lead to improvements in cancer treatment. In this review, we summarized the recent discoveries linking epigenetics and metabolism and their underlying roles in tumorigenesis; and highlighted the promising molecular targets, with an update on the development of small molecule or biologic inhibitors against these abnormalities in cancer.
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He Y, Zheng M, Li Q, Hu Z, Zhu H, Liu J, Wang J, Xue Y, Li H, Zhang Y. Asperspiropene A, a novel fungal metabolite as an inhibitor of cancer-associated mutant isocitrate dehydrogenase 1. Org Chem Front 2017. [DOI: 10.1039/c6qo00847j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In silico screening of an in-house natural product database and confirmatory bioassays led to the identification of asperspiropene A (1) as an inhibitor of cancer-associated mutant IDH1.
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40
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Jones S, Ahmet J, Ayton K, Ball M, Cockerill M, Fairweather E, Hamilton N, Harper P, Hitchin J, Jordan A, Levy C, Lopez R, McKenzie E, Packer M, Plant D, Simpson I, Simpson P, Sinclair I, Somervaille TCP, Small H, Spencer GJ, Thomson G, Tonge M, Waddell I, Walsh J, Waszkowycz B, Wigglesworth M, Wiseman DH, Ogilvie D. Discovery and Optimization of Allosteric Inhibitors of Mutant Isocitrate Dehydrogenase 1 (R132H IDH1) Displaying Activity in Human Acute Myeloid Leukemia Cells. J Med Chem 2016; 59:11120-11137. [PMID: 28002956 DOI: 10.1021/acs.jmedchem.6b01320] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
A collaborative high throughput screen of 1.35 million compounds against mutant (R132H) isocitrate dehydrogenase IDH1 led to the identification of a novel series of inhibitors. Elucidation of the bound ligand crystal structure showed that the inhibitors exhibited a novel binding mode in a previously identified allosteric site of IDH1 (R132H). This information guided the optimization of the series yielding submicromolar enzyme inhibitors with promising cellular activity. Encouragingly, one compound from this series was found to induce myeloid differentiation in primary human IDH1 R132H AML cells in vitro.
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Affiliation(s)
| | | | | | - Matthew Ball
- Manchester Institute of Biotechnology, University of Manchester , Princess Street, Manchester, M1 7DN, U.K
| | | | | | | | | | | | | | - Colin Levy
- Manchester Institute of Biotechnology, University of Manchester , Princess Street, Manchester, M1 7DN, U.K
| | - Ruth Lopez
- Manchester Institute of Biotechnology, University of Manchester , Princess Street, Manchester, M1 7DN, U.K
| | - Eddie McKenzie
- Manchester Institute of Biotechnology, University of Manchester , Princess Street, Manchester, M1 7DN, U.K
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Sullivan LB, Gui DY, Vander Heiden MG. Altered metabolite levels in cancer: implications for tumour biology and cancer therapy. Nat Rev Cancer 2016; 16:680-693. [PMID: 27658530 DOI: 10.1038/nrc.2016.85] [Citation(s) in RCA: 266] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Altered cell metabolism is a characteristic feature of many cancers. Aside from well-described changes in nutrient consumption and waste excretion, altered cancer cell metabolism also results in changes to intracellular metabolite concentrations. Increased levels of metabolites that result directly from genetic mutations and cancer-associated modifications in protein expression can promote cancer initiation and progression. Changes in the levels of specific metabolites, such as 2-hydroxyglutarate, fumarate, succinate, aspartate and reactive oxygen species, can result in altered cell signalling, enzyme activity and/or metabolic flux. In this Review, we discuss the mechanisms that lead to changes in metabolite concentrations in cancer cells, the consequences of these changes for the cells and how they might be exploited to improve cancer therapy.
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Affiliation(s)
- Lucas B Sullivan
- The Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Dan Y Gui
- The Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Matthew G Vander Heiden
- The Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
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42
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Saha SK, Gordan JD, Kleinstiver BP, Vu P, Najem MS, Yeo JC, Shi L, Kato Y, Levin RS, Webber JT, Damon LJ, Egan RK, Greninger P, McDermott U, Garnett MJ, Jenkins RL, Rieger-Christ KM, Sullivan TB, Hezel AF, Liss AS, Mizukami Y, Goyal L, Ferrone CR, Zhu AX, Joung JK, Shokat KM, Benes CH, Bardeesy N. Isocitrate Dehydrogenase Mutations Confer Dasatinib Hypersensitivity and SRC Dependence in Intrahepatic Cholangiocarcinoma. Cancer Discov 2016; 6:727-39. [PMID: 27231123 DOI: 10.1158/2159-8290.cd-15-1442] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 05/16/2016] [Indexed: 01/06/2023]
Abstract
UNLABELLED Intrahepatic cholangiocarcinoma (ICC) is an aggressive liver bile duct malignancy exhibiting frequent isocitrate dehydrogenase (IDH1/IDH2) mutations. Through a high-throughput drug screen of a large panel of cancer cell lines, including 17 biliary tract cancers, we found that IDH mutant (IDHm) ICC cells demonstrate a striking response to the multikinase inhibitor dasatinib, with the highest sensitivity among 682 solid tumor cell lines. Using unbiased proteomics to capture the activated kinome and CRISPR/Cas9-based genome editing to introduce dasatinib-resistant "gatekeeper" mutant kinases, we identified SRC as a critical dasatinib target in IDHm ICC. Importantly, dasatinib-treated IDHm xenografts exhibited pronounced apoptosis and tumor regression. Our results show that IDHm ICC cells have a unique dependency on SRC and suggest that dasatinib may have therapeutic benefit against IDHm ICC. Moreover, these proteomic and genome-editing strategies provide a systematic and broadly applicable approach to define targets of kinase inhibitors underlying drug responsiveness. SIGNIFICANCE IDH mutations define a distinct subtype of ICC, a malignancy that is largely refractory to current therapies. Our work demonstrates that IDHm ICC cells are hypersensitive to dasatinib and critically dependent on SRC activity for survival and proliferation, pointing to new therapeutic strategies against these cancers. Cancer Discov; 6(7); 727-39. ©2016 AACR.This article is highlighted in the In This Issue feature, p. 681.
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Affiliation(s)
- Supriya K Saha
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - John D Gordan
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Benjamin P Kleinstiver
- Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts. Department of Pathology, Harvard Medical School, Boston, Massachusetts
| | - Phuong Vu
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Mortada S Najem
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Jia-Chi Yeo
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Lei Shi
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Yasutaka Kato
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Rebecca S Levin
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California
| | - James T Webber
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Leah J Damon
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Regina K Egan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Patricia Greninger
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | | | | | - Roger L Jenkins
- Department of Transplantation, Lahey Hospital and Medical Center, Burlington, Massachusetts
| | - Kimberly M Rieger-Christ
- Department of Translational Research, Lahey Hospital and Medical Center, Burlington, Massachusetts
| | - Travis B Sullivan
- Department of Translational Research, Lahey Hospital and Medical Center, Burlington, Massachusetts
| | - Aram F Hezel
- University of Rochester School of Medicine, Rochester, New York
| | - Andrew S Liss
- Department of Surgery and the Andrew L. Warshaw, MD, Institute for Pancreatic Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Yusuke Mizukami
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts. Center for Clinical and Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Hokkaido, Japan
| | - Lipika Goyal
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Cristina R Ferrone
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Andrew X Zhu
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - J Keith Joung
- Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts. Department of Pathology, Harvard Medical School, Boston, Massachusetts
| | - Kevan M Shokat
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California. Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California
| | - Cyril H Benes
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts.
| | - Nabeel Bardeesy
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts.
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Merk A, Bartesaghi A, Banerjee S, Falconieri V, Rao P, Davis MI, Pragani R, Boxer MB, Earl LA, Milne JLS, Subramaniam S. Breaking Cryo-EM Resolution Barriers to Facilitate Drug Discovery. Cell 2016; 165:1698-1707. [PMID: 27238019 DOI: 10.1016/j.cell.2016.05.040] [Citation(s) in RCA: 331] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 05/09/2016] [Accepted: 05/09/2016] [Indexed: 11/17/2022]
Abstract
Recent advances in single-particle cryoelecton microscopy (cryo-EM) are enabling generation of numerous near-atomic resolution structures for well-ordered protein complexes with sizes ≥ ∼200 kDa. Whether cryo-EM methods are equally useful for high-resolution structural analysis of smaller, dynamic protein complexes such as those involved in cellular metabolism remains an important question. Here, we present 3.8 Å resolution cryo-EM structures of the cancer target isocitrate dehydrogenase (93 kDa) and identify the nature of conformational changes induced by binding of the allosteric small-molecule inhibitor ML309. We also report 2.8-Å- and 1.8-Å-resolution structures of lactate dehydrogenase (145 kDa) and glutamate dehydrogenase (334 kDa), respectively. With these results, two perceived barriers in single-particle cryo-EM are overcome: (1) crossing 2 Å resolution and (2) obtaining structures of proteins with sizes < 100 kDa, demonstrating that cryo-EM can be used to investigate a broad spectrum of drug-target interactions and dynamic conformational states.
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Affiliation(s)
- Alan Merk
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Alberto Bartesaghi
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Soojay Banerjee
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Veronica Falconieri
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Prashant Rao
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Mindy I Davis
- National Center for Advancing Translational Sciences, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Rajan Pragani
- National Center for Advancing Translational Sciences, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Matthew B Boxer
- National Center for Advancing Translational Sciences, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Lesley A Earl
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Jacqueline L S Milne
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Sriram Subramaniam
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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Chitneni SK, Reitman ZJ, Gooden DM, Yan H, Zalutsky MR. Radiolabeled inhibitors as probes for imaging mutant IDH1 expression in gliomas: Synthesis and preliminary evaluation of labeled butyl-phenyl sulfonamide analogs. Eur J Med Chem 2016; 119:218-30. [PMID: 27163884 DOI: 10.1016/j.ejmech.2016.04.066] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 04/25/2016] [Accepted: 04/26/2016] [Indexed: 11/27/2022]
Abstract
INTRODUCTION Malignant gliomas frequently harbor mutations in the isocitrate dehydrogenase 1 (IDH1) gene. Studies suggest that IDH mutation contributes to tumor pathogenesis through mechanisms that are mediated by the neomorphic metabolite of the mutant IDH1 enzyme, 2-hydroxyglutarate (2-HG). The aim of this work was to synthesize and evaluate radiolabeled compounds that bind to the mutant IDH1 enzyme with the goal of enabling noninvasive imaging of mutant IDH1 expression in gliomas by positron emission tomography (PET). METHODS A small library of nonradioactive analogs were designed and synthesized based on the chemical structure of reported butyl-phenyl sulfonamide inhibitors of mutant IDH1. Enzyme inhibition assays were conducted using purified mutant IDH1 enzyme, IDH1-R132H, to determine the IC50 and the maximal inhibitory efficiency of the synthesized compounds. Selected compounds, 1 and 4, were labeled with radioiodine ((125)I) and/or (18)F using bromo- and phenol precursors, respectively. In vivo behavior of the labeled inhibitors was studied by conducting tissue distribution studies with [(125)I]1 in normal mice. Cell uptake studies were conducted using an isogenic astrocytoma cell line that carried a native IDH1-R132H mutation to evaluate the potential uptake of the labeled inhibitors in IDH1-mutated tumor cells. RESULTS Enzyme inhibition assays showed good inhibitory potency for compounds that have iodine or a fluoroethoxy substituent at the ortho position of the phenyl ring in compounds 1 and 4 with IC50 values of 1.7 μM and 2.3 μM, respectively. Compounds 1 and 4 inhibited mutant IDH1 activity and decreased the production of 2-HG in an IDH1-mutated astrocytoma cell line. Radiolabeling of 1 and 4 was achieved with an average radiochemical yield of 56.6 ± 20.1% for [(125)I]1 (n = 4) and 67.5 ± 6.6% for [(18)F]4 (n = 3). [(125)I]1 exhibited favorable biodistribution characteristics in normal mice, with rapid clearance from the blood and elimination via the hepatobiliary system by 4 h after injection. The uptake of [(125)I]1 in tumor cells positive for IDH1-R132H was significantly higher compared to isogenic WT-IDH1 controls, with a maximal uptake ratio of 1.67 at 3 h post injection. Co-incubation of the labeled inhibitors with the corresponding nonradioactive analogs, and decreasing the normal concentrations of FBS (10%) in the incubation media substantially increased the uptake of the labeled inhibitors in both the IDH1-mutant and WT-IDH1 tumor cell lines, suggesting significant non-specific binding of the synthesized labeled butyl-phenyl sulfonamide inhibitors. CONCLUSIONS These data demonstrate the feasibility of developing radiolabeled probes for the mutant IDH1 enzyme based on enzyme inhibitors. Further optimization of the labeled inhibitors by modifying the chemical structure to decrease the lipophilicity and to increase potency may yield compounds with improved characteristics as probes for imaging mutant IDH1 expression in tumors.
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Affiliation(s)
- Satish K Chitneni
- Department of Radiology, Duke University Medical Center, Durham, NC 27710, USA.
| | - Zachary J Reitman
- Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA
| | - David M Gooden
- Small Molecule Synthesis Facility, Duke University, Durham, NC 27708, USA
| | - Hai Yan
- Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA
| | - Michael R Zalutsky
- Department of Radiology, Duke University Medical Center, Durham, NC 27710, USA
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Cuyàs E, Fernández-Arroyo S, Corominas-Faja B, Rodríguez-Gallego E, Bosch-Barrera J, Martin-Castillo B, De Llorens R, Joven J, Menendez JA. Oncometabolic mutation IDH1 R132H confers a metformin-hypersensitive phenotype. Oncotarget 2016; 6:12279-96. [PMID: 25980580 PMCID: PMC4494938 DOI: 10.18632/oncotarget.3733] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 03/11/2015] [Indexed: 02/07/2023] Open
Abstract
Metabolic flexibility might be particularly constrained in tumors bearing mutations in isocitrate dehydrogenase 1 (IDH1) leading to the production of the oncometabolite 2-hydroxygluratate (2HG). To test the hypothesis that IDH1 mutations could generate metabolic vulnerabilities for therapeutic intervention, we utilized an MCF10A cell line engineered with an arginine-to-histidine conversion at position 132 (R132H) in the catalytic site of IDH1, which equips the enzyme with a neomorphic α-ketoglutarate to 2HG reducing activity in an otherwise isogenic background. IDH1 R132H/+ and isogenic IDH1 +/+ parental cells were screened for their ability to generate energy-rich NADH when cultured in a standardized high-throughput Phenotype MicroArrayplatform comprising >300 nutrients. A radical remodeling of the metabotype occurred in cells carrying the R132H mutation since they presented a markedly altered ability to utilize numerous carbon catabolic fuels. A mitochondria toxicity-screening modality confirmed a severe inability of IDH1-mutated cells to use various carbon substrates that are fed into the electron transport chain at different points. The mitochondrial biguanide poisons, metformin and phenformin, further impaired the intrinsic weakness of IDH1-mutant cells to use certain carbon-energy sources. Additionally, metabolic reprogramming of IDH1-mutant cells increased their sensitivity to metformin in assays of cell proliferation, clonogenic potential, and mammosphere formation. Targeted metabolomics studies revealed that the ability of metformin to interfere with the anaplerotic entry of glutamine into the tricarboxylic acid cycle could explain the hypersensitivity of IDH1-mutant cells to biguanides. Moreover, synergistic interactions occurred when metformin treatment was combined with the selective R132H-IDH1 inhibitor AGI-5198. Together, these results suggest that therapy involving the simultaneous targeting of metabolic vulnerabilities with metformin, and 2HG overproduction with mutant-selective inhibitors (AGI-5198-related AG-120 [Agios]), might represent a worthwhile avenue of exploration in the treatment of IDH1-mutated tumors.
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Affiliation(s)
- Elisabet Cuyàs
- Metabolism and Cancer Group, Translational Research Laboratory, Catalan Institute of Oncology (ICO), Girona, Catalonia, Spain.,Molecular Oncology Group, Girona Biomedical Research Institute (IDIBGI), Girona, Catalonia, Spain
| | - Salvador Fernández-Arroyo
- Unitat de Recerca Biomèdica (URB-CRB), Institut d'Investigació Sanitaria Pere i Virgili (IISPV), Universitat Rovira i Virgili, Reus, Catalonia. Spain
| | - Bruna Corominas-Faja
- Metabolism and Cancer Group, Translational Research Laboratory, Catalan Institute of Oncology (ICO), Girona, Catalonia, Spain.,Molecular Oncology Group, Girona Biomedical Research Institute (IDIBGI), Girona, Catalonia, Spain
| | - Esther Rodríguez-Gallego
- Unitat de Recerca Biomèdica (URB-CRB), Institut d'Investigació Sanitaria Pere i Virgili (IISPV), Universitat Rovira i Virgili, Reus, Catalonia. Spain
| | - Joaquim Bosch-Barrera
- Molecular Oncology Group, Girona Biomedical Research Institute (IDIBGI), Girona, Catalonia, Spain.,Medical Oncology, Catalan Institute of Oncology (ICO), Girona, Catalonia, Spain
| | - Begoña Martin-Castillo
- Molecular Oncology Group, Girona Biomedical Research Institute (IDIBGI), Girona, Catalonia, Spain.,Clinical Research Unit, Catalan Institute of Oncology (ICO), Girona, Catalonia, Spain
| | - Rafael De Llorens
- Biochemistry and Molecular Biology Unit, Department of Biology, University of Girona, Girona, Catalonia, Spain
| | - Jorge Joven
- Unitat de Recerca Biomèdica (URB-CRB), Institut d'Investigació Sanitaria Pere i Virgili (IISPV), Universitat Rovira i Virgili, Reus, Catalonia. Spain
| | - Javier A Menendez
- Metabolism and Cancer Group, Translational Research Laboratory, Catalan Institute of Oncology (ICO), Girona, Catalonia, Spain.,Molecular Oncology Group, Girona Biomedical Research Institute (IDIBGI), Girona, Catalonia, Spain
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46
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Hall MD, Simeonov A, Davis MI. Avoiding Fluorescence Assay Interference-The Case for Diaphorase. Assay Drug Dev Technol 2016; 14:175-9. [PMID: 27078679 PMCID: PMC4840916 DOI: 10.1089/adt.2016.707] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Fluorescence is utilized as the output for a range of assay formats used in high-throughput screening (HTS). Interference with these assays from the compounds in libraries utilized in HTS is a well-recognized phenomenon, particularly for assays relying on UV excitation such as for direct detection of the oxidoreductase cofactors NADH or NADPH. In this study, we discuss these interference challenges and highlight the specific case of the diaphorase/resazurin system that can be coupled to enzymes utilizing NADH or NADPH. We review the utilization of this assay system in the literature and argue that the diaphorase/resazurin system is underutilized in assay development. It is the authors' hope that this Perspective and the accompanying Technical Brief in this issue will stimulate interest in a robust and sensitive coupling system to avoid assay fluorescence interference.
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Affiliation(s)
- Matthew D Hall
- NCATS Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health , Rockville, Maryland
| | - Anton Simeonov
- NCATS Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health , Rockville, Maryland
| | - Mindy I Davis
- NCATS Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health , Rockville, Maryland
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47
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Davis MI, Shen M, Simeonov A, Hall MD. Diaphorase Coupling Protocols for Red-Shifting Dehydrogenase Assays. Assay Drug Dev Technol 2016; 14:207-12. [PMID: 27078681 PMCID: PMC4840998 DOI: 10.1089/adt.2016.706] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Dehydrogenases are an important target for the development of cancer therapeutics. Dehydrogenases either produce or consume NAD(P)H, which is fluorescent but at a wavelength where many compounds found in chemical libraries are also fluorescent. By coupling dehydrogenases to diaphorase, which utilizes NAD(P)H to produce the fluorescent molecule resorufin from resazurin, the assay can be red-shifted into a spectral region that reduces interference from compound libraries. Dehydrogenases that produce NAD(P)H, such as isocitrate dehydrogenase 1 (IDH1), can be read in kinetic mode. Dehydrogenases that consume NAD(P)H, such as mutant IDH1 R132H, can be read in endpoint mode. Here, we report protocols for robust and miniaturized 1,536-well assays for WT IDH1 and IDH1 R132H coupled to diaphorase, and the counterassays used to further detect compound interference with the coupling reagents. This coupling technique is applicable to dehydrogenases that either produce or consume NAD(P)H, and the examples provided here can act as guidelines for the development of high-throughput screens against this enzyme class.
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Affiliation(s)
- Mindy I Davis
- NCATS Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health , Rockville, Maryland
| | - Min Shen
- NCATS Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health , Rockville, Maryland
| | - Anton Simeonov
- NCATS Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health , Rockville, Maryland
| | - Matthew D Hall
- NCATS Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health , Rockville, Maryland
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48
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Gill H, Leung AYH, Kwong YL. Molecular and Cellular Mechanisms of Myelodysplastic Syndrome: Implications on Targeted Therapy. Int J Mol Sci 2016; 17:440. [PMID: 27023522 PMCID: PMC4848896 DOI: 10.3390/ijms17040440] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 03/02/2016] [Accepted: 03/07/2016] [Indexed: 12/11/2022] Open
Abstract
Myelodysplastic syndrome (MDS) is a group of heterogeneous clonal hematopoietic stem cell disorders characterized by cytopenia, ineffective hematopoiesis, and progression to secondary acute myeloid leukemia in high-risk cases. Conventional prognostication relies on clinicopathological parameters supplemented by cytogenetic information. However, recent studies have shown that genetic aberrations also have critical impacts on treatment outcome. Moreover, these genetic alterations may themselves be a target for treatment. The mutation landscape in MDS is shaped by gene aberrations involved in DNA methylation (TET2, DNMT3A, IDH1/2), histone modification (ASXL1, EZH2), the RNA splicing machinery (SF3B1, SRSF2, ZRSR2, U2AF1/2), transcription (RUNX1, TP53, BCOR, PHF6, NCOR, CEBPA, GATA2), tyrosine kinase receptor signaling (JAK2, MPL, FLT3, GNAS, KIT), RAS pathways (KRAS, NRAS, CBL, NF1, PTPN11), DNA repair (ATM, BRCC3, DLRE1C, FANCL), and cohesion complexes (STAG2, CTCF, SMC1A, RAD21). A detailed understanding of the pathogenetic mechanisms leading to transformation is critical for designing single-agent or combinatorial approaches in target therapy of MDS.
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Affiliation(s)
- Harinder Gill
- Department of Medicine, Queen Mary Hospital, Hong Kong, China.
| | | | - Yok-Lam Kwong
- Department of Medicine, Queen Mary Hospital, Hong Kong, China.
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49
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Lue JK, Amengual JE, O'Connor OA. Epigenetics and Lymphoma: Can We Use Epigenetics to Prime or Reset Chemoresistant Lymphoma Programs? Curr Oncol Rep 2016; 17:40. [PMID: 26141799 DOI: 10.1007/s11912-015-0464-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Non-Hodgkin lymphoma is a diverse group of lymphocyte-derived neoplasms. Although a heterogeneous group of malignancies, it has become apparent that epigenetic alterations, such as disturbances of DNA methylation and histone modification, are a common occurrence in both B cell and T cell lymphomas, contributing to lymphomagenesis. As a result, the use of epigenetic targeted therapy has been incorporated into various pre-clinical and clinical studies, demonstrating significant efficacy in lymphoma, with vorinostat becoming the first epigenetic therapy to receive FDA approval in any malignancy. The role of epigenetic drugs is evolving, with its potential use in combination therapy as well as a means of overcoming chemotherapy resistance. In this review, we discuss the epigenetic alterations in non-Hodgkin lymphomas as well as provide an overview of current epigenetic drugs and their role in clinical practice, and on-going clinical trials.
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Affiliation(s)
- Jennifer K Lue
- Center for Lymphoid Malignancies, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, Columbia University, New York, NY, USA
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50
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Keum YS, Choi BY. Isocitrate dehydrogenase mutations: new opportunities for translational research. BMB Rep 2016; 48:266-70. [PMID: 25787993 PMCID: PMC4578565 DOI: 10.5483/bmbrep.2015.48.5.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Indexed: 02/05/2023] Open
Abstract
Over the last decade, comprehensive genome-wide sequencing studies have enabled us to find out unexpected genetic alterations of metabolism in cancer. An example is the identification of arginine missense mutations of isocitrate dehydrogenases-1 and -2 (IDH1/2) in glioma, acute myeloid leukemia (AML), chondrosarcomas, and cholangiocarcinoma. These alterations are closely associated with the production of a new stereospecific metabolite, (R)-2-hydroxyglutarate (R-2HG). A large number of follow-up studies have been performed to address the molecular mechanisms of IDH1/2 mutations underlying how these events contribute to malignant transformation. In the meanwhile, the development of selective mutant IDH1/2 chemical inhibitors is being actively pursued in the scientific community and pharmaceutical industry. The present review article briefly discusses the important findings that highlight the molecular mechanisms of IDH1/2 mutations in cancer and provides a current status for development of selective mutant IDH1/2 chemical inhibitors. [BMB Reports 2015; 48(5): 266-270]
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Affiliation(s)
- Young-Sam Keum
- College of Pharmacy, Dongguk University, Goyang 410-820, Korea
| | - Bu Young Choi
- Department of Pharmaceutical Science and Engineering, Seowon University, Cheongju 361-742, Korea
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