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Cui Y, Zhang J, Zhang G. The Potential Strategies for Overcoming Multidrug Resistance and Reducing Side Effects of Monomer Tubulin Inhibitors for Cancer Therapy. Curr Med Chem 2024; 31:1874-1895. [PMID: 37349994 DOI: 10.2174/0929867330666230622142505] [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: 01/29/2023] [Revised: 04/26/2023] [Accepted: 05/12/2023] [Indexed: 06/24/2023]
Abstract
BACKGROUND Tubulin is an essential target in tumor therapy, and this is attributed to its ability to target MT dynamics and interfere with critical cellular functions, including mitosis, cell signaling, and intracellular trafficking. Several tubulin inhibitors have been approved for clinical application. However, the shortcomings, such as drug resistance and toxic side effects, limit its clinical application. Compared with single-target drugs, multi-target drugs can effectively improve efficacy to reduce side effects and overcome the development of drug resistance. Tubulin protein degraders do not require high concentrations and can be recycled. After degradation, the protein needs to be resynthesized to regain function, which significantly delays the development of drug resistance. METHODS Using SciFinder® as a tool, the publications about tubulin-based dual-target inhibitors and tubulin degraders were surveyed with an exclusion of those published as patents. RESULTS This study presents the research progress of tubulin-based dual-target inhibitors and tubulin degraders as antitumor agents to provide a reference for developing and applying more efficient drugs for cancer therapy. CONCLUSION The multi-target inhibitors and protein degraders have shown a development prospect to overcome multidrug resistance and reduce side effects in the treatment of tumors. Currently, the design of dual-target inhibitors for tubulin needs to be further optimized, and it is worth further clarifying the detailed mechanism of protein degradation.
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Affiliation(s)
- Yingjie Cui
- Department of Pharmacy, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, P.R. China
| | - Jing Zhang
- Department of Pharmacy, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, P.R. China
| | - Guifang Zhang
- Department of Pharmacy, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, P.R. China
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2
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Szabo E, Nagy B, Czajlik A, Komlodi T, Ozohanics O, Tretter L, Ambrus A. Mitochondrial Alpha-Keto Acid Dehydrogenase Complexes: Recent Developments on Structure and Function in Health and Disease. Subcell Biochem 2024; 104:295-381. [PMID: 38963492 DOI: 10.1007/978-3-031-58843-3_13] [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: 07/05/2024]
Abstract
The present work delves into the enigmatic world of mitochondrial alpha-keto acid dehydrogenase complexes discussing their metabolic significance, enzymatic operation, moonlighting activities, and pathological relevance with links to underlying structural features. This ubiquitous family of related but diverse multienzyme complexes is involved in carbohydrate metabolism (pyruvate dehydrogenase complex), the citric acid cycle (α-ketoglutarate dehydrogenase complex), and amino acid catabolism (branched-chain α-keto acid dehydrogenase complex, α-ketoadipate dehydrogenase complex); the complexes all function at strategic points and also participate in regulation in these metabolic pathways. These systems are among the largest multienzyme complexes with at times more than 100 protein chains and weights ranging up to ~10 million Daltons. Our chapter offers a wealth of up-to-date information on these multienzyme complexes for a comprehensive understanding of their significance in health and disease.
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Affiliation(s)
- Eszter Szabo
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Balint Nagy
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Andras Czajlik
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Timea Komlodi
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Oliver Ozohanics
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Laszlo Tretter
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Attila Ambrus
- Department of Biochemistry, Semmelweis University, Budapest, Hungary.
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3
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Liu S, Kormos BL, Knafels JD, Sahasrabudhe PV, Rosado A, Sommese RF, Reyes AR, Ward J, Roth Flach RJ, Wang X, Buzon LM, Reese MR, Bhattacharya SK, Omoto K, Filipski KJ. Structural studies identify angiotensin II receptor blocker-like compounds as branched-chain ketoacid dehydrogenase kinase inhibitors. J Biol Chem 2023; 299:102959. [PMID: 36717078 PMCID: PMC9976451 DOI: 10.1016/j.jbc.2023.102959] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 01/19/2023] [Accepted: 01/25/2023] [Indexed: 01/30/2023] Open
Abstract
The mammalian mitochondrial branched-chain ketoacid dehydrogenase (BCKD) complex is a multienzyme complex involved in the catabolism of branched-chain amino acids. BCKD is regulated by the BCKD kinase, or BCKDK, which binds to the E2 subunit of BCKD, phosphorylates its E1 subunit, and inhibits enzymatic activity. Inhibition of the BCKD complex results in increased levels of branched-chain amino acids and branched-chain ketoacids, and this buildup has been associated with heart failure, type 2 diabetes mellitus, and nonalcoholic fatty liver disease. To find BCKDK inhibitors for potential treatment of these diseases, we performed both NMR and virtual fragment screening and identified tetrazole-bearing fragments that bind BCKDK at multiple sites. Through structure-based virtual screening expanding from these fragments, the angiotensin receptor blocker class antihypertension drugs and angiotensin receptor blocker-like compounds were discovered to be potent BCKDK inhibitors, suggesting potential new avenues for heart failure treatment combining BCKDK inhibition and antihypertension.
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Affiliation(s)
- Shenping Liu
- Medicine Design, Pfizer Inc, Groton, Connecticut, USA.
| | | | | | | | - Amy Rosado
- Medicine Design, Pfizer Inc, Groton, Connecticut, USA
| | | | - Allan R Reyes
- Internal Medicine Research Unit, Pfizer Inc, Cambridge, Massachusetts, USA
| | - Jessica Ward
- Internal Medicine Research Unit, Pfizer Inc, Cambridge, Massachusetts, USA
| | | | - Xiaochun Wang
- Medicine Design, Pfizer Inc, Groton, Connecticut, USA
| | | | | | | | - Kiyoyuki Omoto
- Medicine Design, Pfizer Inc, Cambridge, Massachusetts, USA
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4
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Mobet Y, Liu X, Liu T, Yu J, Yi P. Interplay Between m6A RNA Methylation and Regulation of Metabolism in Cancer. Front Cell Dev Biol 2022; 10:813581. [PMID: 35186927 PMCID: PMC8851358 DOI: 10.3389/fcell.2022.813581] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 01/17/2022] [Indexed: 12/14/2022] Open
Abstract
Methylation of adenosine in RNA to N6-methyladenosine (m6A) is widespread in eukaryotic cells with his integral RNA regulation. This dynamic process is regulated by methylases (editors/writers), demethylases (remover/erasers), and proteins that recognize methylation (effectors/readers). It is now evident that m6A is involved in the proliferation and metastasis of cancer cells, for instance, altering cancer cell metabolism. Thus, determining how m6A dysregulates metabolic pathways could provide potential targets for cancer therapy or early diagnosis. This review focuses on the link between the m6A modification and the reprogramming of metabolism in cancer. We hypothesize that m6A modification could dysregulate the expression of glucose, lipid, amino acid metabolism, and other metabolites or building blocks of cells by adaptation to the hypoxic tumor microenvironment, an increase in glycolysis, mitochondrial dysfunction, and abnormal expression of metabolic enzymes, metabolic receptors, transcription factors as well as oncogenic signaling pathways in both hematological malignancies and solid tumors. These metabolism abnormalities caused by m6A’s modification may affect the metabolic reprogramming of cancer cells and then increase cell proliferation, tumor initiation, and metastasis. We conclude that focusing on m6A could provide new directions in searching for novel therapeutic and diagnostic targets for the early detection and treatment of many cancers.
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Affiliation(s)
- Youchaou Mobet
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Laboratory of Biochemistry, Faculty of Science, University of Douala, Douala, Cameroon
| | - Xiaoyi Liu
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Tao Liu
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
- *Correspondence: Tao Liu, ; Jianhua Yu, ; Ping Yi,
| | - Jianhua Yu
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Los Angeles, CA, United States
- Hematologic Malignancies and Stem Cell Transplantation Institute, City of Hope National Medical Center, Los Angeles, CA, United States
- Comprehensive Cancer Center, City of Hope, Los Angeles, CA, United States
- *Correspondence: Tao Liu, ; Jianhua Yu, ; Ping Yi,
| | - Ping Yi
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
- *Correspondence: Tao Liu, ; Jianhua Yu, ; Ping Yi,
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5
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Soltan OM, Shoman ME, Abdel-Aziz SA, Narumi A, Konno H, Abdel-Aziz M. Molecular hybrids: A five-year survey on structures of multiple targeted hybrids of protein kinase inhibitors for cancer therapy. Eur J Med Chem 2021; 225:113768. [PMID: 34450497 DOI: 10.1016/j.ejmech.2021.113768] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/23/2021] [Accepted: 08/08/2021] [Indexed: 02/07/2023]
Abstract
Protein kinases have grown over the past few years as a crucial target for different cancer types. With the multifactorial nature of cancer, and the fast development of drug resistance for conventional chemotherapeutics, a strategy for designing multi-target agents was suggested to potentially increase drug efficacy, minimize side effects and retain the proper pharmacokinetic properties. Kinase inhibitors were used extensively in such strategy. Different kinase inhibitor agents which target EGFR, VEGFR, c-Met, CDK, PDK and other targets were merged into hybrids with conventional chemotherapeutics such as tubulin polymerization and topoisomerase inhibitors. Other hybrids were designed gathering kinase inhibitors with targeted cancer therapy such as HDAC, PARP, HSP 90 inhibitors. Nitric oxide donor molecules were also merged with kinase inhibitors for cancer therapy. The current review presents the hybrids designed in the past five years discussing their design principles, results and highlights their future perspectives.
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Affiliation(s)
- Osama M Soltan
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Al-Azhar University, Assiut Branch, Assiut, 71524, Egypt
| | - Mai E Shoman
- Department of Medicinal Chemistry, Faculty of Pharmacy, Minia University, 61519, Minia, Egypt.
| | - Salah A Abdel-Aziz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Al-Azhar University, Assiut Branch, Assiut, 71524, Egypt; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Deraya University, 61111, Minia, Egypt
| | - Atsushi Narumi
- Department of Organic Materials Science, Graduate School of Organic Materials Science, Yamagata University, Jonan 4-3-16, Yonezawa, 992-8510, Japan
| | - Hiroyuki Konno
- Department of Biological Engineering, Graduate School of Science and Engineering, Yamagata University, Jonan 4-3-16, Yonezawa, 992-8510, Japan
| | - Mohamed Abdel-Aziz
- Department of Medicinal Chemistry, Faculty of Pharmacy, Minia University, 61519, Minia, Egypt.
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Škerlová J, Berndtsson J, Nolte H, Ott M, Stenmark P. Structure of the native pyruvate dehydrogenase complex reveals the mechanism of substrate insertion. Nat Commun 2021; 12:5277. [PMID: 34489474 PMCID: PMC8421416 DOI: 10.1038/s41467-021-25570-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 08/13/2021] [Indexed: 02/07/2023] Open
Abstract
The pyruvate dehydrogenase complex (PDHc) links glycolysis to the citric acid cycle by converting pyruvate into acetyl-coenzyme A. PDHc encompasses three enzymatically active subunits, namely pyruvate dehydrogenase, dihydrolipoyl transacetylase, and dihydrolipoyl dehydrogenase. Dihydrolipoyl transacetylase is a multidomain protein comprising a varying number of lipoyl domains, a peripheral subunit-binding domain, and a catalytic domain. It forms the structural core of the complex, provides binding sites for the other enzymes, and shuffles reaction intermediates between the active sites through covalently bound lipoyl domains. The molecular mechanism by which this shuttling occurs has remained elusive. Here, we report a cryo-EM reconstruction of the native E. coli dihydrolipoyl transacetylase core in a resting state. This structure provides molecular details of the assembly of the core and reveals how the lipoyl domains interact with the core at the active site.
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Affiliation(s)
- Jana Škerlová
- grid.10548.380000 0004 1936 9377Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Jens Berndtsson
- grid.10548.380000 0004 1936 9377Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Hendrik Nolte
- grid.419502.b0000 0004 0373 6590Max-Planck-Institute for Biology of Ageing, Cologne, Germany
| | - Martin Ott
- grid.10548.380000 0004 1936 9377Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden ,grid.8761.80000 0000 9919 9582Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Pål Stenmark
- grid.10548.380000 0004 1936 9377Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden ,grid.4514.40000 0001 0930 2361Department of Experimental Medical Science, Lund University, Lund, Sweden
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7
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Ferrarini MG, Nisimura LM, Girard RMBM, Alencar MB, Fragoso MSI, Araújo-Silva CA, Veiga ADA, Abud APR, Nardelli SC, Vommaro RC, Silber AM, France-Sagot M, Ávila AR. Dichloroacetate and Pyruvate Metabolism: Pyruvate Dehydrogenase Kinases as Targets Worth Investigating for Effective Therapy of Toxoplasmosis. mSphere 2021; 6:e01002-20. [PMID: 33408226 PMCID: PMC7845590 DOI: 10.1128/msphere.01002-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 12/09/2020] [Indexed: 12/31/2022] Open
Abstract
Toxoplasmosis, a protozoan infection caused by Toxoplasma gondii, is estimated to affect around 2.5 billion people worldwide. Nevertheless, the side effects of drugs combined with the long period of therapy usually result in discontinuation of the treatment. New therapies should be developed by exploring peculiarities of the parasite's metabolic pathways, similarly to what has been well described in cancer cell metabolism. An example is the switch in the metabolism of cancer that blocks the conversion of pyruvate into acetyl coenzyme A in mitochondria. In this context, dichloroacetate (DCA) is an anticancer drug that reverts the tumor proliferation by inhibiting the enzymes responsible for this switch: the pyruvate dehydrogenase kinases (PDKs). DCA has also been used in the treatment of certain symptoms of malaria; however, there is no evidence of how this drug affects apicomplexan species. In this paper, we studied the metabolism of T. gondii and demonstrate that DCA also inhibits T. gondii's in vitro infection with no toxic effects on host cells. DCA caused an increase in the activity of pyruvate dehydrogenase followed by an unbalanced mitochondrial activity. We also observed morphological alterations frequently in mitochondria and in a few apicoplasts, essential organelles for parasite survival. To date, the kinases that potentially regulate the activity of pyruvate metabolism in both organelles have never been described. Here, we confirmed the presence in the genome of two putative kinases (T. gondii PDK [TgPDK] and T. gondii branched-chain α-keto acid dehydrogenase kinase [TgBCKDK]), verified their cellular localization in the mitochondrion, and provided in silico data suggesting that they are potential targets of DCA.IMPORTANCE Currently, the drugs used for toxoplasmosis have severe toxicity to human cells, and the treatment still lacks effective and safer alternatives. The search for novel drug targets is timely. We report here that the treatment of T. gondii with an anticancer drug, dichloroacetate (DCA), was effective in decreasing in vitro infection without toxicity to human cells. It is known that PDK is the main target of DCA in mammals, and this inactivation increases the conversion of pyruvate into acetyl coenzyme A and reverts the proliferation of tumor cells. Moreover, we verified the mitochondrial localization of two kinases that possibly regulate the activity of pyruvate metabolism in T. gondii, which has never been studied. DCA increased pyruvate dehydrogenase (PDH) activity in T. gondii, followed by an unbalanced mitochondrial activity, in a manner similar to what was previously observed in cancer cells. Thus, we propose the conserved kinases as potential regulators of pyruvate metabolism and interesting targets for new therapies.
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Affiliation(s)
- Mariana Galvão Ferrarini
- Laboratoire de Biométrie et Biologie Évolutive, UMR 5558, CNRS, Université de Lyon 1, Villeurbanne, France
| | - Lindice Mitie Nisimura
- Laboratório de Pesquisa em Apicomplexa, Instituto Carlos Chagas, Fiocruz, Paraná, Brazil
| | - Richard Marcel Bruno Moreira Girard
- Laboratory of Biochemistry of Tryps, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Mayke Bezerra Alencar
- Laboratory of Biochemistry of Tryps, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | | | - Carlla Assis Araújo-Silva
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Bioimagens, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alan de Almeida Veiga
- Laboratório de Pesquisa em Apicomplexa, Instituto Carlos Chagas, Fiocruz, Paraná, Brazil
| | | | | | - Rossiane C Vommaro
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Bioimagens, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ariel Mariano Silber
- Laboratory of Biochemistry of Tryps, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Marie France-Sagot
- Laboratoire de Biométrie et Biologie Évolutive, UMR 5558, CNRS, Université de Lyon 1, Villeurbanne, France
- INRIA Grenoble Rhône-Alpes, Montbonnot-Saint-Martin, France
| | - Andréa Rodrigues Ávila
- Laboratório de Pesquisa em Apicomplexa, Instituto Carlos Chagas, Fiocruz, Paraná, Brazil
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8
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Skalidis I, Tüting C, Kastritis PL. Unstructured regions of large enzymatic complexes control the availability of metabolites with signaling functions. Cell Commun Signal 2020; 18:136. [PMID: 32843078 PMCID: PMC7448341 DOI: 10.1186/s12964-020-00631-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/17/2020] [Indexed: 12/23/2022] Open
Abstract
Metabolites produced via traditional biochemical processes affect intracellular communication, inflammation, and malignancy. Unexpectedly, acetyl-CoA, α-ketoglutarate and palmitic acid, which are chemical species of reactions catalyzed by highly abundant, gigantic enzymatic complexes, dubbed as "metabolons", have broad "nonmetabolic" signaling functions. Conserved unstructured regions within metabolons determine the yield of these metabolites. Unstructured regions tether functional protein domains, act as spatial constraints to confine constituent enzyme communication, and, in the case of acetyl-CoA production, tend to be regulated by intricate phosphorylation patterns. This review presents the multifaceted roles of these three significant metabolites and describes how their perturbation leads to altered or transformed cellular function. Their dedicated enzymatic systems are then introduced, namely, the pyruvate dehydrogenase (PDH) and oxoglutarate dehydrogenase (OGDH) complexes, and the fatty acid synthase (FAS), with a particular focus on their structural characterization and the localization of unstructured regions. Finally, upstream metabolite regulation, in which spatial occupancy of unstructured regions within dedicated metabolons may affect metabolite availability and subsequently alter cell functions, is discussed. Video abstract.
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Affiliation(s)
- Ioannis Skalidis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany.,Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle/Saale, Germany
| | - Christian Tüting
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany.,Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle/Saale, Germany
| | - Panagiotis L Kastritis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany. .,Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle/Saale, Germany. .,ZIK HALOmem, Martin Luther University Halle-Wittenberg, Biozentrum, Room A.2.14, Weinbergweg 22, 06120, Halle/Saale, Germany.
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9
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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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10
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Investigation of inhibitory potential of quercetin to the pyruvate dehydrogenase kinase 3: Towards implications in anticancer therapy. Int J Biol Macromol 2019; 136:1076-1085. [DOI: 10.1016/j.ijbiomac.2019.06.158] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/19/2019] [Accepted: 06/21/2019] [Indexed: 12/27/2022]
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11
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Dahiya R, Mohammad T, Gupta P, Haque A, Alajmi MF, Hussain A, Hassan MI. Molecular interaction studies on ellagic acid for its anticancer potential targeting pyruvate dehydrogenase kinase 3. RSC Adv 2019; 9:23302-23315. [PMID: 35514501 PMCID: PMC9067284 DOI: 10.1039/c9ra02864a] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 07/15/2019] [Indexed: 11/21/2022] Open
Abstract
Pyruvate dehydrogenase kinase 3 (PDK3) plays a central role in the cancer metabolic switch through the reversible phosphorylation of pyruvate dehydrogenase complex thereby blocking the entry of pyruvate for its catabolism into the TCA cycle, and thus it is considered as an important drug target for various types of cancers. We have successfully expressed full length human PDK3 and investigated its interaction mechanism with dietary polyphenols in the search for potential inhibitors. Molecular docking analysis revealed that the selected compounds preferentially bind to the ATP-binding pocket of PDK3 and interact with functionally important residues. In silico observations were further complemented by experimental measurements of the fluorescence quenching of PDK3 and confirmed with the isothermal titration calorimetry measurements. Ellagic acid (EA) significantly binds and inhibits the kinase activity of PDK3. In vitro cytotoxicity and the anti-proliferative properties of EA were evaluated by MTT assay. Conformational dynamics of the EA-PDK3 complex during molecular dynamics simulation revealed that a stable complex was maintained by a significant number of hydrogen bonds throughout the 100 ns trajectories. In conclusion, EA may be considered as a promising molecule for PDK3 inhibition and could be exploited as a lead molecule against PDK3 associated diseases. PDK3 plays a central role in cancer through the reversible phosphorylation of PDC thereby blocking the entry of pyruvate into the TCA cycle. PDK3 mediated metabolic switching can be therapeutically targeted for glycolysis addicted cancers.![]()
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Affiliation(s)
- Rashmi Dahiya
- Centre for Interdisciplinary Research in Basic Sciences
- Jamia Millia Islamia
- New Delhi 110025
- India
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences
- Jamia Millia Islamia
- New Delhi 110025
- India
| | - Preeti Gupta
- Centre for Interdisciplinary Research in Basic Sciences
- Jamia Millia Islamia
- New Delhi 110025
- India
| | - Anzarul Haque
- Centre for Interdisciplinary Research in Basic Sciences
- Jamia Millia Islamia
- New Delhi 110025
- India
| | - Mohamed F. Alajmi
- Department of Pharmacognosy College of Pharmacy
- King Saud University
- Riyadh 11451
- Kingdom of Saudi Arabia
| | - Afzal Hussain
- Department of Pharmacognosy College of Pharmacy
- King Saud University
- Riyadh 11451
- Kingdom of Saudi Arabia
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences
- Jamia Millia Islamia
- New Delhi 110025
- India
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12
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Lin HY, Han HW, Sun WX, Yang YS, Tang CY, Lu GH, Qi JL, Wang XM, Yang YH. Design and characterization of α -lipoic acyl shikonin ester twin drugs as tubulin and PDK1 dual inhibitors. Eur J Med Chem 2018; 144:137-150. [DOI: 10.1016/j.ejmech.2017.12.019] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 12/05/2017] [Accepted: 12/06/2017] [Indexed: 01/05/2023]
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13
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Synthesis and biological evaluation of (R)-3,3,3-trifluoro-2-hydroxy-2-methylpropionamides as pyruvate dehydrogenase kinase 1 (PDK1) inhibitors to reduce the growth of cancer cells. Eur J Pharm Sci 2017; 110:87-92. [DOI: 10.1016/j.ejps.2017.03.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 03/13/2017] [Accepted: 03/23/2017] [Indexed: 12/23/2022]
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14
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Fang A, Luo H, Liu L, Fan H, Zhou Y, Yao Y, Zhang Y. Identification of pyruvate dehydrogenase kinase 1 inhibitors with anti-osteosarcoma activity. Bioorg Med Chem Lett 2017; 27:5450-5453. [PMID: 29150396 DOI: 10.1016/j.bmcl.2017.10.073] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 10/25/2017] [Accepted: 10/28/2017] [Indexed: 02/05/2023]
Abstract
Overexpression of pyruvate dehydrogenase kinases (PDKs), especially PDK1 has been observed in a variety of cancers. Thus, targeting PDK1 offers an attractive opportunity for the development of cancer therapies. In this letter, we reported the identification of two novel PDK1 inhibitors as anti-osteosarcoma agents. We found that TM-1 and TM-2 inhibited PDK1 with the IC50 values of 2.97 and 3.41 μM, respectively. Furthermore, TM-1 and TM-2 dose-dependently reduced phosphorylation of pyruvate dehydrogenase complex in MG-63 osteosarcoma cells. Finally, TM-1 and TM-2 were found to inhibit the proliferation of MG-63 cells with the EC50 values of 14.5, and 11.0 μM, respectively, meaning TM-1 and TM-2 could be promising leads for the discovery of potent PDK1 inhibitors.
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Affiliation(s)
- Aiping Fang
- West China School of Public Health/No. 4 West China Teaching Hospital, Sichuan University, Chengdu 610041, PR China; State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Huiqiang Luo
- West China School of Public Health/No. 4 West China Teaching Hospital, Sichuan University, Chengdu 610041, PR China
| | - Liping Liu
- Department of Hepatobiliary and Pancreas Surgery, The Second Clinical Medical College of Jinan University, (Shenzhen People's Hospital), Shenzhen 518020, Guangdong Province, PR China
| | - Haibo Fan
- Department of Hepatobiliary and Pancreas Surgery, The Second Clinical Medical College of Jinan University, (Shenzhen People's Hospital), Shenzhen 518020, Guangdong Province, PR China
| | - Yaying Zhou
- Department of Hepatobiliary and Pancreas Surgery, The Second Clinical Medical College of Jinan University, (Shenzhen People's Hospital), Shenzhen 518020, Guangdong Province, PR China
| | - Yuqin Yao
- West China School of Public Health/No. 4 West China Teaching Hospital, Sichuan University, Chengdu 610041, PR China; State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Yue Zhang
- Department of Hepatobiliary and Pancreas Surgery, The Second Clinical Medical College of Jinan University, (Shenzhen People's Hospital), Shenzhen 518020, Guangdong Province, PR China.
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15
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Zhang SL, Hu X, Zhang W, Tam KY. Unexpected Discovery of Dichloroacetate Derived Adenosine Triphosphate Competitors Targeting Pyruvate Dehydrogenase Kinase To Inhibit Cancer Proliferation. J Med Chem 2016; 59:3562-8. [PMID: 27006991 DOI: 10.1021/acs.jmedchem.5b01828] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Pyruvate dehydrogenase kinases (PDKs) have recently emerged as an attractive target for cancer therapy. Herein, we prepared a series of compounds derived from dichloroacetate (DCA) which inhibited cancer cells proliferation. For the first time, we have successfully developed DCA derived inhibitors that preferentially bind to the adenosine triphosphate (ATP) pocket of PDK isoform 1 (PDK1).
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Affiliation(s)
- Shao-Lin Zhang
- Drug Development Core, Faculty of Health Sciences, University of Macau , Taipa, Macau, China
| | - Xiaohui Hu
- Drug Development Core, Faculty of Health Sciences, University of Macau , Taipa, Macau, China
| | - Wen Zhang
- Drug Development Core, Faculty of Health Sciences, University of Macau , Taipa, Macau, China
| | - Kin Yip Tam
- Drug Development Core, Faculty of Health Sciences, University of Macau , Taipa, Macau, China
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16
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Zhang W, Zhang SL, Hu X, Tam KY. Targeting Tumor Metabolism for Cancer Treatment: Is Pyruvate Dehydrogenase Kinases (PDKs) a Viable Anticancer Target? Int J Biol Sci 2015; 11:1390-400. [PMID: 26681918 PMCID: PMC4671996 DOI: 10.7150/ijbs.13325] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 09/07/2015] [Indexed: 01/07/2023] Open
Abstract
Cancer remains a lethal threat to global lives. Development of novel anticancer therapeutics is still a challenge to scientists in the field of biomedicine. In cancer cells, the metabolic features are significantly different from those of normal ones, which are hallmarks of several malignancies. Recent studies brought atypical cellular metabolism, such as aerobic glycolysis or the Warburg effect, into the scientific limelight. Targeting these altered metabolic pathways in cancer cells presents a promising therapeutic strategy. Pyruvate dehydrogenase kinases (PDKs), key enzymes in the pathway of glucose metabolism, could inactivate the pyruvate dehydrogenase complex (PDC) by phosphorylating it and preserving the substrates pyruvate, lactate and alanine for gluconeogenesis. Overexpression of PDKs could block the oxidative decarboxylation of pyruvate to satisfy high oxygen demand in cancer cells, while inhibition of PDKs could upregulate the activity of PDC and rectify the balance between the demand and supply of oxygen, which could lead to cancer cell death. Thus, inhibitors targeting PDKs represent a promising strategy for cancer treatment by acting on glycolytic tumors while showing minimal side effects on the oxidative healthy organs. This review considers the role of PDKs as regulator of PDC that catalyzes the oxidative decarboxylation of pyruvate in mitochondrion. It is concluded that PDKs are solid therapeutic targets. Inhibition of PDKs could be an attractive therapeutic approach for the development of anti-cancer drugs.
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Affiliation(s)
- Wen Zhang
- Drug Development Core, Faculty of Health Sciences, University of Macau, Macau, China
| | - Shao-Lin Zhang
- Drug Development Core, Faculty of Health Sciences, University of Macau, Macau, China
| | - Xiaohui Hu
- Drug Development Core, Faculty of Health Sciences, University of Macau, Macau, China
| | - Kin Yip Tam
- Drug Development Core, Faculty of Health Sciences, University of Macau, Macau, China
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17
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Zhang SL, Hu X, Zhang W, Yao H, Tam KY. Development of pyruvate dehydrogenase kinase inhibitors in medicinal chemistry with particular emphasis as anticancer agents. Drug Discov Today 2015; 20:1112-9. [PMID: 25842042 DOI: 10.1016/j.drudis.2015.03.012] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 03/10/2015] [Accepted: 03/25/2015] [Indexed: 12/25/2022]
Abstract
Many cancer cells demonstrate a high rate of glucose consumption via glycolysis to provide intermediates for macromolecule biosynthesis. To accomplish this metabolic change, the expression of pyruvate dehydrogenase kinases (PDKs) is rapidly increased in cancer cells. Inhibition of PDKs could promote the function of mitochondria by increasing the oxidative metabolism of pyruvate, resulting in the death of cancer cells. In this review, we provide an overview of the structural information available for PDKs and their connections to known therapeutic effects. We then describe the development of small molecule PDK inhibitors in medicinal chemistry with particular emphasis as anticancer agents. Finally, directions for further development of PDK inhibitors as potential anticancer agents are discussed.
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Affiliation(s)
- Shao-Lin Zhang
- Drug Development Core, Faculty of Health Sciences, University of Macau, Macau, China
| | - Xiaohui Hu
- Drug Development Core, Faculty of Health Sciences, University of Macau, Macau, China
| | - Wen Zhang
- Drug Development Core, Faculty of Health Sciences, University of Macau, Macau, China
| | - Huankai Yao
- Drug Development Core, Faculty of Health Sciences, University of Macau, Macau, China
| | - Kin Yip Tam
- Drug Development Core, Faculty of Health Sciences, University of Macau, Macau, China.
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18
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Elucidation of the interaction loci of the human pyruvate dehydrogenase complex E2·E3BP core with pyruvate dehydrogenase kinase 1 and kinase 2 by H/D exchange mass spectrometry and nuclear magnetic resonance. Biochemistry 2014; 54:69-82. [PMID: 25436986 PMCID: PMC4295793 DOI: 10.1021/bi5013113] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
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The human pyruvate dehydrogenase
complex (PDC) comprises three
principal catalytic components for its mission: E1, E2, and E3. The
core of the complex is a strong subcomplex between E2 and an E3-binding
protein (E3BP). The PDC is subject to regulation at E1 by serine phosphorylation
by four kinases (PDK1–4), an inactivation reversed by the action
of two phosphatases (PDP1 and -2). We report H/D exchange mass spectrometric
(HDX-MS) and nuclear magnetic resonance (NMR) studies in the first
attempt to define the interaction loci between PDK1 and PDK2 with
the intact E2·E3BP core and their C-terminally truncated proteins.
While the three lipoyl domains (L1 and L2 on E2 and L3 on E3BP) lend
themselves to NMR studies and determination of interaction maps with
PDK1 and PDK2 at the individual residue level, HDX-MS allowed studies
of interaction loci on both partners in the complexes, PDKs, and other
regions of the E2·E3BP core, as well, at the peptide level. HDX-MS
suggested that the intact E2·E3BP core enhances the binding specificity
of L2 for PDK2 over PDK1, while NMR studies detected lipoyl domain
residues unique to interaction with PDK1 and PDK2. The E2·E3BP
core induced more changes on PDKs than any C-terminally truncated
protein, with clear evidence of greater plasticity of PDK1 than of
PDK2. The effect of L1L2S paralleled HDX-MS results obtained with
the intact E2·E3BP core; hence, L1L2S is an excellent candidate
with which to define interaction loci with these two PDKs. Surprisingly,
L3S′ induced moderate interaction with both PDKs according
to both methods.
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19
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Patel MS, Nemeria NS, Furey W, Jordan F. The pyruvate dehydrogenase complexes: structure-based function and regulation. J Biol Chem 2014; 289:16615-23. [PMID: 24798336 DOI: 10.1074/jbc.r114.563148] [Citation(s) in RCA: 381] [Impact Index Per Article: 38.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The pyruvate dehydrogenase complexes (PDCs) from all known living organisms comprise three principal catalytic components for their mission: E1 and E2 generate acetyl-coenzyme A, whereas the FAD/NAD(+)-dependent E3 performs redox recycling. Here we compare bacterial (Escherichia coli) and human PDCs, as they represent the two major classes of the superfamily of 2-oxo acid dehydrogenase complexes with different assembly of, and interactions among components. The human PDC is subject to inactivation at E1 by serine phosphorylation by four kinases, an inactivation reversed by the action of two phosphatases. Progress in our understanding of these complexes important in metabolism is reviewed.
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Affiliation(s)
- Mulchand S Patel
- From the Department of Biochemistry, School of Medicine and Biomedical Sciences, University at Buffalo, the State University of New York, Buffalo, New York 14214,
| | - Natalia S Nemeria
- the Department of Chemistry, Rutgers, the State University of New Jersey, Newark, New Jersey 07102
| | - William Furey
- the Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, and the Veterans Affairs Medical Center, Pittsburgh, Pennsylvania 15240
| | - Frank Jordan
- the Department of Chemistry, Rutgers, the State University of New Jersey, Newark, New Jersey 07102,
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20
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Gray LR, Tompkins SC, Taylor EB. Regulation of pyruvate metabolism and human disease. Cell Mol Life Sci 2013; 71:2577-604. [PMID: 24363178 PMCID: PMC4059968 DOI: 10.1007/s00018-013-1539-2] [Citation(s) in RCA: 517] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 11/24/2013] [Accepted: 12/02/2013] [Indexed: 12/31/2022]
Abstract
Pyruvate is a keystone molecule critical for numerous aspects of eukaryotic and human metabolism. Pyruvate is the end-product of glycolysis, is derived from additional sources in the cellular cytoplasm, and is ultimately destined for transport into mitochondria as a master fuel input undergirding citric acid cycle carbon flux. In mitochondria, pyruvate drives ATP production by oxidative phosphorylation and multiple biosynthetic pathways intersecting the citric acid cycle. Mitochondrial pyruvate metabolism is regulated by many enzymes, including the recently discovered mitochondria pyruvate carrier, pyruvate dehydrogenase, and pyruvate carboxylase, to modulate overall pyruvate carbon flux. Mutations in any of the genes encoding for proteins regulating pyruvate metabolism may lead to disease. Numerous cases have been described. Aberrant pyruvate metabolism plays an especially prominent role in cancer, heart failure, and neurodegeneration. Because most major diseases involve aberrant metabolism, understanding and exploiting pyruvate carbon flux may yield novel treatments that enhance human health.
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Affiliation(s)
- Lawrence R Gray
- Department of Biochemistry, Fraternal Order of the Eagles Diabetes Research Center, and François M. Abboud Cardiovascular Research Center, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, 51 Newton Rd, 4-403 BSB, Iowa City, IA, 52242, USA
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21
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Kennerson ML, Yiu EM, Chuang DT, Kidambi A, Tso SC, Ly C, Chaudhry R, Drew AP, Rance G, Delatycki MB, Züchner S, Ryan MM, Nicholson GA. A new locus for X-linked dominant Charcot-Marie-Tooth disease (CMTX6) is caused by mutations in the pyruvate dehydrogenase kinase isoenzyme 3 (PDK3) gene. Hum Mol Genet 2013; 22:1404-16. [PMID: 23297365 PMCID: PMC3596851 DOI: 10.1093/hmg/dds557] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 12/16/2012] [Accepted: 12/27/2012] [Indexed: 01/30/2023] Open
Abstract
Hereditary motor and sensory disorders of the peripheral nerve form one of the most common groups of human genetic diseases collectively called Charcot-Marie-Tooth (CMT) neuropathy. Using linkage analysis in a three generation kindred, we have mapped a new locus for X-linked dominant CMT to chromosome Xp22.11. A microsatellite scan of the X chromosome established significant linkage to several markers including DXS993 (Zmax = 3.16; θ = 0.05). Extended haplotype analysis refined the linkage region to a 1.43-Mb interval flanked by markers DXS7110 and DXS8027. Whole exome sequencing identified a missense mutation c.G473A (p.R158H) in the pyruvate dehydrogenase kinase isoenzyme 3 (PDK3) gene. The change localized within the 1.43-Mb linkage interval, segregated with the affected phenotype and was excluded in ethnically matched control chromosomes. PDK3 is one of the four isoenzymes regulating the pyruvate dehydrogenase complex (PDC), by reversible phosphorylation, and is a nuclear-coded protein located in the mitochondrial matrix. PDC catalyzes the oxidative decarboxylation of pyruvate to acetyl CoA and is a key enzyme linking glycolysis to the energy-producing Krebs cycle and lipogenic pathways. We found that the R158H mutation confers enzyme hyperactivity and binds with stronger affinity than the wild-type to the inner-lipoyl (L2) domain of the E2p chain of PDC. Our findings suggest a reduced pyruvate flux due to R158H mutant PDK3-mediated hyper-phosphorylation of the PDC as the underlying pathogenic cause of peripheral neuropathy. The results highlight an important causative link between peripheral nerve degeneration and an essential bioenergetic or biosynthetic pathway required for the maintenance of peripheral nerves.
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Affiliation(s)
- Marina L Kennerson
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, NSW, Australia.
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22
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Hiromasa Y, Yan X, Roche TE. Specific ion influences on self-association of pyruvate dehydrogenase kinase isoform 2 (PDHK2), binding of PDHK2 to the L2 lipoyl domain, and effects of the lipoyl group-binding site inhibitor, Nov3r. Biochemistry 2008; 47:2312-24. [PMID: 18220415 DOI: 10.1021/bi7014772] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Association of the PDHK2 and GST-L2 (glutathione-S-transferase fused to the inner lipoyl domain (L2) of dihydrolipoyl acetyltransferase (E2)) dimers was enhanced by K+ with higher affinity K+ binding than occurs at the PDHK2 active site. Supporting a distinct K+ binding site, the NH4+ ion did not effectively replace K+ in aiding GST-L2 binding. With 50 mM K+, Pi enhanced interference by ADP, ATP, or pyruvate of PDHK2 binding to GST-L2. The inclusion of Pi with ADP or ATP plus pyruvate greatly hindered PDHK2 binding to GST-L2 and promoted PDHK2 forming a tetramer. Reciprocally, GST-L2 interference with ATP/ADP binding also required elevated K+ and was increased by Pi. Potent inhibition by Nov3r of E2-activated PDHK2 activity (IC50 of approximately 7.8 nM) required elevated K+ and Pi. Nov3r only modestly inhibited the low activity of PDHK2 without E2. By binding at the lipoyl group binding site, Nov3r prevented PDHK2 binding to E2 and GST-L2. Nov3r interfered with high-affinity binding of ADP and pyruvate via a Pi-dependent mechanism. Thus, GST-L2 binding to PDHK2 is supported by K+ binding at a site distinct from the active site. Pi makes major contributions to ligands interfering with PDHK2 binding to GST-L2, the conversion of PDHK2 dimer to a tetramer, and Nov3r (an acetyl-lipoate analog) interfering with binding of ADP and pyruvate. Pi is suggested to facilitate transmission within PDHK2 of the stimulatory signal of acetylation from the distal lipoyl-group binding site to the active site.
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Affiliation(s)
- Yasuaki Hiromasa
- Department of Biochemistry, Kansas State University, Manhattan, Kansas 66506, USA
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23
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Kato M, Li J, Chuang JL, Chuang DT. Distinct structural mechanisms for inhibition of pyruvate dehydrogenase kinase isoforms by AZD7545, dichloroacetate, and radicicol. Structure 2007; 15:992-1004. [PMID: 17683942 PMCID: PMC2871385 DOI: 10.1016/j.str.2007.07.001] [Citation(s) in RCA: 166] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2007] [Revised: 07/10/2007] [Accepted: 07/10/2007] [Indexed: 01/07/2023]
Abstract
Pyruvate dehydrogenase kinase (PDK) isoforms are molecular switches that downregulate the pyruvate dehydrogenase complex (PDC) by reversible phosphorylation in mitochondria. We have determined structures of human PDK1 or PDK3 bound to the inhibitors AZD7545, dichloroacetate (DCA), and radicicol. We show that the trifluoromethylpropanamide end of AZD7545 projects into the lipoyl-binding pocket of PDK1. This interaction results in inhibition of PDK1 and PDK3 activities by aborting kinase binding to the PDC scaffold. Paradoxically, AZD7545 at saturating concentrations robustly increases scaffold-free PDK3 activity, similar to the inner lipoyl domain. Good DCA density is present in the helix bundle in the N-terminal domain of PDK1. Bound DCA promotes local conformational changes that are communicated to both nucleotide-binding and lipoyl-binding pockets of PDK1, leading to the inactivation of kinase activity. Finally, radicicol inhibits kinase activity by binding directly to the ATP-binding pocket of PDK3, similar to Hsp90 and Topo VI from the same ATPase/kinase superfamily.
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Affiliation(s)
- Masato Kato
- Department of Internal Medicine University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jun Li
- Department of Biochemistry University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jacinta L. Chuang
- Department of Biochemistry University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - David T. Chuang
- Department of Internal Medicine University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Biochemistry University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Correspondence:
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24
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Vassylyev DG, Symersky J. Crystal structure of pyruvate dehydrogenase phosphatase 1 and its functional implications. J Mol Biol 2007; 370:417-26. [PMID: 17532339 PMCID: PMC1994205 DOI: 10.1016/j.jmb.2007.05.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2006] [Revised: 04/18/2007] [Accepted: 05/03/2007] [Indexed: 11/22/2022]
Abstract
Pyruvate dehydrogenase phosphatase 1 (PDP1) catalyzes dephosphorylation of pyruvate dehydrogenase (E1) in the mammalian pyruvate dehydrogenase complex (PDC), whose activity is regulated by the phosphorylation-dephosphorylation cycle by the corresponding protein kinases (PDHKs) and phosphatases. The activity of PDP1 is greatly enhanced through Ca2+ -dependent binding of the catalytic subunit (PDP1c) to the L2 (inner lipoyl) domain of dihydrolipoyl acetyltransferase (E2), which is also integrated in PDC. Here, we report the crystal structure of the rat PDP1c at 1.8 A resolution. The structure reveals that PDP1 belongs to the PPM family of protein serine/threonine phosphatases, which, in spite of a low level of sequence identity, share the structural core consisting of the central beta-sandwich flanked on both sides by loops and alpha-helices. Consistent with the previous studies, two well-fixed magnesium ions are coordinated by five active site residues and five water molecules in the PDP1c catalytic center. Structural analysis indicates that, while the central portion of the PDP1c molecule is highly conserved among the members of the PPM protein family, a number of structural insertions and deletions located at the periphery of PDP1c likely define its functional specificity towards the PDC. One notable feature of PDP1c is a long insertion (residues 98-151) forming a unique hydrophobic pocket on the surface that likely accommodates the lipoyl moiety of the E2 domain in a fashion similar to that of PDHKs. The cavity, however, appears more open than in PDHK, suggesting that its closure may be required to achieve tight, specific binding of the lipoic acid. We propose a mechanism in which the closure of the lipoic acid binding site is triggered by the formation of the intermolecular (PDP1c/L2) Ca2+ binding site in a manner reminiscent of the Ca2+ -induced closure of the regulatory domain of troponin C.
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Affiliation(s)
- Dmitry G Vassylyev
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, School of Medicine and Dentistry, Kaul Genetics Building, Birmingham, Al 35294, USA.
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