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Li Y, Xie Z, Lei X, Yang X, Huang S, Yuan W, Deng X, Wang Z, Tang G. Recent advances in pyruvate dehydrogenase kinase inhibitors: Structures, inhibitory mechanisms and biological activities. Bioorg Chem 2024; 144:107160. [PMID: 38301426 DOI: 10.1016/j.bioorg.2024.107160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 01/23/2024] [Accepted: 01/27/2024] [Indexed: 02/03/2024]
Abstract
Metabolism is reprogrammed in a variety of cancer cells to ensure their rapid proliferation. Cancer cells prefer to utilize glycolysis to produce energy as well as to provide large amounts of precursors for their division. In this process, cancer cells inhibit the activity of pyruvate dehydrogenase complex (PDC) by upregulating the expression of pyruvate dehydrogenase kinases (PDKs). Inhibiting the activity of PDKs in cancer cells can effectively block this metabolic transition in cancer cells, while also activating mitochondrial oxidative metabolism and promoting apoptosis of cancer cells. To this day, the study of PDKs inhibitors has become one of the research hotspots in the field of medicinal chemistry. Novel structures targeting PDKs are constantly being discovered, and some inhibitors have entered the clinical research stage. Here, we reviewed the research progress of PDKs inhibitors in recent years and classified them according to the PDKs binding sites they acted on, aiming to summarize the structural characteristics of inhibitors acting on different binding sites and explore their clinical application value. Finally, the shortcomings of some PDKs inhibitors and the further development direction of PDKs inhibitors are discussed.
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Affiliation(s)
- Yiyang Li
- Institute of Pharmacy and Pharmacology, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Zhizhong Xie
- Institute of Pharmacy and Pharmacology, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Xiaoyong Lei
- Institute of Pharmacy and Pharmacology, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Xiaoyan Yang
- Institute of Pharmacy and Pharmacology, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Sheng Huang
- Jiuzhitang Co., Ltd, Changsha, Hunan 410007, China
| | - Weixi Yuan
- Institute of Pharmacy and Pharmacology, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Xiangping Deng
- The First Affiliated Hospital, Department of Pharmacy, Hengyang Medical School, University of South China, Hengyang 421001, Hunan, China.
| | - Zhe Wang
- The Second Affiliated Hospital, Department of Pharmacy, Hengyang Medical School, University of South China, Hengyang 421001, Hunan, China.
| | - Guotao Tang
- Institute of Pharmacy and Pharmacology, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China.
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Yue J, Xu J, Yin Y, Shu Y, Li Y, Li T, Zou Z, Wang Z, Li F, Zhang M, Liang S, He X, Liu Z, Wang Y. Targeting the PDK/PDH axis to reverse metabolic abnormalities by structure-based virtual screening with in vitro and in vivo experiments. Int J Biol Macromol 2024; 262:129970. [PMID: 38325689 DOI: 10.1016/j.ijbiomac.2024.129970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 02/09/2024]
Abstract
In humans and animals, the pyruvate dehydrogenase kinase (PDK) family proteins (PDKs 1-4) are excessively activated in metabolic disorders such as obesity, diabetes, and cancer, inhibiting the activity of pyruvate dehydrogenase (PDH) which plays a crucial role in energy and fatty acid metabolism and impairing its function. Intervention and regulation of PDH activity have become important research approaches for the treatment of various metabolic disorders. In this study, a small molecule (g25) targeting PDKs and activating PDH, was identified through multi-level computational screening methods. In vivo and in vitro experiments have shown that g25 activated the activity of PDH and reduced plasma lactate and triglyceride level. Besides, g25 significantly decreased hepatic fat deposition in a diet-induced obesity mouse model. Furthermore, g25 enhanced the tumor-inhibiting activity of cisplatin when used in combination. Molecular dynamics simulations and in vitro kinase assay also revealed the specificity of g25 towards PDK2. Overall, these findings emphasize the importance of targeting the PDK/PDH axis to regulate PDH enzyme activity in the treatment of metabolic disorders, providing directions for future related research. This study provides a possible lead compound for the PDK/PDH axis related diseases and offers insights into the regulatory mechanisms of this pathway in diseases.
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Affiliation(s)
- Jianda Yue
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China; Peptide and Small Molecule Drug R&D Plateform, Furong Laboratory, Hunan Normal University, Changsha 410081, Hunan, China; Institute of Interdisciplinary Studies, Hunan Normal University, Changsha 410081, China
| | - Jiawei Xu
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China; Peptide and Small Molecule Drug R&D Plateform, Furong Laboratory, Hunan Normal University, Changsha 410081, Hunan, China; Institute of Interdisciplinary Studies, Hunan Normal University, Changsha 410081, China
| | - Yekui Yin
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China; Peptide and Small Molecule Drug R&D Plateform, Furong Laboratory, Hunan Normal University, Changsha 410081, Hunan, China; Institute of Interdisciplinary Studies, Hunan Normal University, Changsha 410081, China
| | - Yuanyuan Shu
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China; Peptide and Small Molecule Drug R&D Plateform, Furong Laboratory, Hunan Normal University, Changsha 410081, Hunan, China; Institute of Interdisciplinary Studies, Hunan Normal University, Changsha 410081, China
| | - Yaqi Li
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China; Peptide and Small Molecule Drug R&D Plateform, Furong Laboratory, Hunan Normal University, Changsha 410081, Hunan, China
| | - Tingting Li
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China; Peptide and Small Molecule Drug R&D Plateform, Furong Laboratory, Hunan Normal University, Changsha 410081, Hunan, China; Institute of Interdisciplinary Studies, Hunan Normal University, Changsha 410081, China
| | - Zirui Zou
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China; Peptide and Small Molecule Drug R&D Plateform, Furong Laboratory, Hunan Normal University, Changsha 410081, Hunan, China; Institute of Interdisciplinary Studies, Hunan Normal University, Changsha 410081, China
| | - Zihan Wang
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China; Peptide and Small Molecule Drug R&D Plateform, Furong Laboratory, Hunan Normal University, Changsha 410081, Hunan, China; Institute of Interdisciplinary Studies, Hunan Normal University, Changsha 410081, China
| | - Fengjiao Li
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China; Peptide and Small Molecule Drug R&D Plateform, Furong Laboratory, Hunan Normal University, Changsha 410081, Hunan, China; Institute of Interdisciplinary Studies, Hunan Normal University, Changsha 410081, China
| | - Mengqi Zhang
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China; Peptide and Small Molecule Drug R&D Plateform, Furong Laboratory, Hunan Normal University, Changsha 410081, Hunan, China; Institute of Interdisciplinary Studies, Hunan Normal University, Changsha 410081, China
| | - Songping Liang
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China; Peptide and Small Molecule Drug R&D Plateform, Furong Laboratory, Hunan Normal University, Changsha 410081, Hunan, China; Institute of Interdisciplinary Studies, Hunan Normal University, Changsha 410081, China
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China; New York University-East China Normal University Center for Computational Chemistry, New York University Shanghai, Shanghai 200062, China
| | - Zhonghua Liu
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China; Peptide and Small Molecule Drug R&D Plateform, Furong Laboratory, Hunan Normal University, Changsha 410081, Hunan, China; Institute of Interdisciplinary Studies, Hunan Normal University, Changsha 410081, China.
| | - Ying Wang
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China; Peptide and Small Molecule Drug R&D Plateform, Furong Laboratory, Hunan Normal University, Changsha 410081, Hunan, China; Institute of Interdisciplinary Studies, Hunan Normal University, Changsha 410081, China.
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Dou X, Fu Q, Long Q, Liu S, Zou Y, Fu D, Xu Q, Jiang Z, Ren X, Zhang G, Wei X, Li Q, Campisi J, Zhao Y, Sun Y. PDK4-dependent hypercatabolism and lactate production of senescent cells promotes cancer malignancy. Nat Metab 2023; 5:1887-1910. [PMID: 37903887 PMCID: PMC10663165 DOI: 10.1038/s42255-023-00912-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 09/22/2023] [Indexed: 11/01/2023]
Abstract
Senescent cells remain metabolically active, but their metabolic landscape and resulting implications remain underexplored. Here, we report upregulation of pyruvate dehydrogenase kinase 4 (PDK4) upon senescence, particularly in some stromal cell lines. Senescent cells display a PDK4-dependent increase in aerobic glycolysis and enhanced lactate production but maintain mitochondrial respiration and redox activity, thus adopting a special form of metabolic reprogramming. Medium from PDK4+ stromal cells promotes the malignancy of recipient cancer cells in vitro, whereas inhibition of PDK4 causes tumor regression in vivo. We find that lactate promotes reactive oxygen species production via NOX1 to drive the senescence-associated secretory phenotype, whereas PDK4 suppression reduces DNA damage severity and restrains the senescence-associated secretory phenotype. In preclinical trials, PDK4 inhibition alleviates physical dysfunction and prevents age-associated frailty. Together, our study confirms the hypercatabolic nature of senescent cells and reveals a metabolic link between cellular senescence, lactate production, and possibly, age-related pathologies, including but not limited to cancer.
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Affiliation(s)
- Xuefeng Dou
- Key Laboratory of Tissue Microenvironment and Tumour, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Qiang Fu
- Department of Pharmacology, Institute of Aging Medicine, Binzhou Medical University, Yantai, China
| | - Qilai Long
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Shuning Liu
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Yejun Zou
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
- Research Unit of New Techniques for Live-cell Metabolic Imaging, Chinese Academy of Medical Sciences, Beijing, China
| | - Da Fu
- Department of General Surgery, Pancreatic Disease Institute, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qixia Xu
- Key Laboratory of Tissue Microenvironment and Tumour, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zhirui Jiang
- Key Laboratory of Tissue Microenvironment and Tumour, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiaohui Ren
- Key Laboratory of Tissue Microenvironment and Tumour, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Guilong Zhang
- Department of Pharmacology, Institute of Aging Medicine, Binzhou Medical University, Yantai, China
- Department of Pharmacology, Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Binzhou Medical University, Yantai, China
| | - Xiaoling Wei
- Department of Endodontics, Shanghai Stomatological Hospital and School of Stomatology, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Craniomaxillofacial Development and Diseases, Fudan University, Shanghai, China
| | - Qingfeng Li
- Department of Plastic & Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Judith Campisi
- Buck Institute for Research on Aging, Novato, CA, USA
- Lawrence Berkeley National Laboratory, University of California, Berkeley, CA, USA
| | - Yuzheng Zhao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China.
- Research Unit of New Techniques for Live-cell Metabolic Imaging, Chinese Academy of Medical Sciences, Beijing, China.
| | - Yu Sun
- Key Laboratory of Tissue Microenvironment and Tumour, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
- Department of Pharmacology, Institute of Aging Medicine, Binzhou Medical University, Yantai, China.
- Department of Medicine and VAPSHCS, University of Washington, Seattle, WA, USA.
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Guo Y, Zhou Y, Wu P, Ran M, Xu N, Shan W, Sha O, Tam KY. Dichloroacetophenone biphenylsulfone ethers as anticancer pyruvate dehydrogenase kinase inhibitors in non-small cell lung cancer models. Chem Biol Interact 2023; 378:110467. [PMID: 37004952 DOI: 10.1016/j.cbi.2023.110467] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 03/16/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023]
Abstract
Pyruvate dehydrogenase kinase 1 (PDK1) is an important metabolic enzyme which is often overexpressed in many types of cancers, including non-small-cell lung cancers (NSCLC). Targeting PDK1 appears to be an attractive anticancer strategy. Based on a previously reported moderate potent anticancer PDK1 inhibitor, 64, we developed three dichloroacetophenone biphenylsulfone ethers, 30, 31 and 32, which showed strong PDK1 inhibitions of 74%, 83% and 72% at 10 μM, respectively. Then we investigated the anticancer effects of 31 in two NSCLC cell lines, namely, NCI-H1299 and NCI-H1975. It was found that 31 exhibited sub-micromolar cancer cell IC50s, suppressed colony formation, induced mitochondrial membrane potential depolarization, triggered apoptosis, altered cellular glucose metabolism, with concomitant reductions in extracellular lactate levels and enhanced the generation of reactive oxygen species in NSCLC cells. Moreover, 31 significantly suppressed the tumor growth in an NCI-H1975 mouse xenograft model, outperforming the anticancer effects of 64. Taken together our results suggested that inhibition of PDK1 via dichloroacetophenone biphenylsulfone ethers may provide a novel direction leading to an alternative treatment option in NSCLC therapy.
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Lee H, Jeon JH, Lee YJ, Kim MJ, Kwon WH, Chanda D, Thoudam T, Pagire HS, Pagire SH, Ahn JH, Harris RA, Kim ES, Lee IK. Inhibition of Pyruvate Dehydrogenase Kinase 4 in CD4 + T Cells Ameliorates Intestinal Inflammation. Cell Mol Gastroenterol Hepatol 2022; 15:439-461. [PMID: 36229019 PMCID: PMC9791136 DOI: 10.1016/j.jcmgh.2022.09.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 09/28/2022] [Accepted: 09/29/2022] [Indexed: 01/28/2023]
Abstract
BACKGROUND & AIMS Despite recent evidence supporting the metabolic plasticity of CD4+ T cells, it is uncertain whether the metabolic checkpoint pyruvate dehydrogenase kinase (PDK) in T cells plays a role in the pathogenesis of colitis. METHODS To investigate the role of PDK4 in colitis, we used dextran sulfate sodium (DSS)-induced colitis and T-cell transfer colitis models based on mice with constitutive knockout (KO) or CD4+ T-cell-specific KO of PDK4 (Pdk4fl/flCD4Cre). The effect of PDK4 deletion on T-cell activation was also studied in vitro. Furthermore, we examined the effects of a pharmacologic inhibitor of PDK4 on colitis. RESULTS Expression of PDK4 increased during colitis development in a DSS-induced colitis model. Phosphorylated PDHE1α, a substrate of PDK4, accumulated in CD4+ T cells in the lamina propria of patients with inflammatory bowel disease. Both constitutive KO and CD4+ T-cell-specific deletion of PDK4 delayed DSS-induced colitis. Adoptive transfer of PDK4-deficient CD4+ T cells attenuated murine colitis, and PDK4 deficiency resulted in decreased activation of CD4+ T cells and attenuated aerobic glycolysis. Mechanistically, there were fewer endoplasmic reticulum-mitochondria contact sites, which are responsible for interorganelle calcium transfer, in PDK4-deficient CD4+ T cells. Consistent with this, GM-10395, a novel inhibitor of PDK4, suppressed T-cell activation by reducing endoplasmic reticulum-mitochondria calcium transfer, thereby ameliorating murine colitis. CONCLUSIONS PDK4 deletion from CD4+ T cells mitigates colitis by metabolic and calcium signaling modulation, suggesting PDK4 as a potential therapeutic target for IBD.
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Affiliation(s)
- Hoyul Lee
- Research Institute of Aging and Metabolism, Kyungpook National University, Daegu, Republic of Korea
| | - Jae Han Jeon
- Research Institute of Aging and Metabolism, Kyungpook National University, Daegu, Republic of Korea,Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Chilgok Hospital, Daegu, Republic of Korea
| | - Yu-Jeong Lee
- Cell & Matrix Research Institute, Kyungpook National University, Daegu, Republic of Korea
| | - Mi-Jin Kim
- Research Institute of Aging and Metabolism, Kyungpook National University, Daegu, Republic of Korea
| | - Woong Hee Kwon
- Leading-Edge Research Center for Drug Discovery and Development for Diabetes and Metabolic Disease, Kyungpook National University Hospital, Daegu, Republic of Korea
| | - Dipanjan Chanda
- Research Institute of Aging and Metabolism, Kyungpook National University, Daegu, Republic of Korea
| | - Themis Thoudam
- Research Institute of Aging and Metabolism, Kyungpook National University, Daegu, Republic of Korea
| | - Haushabhau S. Pagire
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea
| | - Suvarna H. Pagire
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea
| | - Jin Hee Ahn
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea
| | - Robert A. Harris
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas
| | - Eun Soo Kim
- Division of Gastroenterology, Department of Internal Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu, Republic of Korea,Correspondence Address correspondence to: Eun Soo Kim, MD, PhD, Division of Gastroenterology, Department of Internal Medicine, School of Medicine, Kyungpook National University, 130 Dongdeok-ro, Jung-gu, Daegu, Republic of Korea 41944. fax: +82-53-200-5879.
| | - In-Kyu Lee
- Research Institute of Aging and Metabolism, Kyungpook National University, Daegu, Republic of Korea,Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu, Republic of Korea,In-Kyu Lee, MD, PhD, Department of Internal Medicine, School of Medicine, Kyungpook National University, 130 Dongdeok-ro, Jung-gu, Daegu, Republic of Korea 41944.
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Evaluation of Substituted Pyrazole-Based Kinase Inhibitors in One Decade (2011-2020): Current Status and Future Prospects. Molecules 2022; 27:molecules27010330. [PMID: 35011562 PMCID: PMC8747022 DOI: 10.3390/molecules27010330] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/29/2021] [Accepted: 12/31/2021] [Indexed: 11/17/2022] Open
Abstract
Pyrazole has been recognized as a pharmacologically important privileged scaffold whose derivatives produce almost all types of pharmacological activities and have attracted much attention in the last decades. Of the various pyrazole derivatives reported as potential therapeutic agents, this article focuses on pyrazole-based kinase inhibitors. Pyrazole-possessing kinase inhibitors play a crucial role in various disease areas, especially in many cancer types such as lymphoma, breast cancer, melanoma, cervical cancer, and others in addition to inflammation and neurodegenerative disorders. In this article, we reviewed the structural and biological characteristics of the pyrazole derivatives recently reported as kinase inhibitors and classified them according to their target kinases in a chronological order. We reviewed the reports including pyrazole derivatives as kinase inhibitors published during the past decade (2011-2020).
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Kim SE, Ji SB, Kim E, Jeong M, Kim J, Lee GM, Seo HJ, Bae S, Jeong Y, Lee S, Kim S, Lee T, Cho SJ, Liu KH. Nontargeted Metabolomics by High-Resolution Mass Spectrometry to Study the In Vitro Metabolism of a Dual Inverse Agonist of Estrogen-Related Receptors β and γ, DN203368. Pharmaceutics 2021; 13:pharmaceutics13060776. [PMID: 34072800 PMCID: PMC8230175 DOI: 10.3390/pharmaceutics13060776] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/21/2021] [Accepted: 05/24/2021] [Indexed: 02/07/2023] Open
Abstract
DN203368 ((E)-3-[1-(4-[4-isopropylpiperazine-1-yl]phenyl) 3-methyl-2-phenylbut-1-en-1-yl] phenol) is a 4-hydroxy tamoxifen analog that is a dual inverse agonist of estrogen-related receptor β/γ (ERRβ/γ). ERRγ is an orphan nuclear receptor that plays an important role in development and homeostasis and holds potential as a novel therapeutic target in metabolic diseases such as diabetes mellitus, obesity, and cancer. ERRβ is also one of the orphan nuclear receptors critical for many biological processes, such as development. We investigated the in vitro metabolism of DN203368 by conventional and metabolomic approaches using high-resolution mass spectrometry. The compound (100 μM) was incubated with rat and human liver microsomes in the presence of NADPH. In the metabolomic approach, the m/z value and retention time information obtained from the sample and heat-inactivated control group were statistically evaluated using principal component analysis and orthogonal partial least-squares discriminant analysis. Significant features responsible for group separation were then identified using tandem mass spectra. Seven metabolites of DN203368 were identified in rat liver microsomes and the metabolic pathways include hydroxylation (M1-3), N-oxidation (M4), N-deisopropylation (M5), N,N-dealkylation (M6), and oxidation and dehydrogenation (M7). Only five metabolites (M2, M3, and M5-M7) were detected in human liver microsomes. In the conventional approach using extracted ion monitoring for values of mass increase or decrease by known metabolic reactions, only five metabolites (M1-M5) were found in rat liver microsomes, whereas three metabolites (M2, M3, and M5) were found in human liver microsomes. This study revealed that nontargeted metabolomics combined with high-resolution mass spectrometry and multivariate analysis could be a more efficient tool for drug metabolite identification than the conventional approach. These results might also be useful for understanding the pharmacokinetics and metabolism of DN203368 in animals and humans.
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Affiliation(s)
- Sin-Eun Kim
- BK21 FOUR KNU Community-Based Intelligent Novel Drug Discovery Education Unit, College of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu 41566, Korea; (S.-E.K.); (S.-B.J.); (E.K.); (G.-M.L.); (H.-J.S.); (S.B.); (Y.J.); (S.L.); (T.L.)
| | - Seung-Bae Ji
- BK21 FOUR KNU Community-Based Intelligent Novel Drug Discovery Education Unit, College of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu 41566, Korea; (S.-E.K.); (S.-B.J.); (E.K.); (G.-M.L.); (H.-J.S.); (S.B.); (Y.J.); (S.L.); (T.L.)
| | - Euihyeon Kim
- BK21 FOUR KNU Community-Based Intelligent Novel Drug Discovery Education Unit, College of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu 41566, Korea; (S.-E.K.); (S.-B.J.); (E.K.); (G.-M.L.); (H.-J.S.); (S.B.); (Y.J.); (S.L.); (T.L.)
| | - Minseon Jeong
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu 41061, Korea; (M.J.); (J.K.)
| | - Jina Kim
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu 41061, Korea; (M.J.); (J.K.)
| | - Gyung-Min Lee
- BK21 FOUR KNU Community-Based Intelligent Novel Drug Discovery Education Unit, College of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu 41566, Korea; (S.-E.K.); (S.-B.J.); (E.K.); (G.-M.L.); (H.-J.S.); (S.B.); (Y.J.); (S.L.); (T.L.)
| | - Hyung-Ju Seo
- BK21 FOUR KNU Community-Based Intelligent Novel Drug Discovery Education Unit, College of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu 41566, Korea; (S.-E.K.); (S.-B.J.); (E.K.); (G.-M.L.); (H.-J.S.); (S.B.); (Y.J.); (S.L.); (T.L.)
| | - Subin Bae
- BK21 FOUR KNU Community-Based Intelligent Novel Drug Discovery Education Unit, College of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu 41566, Korea; (S.-E.K.); (S.-B.J.); (E.K.); (G.-M.L.); (H.-J.S.); (S.B.); (Y.J.); (S.L.); (T.L.)
| | - Yeojin Jeong
- BK21 FOUR KNU Community-Based Intelligent Novel Drug Discovery Education Unit, College of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu 41566, Korea; (S.-E.K.); (S.-B.J.); (E.K.); (G.-M.L.); (H.-J.S.); (S.B.); (Y.J.); (S.L.); (T.L.)
| | - Sangkyu Lee
- BK21 FOUR KNU Community-Based Intelligent Novel Drug Discovery Education Unit, College of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu 41566, Korea; (S.-E.K.); (S.-B.J.); (E.K.); (G.-M.L.); (H.-J.S.); (S.B.); (Y.J.); (S.L.); (T.L.)
- Mass Spectrometry Based Convergence Research Institute, Kyungpook National University, Daegu 41566, Korea;
| | - Sunghwan Kim
- Mass Spectrometry Based Convergence Research Institute, Kyungpook National University, Daegu 41566, Korea;
- Department of Chemistry, Kyungpook National University, Daegu 41566, Korea
| | - Taeho Lee
- BK21 FOUR KNU Community-Based Intelligent Novel Drug Discovery Education Unit, College of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu 41566, Korea; (S.-E.K.); (S.-B.J.); (E.K.); (G.-M.L.); (H.-J.S.); (S.B.); (Y.J.); (S.L.); (T.L.)
| | - Sung Jin Cho
- Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, Korea Institute of Science and Technology, Seoul 02792, Korea
- Correspondence: (S.J.C.); (K.-H.L.); Tel.: +82-2-958-5137 (S.-J.C.); +82-53-950-8567 (K.-H.L.); Fax: +82-2-958-5137 (S.J.C.); +82-53-950-8557 (K.-H.L.)
| | - Kwang-Hyeon Liu
- BK21 FOUR KNU Community-Based Intelligent Novel Drug Discovery Education Unit, College of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu 41566, Korea; (S.-E.K.); (S.-B.J.); (E.K.); (G.-M.L.); (H.-J.S.); (S.B.); (Y.J.); (S.L.); (T.L.)
- Mass Spectrometry Based Convergence Research Institute, Kyungpook National University, Daegu 41566, Korea;
- Correspondence: (S.J.C.); (K.-H.L.); Tel.: +82-2-958-5137 (S.-J.C.); +82-53-950-8567 (K.-H.L.); Fax: +82-2-958-5137 (S.J.C.); +82-53-950-8557 (K.-H.L.)
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8
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Jane EP, Premkumar DR, Rajasundaram D, Thambireddy S, Reslink MC, Agnihotri S, Pollack IF. Reversing tozasertib resistance in glioma through inhibition of pyruvate dehydrogenase kinases. Mol Oncol 2021; 16:219-249. [PMID: 34058053 PMCID: PMC8732347 DOI: 10.1002/1878-0261.13025] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 04/23/2021] [Accepted: 05/28/2021] [Indexed: 12/19/2022] Open
Abstract
Acquired resistance to conventional chemotherapeutic agents limits their effectiveness and can cause cancer treatment to fail. Because enzymes in the aurora kinase family are vital regulators of several mitotic events, we reasoned that targeting these kinases with tozasertib, a pan‐aurora kinase inhibitor, would not only cause cytokinesis defects, but also induce cell death in high‐grade pediatric and adult glioma cell lines. We found that tozasertib induced cell cycle arrest, increased mitochondrial permeability and reactive oxygen species generation, inhibited cell growth and migration, and promoted cellular senescence and pro‐apoptotic activity. However, sustained exposure to tozasertib at clinically relevant concentrations conferred resistance, which led us to examine the mechanistic basis for the emergence of drug resistance. RNA‐sequence analysis revealed a significant upregulation of the gene encoding pyruvate dehydrogenase kinase isoenzyme 4 (PDK4), a pyruvate dehydrogenase (PDH) inhibitory kinase that plays a crucial role in the control of metabolic flexibility under various physiological conditions. Upregulation of PDK1, PDK2, PDK3, or PDK4 protein levels was positively correlated with tozasertib‐induced resistance through inhibition of PDH activity. Tozasertib‐resistant cells exhibited increased mitochondrial mass as measured by 10‐N‐nonyl‐Acridine Orange. Inhibition of PDK with dichloroacetate resulted in increased mitochondrial permeability and cell death in tozasertib‐resistant glioma cell lines. Based on these results, we believe that PDK is a selective target for the tozasertib resistance phenotype and should be considered for further preclinical evaluations.
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Affiliation(s)
- Esther P Jane
- Department of Neurosurgery, University of Pittsburgh School of Medicine, PA, USA
| | - Daniel R Premkumar
- Department of Neurosurgery, University of Pittsburgh School of Medicine, PA, USA.,Department of Neurosurgery, UPMC Hillman Cancer Center, PA, USA
| | | | - Swetha Thambireddy
- Department of Neurosurgery, University of Pittsburgh School of Medicine, PA, USA
| | - Matthew C Reslink
- Department of Neurosurgery, University of Pittsburgh School of Medicine, PA, USA
| | - Sameer Agnihotri
- Department of Neurosurgery, University of Pittsburgh School of Medicine, PA, USA.,Department of Neurosurgery, UPMC Hillman Cancer Center, PA, USA
| | - Ian F Pollack
- Department of Neurosurgery, University of Pittsburgh School of Medicine, PA, USA.,Department of Neurosurgery, UPMC Hillman Cancer Center, PA, USA
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9
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Anwar S, Shamsi A, Mohammad T, Islam A, Hassan MI. Targeting pyruvate dehydrogenase kinase signaling in the development of effective cancer therapy. Biochim Biophys Acta Rev Cancer 2021; 1876:188568. [PMID: 34023419 DOI: 10.1016/j.bbcan.2021.188568] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/06/2021] [Accepted: 05/11/2021] [Indexed: 02/06/2023]
Abstract
Pyruvate is irreversibly decarboxylated to acetyl coenzyme A by mitochondrial pyruvate dehydrogenase complex (PDC). Decarboxylation of pyruvate is considered a crucial step in cell metabolism and energetics. The cancer cells prefer aerobic glycolysis rather than mitochondrial oxidation of pyruvate. This attribute of cancer cells allows them to sustain under indefinite proliferation and growth. Pyruvate dehydrogenase kinases (PDKs) play critical roles in many diseases because they regulate PDC activity. Recent findings suggest an altered metabolism of cancer cells is associated with impaired mitochondrial function due to PDC inhibition. PDKs inhibit the PDC activity via phosphorylation of the E1a subunit and subsequently cause a glycolytic shift. Thus, inhibition of PDK is an attractive strategy in anticancer therapy. This review highlights that PDC/PDK axis could be implicated in cancer's therapeutic management by developing potential small-molecule PDK inhibitors. In recent years, a dramatic increase in the targeting of the PDC/PDK axis for cancer treatment gained an attention from the scientific community. We further discuss breakthrough findings in the PDC-PDK axis. In addition, structural features, functional significance, mechanism of activation, involvement in various human pathologies, and expression of different forms of PDKs (PDK1-4) in different types of cancers are discussed in detail. We further emphasized the gene expression profiling of PDKs in cancer patients to prognosis and therapeutic manifestations. Additionally, inhibition of the PDK/PDC axis by small molecule inhibitors and natural compounds at different clinical evaluation stages has also been discussed comprehensively.
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Affiliation(s)
- Saleha Anwar
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Anas Shamsi
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.
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10
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Su Z, Liu Y, Zhang H. Adaptive Cardiac Metabolism Under Chronic Hypoxia: Mechanism and Clinical Implications. Front Cell Dev Biol 2021; 9:625524. [PMID: 33604337 PMCID: PMC7884626 DOI: 10.3389/fcell.2021.625524] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 01/11/2021] [Indexed: 11/29/2022] Open
Abstract
Chronic hypoxia is an essential component in many cardiac diseases. The heart consumes a substantial amount of energy and it is important to maintain the balance of energy supply and demand when oxygen is limited. Previous studies showed that the heart switches from fatty acid to glucose to maintain metabolic efficiency in the adaptation to chronic hypoxia. However, the underlying mechanism of this adaptive cardiac metabolism remains to be fully characterized. Moreover, how the altered cardiac metabolism affects the heart function in patients with chronic hypoxia has not been discussed in the current literature. In this review, we summarized new findings from animal and human studies to illustrate the mechanism underlying the adaptive cardiac metabolism under chronic hypoxia. Clinical focus is given to certain patients that are subject to the impact of chronic hypoxia, and potential treatment strategies that modulate cardiac metabolism and may improve the heart function in these patients are also summarized.
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Affiliation(s)
- Zhanhao Su
- State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yiwei Liu
- Heart center and Shanghai Institute of Pediatric Congenital Heart Disease, Shanghai Children's Medical Center, National Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Hao Zhang
- Heart center and Shanghai Institute of Pediatric Congenital Heart Disease, Shanghai Children's Medical Center, National Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
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11
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Xie Z, Yang X, Duan Y, Han J, Liao C. Small-Molecule Kinase Inhibitors for the Treatment of Nononcologic Diseases. J Med Chem 2021; 64:1283-1345. [PMID: 33481605 DOI: 10.1021/acs.jmedchem.0c01511] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Great successes have been achieved in developing small-molecule kinase inhibitors as anticancer therapeutic agents. However, kinase deregulation plays essential roles not only in cancer but also in almost all major disease areas. Accumulating evidence has revealed that kinases are promising drug targets for different diseases, including cancer, autoimmune diseases, inflammatory diseases, cardiovascular diseases, central nervous system disorders, viral infections, and malaria. Indeed, the first small-molecule kinase inhibitor for treatment of a nononcologic disease was approved in 2011 by the U.S. FDA. To date, 10 such inhibitors have been approved, and more are in clinical trials for applications other than cancer. This Perspective discusses a number of kinases and their small-molecule inhibitors for the treatment of diseases in nononcologic therapeutic fields. The opportunities and challenges in developing such inhibitors are also highlighted.
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Affiliation(s)
- Zhouling Xie
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Xiaoxiao Yang
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Yajun Duan
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Jihong Han
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Chenzhong Liao
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
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12
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Jeon JH, Thoudam T, Choi EJ, Kim MJ, Harris RA, Lee IK. Loss of metabolic flexibility as a result of overexpression of pyruvate dehydrogenase kinases in muscle, liver and the immune system: Therapeutic targets in metabolic diseases. J Diabetes Investig 2020; 12:21-31. [PMID: 32628351 PMCID: PMC7779278 DOI: 10.1111/jdi.13345] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 06/26/2020] [Accepted: 06/29/2020] [Indexed: 12/12/2022] Open
Abstract
Good health depends on the maintenance of metabolic flexibility, which in turn is dependent on the maintenance of regulatory flexibility of a large number of regulatory enzymes, but especially the pyruvate dehydrogenase complex (PDC), because of its central role in carbohydrate metabolism. Flexibility in regulation of PDC is dependent on rapid changes in the phosphorylation state of PDC determined by the relative activities of the pyruvate dehydrogenase kinases (PDKs) and the pyruvate dehydrogenase phosphatases. Inactivation of the PDC by overexpression of PDK4 contributes to hyperglycemia, and therefore the serious health problems associated with diabetes. Loss of regulatory flexibility of PDC occurs in other disease states and pathological conditions that have received less attention than diabetes. These include cancers, non‐alcoholic fatty liver disease, cancer‐induced cachexia, diabetes‐induced nephropathy, sepsis and amyotrophic lateral sclerosis. Overexpression of PDK4, and in some situations, the other PDKs, as well as under expression of the pyruvate dehydrogenase phosphatases, leads to inactivation of the PDC, mitochondrial dysfunction and deleterious effects with health consequences. The possible basis for this phenomenon, along with evidence that overexpression of PDK4 results in phosphorylation of “off‐target” proteins and promotes excessive transport of Ca2+ into mitochondria through mitochondria‐associated endoplasmic reticulum membranes are discussed. Recent efforts to find small molecule PDK inhibitors with therapeutic potential are also reviewed.
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Affiliation(s)
- Jae-Han Jeon
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu, Korea.,Leading-Edge Research Center for Drug Discovery and Development for Diabetes and Metabolic Disease, Kyungpook National University Hospital, Daegu, Korea
| | - Themis Thoudam
- Research Institute of Aging and Metabolism, Kyungpook National University, Daegu, Korea
| | - Eun Jung Choi
- Department of Biomedical Science, The Graduate School, Kyungpook National University, Daegu, Korea
| | - Min-Ji Kim
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu, Korea
| | - Robert A Harris
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - In-Kyu Lee
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu, Korea.,Leading-Edge Research Center for Drug Discovery and Development for Diabetes and Metabolic Disease, Kyungpook National University Hospital, Daegu, Korea.,Research Institute of Aging and Metabolism, Kyungpook National University, Daegu, Korea.,Department of Biomedical Science, The Graduate School, Kyungpook National University, Daegu, Korea
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13
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Lee K, Moon S, Park MJ, Koh IU, Choi NH, Yu HY, Kim YJ, Kong J, Kang HG, Kim SC, Kim BJ. Integrated Analysis of Tissue-Specific Promoter Methylation and Gene Expression Profile in Complex Diseases. Int J Mol Sci 2020; 21:E5056. [PMID: 32709145 PMCID: PMC7404266 DOI: 10.3390/ijms21145056] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/14/2020] [Accepted: 07/16/2020] [Indexed: 02/06/2023] Open
Abstract
This study investigated whether the promoter region of DNA methylation positively or negatively regulates tissue-specific genes (TSGs) and if it correlates with disease pathophysiology. We assessed tissue specificity metrics in five human tissues, using sequencing-based approaches, including 52 whole genome bisulfite sequencing (WGBS), 52 RNA-seq, and 144 chromatin immunoprecipitation sequencing (ChIP-seq) data. A correlation analysis was performed between the gene expression and DNA methylation levels of the TSG promoter region. The TSG enrichment analyses were conducted in the gene-disease association network (DisGeNET). The epigenomic association analyses of CpGs in enriched TSG promoters were performed using 1986 Infinium MethylationEPIC array data. A correlation analysis showed significant associations between the promoter methylation and 449 TSGs' expression. A disease enrichment analysis showed that diabetes- and obesity-related diseases were high-ranked. In an epigenomic association analysis based on obesity, 62 CpGs showed statistical significance. Among them, three obesity-related CpGs were newly identified and replicated with statistical significance in independent data. In particular, a CpG (cg17075888 of PDK4), considered as potential therapeutic targets, were associated with complex diseases, including obesity and type 2 diabetes. The methylation changes in a substantial number of the TSG promoters showed a significant association with metabolic diseases. Collectively, our findings provided strong evidence of the relationship between tissue-specific patterns of epigenetic changes and metabolic diseases.
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Affiliation(s)
- Kibaick Lee
- Division of Genome Research, Center for Genome Science, Korea National Institute of Health, Chungcheongbuk-do 28519, Korea; (K.L.); (S.M.); (M.-J.P.); (I.-U.K.); (N.-H.C.); (H.-Y.Y.); (Y.J.K.); (J.K.)
| | - Sanghoon Moon
- Division of Genome Research, Center for Genome Science, Korea National Institute of Health, Chungcheongbuk-do 28519, Korea; (K.L.); (S.M.); (M.-J.P.); (I.-U.K.); (N.-H.C.); (H.-Y.Y.); (Y.J.K.); (J.K.)
| | - Mi-Jin Park
- Division of Genome Research, Center for Genome Science, Korea National Institute of Health, Chungcheongbuk-do 28519, Korea; (K.L.); (S.M.); (M.-J.P.); (I.-U.K.); (N.-H.C.); (H.-Y.Y.); (Y.J.K.); (J.K.)
| | - In-Uk Koh
- Division of Genome Research, Center for Genome Science, Korea National Institute of Health, Chungcheongbuk-do 28519, Korea; (K.L.); (S.M.); (M.-J.P.); (I.-U.K.); (N.-H.C.); (H.-Y.Y.); (Y.J.K.); (J.K.)
| | - Nak-Hyeon Choi
- Division of Genome Research, Center for Genome Science, Korea National Institute of Health, Chungcheongbuk-do 28519, Korea; (K.L.); (S.M.); (M.-J.P.); (I.-U.K.); (N.-H.C.); (H.-Y.Y.); (Y.J.K.); (J.K.)
| | - Ho-Yeong Yu
- Division of Genome Research, Center for Genome Science, Korea National Institute of Health, Chungcheongbuk-do 28519, Korea; (K.L.); (S.M.); (M.-J.P.); (I.-U.K.); (N.-H.C.); (H.-Y.Y.); (Y.J.K.); (J.K.)
| | - Young Jin Kim
- Division of Genome Research, Center for Genome Science, Korea National Institute of Health, Chungcheongbuk-do 28519, Korea; (K.L.); (S.M.); (M.-J.P.); (I.-U.K.); (N.-H.C.); (H.-Y.Y.); (Y.J.K.); (J.K.)
| | - Jinhwa Kong
- Division of Genome Research, Center for Genome Science, Korea National Institute of Health, Chungcheongbuk-do 28519, Korea; (K.L.); (S.M.); (M.-J.P.); (I.-U.K.); (N.-H.C.); (H.-Y.Y.); (Y.J.K.); (J.K.)
| | - Hee Gyung Kang
- Department of Pediatrics, Seoul National University College of Medicine, Seoul 03080, Korea;
| | - Song Cheol Kim
- Department of Surgery, Asan Medical Center, AMIST, University of Ulsan College of Medicine, Seoul 05505, Korea
| | - Bong-Jo Kim
- Division of Genome Research, Center for Genome Science, Korea National Institute of Health, Chungcheongbuk-do 28519, Korea; (K.L.); (S.M.); (M.-J.P.); (I.-U.K.); (N.-H.C.); (H.-Y.Y.); (Y.J.K.); (J.K.)
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14
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Kang J, Pagire HS, Kang D, Song YH, Lee IK, Lee KT, Park CJ, Ahn JH, Kim J. Structural basis for the inhibition of PDK2 by novel ATP- and lipoyl-binding site targeting compounds. Biochem Biophys Res Commun 2020; 527:778-784. [PMID: 32444142 DOI: 10.1016/j.bbrc.2020.04.102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 04/20/2020] [Indexed: 11/19/2022]
Abstract
Pyruvate dehydrogenase kinase (PDK) controls the activity of pyruvate decarboxylase complex (PDC) by phosphorylating key serine residues on the E1 subunit, which leads to a decreased oxidative phosphorylation in mitochondria. Inhibition of PDK activity by natural/synthetic compounds has been shown to reverse the Warburg effect, a characteristic metabolism in cancer cells. PDK-PDC axis also has been associated with diabetes and heart disease. Therefore, regulation of PDK activity has been considered as a promising strategy to treat related diseases. Here we present the X-ray crystal structure of PDK2 complexed with a recently identified PDK4 inhibitor, compound 8c, which has been predicted to bind at the lipoyl-binding site and interrupt intermolecular interactions with the E2-E3bp subunits of PDC. The co-crystal structure confirmed the specific binding location of compound 8c and revealed the remote conformational change in the ATP-binding pocket. In addition, two novel 4,5-diarylisoxazole derivatives, GM10030 and GM67520, were synthesized and used for structural studies, which target the ATP-binding site of PDK2. These compounds bind to PDK2 with a sub-100nM affinity as determined by isothermal titration calorimetry experiments. Notably, the crystal structure of the PDK2-GM10030 complex displays unprecedented asymmetric conformation of human PDK2 dimer, especially in the ATP-lids and C-terminal tails.
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Affiliation(s)
- Jihoon Kang
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea
| | - Haushabhau S Pagire
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea
| | - Donguk Kang
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea
| | - Yo Han Song
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea
| | - In Kyu Lee
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu, 41944, Republic of Korea
| | - Kang Taek Lee
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea
| | - Chin-Ju Park
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea
| | - Jin Hee Ahn
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea
| | - Jungwook Kim
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea.
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15
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Affiliation(s)
- Matthew D. Lloyd
- Drug & Target Development, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, U.K
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16
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Cho H, Shin I, Cho K, Yoon H, Yoo EK, Kim MJ, Park S, Lee IK, Kim ND, Sim T. Identification of Novel Resorcinol Amide Derivatives as Potent and Specific Pyruvate Dehydrogenase Kinase (PDHK) Inhibitors. J Med Chem 2019; 62:8461-8479. [DOI: 10.1021/acs.jmedchem.9b00565] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Hanna Cho
- KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Injae Shin
- KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Kyungseon Cho
- Chemical Kinomics Research Center, Korea Institute of Science and Technology (KIST), 5 Hwarangro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Hojong Yoon
- Chemical Kinomics Research Center, Korea Institute of Science and Technology (KIST), 5 Hwarangro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Eun Kyung Yoo
- Leading-Edge Research Center for Drug Discovery and Development for Diabetes and Metabolic Disease, Kyungpook National University Hospital, Daegu 41404, Republic of Korea
| | - Mi-Jin Kim
- Leading-Edge Research Center for Drug Discovery and Development for Diabetes and Metabolic Disease, Kyungpook National University Hospital, Daegu 41404, Republic of Korea
| | - Sungmi Park
- Leading-Edge Research Center for Drug Discovery and Development for Diabetes and Metabolic Disease, Kyungpook National University Hospital, Daegu 41404, Republic of Korea
| | - In-Kyu Lee
- Leading-Edge Research Center for Drug Discovery and Development for Diabetes and Metabolic Disease, Kyungpook National University Hospital, Daegu 41404, Republic of Korea
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu 41944, Republic of Korea
| | - Nam Doo Kim
- Daegu-Gyeongbuk Medical Innovation Foundation, 2387 Dalgubeol-daero, Suseong-gu, Daegu 42019, Republic of Korea
- NDBio Therapeutics Inc., 32 Songdogwahak-ro, Yeonsu-gu, Incheon 21984, Republic of Korea
| | - Taebo Sim
- KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
- Chemical Kinomics Research Center, Korea Institute of Science and Technology (KIST), 5 Hwarangro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea
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