1
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Anwar S, Khan S, Hussain A, Alajmi MF, Shamsi A, Hassan MI. Investigating Pyruvate Dehydrogenase Kinase 3 Inhibitory Potential of Myricetin Using Integrated Computational and Spectroscopic Approaches. ACS OMEGA 2024; 9:29633-29643. [PMID: 39005765 PMCID: PMC11238318 DOI: 10.1021/acsomega.4c03001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/13/2024] [Accepted: 06/07/2024] [Indexed: 07/16/2024]
Abstract
Protein kinases are involved in various diseases and currently represent potential targets for drug discovery. These kinases play major roles in regulating the cellular machinery and control growth, homeostasis, and cell signaling. Dysregulation of kinase expression is associated with various disorders such as cancer and neurodegeneration. Pyruvate dehydrogenase kinase 3 (PDK3) is implicated in cancer therapeutics as a potential drug target. In this current study, a molecular docking exhibited a strong binding affinity of myricetin to PDK3. Further, a 100 ns all-atom molecular dynamics (MD) simulation study provided insights into the structural dynamics and stability of the PDK3-myricetin complex, revealing the formation of a stable complex with minimal structural alterations upon ligand binding. Additionally, the actual affinity was ascertained by fluorescence binding studies, and myricetin showed appreciable binding affinity to PDK3. Further, the kinase inhibition assay suggested significant inhibition of PDK3 by myricetin, revealing an excellent inhibitory potential with an IC50 value of 3.3 μM. In conclusion, this study establishes myricetin as a potent PDK3 inhibitor that can be implicated in therapeutic targeting cancer and PDK3-associated diseases. In addition, this study underscores the efficacy of myricetin as a potential lead to drug discovery and provides valuable insights into the inhibition mechanism, enabling advancements in cancer therapeutics.
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Affiliation(s)
- Saleha Anwar
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Shama Khan
- South
African Medical Research Council, Vaccines and Infectious Diseases
Analytics Research Unit, Faculty of Health Science, School of Pathology, University of the Witwatersrand, Johannesburg, 2193, South Africa
| | - Afzal Hussain
- Department
of Pharmacognosy, College of Pharmacy, King
Saud University, Riyadh, 4545, Saudi Arabia
| | - Mohamed F. Alajmi
- Department
of Pharmacognosy, College of Pharmacy, King
Saud University, Riyadh, 4545, Saudi Arabia
| | - Anas Shamsi
- Centre
of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman 364, United Arab
Emirates
| | - Md. Imtaiyaz Hassan
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
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2
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Zhang J, Wu X. The Whole Genome DNA Methylation Signatures of Hindlimb Muscles in Chinese Alligators during Hibernation and Active Periods. Animals (Basel) 2024; 14:1972. [PMID: 38998084 PMCID: PMC11240547 DOI: 10.3390/ani14131972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 06/12/2024] [Accepted: 07/02/2024] [Indexed: 07/14/2024] Open
Abstract
Many ectotherms hibernate to increase their chances of survival during harsh winter conditions. The role of DNA methylation in regulating gene expression related to hibernation in ectotherms remains unclear. Here, we employed whole-genome bisulfite sequencing (WGBS) technology to construct a comprehensive genome-wide DNA methylation landscape of the hindlimb muscles in the Chinese alligator during hibernation and active periods. The results indicated that methylation modifications were most abundant at CG sites, identifying 9447 differentially methylated regions (DMRs) and 2329 differentially methylated genes (DMGs). KEGG pathway enrichment analysis of the DMGs revealed significant enrichment in major pathways such as the neurotrophin signaling pathway, the MAPK signaling pathway, the GnRH signaling pathway, the biosynthesis of amino acids, and the regulation of the actin cytoskeleton, which are closely related to lipid metabolism, energy metabolism, and amino acid metabolism. Among these, 412 differentially methylated genes were located in promoter regions, including genes related to energy metabolism such as ATP5F1C, ATP5MD, PDK3, ANGPTL1, and ANGPTL2, and genes related to ubiquitin-proteasome degradation such as FBXO28, FBXO43, KLHL40, and PSMD5. These findings suggest that methylation in promoter regions may play a significant role in regulating the adaptive hibernation mechanisms in the Chinese alligator. This study contributes to a further understanding of the epigenetic mechanisms behind the hibernation of the Chinese alligator.
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Affiliation(s)
- Jihui Zhang
- School of Food Science and Biology Engineering, Wuhu Institute of Technology, Wuhu 241000, China
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Xiaobing Wu
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
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3
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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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Sha R, Dong X, Yan S, Dai H, Sun A, You L, Guo Z. Cuproptosis-related genes predict prognosis and trastuzumab therapeutic response in HER2-positive breast cancer. Sci Rep 2024; 14:2908. [PMID: 38316885 PMCID: PMC10844230 DOI: 10.1038/s41598-024-52638-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 01/22/2024] [Indexed: 02/07/2024] Open
Abstract
Breast cancer is the most common diagnosed cancer, the HER2-positive subtype account for 15% of all breast cancer. HER2-targeted therapy is the mainstay treatment for HER2-positive breast cancer. Cuproptosis is a novel form of programmed cell death, and is caused by mitochondrial lipoylation and destabilization of iron-sulfur proteins triggered by copper, which was considered as a key player in various biological processes. However, the roles of cuproptosis-related genes in HER2-positive breast cancer remain largely unknown. In the present study, we constructed a prognostic prediction model of HER2-positive breast cancer patients using TCGA database. Dysregulated genes for cells resistant to HER2-targeted therapy were analyzed in the GEO dataset. KEGG pathway, GO enrichment and GSEA was performed respectively. The immune landscape of DLAT was analyzed by CIBERSORT algorithm and TIDE algorithm. HER2-positive breast cancer patients with high CRGs risk score showed shorter OS. DLAT was downregulated and correlated with better survival of HER2-positive breast cancer patients (HR = 3.30, p = 0.022). High expressed DLAT was associated with resistant to HER2-targeted therapy. Knocking down DLAT with siRNA increased sensitivity of breast cancer to trastuzumab. KEGG pathway and GO enrichment of DEGs indicated that DLAT participates in various pathways correlated with organelle fission, chromosome segregation, nuclear division, hormone-mediated signaling pathway, regulation of intracellular estrogen receptor signaling pathway, condensed chromosome and PPAR signaling pathway. There was a negative correlation between TIDE and DLAT expression (r = - 0.292, p < 0.001), which means high DLAT expression is an indicator of sensitivity to immunotherapy. In conclusion, our study constructed a four CRGs signature prognostic prediction model and identified DLAT as an independent prognostic factor and associated with resistant to HER2-targeted therapy for HER2-positive breast cancer patients.
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Affiliation(s)
- Rui Sha
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), 2 Zheshan West Road, Wuhu, 241001, Anhui, China
| | - Xinrui Dong
- Department of Breast Surgery, The First Affiliated Hospital With Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu, China
| | - Shanshan Yan
- Center for Medical Ultrasound, Suzhou Municipal Hospital, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou, 215000, Jiangsu, China
| | - Huijuan Dai
- Renji Hospital, School of Medicine, Shanghai Jiaotong University, 1630 Dongfang Road, Shanghai, 200127, China
| | - Aijun Sun
- Department of Thyroid and Breast Oncological Surgery, Xuzhou Medical College Affiliated Huaian Hospital, 62 Huaihai South Road, Huaian, 223001, Jiangsu, China.
| | - Liuxia You
- Department of Clinical Laboratory, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, 362000, Fujian, China.
| | - Zongjin Guo
- Department of Interventional Radiology, The University of HongKong-Shenzhen Hospital, Shenzhen, 518053, China.
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5
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Jairajpuri DS, Khan S, Anwar S, Hussain A, Alajmi MF, Hassan I. Investigating the role of thymol as a promising inhibitor of pyruvate dehydrogenase kinase 3 for targeted cancer therapy. Int J Biol Macromol 2024; 259:129314. [PMID: 38211912 DOI: 10.1016/j.ijbiomac.2024.129314] [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: 09/29/2023] [Revised: 12/17/2023] [Accepted: 01/05/2024] [Indexed: 01/13/2024]
Abstract
Protein kinases have emerged as major contributors to various diseases. They are currently exploited as a potential target in drug discovery because they play crucial roles in cell signaling, growth, and regulation. Their dysregulation is associated with inflammatory disorders, cancer, and neurodegenerative diseases. Pyruvate dehydrogenase kinase 3 (PDK3) has become an attractive drug target in cancer therapeutics. In the present study, we investigated the effective role of thymol in PDK3 inhibition due to the high affinity predicted through molecular docking studies. Hence, to better understand this inhibition mechanism, we carried out a 100 ns molecular dynamics (MD) simulation to analyse the dynamics and stability of the PDK3-thymol complex. The PDK3-thymol complex was stable and energetically favourable, with many intramolecular hydrogen bond interactions in the PDK3-thymol complex. Enzyme inhibition assay showed significant inhibition of PDK3 by thymol, revealing potential inhibitory action of thymol towards PDK3 (IC50 = 2.66 μM). In summary, we established thymol as one of the potential inhibitors of PDK3, proposing promising therapeutic implications for severe diseases associated with PDK3 dysregulation. This study further advances our understanding of thymol's therapeutic capabilities and potential role in cancer treatment.
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Affiliation(s)
- Deeba Shamim Jairajpuri
- Department of Medical Biochemistry, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, Bahrain
| | - Shama Khan
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Science, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Saleha Anwar
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Afzal Hussain
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohamed F Alajmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.
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6
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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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7
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Pecoraro C, De Franco M, Carbone D, Bassani D, Pavan M, Cascioferro S, Parrino B, Cirrincione G, Dall'Acqua S, Moro S, Gandin V, Diana P. 1,2,4-Amino-triazine derivatives as pyruvate dehydrogenase kinase inhibitors: Synthesis and pharmacological evaluation. Eur J Med Chem 2023; 249:115134. [PMID: 36709650 DOI: 10.1016/j.ejmech.2023.115134] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/08/2023] [Accepted: 01/16/2023] [Indexed: 01/25/2023]
Abstract
Among the different hallmarks of cancer, deregulation of cellular metabolism turned out to be an essential mechanism in promoting cancer resistance and progression. The pyruvate dehydrogenase kinases (PDKs) are well known as key regulators in cells metabolic process and their activity was found to be overexpressed in different metabolic alerted types of cancer, including the high aggressive pancreatic ductal adenocarcinoma (PDAC). To date few PDK inhibitors have been reported, and the different molecules developed are characterized by structural chemical diversity. In an attempt to find novel classes of potential PDK inhibitors, the molecular hybridization approach, which combine two or more active scaffolds in a single structure, was employed. Herein we report the synthesis and the pharmacological evaluation of the novel hybrid molecules, characterized by the fusion of three different pharmacophoric sub-units such as 1,2,4-amino triazines, 7-azaindoles and indoles, in a single structure. The synthesized derivatives demonstrated a promising ability in hampering the enzymatic activity of PDK1 and 4, further confirmed by docking studies. Interestingly, these derivatives retained a strong antiproliferative activity against pancreatic cancer cells either in 2D and 3D models. Mechanistic studies in highly aggressive PDAC cells confirmed their ability to hamper PDK axis and to induce cancer cell death by apoptosis. Moreover, in vivo translational studies in a murine syngeneic solid tumor model confirmed the ability of the most representative compounds to target the PDK system and highlight the ability to reduce the tumor growth without inducing substantial body weight changes in the treated mice.
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Affiliation(s)
- Camilla Pecoraro
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, via Archirafi 32, 90123, Palermo, Italy
| | - Michele De Franco
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via F. Marzolo 5, 35131, Padova, Italy
| | - Daniela Carbone
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, via Archirafi 32, 90123, Palermo, Italy
| | - Davide Bassani
- Department of Pharmaceutical and Pharmacological Sciences, Molecular Modeling Section (MMS), University of Padova, via F. Marzolo 5, 35131, Padova, Italy
| | - Matteo Pavan
- Department of Pharmaceutical and Pharmacological Sciences, Molecular Modeling Section (MMS), University of Padova, via F. Marzolo 5, 35131, Padova, Italy
| | - Stella Cascioferro
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, via Archirafi 32, 90123, Palermo, Italy
| | - Barbara Parrino
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, via Archirafi 32, 90123, Palermo, Italy
| | - Girolamo Cirrincione
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, via Archirafi 32, 90123, Palermo, Italy
| | - Stefano Dall'Acqua
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via F. Marzolo 5, 35131, Padova, Italy
| | - Stefano Moro
- Department of Pharmaceutical and Pharmacological Sciences, Molecular Modeling Section (MMS), University of Padova, via F. Marzolo 5, 35131, Padova, Italy
| | - Valentina Gandin
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via F. Marzolo 5, 35131, Padova, Italy.
| | - Patrizia Diana
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, via Archirafi 32, 90123, Palermo, Italy.
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Carbone D, De Franco M, Pecoraro C, Bassani D, Pavan M, Cascioferro S, Parrino B, Cirrincione G, Dall’Acqua S, Moro S, Gandin V, Diana P. Discovery of the 3-Amino-1,2,4-triazine-Based Library as Selective PDK1 Inhibitors with Therapeutic Potential in Highly Aggressive Pancreatic Ductal Adenocarcinoma. Int J Mol Sci 2023; 24:ijms24043679. [PMID: 36835086 PMCID: PMC9959349 DOI: 10.3390/ijms24043679] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/06/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
Pyruvate dehydrogenase kinases (PDKs) are serine/threonine kinases, that are directly involved in altered cancer cell metabolism, resulting in cancer aggressiveness and resistance. Dichloroacetic acid (DCA) is the first PDK inhibitor that has entered phase II clinical; however, several side effects associated with weak anticancer activity and excessive drug dose (100 mg/kg) have led to its limitation in clinical application. Building upon a molecular hybridization approach, a small library of 3-amino-1,2,4-triazine derivatives has been designed, synthesized, and characterized for their PDK inhibitory activity using in silico, in vitro, and in vivo assays. Biochemical screenings showed that all synthesized compounds are potent and subtype-selective inhibitors of PDK. Accordingly, molecular modeling studies revealed that a lot of ligands can be properly placed inside the ATP-binding site of PDK1. Interestingly, 2D and 3D cell studies revealed their ability to induce cancer cell death at low micromolar doses, being extremely effective against human pancreatic KRAS mutated cancer cells. Cellular mechanistic studies confirm their ability to hamper the PDK/PDH axis, thus leading to metabolic/redox cellular impairment, and to ultimately trigger apoptotic cancer cell death. Remarkably, preliminary in vivo studies performed on a highly aggressive and metastatic Kras-mutant solid tumor model confirm the ability of the most representative compound 5i to target the PDH/PDK axis in vivo and highlighted its equal efficacy and better tolerability profile with respect to those elicited by the reference FDA approved drugs, cisplatin and gemcitabine. Collectively, the data highlights the promising anticancer potential of these novel PDK-targeting derivatives toward obtaining clinical candidates for combatting highly aggressive KRAS-mutant pancreatic ductal adenocarcinomas.
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Affiliation(s)
- Daniela Carbone
- Department of Biological, Chemical, and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Michele De Franco
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via F. Marzolo 5, 35131 Padova, Italy
| | - Camilla Pecoraro
- Department of Biological, Chemical, and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Davide Bassani
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via F. Marzolo 5, 35131 Padova, Italy
| | - Matteo Pavan
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via F. Marzolo 5, 35131 Padova, Italy
| | - Stella Cascioferro
- Department of Biological, Chemical, and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Barbara Parrino
- Department of Biological, Chemical, and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Girolamo Cirrincione
- Department of Biological, Chemical, and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Stefano Dall’Acqua
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via F. Marzolo 5, 35131 Padova, Italy
| | - Stefano Moro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via F. Marzolo 5, 35131 Padova, Italy
| | - Valentina Gandin
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via F. Marzolo 5, 35131 Padova, Italy
- Correspondence: (V.G.); (P.D.)
| | - Patrizia Diana
- Department of Biological, Chemical, and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Via Archirafi 32, 90123 Palermo, Italy
- Correspondence: (V.G.); (P.D.)
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9
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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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10
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Anwar S, DasGupta D, Shafie A, Alhumaydhi FA, Alsagaby SA, Shahwan M, Anjum F, Al Abdulmonem W, Sharaf SE, Imtaiyaz Hassan M. Implications of tempol in pyruvate dehydrogenase kinase 3 targeted anticancer therapeutics: Computational, spectroscopic, and calorimetric studies. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.118581] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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11
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Tüting C, Kyrilis FL, Müller J, Sorokina M, Skalidis I, Hamdi F, Sadian Y, Kastritis PL. Cryo-EM snapshots of a native lysate provide structural insights into a metabolon-embedded transacetylase reaction. Nat Commun 2021; 12:6933. [PMID: 34836937 PMCID: PMC8626477 DOI: 10.1038/s41467-021-27287-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 11/08/2021] [Indexed: 11/23/2022] Open
Abstract
Found across all kingdoms of life, 2-keto acid dehydrogenase complexes possess prominent metabolic roles and form major regulatory sites. Although their component structures are known, their higher-order organization is highly heterogeneous, not only across species or tissues but also even within a single cell. Here, we report a cryo-EM structure of the fully active Chaetomium thermophilum pyruvate dehydrogenase complex (PDHc) core scaffold at 3.85 Å resolution (FSC = 0.143) from native cell extracts. By combining cryo-EM with macromolecular docking and molecular dynamics simulations, we resolve all PDHc core scaffold interfaces and dissect the residing transacetylase reaction. Electrostatics attract the lipoyl domain to the transacetylase active site and stabilize the coenzyme A, while apolar interactions position the lipoate in its binding cleft. Our results have direct implications on the structural determinants of the transacetylase reaction and the role of flexible regions in the context of the overall 10 MDa PDHc metabolon architecture.
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Affiliation(s)
- Christian Tüting
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany
| | - Fotis L Kyrilis
- 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
| | - Johannes Müller
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle/Saale, Germany
| | - Marija Sorokina
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle/Saale, Germany
- RGCC International GmbH, Baarerstrasse 95, Zug, 6300, Switzerland
- BioSolutions GmbH Weinbergweg 22, 06120, Halle/Saale, Germany
| | - 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
| | - Farzad Hamdi
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany
| | - Yashar Sadian
- Bioimaging Center (cryoGEnic), Université de Genève, Sciences II, 1211, Genève 4, Switzerland
| | - 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.
- Biozentrum, Martin Luther University Halle-Wittenberg, Weinbergweg 22, Halle/Saale, Germany.
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12
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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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13
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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: 62] [Impact Index Per Article: 20.7] [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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14
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Abstract
Neoplastic transformation is reportedly associated with alterations of the potassium transport across plasma and intracellular membranes. These alterations have been identified as crucial elements of the tumourigenic reprogramming of cells. Potassium channels may contribute to cancer initiation, malignant progression and therapy resistance of tumour cells. The book chapter focusses on (oncogenic) potassium channels frequently upregulated in different tumour entities, upstream and downstream signalling of these channels, their contribution to the maintenance of cancer stemness and the formation of an immunosuppressive tumour microenvironment. In addition, their role in adaptation to tumour hypoxia, metabolic reprogramming, as well as tumour spreading and metastasis is discussed. Finally, we discuss how (oncogenic) potassium channels may confer treatment resistance of tumours against radiation and chemotherapy and thus might be harnessed for new therapy strategies, for instance, by repurposing approved drugs known to target potassium channels.
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15
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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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16
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Guo Y, Qiu W, Roche TE, Hackert ML. Crystal structure of the catalytic subunit of bovine pyruvate dehydrogenase phosphatase. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2020; 76:292-301. [PMID: 32627744 DOI: 10.1107/s2053230x20007943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 06/11/2020] [Indexed: 11/11/2022]
Abstract
Mammalian pyruvate dehydrogenase (PDH) activity is tightly regulated by phosphorylation and dephosphorylation, which is catalyzed by PDH kinase isomers and PDH phosphatase isomers, respectively. PDH phosphatase isomer 1 (PDP1) is a heterodimer consisting of a catalytic subunit (PDP1c) and a regulatory subunit (PDP1r). Here, the crystal structure of bovine PDP1c determined at 2.1 Å resolution is reported. The crystals belonged to space group P3221, with unit-cell parameters a = b = 75.3, c = 173.2 Å. The structure was solved by molecular-replacement methods and refined to a final R factor of 21.9% (Rfree = 24.7%). The final model consists of 402 of a possible 467 amino-acid residues of the PDP1c monomer, two Mn2+ ions in the active site, an additional Mn2+ ion coordinated by His410 and His414, two MnSO4 ion pairs at special positions near the crystallographic twofold symmetry axis and 226 water molecules. Several new features of the PDP1c structure are revealed. The requirements are described and plausible bases are deduced for the interaction of PDP1c with PDP1r and other components of the pyruvate dehydrogenase complex.
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Affiliation(s)
- Youzhong Guo
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Weihua Qiu
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Thomas E Roche
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA
| | - Marvin L Hackert
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
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17
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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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18
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Anwar S, Mohammad T, Shamsi A, Queen A, Parveen S, Luqman S, Hasan GM, Alamry KA, Azum N, Asiri AM, Hassan MI. Discovery of Hordenine as a Potential Inhibitor of Pyruvate Dehydrogenase Kinase 3: Implication in Lung Cancer Therapy. Biomedicines 2020; 8:E119. [PMID: 32422877 PMCID: PMC7277448 DOI: 10.3390/biomedicines8050119] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/09/2020] [Accepted: 05/11/2020] [Indexed: 11/16/2022] Open
Abstract
Design and development of potential pyruvate dehydrogenase kinase 3 (PDK3) inhibitors have gained attention because of their possible therapeutic uses in lung cancer therapy. In the present study, the binding affinity of naturally occurring alkaloids, hordenine, vincamine, tryptamine, cinchonine, and colcemid was measured with PDK3. The molecular docking and fluorescence binding studies suggested that all these compounds show a considerable binding affinity for PDK3. Among them, the affinity of hordenine to the PDK3 was excellent (K = 106 M-1) which was further complemented by isothermal titration calorimetric measurements. Hordenine binds in the active site pocket of PDK3 and forms a significant number of non-covalent interactions with functionally important residues. All-atom molecular dynamics (MD) simulation study suggested that the PDK3-hordenine complex is stabilized throughout the trajectory of 100ns and leads to fewer conformational changes. The enzyme inhibition studies showed that hordenine inhibits the activity of PDK3 with an IC50 value of 5.4 µM. Furthermore, hordenine showed a cytotoxic effect on human lung cancer cells (A549 and H1299) with an admirable IC50 value. However, it did not inhibit the growth of HEK293 cells up to 200 µM, indicating its non-toxicity to non-cancerous cell lines. In summary, our findings provide the basis for the therapeutic implication of hordenine and its derivatives in lung cancer and PDK3-related diseases after required in vivo validation.
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Affiliation(s)
- Saleha Anwar
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India; (S.A.); (T.M.); (A.S.)
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India; (S.A.); (T.M.); (A.S.)
| | - Anas Shamsi
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India; (S.A.); (T.M.); (A.S.)
| | - Aarfa Queen
- Department of Chemistry, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India;
| | - Shahnaz Parveen
- Molecular Bioprospection Department, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, India; (S.P.); (S.L.)
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Suaib Luqman
- Molecular Bioprospection Department, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, India; (S.P.); (S.L.)
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Gulam Mustafa Hasan
- Department of Biochemistry, College of Medicine, Prince Sattam Bin Abdulaziz University, P.O. Box 173, Al-Kharj 11942, Saudi Arabia;
| | - Khalid A. Alamry
- Chemistry Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; (K.A.A.); (N.A.); (A.M.A.)
| | - Naved Azum
- Chemistry Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; (K.A.A.); (N.A.); (A.M.A.)
| | - Abdullah M. Asiri
- Chemistry Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; (K.A.A.); (N.A.); (A.M.A.)
- Center of Excellence for Advanced Materials Research (CEAMR), King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India; (S.A.); (T.M.); (A.S.)
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19
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Anwar S, Kar RK, Haque MA, Dahiya R, Gupta P, Islam A, Ahmad F, Hassan MI. Effect of pH on the structure and function of pyruvate dehydrogenase kinase 3: Combined spectroscopic and MD simulation studies. Int J Biol Macromol 2020; 147:768-777. [PMID: 31982536 DOI: 10.1016/j.ijbiomac.2020.01.218] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 01/21/2020] [Accepted: 01/22/2020] [Indexed: 12/22/2022]
Abstract
Pyruvate dehydrogenase kinase-3 (PDK3) plays important role in the glucose metabolism and is associated with cancer progression, and thus being considered as an attractive target for cancer therapy. In this study, we employed spectroscopic techniques to study the structural and conformational changes in the PDK3 at varying pH conditions ranging from pH 2.0 to 12.0. UV/Vis, fluorescence and circular dichroism spectroscopic measurements revealed that PDK3 maintains its native-like structure (both secondary and tertiary) in the alkaline conditions (pH 7.0-12.0). However, a significant loss in the structure was observed under acidic conditions (pH 2.0-6.0). The propensity of aggregate formation at pH 4.0 was estimated by thioflavin T fluorescence measurements. To further complement structural data, kinase activity assay was performed, and maximum activity of PDK3 was observed at pH 7.0-8.0 range; whereas, its activity was lost under acidic pH. To further see conformational changes at atomistic level we have performed all-atom molecular dynamics at different pH conditions for 150 ns. A well defined correlation was observed between experimental and computational studies. This work highlights the significance of structural dependence of pH for wide implications in protein-protein interaction, biological function and drug design procedures.
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Affiliation(s)
- Saleha Anwar
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Rajiv K Kar
- Fritz Haber Center for Molecular Dynamic Research, Hebrew University of Jerusalem, Israel
| | - Md Anzarul Haque
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Rashmi Dahiya
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Preeti Gupta
- 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
| | - Faizan Ahmad
- 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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20
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Mohammad T, Arif K, Alajmi MF, Hussain A, Islam A, Rehman MT, Hassan I. Identification of high-affinity inhibitors of pyruvate dehydrogenase kinase-3: towards therapeutic management of cancer. J Biomol Struct Dyn 2020; 39:586-594. [DOI: 10.1080/07391102.2020.1711810] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Kaynat Arif
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Mohamed F. Alajmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Afzal Hussain
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Md. Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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21
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Martins-Noguerol R, Moreno-Pérez AJ, Acket S, Makni S, Garcés R, Troncoso-Ponce A, Salas JJ, Thomasset B, Martínez-Force E. Lipidomic Analysis of Plastidial Octanoyltransferase Mutants of Arabidopsis thaliana. Metabolites 2019; 9:metabo9100209. [PMID: 31569524 PMCID: PMC6835903 DOI: 10.3390/metabo9100209] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 09/27/2019] [Accepted: 09/27/2019] [Indexed: 01/19/2023] Open
Abstract
Plant de novo fatty acid synthesis takes place in the plastid using acetyl-coenzyme A (acetyl-CoA) as the main precursor. This first intermediate is produced from pyruvate through the action of the plastidial pyruvate dehydrogenase complex (PDH), which catalyses the oxidative decarboxylation of pyruvate to produce acetyl-CoA, CO2, and NADH. For the proper functioning of this complex, lipoic acid is required to be bound to the dihydrolipoamide S-acetyltransferase E2 subunit of PDH. Octanoyltransferase (LIP2; EC 2.3.1.181) and lipoyl synthase (LIP1; EC 2.8.1.8) are the enzymes involved in the biosynthesis of this essential cofactor. In Arabidopsis plastids, an essential lipoyl synthase (AtLIP1p) and two redundant octanoyltransferases (AtLIP2p1 and AtLIP2p2) have been described. In the present study, the lipidomic characterization of Arabidopsis octanoyltransferase mutants reveals new insight into the lipoylation functions within plastid metabolism. Lipids and fatty acids from mature seeds and seedlings from Atlip2p1 and Atlip2p2 mutants were analysed by gas chromatography (GC) and liquid chromatography–electrospray ionization high-resolution mass spectrometry (LC-ESI-HRMS2), the analysis revealed changes in fatty acid profiles that showed similar patterns in both mutant seeds and seedlings and in the lipid species containing those fatty acids. Although both mutants showed similar tendencies, the lack of the AtLIP2p2 isoform produced a more acute variation in its lipids profile. These changes in fatty acid composition and the increase in their content per seed point to the interference of octanoyltransferases in the fatty acid synthesis flux in Arabidopsis thaliana seeds.
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Affiliation(s)
- Raquel Martins-Noguerol
- Instituto de la Grasa-CSIC, Building 46, UPO Campus, Ctra. de Utrera km 1, 41013 Seville, Spain.
- Alliance Sorbonne Université, Université de Technologie de Compiègne, Génie Enzymatique et Cellulaire (GEC), UMR-CNRS 7025, CS 60319, 60203 Compiègne CEDEX, France.
| | - Antonio Javier Moreno-Pérez
- Instituto de la Grasa-CSIC, Building 46, UPO Campus, Ctra. de Utrera km 1, 41013 Seville, Spain.
- Alliance Sorbonne Université, Université de Technologie de Compiègne, Génie Enzymatique et Cellulaire (GEC), UMR-CNRS 7025, CS 60319, 60203 Compiègne CEDEX, France.
| | - Sebastien Acket
- Alliance Sorbonne Université, Université de Technologie de Compiègne, Génie Enzymatique et Cellulaire (GEC), UMR-CNRS 7025, CS 60319, 60203 Compiègne CEDEX, France.
| | - Salim Makni
- Alliance Sorbonne Université, Université de Technologie de Compiègne, Génie Enzymatique et Cellulaire (GEC), UMR-CNRS 7025, CS 60319, 60203 Compiègne CEDEX, France.
| | - Rafael Garcés
- Instituto de la Grasa-CSIC, Building 46, UPO Campus, Ctra. de Utrera km 1, 41013 Seville, Spain.
| | - Adrián Troncoso-Ponce
- Alliance Sorbonne Université, Université de Technologie de Compiègne, Génie Enzymatique et Cellulaire (GEC), UMR-CNRS 7025, CS 60319, 60203 Compiègne CEDEX, France.
| | - Joaquín J Salas
- Instituto de la Grasa-CSIC, Building 46, UPO Campus, Ctra. de Utrera km 1, 41013 Seville, Spain.
| | - Brigitte Thomasset
- Alliance Sorbonne Université, Université de Technologie de Compiègne, Génie Enzymatique et Cellulaire (GEC), UMR-CNRS 7025, CS 60319, 60203 Compiègne CEDEX, France.
| | - Enrique Martínez-Force
- Instituto de la Grasa-CSIC, Building 46, UPO Campus, Ctra. de Utrera km 1, 41013 Seville, Spain.
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22
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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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23
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Live-Cell Imaging of Physiologically Relevant Metal Ions Using Genetically Encoded FRET-Based Probes. Cells 2019; 8:cells8050492. [PMID: 31121936 PMCID: PMC6562680 DOI: 10.3390/cells8050492] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 05/17/2019] [Accepted: 05/21/2019] [Indexed: 01/02/2023] Open
Abstract
Essential biochemical reactions and processes within living organisms are coupled to subcellular fluctuations of metal ions. Disturbances in cellular metal ion homeostasis are frequently associated with pathological alterations, including neurotoxicity causing neurodegeneration, as well as metabolic disorders or cancer. Considering these important aspects of the cellular metal ion homeostasis in health and disease, measurements of subcellular ion signals are of broad scientific interest. The investigation of the cellular ion homeostasis using classical biochemical methods is quite difficult, often even not feasible or requires large cell numbers. Here, we report of genetically encoded fluorescent probes that enable the visualization of metal ion dynamics within individual living cells and their organelles with high temporal and spatial resolution. Generally, these probes consist of specific ion binding domains fused to fluorescent protein(s), altering their fluorescent properties upon ion binding. This review focuses on the functionality and potential of these genetically encoded fluorescent tools which enable monitoring (sub)cellular concentrations of alkali metals such as K+, alkaline earth metals including Mg2+ and Ca2+, and transition metals including Cu+/Cu2+ and Zn2+. Moreover, we discuss possible approaches for the development and application of novel metal ion biosensors for Fe2+/Fe3+, Mn2+ and Na+.
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24
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Zdraljevic S, Fox BW, Strand C, Panda O, Tenjo FJ, Brady SC, Crombie TA, Doench JG, Schroeder FC, Andersen EC. Natural variation in C. elegans arsenic toxicity is explained by differences in branched chain amino acid metabolism. eLife 2019; 8:40260. [PMID: 30958264 PMCID: PMC6453569 DOI: 10.7554/elife.40260] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Accepted: 03/26/2019] [Indexed: 12/29/2022] Open
Abstract
We find that variation in the dbt-1 gene underlies natural differences in Caenorhabditis elegans responses to the toxin arsenic. This gene encodes the E2 subunit of the branched-chain α-keto acid dehydrogenase (BCKDH) complex, a core component of branched-chain amino acid (BCAA) metabolism. We causally linked a non-synonymous variant in the conserved lipoyl domain of DBT-1 to differential arsenic responses. Using targeted metabolomics and chemical supplementation, we demonstrate that differences in responses to arsenic are caused by variation in iso-branched chain fatty acids. Additionally, we show that levels of branched chain fatty acids in human cells are perturbed by arsenic treatment. This finding has broad implications for arsenic toxicity and for arsenic-focused chemotherapeutics across human populations. Our study implicates the BCKDH complex and BCAA metabolism in arsenic responses, demonstrating the power of C. elegans natural genetic diversity to identify novel mechanisms by which environmental toxins affect organismal physiology. Editorial note: This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).
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Affiliation(s)
- Stefan Zdraljevic
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, United States.,Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Bennett William Fox
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, United States
| | | | - Oishika Panda
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, United States.,The Buck Institute for Research on Aging, Novato, United States
| | - Francisco J Tenjo
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, United States
| | - Shannon C Brady
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, United States.,Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Tim A Crombie
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - John G Doench
- Broad Institute of MIT and Harvard, Cambridge, United States
| | - Frank C Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, United States
| | - Erik C Andersen
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, United States.,Department of Molecular Biosciences, Northwestern University, Evanston, United States.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Northwestern University, Chicago, United States
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25
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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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26
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Michelakis ED, Gurtu V, Webster L, Barnes G, Watson G, Howard L, Cupitt J, Paterson I, Thompson RB, Chow K, O'Regan DP, Zhao L, Wharton J, Kiely DG, Kinnaird A, Boukouris AE, White C, Nagendran J, Freed DH, Wort SJ, Gibbs JSR, Wilkins MR. Inhibition of pyruvate dehydrogenase kinase improves pulmonary arterial hypertension in genetically susceptible patients. Sci Transl Med 2018; 9:9/413/eaao4583. [PMID: 29070699 DOI: 10.1126/scitranslmed.aao4583] [Citation(s) in RCA: 183] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 09/22/2017] [Indexed: 12/17/2022]
Abstract
Pulmonary arterial hypertension (PAH) is a progressive vascular disease with a high mortality rate. It is characterized by an occlusive vascular remodeling due to a pro-proliferative and antiapoptotic environment in the wall of resistance pulmonary arteries (PAs). Proliferating cells exhibit a cancer-like metabolic switch where mitochondrial glucose oxidation is suppressed, whereas glycolysis is up-regulated as the major source of adenosine triphosphate production. This multifactorial mitochondrial suppression leads to inhibition of apoptosis and downstream signaling promoting proliferation. We report an increase in pyruvate dehydrogenase kinase (PDK), an inhibitor of the mitochondrial enzyme pyruvate dehydrogenase (PDH, the gatekeeping enzyme of glucose oxidation) in the PAs of human PAH compared to healthy lungs. Treatment of explanted human PAH lungs with the PDK inhibitor dichloroacetate (DCA) ex vivo activated PDH and increased mitochondrial respiration. In a 4-month, open-label study, DCA (3 to 6.25 mg/kg b.i.d.) administered to patients with idiopathic PAH (iPAH) already on approved iPAH therapies led to reduction in mean PA pressure and pulmonary vascular resistance and improvement in functional capacity, but with a range of individual responses. Lack of ex vivo and clinical response was associated with the presence of functional variants of SIRT3 and UCP2 that predict reduced protein function. Impaired function of these proteins causes PDK-independent mitochondrial suppression and pulmonary hypertension in mice. This first-in-human trial of a mitochondria-targeting drug in iPAH demonstrates that PDK is a druggable target and offers hemodynamic improvement in genetically susceptible patients, paving the way for novel precision medicine approaches in this disease.
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Affiliation(s)
| | - Vikram Gurtu
- Department of Medicine, University of Alberta, Edmonton, Alberta T6G2B7, Canada
| | - Linda Webster
- Department of Medicine, University of Alberta, Edmonton, Alberta T6G2B7, Canada
| | - Gareth Barnes
- Department of Medicine, Imperial College London, London W12 0NN, UK
| | - Geoffrey Watson
- Department of Medicine, Imperial College London, London W12 0NN, UK
| | - Luke Howard
- National Pulmonary Hypertension Service, Imperial College Healthcare National Health Service Trust, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - John Cupitt
- Department of Medicine, Imperial College London, London W12 0NN, UK
| | - Ian Paterson
- Department of Medicine, University of Alberta, Edmonton, Alberta T6G2B7, Canada
| | - Richard B Thompson
- Department of Biomedical Engineering, University of Alberta, Edmonton, Alberta T6G2B7, Canada
| | - Kelvin Chow
- Department of Biomedical Engineering, University of Alberta, Edmonton, Alberta T6G2B7, Canada
| | - Declan P O'Regan
- Medical Research Council, London Institute of Medical Sciences, Hammersmith Hospital Campus, Imperial College London, London W12 0NN, UK
| | - Lan Zhao
- Department of Medicine, Imperial College London, London W12 0NN, UK
| | - John Wharton
- Department of Medicine, Imperial College London, London W12 0NN, UK
| | - David G Kiely
- Sheffield Pulmonary Vascular Disease Unit, Royal Hallamshire Hospital, Sheffield S10 2JF, UK
| | - Adam Kinnaird
- Department of Medicine, University of Alberta, Edmonton, Alberta T6G2B7, Canada
| | | | - Chris White
- Department of Surgery, University of Alberta, Edmonton, Alberta T6G2B7, Canada
| | - Jayan Nagendran
- Department of Surgery, University of Alberta, Edmonton, Alberta T6G2B7, Canada
| | - Darren H Freed
- Department of Surgery, University of Alberta, Edmonton, Alberta T6G2B7, Canada
| | - Stephen J Wort
- National Heart and Lung Institute, Imperial College London, Dovehouse Street, London SW3 6LY, UK
| | - J Simon R Gibbs
- National Pulmonary Hypertension Service, Imperial College Healthcare National Health Service Trust, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Martin R Wilkins
- Department of Medicine, Imperial College London, London W12 0NN, UK.
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27
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Woo SH, Seo SK, Park Y, Kim EK, Seong MK, Kim HA, Song JY, Hwang SG, Lee JK, Noh WC, Park IC. Dichloroacetate potentiates tamoxifen-induced cell death in breast cancer cells via downregulation of the epidermal growth factor receptor. Oncotarget 2018; 7:59809-59819. [PMID: 27494858 PMCID: PMC5312350 DOI: 10.18632/oncotarget.10999] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 07/22/2016] [Indexed: 01/01/2023] Open
Abstract
Metabolic reprogramming in cancer cells has recently been recognized as an essential hallmark of neoplasia. In this context, metabolic alterations represent an attractive therapeutic target, and encouraging results with drugs targeting various metabolic processes have been obtained in preclinical studies. Recently, several studies have suggested that dichloroacetate (DCA), a specific pyruvate dehydrogenase kinase inhibitor, may be a potential anticancer drug in a large number of diverse tumors. However, the precise mechanism is not fully understood, which is important for the use of DCA in cancer treatment. In the present study, we found that DCA sensitized MCF7 breast cancer cells to tamoxifen-induced cell death by decreasing epidermal growth factor receptor (EGFR) expression. The downregulation of EGFR was caused by degradation of the protein. Furthermore, p38 mitogen-activated protein kinase played an important role in DCA/tamoxifen-induced EGFR degradation. Finally, DCA also promoted comparable tamoxifen-induced cell death in tamoxifen-resistant MCF7 cells, which were established by long-term treatment with tamoxifen. In summary, our results suggest that DCA is an attractive potential drug that sensitizes cells to tamoxifen-induced cell death and overcome tamoxifen resistance via downregulation of EGFR expression in breast cancer cells.
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Affiliation(s)
- Sang Hyeok Woo
- Division of Radiation Cancer Research, Korea Institute of Radiological and Medical Sciences, Nowon-gu, Seoul, 01812, Republic of Korea
| | - Sung-Keum Seo
- Division of Radiation Cancer Research, Korea Institute of Radiological and Medical Sciences, Nowon-gu, Seoul, 01812, Republic of Korea
| | - Yoonhwa Park
- Division of Radiation Cancer Research, Korea Institute of Radiological and Medical Sciences, Nowon-gu, Seoul, 01812, Republic of Korea.,School of Life Science and Biotechnology, Korea University, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Eun-Kyu Kim
- Department of Surgery, Breast Cancer Center, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Bundang-gu, Seongnam, 13620, Republic of Korea
| | - Min-Ki Seong
- Department of Surgery, Korea Cancer Center Hospital, Korea Institute of Radiological and Medical Sciences, Nowon-gu, Seoul, 01812, Republic of Korea
| | - Hyun-Ah Kim
- Department of Surgery, Korea Cancer Center Hospital, Korea Institute of Radiological and Medical Sciences, Nowon-gu, Seoul, 01812, Republic of Korea
| | - Jie-Young Song
- Division of Radiation Cancer Research, Korea Institute of Radiological and Medical Sciences, Nowon-gu, Seoul, 01812, Republic of Korea
| | - Sang-Gu Hwang
- Division of Radiation Cancer Research, Korea Institute of Radiological and Medical Sciences, Nowon-gu, Seoul, 01812, Republic of Korea
| | - Jin Kyung Lee
- KIRAMS Radiation Biobank, Korea Institute of Radiological and Medical Sciences, Nowon-gu, Seoul, 01812, Republic of Korea
| | - Woo Chul Noh
- Department of Surgery, Korea Cancer Center Hospital, Korea Institute of Radiological and Medical Sciences, Nowon-gu, Seoul, 01812, Republic of Korea
| | - In-Chul Park
- Division of Radiation Cancer Research, Korea Institute of Radiological and Medical Sciences, Nowon-gu, Seoul, 01812, Republic of Korea
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28
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Dad A, Jeong CH, Wagner ED, Plewa MJ. Haloacetic Acid Water Disinfection Byproducts Affect Pyruvate Dehydrogenase Activity and Disrupt Cellular Metabolism. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:1525-1532. [PMID: 29261292 DOI: 10.1021/acs.est.7b04290] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The disinfection of drinking water has been a major public health achievement. However, haloacetic acids (HAAs), generated as byproducts of water disinfection, are cytotoxic, genotoxic, mutagenic, carcinogenic, and teratogenic. Previous studies of monoHAA-induced genotoxicity and cell stress demonstrated that the toxicity was due to inhibition of glyceraldehyde-3-phosphate dehydrogenase (GAPDH), leading to disruption of cellular metabolism and energy homeostasis. DiHAAs and triHAAs are also produced during water disinfection, and whether they share mechanisms of action with monoHAAs is unknown. In this study, we evaluated the effects of mono-, di-, and tri-HAAs on cellular GAPDH enzyme kinetics, cellular ATP levels, and pyruvate dehydrogenase complex (PDC) activity. Here, treatments conducted in Chinese hamster ovary (CHO) cells revealed differences among mono-, di-, and triHAAs in their molecular targets. The monoHAAs, iodoacetic acid and bromoacetic acid, were the strongest inhibitors of GAPDH and greatly reduced cellular ATP levels. Chloroacetic acid, diHAAs, and triHAAs were weaker inhibitors of GAPDH and some increased the levels of cellular ATP. HAAs also affected PDC activity, with most HAAs activating PDC. The primary finding of this work is that mono- versus multi-HAAs address different molecular targets, and the results are generally consistent with a model in which monoHAAs activate the PDC through GAPDH inhibition-mediated disruption in cellular metabolites, including altering ATP-to-ADP and NADH-to-NAD ratios. The monoHAA-mediated reduction in cellular metabolites results in accelerated PDC activity by way of metabolite-ratio-dependent PDC regulation. DiHAAs and triHAAs are weaker inhibitors of GAPDH, but many also increase cellular ATP levels, and we suggest that they increase PDC activity by inhibiting pyruvate dehydrogenase kinase.
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Affiliation(s)
- Azra Dad
- Safe Global Water Institute and ‡Department of Crop Sciences, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | | | - Elizabeth D Wagner
- Safe Global Water Institute and ‡Department of Crop Sciences, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Michael J Plewa
- Safe Global Water Institute and ‡Department of Crop Sciences, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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29
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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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30
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Liu Y, Xie Z, Zhao D, Zhu J, Mao F, Tang S, Xu H, Luo C, Geng M, Huang M, Li J. Development of the First Generation of Disulfide-Based Subtype-Selective and Potent Covalent Pyruvate Dehydrogenase Kinase 1 (PDK1) Inhibitors. J Med Chem 2017; 60:2227-2244. [PMID: 28230989 DOI: 10.1021/acs.jmedchem.6b01245] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Pyruvate dehydrogenase kinases (PDKs) are overexpressed in most cancer cells and are responsible for aberrant glucose metabolism. We previously described bis(4-morpholinyl thiocarbonyl)-disulfide (JX06, 16) as the first covalent inhibitor of PDK1. Here, on the basis of the scaffold of 16, we identify two novel types of disulfide-based PDK1 inhibitors. The most potent analogue, 3a, effectively inhibits PDK1 both at the molecular (kinact/Ki = 4.17 × 103 M-1 s-1) and the cellular level (down to 0.1 μM). In contrast to 16, 3a is a potent and subtype-selective inhibitor of PDK1 with >40-fold selectivity for PDK2-4. 3a also significantly alters glucose metabolic pathways in A549 cells by decreasing ECAR and increasing ROS. Moreover, in the xenograft models, 3a shows significant antitumor activity with no negative effect to the mice weight. Collectively, these data demonstrate that 3a may be an excellent lead compound for the treatment of cancer as a first-generation subtype-selective and covalent PDK1 inhibitor.
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Affiliation(s)
- Yifu Liu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology , Shanghai 200237, China
| | - Zuoquan Xie
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203, China
| | - Dan Zhao
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203, China
| | - Jin Zhu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology , Shanghai 200237, China
| | - Fei Mao
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology , Shanghai 200237, China
| | - Shuai Tang
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203, China
| | - Hui Xu
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203, China
| | - Cheng Luo
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203, China
| | - Meiyu Geng
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203, China
| | - Min Huang
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203, China
| | - Jian Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology , Shanghai 200237, China
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31
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Global view of cognate kinase activation by the human pyruvate dehydrogenase complex. Sci Rep 2017; 7:42760. [PMID: 28230160 PMCID: PMC5322387 DOI: 10.1038/srep42760] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 01/13/2017] [Indexed: 12/11/2022] Open
Abstract
The human pyruvate dehydrogenase complex (PDC) comprises four multidomain components, E1, E3, E2 and an E3-binding protein (E3BP), the latter two forming the core as E2·E3BP sub-complex. Pyruvate flux through PDC is regulated via phosphorylation (inactivation) at E1 by four PDC kinases (PDKs), and reactivation by two PDC phosphatases. Up-regulation of PDK isoform gene expression is reported in several forms of cancer, while PDKs may be further activated by PDC by binding to the E2·E3BP core. Hence, the PDK: E2·E3BP interaction provides new therapeutic targets. We carried out both functional kinetic and thermodynamic studies to demonstrate significant differences in the activation of PDK isoforms by binding to the E2·E3BP core: (i) PDK2 needs no activation by E2·E3BP for efficient functioning, while PDK4 was the least effective of the four isoforms, and could not be activated by E2·E3BP. Hence, development of inhibitors to the interaction of PDK2 and PDK4 with E2·E3BP is not promising; (ii) Design of inhibitors to interfere with interaction of E2·E3BP with PDK1 and PDK3 is promising. PDK3 needs E2·E3BP core for activation, an activation best achieved by synergistic combination of E2-derived catalytic domain and tridomain.
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32
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Tso SC, Lou M, Wu CY, Gui WJ, Chuang JL, Morlock LK, Williams NS, Wynn RM, Qi X, Chuang DT. Development of Dihydroxyphenyl Sulfonylisoindoline Derivatives as Liver-Targeting Pyruvate Dehydrogenase Kinase Inhibitors. J Med Chem 2017; 60:1142-1150. [PMID: 28085286 DOI: 10.1021/acs.jmedchem.6b01540] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Pyruvate dehydrogenase kinases 1-4 (PDK1-4) negatively control activity of the pyruvate dehydrogenase complex (PDC) and are up-regulated in obesity, diabetes, heart failure, and cancer. We reported earlier two novel pan-PDK inhibitors PS8 [4-((5-hydroxyisoindolin-2-yl)sulfonyl)benzene-1,3-diol] (1) and PS10 [2-((2,4-dihydroxyphenyl)sulfonyl)isoindoline-4,6-diol] (2) that targeted the ATP-binding pocket in PDKs. Here, we developed a new generation of PDK inhibitors by extending the dihydroxyphenyl sulfonylisoindoline scaffold in 1 and 2 to the entrance region of the ATP-binding pocket in PDK2. The lead inhibitor (S)-3-amino-4-(4-((2-((2,4-dihydroxyphenyl)sulfonyl)isoindolin-5-yl)amino)piperidin-1-yl)-4-oxobutanamide (17) shows a ∼8-fold lower IC50 (58 nM) than 2 (456 nM). In the crystal structure, the asparagine moiety in 17 provides additional interactions with Glu-262 from PDK2. Treatment of diet-induced obese mice with 17 resulted in significant liver-specific augmentation of PDC activity, accompanied by improved glucose tolerance and drastically reduced hepatic steatosis. These findings support 17 as a potential glucose-lowering therapeutic targeting liver for obesity and type 2 diabetes.
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Affiliation(s)
| | - Mingliang Lou
- Chemistry Center, National Institute of Biological Science , Beijing 102206, China.,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences , Beijing 100730, China
| | | | | | | | | | | | | | - Xiangbing Qi
- Chemistry Center, National Institute of Biological Science , Beijing 102206, China.,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences , Beijing 100730, China
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33
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Vigorito A, Calabrese C, Paltanin E, Melandri S, Maris A. Regarding the torsional flexibility of the dihydrolipoic acid's pharmacophore: 1,3-propanedithiol. Phys Chem Chem Phys 2017; 19:496-502. [PMID: 27905582 DOI: 10.1039/c6cp05606g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The great flexibility of 1,3-propanedithiol is probed using freejet absorption microwave spectroscopy and quantum chemistry calculations.
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Affiliation(s)
- Annalisa Vigorito
- Dipartimento di Chimica G. Ciamician
- Università degli Studi di Bologna
- 40126 Bologna
- Italy
| | - Camilla Calabrese
- Dipartimento di Chimica G. Ciamician
- Università degli Studi di Bologna
- 40126 Bologna
- Italy
| | - Ettore Paltanin
- Dipartimento di Chimica G. Ciamician
- Università degli Studi di Bologna
- 40126 Bologna
- Italy
| | - Sonia Melandri
- Dipartimento di Chimica G. Ciamician
- Università degli Studi di Bologna
- 40126 Bologna
- Italy
| | - Assimo Maris
- Dipartimento di Chimica G. Ciamician
- Università degli Studi di Bologna
- 40126 Bologna
- Italy
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34
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Abstract
The family of 2-oxoacid dehydrogenase complexes (2-OADC), typified by the pyruvate dehydrogenase multi-enzyme complex (PDC) as its most prominent member, are massive molecular machines (Mr, 4-10 million) controlling key steps in glucose homeostasis (PDC), citric acid cycle flux (OGDC, 2-oxoglutarate dehydrogenase) and the metabolism of the branched-chain amino acids, leucine, isoleucine and valine (BCOADC, branched-chain 2-OADC). These highly organised mitochondrial arrays, composed of multiple copies of three separate enzymes, have been widely studied as paradigms for the analysis of enzyme cooperativity, substrate channelling, protein-protein interactions and the regulation of activity by phosphorylation . This chapter will highlight recent advances in our understanding of the structure-function relationships, the overall organisation and the transport and assembly of PDC in particular, focussing on both native and recombinant forms of the complex and their individual components or constituent domains. Biophysical approaches, including X-ray crystallography (MX), nuclear magnetic resonance spectroscopy (NMR), cryo-EM imaging, analytical ultracentrifugation (AUC) and small angle X-ray and neutron scattering (SAXS and SANS), have all contributed significant new information on PDC subunit organisation, stoichiometry, regulatory mechanisms and mode of assembly. Moreover, the recognition of specific genetic defects linked to PDC deficiency, in combination with the ability to analyse recombinant PDCs housing both novel naturally-occurring and engineered mutations, have all stimulated renewed interest in these classical metabolic assemblies. In addition, the role played by PDC, and its constituent proteins, in certain disease states will be briefly reviewed, focussing on the development of new and exciting areas of medical and immunological research.
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Affiliation(s)
- Olwyn Byron
- School of Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - John Gordon Lindsay
- Institute of Molecular, Cell and Systems Biology, Davidson Building, College of Medicine, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.
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35
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Gohara DW, Di Cera E. Molecular Mechanisms of Enzyme Activation by Monovalent Cations. J Biol Chem 2016; 291:20840-20848. [PMID: 27462078 DOI: 10.1074/jbc.r116.737833] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Regulation of enzymes through metal ion complexation is widespread in biology and underscores a physiological need for stability and high catalytic activity that likely predated proteins in the RNA world. In addition to divalent metals such as Ca2+, Mg2+, and Zn2+, monovalent cations often function as efficient and selective promoters of catalysis. Advances in structural biology unravel a rich repertoire of molecular mechanisms for enzyme activation by Na+ and K+ Strategies range from short-range effects mediated by direct participation in substrate binding, to more distributed effects that propagate long-range to catalytic residues. This review addresses general considerations and examples.
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Affiliation(s)
- David W Gohara
- From the Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104
| | - Enrico Di Cera
- From the Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104
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36
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Perez-Siles G, Ly C, Grant A, Drew AP, Yiu EM, Ryan MM, Chuang DT, Tso SC, Nicholson GA, Kennerson ML. Pathogenic mechanisms underlying X-linked Charcot-Marie-Tooth neuropathy (CMTX6) in patients with a pyruvate dehydrogenase kinase 3 mutation. Neurobiol Dis 2016; 94:237-44. [PMID: 27388934 DOI: 10.1016/j.nbd.2016.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 06/22/2016] [Accepted: 07/03/2016] [Indexed: 10/21/2022] Open
Abstract
Charcot-Marie-Tooth disease (CMT) is the most common inherited peripheral neuropathy. An X-linked form of CMT (CMTX6) is caused by a missense mutation (R158H) in the pyruvate dehydrogenase kinase isoenzyme 3 (PDK3) gene. PDK3 is one of 4 isoenzymes that negatively regulate the activity of the pyruvate dehydrogenase complex (PDC) by reversible phosphorylation of its first catalytic component pyruvate dehydrogenase (designated as E1). Mitochondrial PDC catalyses the oxidative decarboxylation of pyruvate to acetyl CoA and links glycolysis to the energy-producing Krebs cycle. We have previously shown the R158H mutation confers PDK3 enzyme hyperactivity. In this study we demonstrate that the increased PDK3 activity in patient fibroblasts (PDK3(R158H)) leads to the attenuation of PDC through hyper-phosphorylation of E1 at selected serine residues. This hyper-phosphorylation can be reversed by treating the PDK3(R158H) fibroblasts with the PDK inhibitor dichloroacetate (DCA). In the patient cells, down-regulation of PDC leads to increased lactate, decreased ATP and alteration of the mitochondrial network. Our findings highlight the potential to develop specific drug targeting of the mutant PDK3 as a therapeutic approach to treating CMTX6.
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Affiliation(s)
- Gonzalo Perez-Siles
- Northcott Neuroscience Laboratory, ANZAC Research Institute, University of Sydney, Concord, NSW, Australia; Sydney Medical School, University of Sydney, Sydney, NSW, Australia.
| | - Carolyn Ly
- Northcott Neuroscience Laboratory, ANZAC Research Institute, University of Sydney, Concord, NSW, Australia
| | - Adrienne Grant
- Northcott Neuroscience Laboratory, ANZAC Research Institute, University of Sydney, Concord, NSW, Australia
| | - Alexander P Drew
- Northcott Neuroscience Laboratory, ANZAC Research Institute, University of Sydney, Concord, NSW, Australia
| | - Eppie M Yiu
- Department of Neurology, Royal Children's Hospital, Flemington Road, Parkville, VIC, Australia; Neuroscience Research, Murdoch Childrens Research Institute, Melbourne, VIC, Australia; Department of Pediatrics, The University of Melbourne, VIC, Australia
| | - Monique M Ryan
- Department of Neurology, Royal Children's Hospital, Flemington Road, Parkville, VIC, Australia; Neuroscience Research, Murdoch Childrens Research Institute, Melbourne, VIC, Australia; Department of Pediatrics, The University of Melbourne, VIC, Australia
| | - David T Chuang
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Shih-Chia Tso
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Garth A Nicholson
- Northcott Neuroscience Laboratory, ANZAC Research Institute, University of Sydney, Concord, NSW, Australia; Molecular Medicine Laboratory, Concord Hospital, Concord, NSW, Australia; Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Marina L Kennerson
- Northcott Neuroscience Laboratory, ANZAC Research Institute, University of Sydney, Concord, NSW, Australia; Molecular Medicine Laboratory, Concord Hospital, Concord, NSW, Australia; Sydney Medical School, University of Sydney, Sydney, NSW, Australia.
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37
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Vašák M, Schnabl J. Sodium and Potassium Ions in Proteins and Enzyme Catalysis. Met Ions Life Sci 2016; 16:259-90. [DOI: 10.1007/978-3-319-21756-7_8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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38
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Moxley MA, Beard DA, Bazil JN. Global Kinetic Analysis of Mammalian E3 Reveals pH-dependent NAD+/NADH Regulation, Physiological Kinetic Reversibility, and Catalytic Optimum. J Biol Chem 2015; 291:2712-30. [PMID: 26644471 DOI: 10.1074/jbc.m115.676619] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Indexed: 12/11/2022] Open
Abstract
Mammalian E3 is an essential mitochondrial enzyme responsible for catalyzing the terminal reaction in the oxidative catabolism of several metabolites. E3 is a key regulator of metabolic fuel selection as a component of the pyruvate dehydrogenase complex (PDHc). E3 regulates PDHc activity by altering the affinity of pyruvate dehydrogenase kinase, an inhibitor of the enzyme complex, through changes in reduction and acetylation state of lipoamide moieties set by the NAD(+)/NADH ratio. Thus, an accurate kinetic model of E3 is needed to predict overall mammalian PDHc activity. Here, we have combined numerous literature data sets and new equilibrium spectroscopic experiments with a multitude of independently collected forward and reverse steady-state kinetic assays using pig heart E3. The latter kinetic assays demonstrate a pH-dependent transition of NAD(+) activation to inhibition, shown here, to our knowledge, for the first time in a single consistent data set. Experimental data were analyzed to yield a thermodynamically constrained four-redox-state model of E3 that simulates pH-dependent activation/inhibition and active site redox states for various conditions. The developed model was used to determine substrate/product conditions that give maximal E3 rates and show that, due to non-Michaelis-Menten behavior, the maximal flux is different compared with the classically defined kcat.
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Affiliation(s)
- Michael A Moxley
- From the Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan 48109
| | - Daniel A Beard
- From the Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan 48109
| | - Jason N Bazil
- From the Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan 48109
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39
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Walter W, Thomalla J, Bruhn J, Fagan DH, Zehowski C, Yee D, Skildum A. Altered regulation of PDK4 expression promotes antiestrogen resistance in human breast cancer cells. SPRINGERPLUS 2015; 4:689. [PMID: 26576332 PMCID: PMC4641142 DOI: 10.1186/s40064-015-1444-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 10/19/2015] [Indexed: 11/10/2022]
Abstract
Acquired or de novo resistance to the selective estrogen receptor modulators tamoxifen and fulvestrant (ICI) is a major barrier to successful treatment of breast cancer. Gene expression patterns in tamoxifen resistant (TamR-MCF-7) cells were compared to their parental cells (MCF-7L) to identify an aberrantly regulated metabolic pathway. TamR-MCF-7 cells are cross resistant to ICI and doxorubicin, and have increased mitochondrial DNA. A small subset of genes had altered expression in TamR-MCF-7 relative to MCF-7L cells. One of the genes, pyruvate dehydrogenase kinase-4 (PDK4), phosphorylates pyruvate dehydrogenase (PDH). PDK4 expression was elevated in TamR-MCF-7 cells; this result was also observed in a second model of acquired antiestrogen resistance. PDK4 expression is controlled in part by glucocorticoid response elements in the PDK4 gene promoter. In MCF-7L cells, PDK4 mRNA expression was insensitive to glucocorticoid receptor agonists, while dexamethasone dramatically increased PDK4 expression in TamR-MCF-7 cells. Using siRNA to knock down PDK4 expression increased TamR-MCF-7 sensitivity to ICI; in contrast adapting cells to growth in glucose depleted media did not affect ICI sensitivity. Despite TamR-MCF-7 cells high levels of PDK4 mRNA relative to MCF-7L, TamR-MCF-7 cells have increased PDH activity. Wild type MCF-7 cells are reported to be heterozygous for a G to A mutation that results in a substitution of threonine for alanine near PDK4′s catalytic site. We found loss of heterozygosity in TamR-MCF-7 cells; TamR-MCF-7 are homozygous for the wild type allele. These data support a role for altered regulation of PDH by PDK4 and altered substrate utilization in the development of drug resistance in human breast cancer cells.
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Affiliation(s)
- William Walter
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth Campus, Duluth, MN USA
| | - Jennifer Thomalla
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth Campus, Duluth, MN USA
| | - Josh Bruhn
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth Campus, Duluth, MN USA
| | - Dedra H Fagan
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN USA
| | - Cheryl Zehowski
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth Campus, Duluth, MN USA
| | - Douglas Yee
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN USA
| | - Andrew Skildum
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth Campus, Duluth, MN USA ; Masonic Cancer Center, University of Minnesota, Minneapolis, MN USA
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40
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Sun W, Xie Z, Liu Y, Zhao D, Wu Z, Zhang D, Lv H, Tang S, Jin N, Jiang H, Tan M, Ding J, Luo C, Li J, Huang M, Geng M. JX06 Selectively Inhibits Pyruvate Dehydrogenase Kinase PDK1 by a Covalent Cysteine Modification. Cancer Res 2015; 75:4923-36. [PMID: 26483203 DOI: 10.1158/0008-5472.can-15-1023] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 08/04/2015] [Indexed: 11/16/2022]
Abstract
Pyruvate dehydrogenase kinase PDK1 is a metabolic enzyme responsible for switching glucose metabolism from mitochondrial oxidation to aerobic glycolysis in cancer cells, a general hallmark of malignancy termed the Warburg effect. Herein we report the identification of JX06 as a selective covalent inhibitor of PDK1 in cells. JX06 forms a disulfide bond with the thiol group of a conserved cysteine residue (C240) based on recognition of a hydrophobic pocket adjacent to the ATP pocket of the PDK1 enzyme. Our investigations of JX06 mechanism suggested that covalent modification at C240 induced conformational changes at Arginine 286 through Van der Waals forces, thereby hindering access of ATP to its binding pocket and in turn impairing PDK1 enzymatic activity. Notably, cells with a higher dependency on glycolysis were more sensitive to PDK1 inhibition, reflecting a metabolic shift that promoted cellular oxidative stress and apoptosis. Our findings offer new mechanistic insights including how to therapeutically target PDK1 by covalently modifying the C240 residue.
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Affiliation(s)
- Wenyi Sun
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Zuoquan Xie
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yifu Liu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Dan Zhao
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Zhixiang Wu
- The Chemical Proteomics Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Dadong Zhang
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Hao Lv
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Shuai Tang
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Nan Jin
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Hualiang Jiang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Minjia Tan
- The Chemical Proteomics Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Jian Ding
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Cheng Luo
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
| | - Jian Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China.
| | - Min Huang
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
| | - Meiyu Geng
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
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Ferriero R, Iannuzzi C, Manco G, Brunetti-Pierri N. Differential inhibition of PDKs by phenylbutyrate and enhancement of pyruvate dehydrogenase complex activity by combination with dichloroacetate. J Inherit Metab Dis 2015; 38:895-904. [PMID: 25601413 PMCID: PMC4551558 DOI: 10.1007/s10545-014-9808-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 12/13/2014] [Accepted: 12/19/2014] [Indexed: 12/13/2022]
Abstract
Pyruvate dehydrogenase complex (PDHC) is a key enzyme in metabolism linking glycolysis to tricarboxylic acid cycle and its activity is tightly regulated by phosphorylation catalyzed by four pyruvate dehydrogenase kinase (PDK) isoforms. PDKs are pharmacological targets for several human diseases including cancer, diabetes, obesity, heart failure, and inherited PDHC deficiency. We investigated the inhibitory activity of phenylbutyrate toward PDKs and found that PDK isoforms 1-to-3 are inhibited whereas PDK4 is unaffected. Moreover, docking studies revealed putative binding sites of phenylbutyrate on PDK2 and 3 that are located on different sites compared to dichloroacetate (DCA), a previously known PDK inhibitor. Based on these findings, we showed both in cells and in mice that phenylbutyrate combined to DCA results in greater increase of PDHC activity compared to each drug alone. These results suggest that therapeutic efficacy can be enhanced by combination of drugs increasing PDHC enzyme activity.
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Affiliation(s)
- Rosa Ferriero
- Telethon Institute of Genetics and Medicine, Via Campi Felgrei, 34, 80078 Pozzuoli, Naples Italy
| | - Clara Iannuzzi
- Institute of Protein Biochemistry (IBP), Naples, Italy
- Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, Naples, Italy
| | | | - Nicola Brunetti-Pierri
- Telethon Institute of Genetics and Medicine, Via Campi Felgrei, 34, 80078 Pozzuoli, Naples Italy
- Department of Translational Medicine, Federico II University of Naples, Naples, Italy
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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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43
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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
![]()
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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44
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Broz AK, Tovar-Méndez A, Mooney BP, Johnston ML, Miernyk JA, Randall DD. A novel regulatory mechanism based upon a dynamic core structure for the mitochondrial pyruvate dehydrogenase complex? Mitochondrion 2014; 19 Pt B:144-53. [DOI: 10.1016/j.mito.2014.05.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 05/06/2014] [Accepted: 05/12/2014] [Indexed: 12/11/2022]
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45
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Sutendra G, Kinnaird A, Dromparis P, Paulin R, Stenson TH, Haromy A, Hashimoto K, Zhang N, Flaim E, Michelakis ED. A nuclear pyruvate dehydrogenase complex is important for the generation of acetyl-CoA and histone acetylation. Cell 2014; 158:84-97. [PMID: 24995980 DOI: 10.1016/j.cell.2014.04.046] [Citation(s) in RCA: 402] [Impact Index Per Article: 40.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Revised: 03/19/2014] [Accepted: 04/18/2014] [Indexed: 01/07/2023]
Abstract
DNA transcription, replication, and repair are regulated by histone acetylation, a process that requires the generation of acetyl-coenzyme A (CoA). Here, we show that all the subunits of the mitochondrial pyruvate dehydrogenase complex (PDC) are also present and functional in the nucleus of mammalian cells. We found that knockdown of nuclear PDC in isolated functional nuclei decreased the de novo synthesis of acetyl-CoA and acetylation of core histones. Nuclear PDC levels increased in a cell-cycle-dependent manner and in response to serum, epidermal growth factor, or mitochondrial stress; this was accompanied by a corresponding decrease in mitochondrial PDC levels, suggesting a translocation from the mitochondria to the nucleus. Inhibition of nuclear PDC decreased acetylation of specific lysine residues on histones important for G1-S phase progression and expression of S phase markers. Dynamic translocation of mitochondrial PDC to the nucleus provides a pathway for nuclear acetyl-CoA synthesis required for histone acetylation and epigenetic regulation.
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Affiliation(s)
- Gopinath Sutendra
- Department of Medicine, University of Alberta, Edmonton, AB T6G 2B7, Canada.
| | - Adam Kinnaird
- Department of Medicine, University of Alberta, Edmonton, AB T6G 2B7, Canada
| | - Peter Dromparis
- Department of Medicine, University of Alberta, Edmonton, AB T6G 2B7, Canada
| | - Roxane Paulin
- Department of Medicine, University of Alberta, Edmonton, AB T6G 2B7, Canada
| | - Trevor H Stenson
- Department of Medicine, University of Alberta, Edmonton, AB T6G 2B7, Canada
| | - Alois Haromy
- Department of Medicine, University of Alberta, Edmonton, AB T6G 2B7, Canada
| | - Kyoko Hashimoto
- Department of Medicine, University of Alberta, Edmonton, AB T6G 2B7, Canada
| | - Nancy Zhang
- nanoFAB Fabrication and Characterization Facility, University of Alberta, Edmonton, AB T6G 2B7, Canada
| | - Eric Flaim
- nanoFAB Fabrication and Characterization Facility, University of Alberta, Edmonton, AB T6G 2B7, Canada
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46
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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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47
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Tso SC, Qi X, Gui WJ, Wu CY, Chuang JL, Wernstedt-Asterholm I, Morlock LK, Owens KR, Scherer PE, Williams NS, Tambar UK, Wynn RM, Chuang DT. Structure-guided development of specific pyruvate dehydrogenase kinase inhibitors targeting the ATP-binding pocket. J Biol Chem 2013; 289:4432-43. [PMID: 24356970 DOI: 10.1074/jbc.m113.533885] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Pyruvate dehydrogenase kinase isoforms (PDKs 1-4) negatively regulate activity of the mitochondrial pyruvate dehydrogenase complex by reversible phosphorylation. PDK isoforms are up-regulated in obesity, diabetes, heart failure, and cancer and are potential therapeutic targets for these important human diseases. Here, we employed a structure-guided design to convert a known Hsp90 inhibitor to a series of highly specific PDK inhibitors, based on structural conservation in the ATP-binding pocket. The key step involved the substitution of a carbonyl group in the parent compound with a sulfonyl in the PDK inhibitors. The final compound of this series, 2-[(2,4-dihydroxyphenyl)sulfonyl]isoindoline-4,6-diol, designated PS10, inhibits all four PDK isoforms with IC50 = 0.8 μM for PDK2. The administration of PS10 (70 mg/kg) to diet-induced obese mice significantly augments pyruvate dehydrogenase complex activity with reduced phosphorylation in different tissues. Prolonged PS10 treatments result in improved glucose tolerance and notably lessened hepatic steatosis in the mouse model. The results support the pharmacological approach of targeting PDK to control both glucose and fat levels in obesity and type 2 diabetes.
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48
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Structure-based design and mechanisms of allosteric inhibitors for mitochondrial branched-chain α-ketoacid dehydrogenase kinase. Proc Natl Acad Sci U S A 2013; 110:9728-33. [PMID: 23716694 DOI: 10.1073/pnas.1303220110] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The branched-chain amino acids (BCAAs) leucine, isoleucine, and valine are elevated in maple syrup urine disease, heart failure, obesity, and type 2 diabetes. BCAA homeostasis is controlled by the mitochondrial branched-chain α-ketoacid dehydrogenase complex (BCKDC), which is negatively regulated by the specific BCKD kinase (BDK). Here, we used structure-based design to develop a BDK inhibitor, (S)-α-chloro-phenylpropionic acid [(S)-CPP]. Crystal structures of the BDK-(S)-CPP complex show that (S)-CPP binds to a unique allosteric site in the N-terminal domain, triggering helix movements in BDK. These conformational changes are communicated to the lipoyl-binding pocket, which nullifies BDK activity by blocking its binding to the BCKDC core. Administration of (S)-CPP to mice leads to the full activation and dephosphorylation of BCKDC with significant reduction in plasma BCAA concentrations. The results buttress the concept of targeting mitochondrial BDK as a pharmacological approach to mitigate BCAA accumulation in metabolic diseases and heart failure.
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49
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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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50
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Hurd TR, Collins Y, Abakumova I, Chouchani ET, Baranowski B, Fearnley IM, Prime TA, Murphy MP, James AM. Inactivation of pyruvate dehydrogenase kinase 2 by mitochondrial reactive oxygen species. J Biol Chem 2012; 287:35153-35160. [PMID: 22910903 DOI: 10.1074/jbc.m112.400002] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Reactive oxygen species are byproducts of mitochondrial respiration and thus potential regulators of mitochondrial function. Pyruvate dehydrogenase kinase 2 (PDHK2) inhibits the pyruvate dehydrogenase complex, thereby regulating entry of carbohydrates into the tricarboxylic acid (TCA) cycle. Here we show that PDHK2 activity is inhibited by low levels of hydrogen peroxide (H(2)O(2)) generated by the respiratory chain. This occurs via reversible oxidation of cysteine residues 45 and 392 on PDHK2 and results in increased pyruvate dehydrogenase complex activity. H(2)O(2) derives from superoxide (O(2)(.)), and we show that conditions that inhibit PDHK2 also inactivate the TCA cycle enzyme, aconitase. These findings suggest that under conditions of high mitochondrial O(2)(.) production, such as may occur under nutrient excess and low ATP demand, the increase in O(2)() and H(2)O(2) may provide feedback signals to modulate mitochondrial metabolism.
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Affiliation(s)
- Thomas R Hurd
- Mitochondrial Biology Unit, Medical Research Council, Cambridge CB2 0XY, United Kingdom
| | - Yvonne Collins
- Mitochondrial Biology Unit, Medical Research Council, Cambridge CB2 0XY, United Kingdom
| | - Irina Abakumova
- Mitochondrial Biology Unit, Medical Research Council, Cambridge CB2 0XY, United Kingdom
| | - Edward T Chouchani
- Mitochondrial Biology Unit, Medical Research Council, Cambridge CB2 0XY, United Kingdom
| | - Bartlomiej Baranowski
- Mitochondrial Biology Unit, Medical Research Council, Cambridge CB2 0XY, United Kingdom
| | - Ian M Fearnley
- Mitochondrial Biology Unit, Medical Research Council, Cambridge CB2 0XY, United Kingdom
| | - Tracy A Prime
- Mitochondrial Biology Unit, Medical Research Council, Cambridge CB2 0XY, United Kingdom
| | - Michael P Murphy
- Mitochondrial Biology Unit, Medical Research Council, Cambridge CB2 0XY, United Kingdom.
| | - Andrew M James
- Mitochondrial Biology Unit, Medical Research Council, Cambridge CB2 0XY, United Kingdom
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