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Mendez R, Shaikh M, Lemke MC, Yuan K, Libby AH, Bai DL, Ross MM, Harris TE, Hsu KL. Predicting small molecule binding pockets on diacylglycerol kinases using chemoproteomics and AlphaFold. RSC Chem Biol 2023; 4:422-430. [PMID: 37292058 PMCID: PMC10246554 DOI: 10.1039/d3cb00057e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 05/13/2023] [Indexed: 06/10/2023] Open
Abstract
Diacylglycerol kinases (DGKs) are metabolic kinases involved in regulating cellular levels of diacylglycerol and phosphatidic lipid messengers. The development of selective inhibitors for individual DGKs would benefit from discovery of protein pockets available for inhibitor binding in cellular environments. Here we utilized a sulfonyl-triazole probe (TH211) bearing a DGK fragment ligand for covalent binding to tyrosine and lysine sites on DGKs in cells that map to predicted small molecule binding pockets in AlphaFold structures. We apply this chemoproteomics-AlphaFold approach to evaluate probe binding of DGK chimera proteins engineered to exchange regulatory C1 domains between DGK subtypes (DGKα and DGKζ). Specifically, we discovered loss of TH211 binding to a predicted pocket in the catalytic domain when C1 domains on DGKα were exchanged that correlated with impaired biochemical activity as measured by a DAG phosphorylation assay. Collectively, we provide a family-wide assessment of accessible sites for covalent targeting that combined with AlphaFold revealed predicted small molecule binding pockets for guiding future inhibitor development of the DGK superfamily.
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Affiliation(s)
- Roberto Mendez
- Department of Chemistry, University of Virginia Charlottesville Virginia 22904 USA +1 434-297-4864
| | - Minhaj Shaikh
- Department of Chemistry, University of Virginia Charlottesville Virginia 22904 USA +1 434-297-4864
| | - Michael C Lemke
- Department of Pharmacology, University of Virginia School of Medicine Charlottesville Virginia 22908 USA
| | - Kun Yuan
- Department of Chemistry, University of Virginia Charlottesville Virginia 22904 USA +1 434-297-4864
| | - Adam H Libby
- Department of Chemistry, University of Virginia Charlottesville Virginia 22904 USA +1 434-297-4864
- University of Virginia Cancer Center, University of Virginia Charlottesville VA 22903 USA
| | - Dina L Bai
- Department of Chemistry, University of Virginia Charlottesville Virginia 22904 USA +1 434-297-4864
| | - Mark M Ross
- Department of Chemistry, University of Virginia Charlottesville Virginia 22904 USA +1 434-297-4864
| | - Thurl E Harris
- Department of Pharmacology, University of Virginia School of Medicine Charlottesville Virginia 22908 USA
| | - Ku-Lung Hsu
- Department of Chemistry, University of Virginia Charlottesville Virginia 22904 USA +1 434-297-4864
- Department of Pharmacology, University of Virginia School of Medicine Charlottesville Virginia 22908 USA
- Department of Molecular Physiology and Biological Physics, University of Virginia Charlottesville Virginia 22908 USA
- University of Virginia Cancer Center, University of Virginia Charlottesville VA 22903 USA
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Alizadeh J, Kavoosi M, Singh N, Lorzadeh S, Ravandi A, Kidane B, Ahmed N, Mraiche F, Mowat MR, Ghavami S. Regulation of Autophagy via Carbohydrate and Lipid Metabolism in Cancer. Cancers (Basel) 2023; 15:cancers15082195. [PMID: 37190124 DOI: 10.3390/cancers15082195] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/21/2023] [Accepted: 03/28/2023] [Indexed: 05/17/2023] Open
Abstract
Metabolic changes are an important component of tumor cell progression. Tumor cells adapt to environmental stresses via changes to carbohydrate and lipid metabolism. Autophagy, a physiological process in mammalian cells that digests damaged organelles and misfolded proteins via lysosomal degradation, is closely associated with metabolism in mammalian cells, acting as a meter of cellular ATP levels. In this review, we discuss the changes in glycolytic and lipid biosynthetic pathways in mammalian cells and their impact on carcinogenesis via the autophagy pathway. In addition, we discuss the impact of these metabolic pathways on autophagy in lung cancer.
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Affiliation(s)
- Javad Alizadeh
- Department of Human Anatomy and Cell Science, College of Medicine, University of Manitoba, Winnipeg, MB R3E 0V9, Canada
| | - Mahboubeh Kavoosi
- Department of Human Anatomy and Cell Science, College of Medicine, University of Manitoba, Winnipeg, MB R3E 0V9, Canada
| | - Navjit Singh
- Department of Human Anatomy and Cell Science, College of Medicine, University of Manitoba, Winnipeg, MB R3E 0V9, Canada
| | - Shahrokh Lorzadeh
- Department of Human Anatomy and Cell Science, College of Medicine, University of Manitoba, Winnipeg, MB R3E 0V9, Canada
| | - Amir Ravandi
- Department of Physiology and Pathophysiology, Rady Faculty of Health Sciences, Institute of Cardiovascular Sciences, Albrechtsen Research Centre, St. Boniface Hospital, Winnipeg, MB R2H 2A6, Canada
| | - Biniam Kidane
- Section of Thoracic Surgery, Department of Surgery, Health Sciences Centre, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3T 6C5, Canada
- CancerCare Manitoba Research Institute, Winnipeg, MB R3E 0V9, Canada
| | - Naseer Ahmed
- CancerCare Manitoba Research Institute, Winnipeg, MB R3E 0V9, Canada
- Department of Radiology, Section of Radiation Oncology, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Fatima Mraiche
- College of Pharmacy, QU Health, Qatar University, Doha 2713, Qatar
- Department of Pharmacology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Michael R Mowat
- CancerCare Manitoba Research Institute, Winnipeg, MB R3E 0V9, Canada
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Saeid Ghavami
- Department of Human Anatomy and Cell Science, College of Medicine, University of Manitoba, Winnipeg, MB R3E 0V9, Canada
- Research Institute of Oncology and Hematology, Winnipeg, MB R3E 0V9, Canada
- Faculty of Medicine in Zabrze, Academia of Silesia, 41-800 Zabrze, Poland
- Biology of Breathing Theme, Children Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB R3E 3P5, Canada
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Granade ME, Manigat LC, Lemke MC, Purow BW, Harris TE. Identification of ritanserin analogs that display DGK isoform specificity. Biochem Pharmacol 2022; 197:114908. [PMID: 34999054 PMCID: PMC8858877 DOI: 10.1016/j.bcp.2022.114908] [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: 11/08/2021] [Revised: 12/28/2021] [Accepted: 01/01/2022] [Indexed: 11/15/2022]
Abstract
The diacylglycerol kinase (DGK) family of lipid enzymes catalyzes the conversion of diacylglycerol (DAG) to phosphatidic acid (PA). Both DAG and PA are lipid signaling molecules that are of notable importance in regulating cell processes such as proliferation, apoptosis, and migration. There are ten mammalian DGK enzymes that appear to have distinct biological functions. DGKα has emerged as a promising therapeutic target in numerous cancers including glioblastoma (GBM) and melanoma as treatment with small molecule DGKα inhibitors results in reduced tumor sizes and prolonged survival. Importantly, DGKα has also been identified as an immune checkpoint due to its promotion of T cell anergy, and its inhibition has been shown to improve T cell activation. There are few small molecule DGKα inhibitors currently available, and the application of existing compounds to clinical settings is hindered by species-dependent variability in potency, as well as concerns regarding isotype specificity particularly amongst other type I DGKs. In order to resolve these issues, we have screened a library of compounds structurally analogous to the DGKα inhibitor, ritanserin, in an effort to identify more potent and specific alternatives. We identified two compounds that more potently and selectively inhibit DGKα, one of which (JNJ-3790339) demonstrates similar cytotoxicity in GBM and melanoma cells as ritanserin. Consistent with its inhibitor profile towards DGKα, JNJ-3790339 also demonstrated improved activation of T cells compared with ritanserin. Together our data support efforts to identify DGK isoform-selective inhibitors as a mechanism to produce pharmacologically relevant cancer therapies.
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Affiliation(s)
- Mitchell E Granade
- University of Virginia, School of Medicine, Department of Pharmacology, Charlottesville, VA, United States
| | - Laryssa C Manigat
- University of Virginia, School of Medicine, Department of Pathology, Charlottesville, VA, United States
| | - Michael C Lemke
- University of Virginia, School of Medicine, Department of Pharmacology, Charlottesville, VA, United States
| | - Benjamin W Purow
- University of Virginia, Department of Neurology, Division of Neuro-Oncology, Charlottesville, VA, United States.
| | - Thurl E Harris
- University of Virginia, School of Medicine, Department of Pharmacology, Charlottesville, VA, United States.
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Hennessy M, Granade ME, Hassaninasab A, Wang D, Kwiatek JM, Han GS, Harris TE, Carman GM. Casein kinase II-mediated phosphorylation of lipin 1β phosphatidate phosphatase at Ser-285 and Ser-287 regulates its interaction with 14-3-3β protein. J Biol Chem 2019; 294:2365-2374. [PMID: 30617183 DOI: 10.1074/jbc.ra118.007246] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/04/2019] [Indexed: 12/20/2022] Open
Abstract
The mammalian lipin 1 phosphatidate phosphatase is a key regulatory enzyme in lipid metabolism. By catalyzing phosphatidate dephosphorylation, which produces diacylglycerol, the enzyme plays a major role in the synthesis of triacylglycerol and membrane phospholipids. The importance of lipin 1 to lipid metabolism is exemplified by cellular defects and lipid-based diseases associated with its loss or overexpression. Phosphorylation of lipin 1 governs whether it is associated with the cytoplasm apart from its substrate or with the endoplasmic reticulum membrane where its enzyme reaction occurs. Lipin 1β is phosphorylated on multiple sites, but less than 10% of them are ascribed to a specific protein kinase. Here, we demonstrate that lipin 1β is a bona fide substrate for casein kinase II (CKII), a protein kinase that is essential to viability and cell cycle progression. Phosphoamino acid analysis and phosphopeptide mapping revealed that lipin 1β is phosphorylated by CKII on multiple serine and threonine residues, with the former being major sites. Mutational analysis of lipin 1β and its peptides indicated that Ser-285 and Ser-287 are both phosphorylated by CKII. Substitutions of Ser-285 and Ser-287 with nonphosphorylatable alanine attenuated the interaction of lipin 1β with 14-3-3β protein, a regulatory hub that facilitates the cytoplasmic localization of phosphorylated lipin 1. These findings advance our understanding of how phosphorylation of lipin 1β phosphatidate phosphatase regulates its interaction with 14-3-3β protein and intracellular localization and uncover a mechanism by which CKII regulates cellular physiology.
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Affiliation(s)
- Meagan Hennessy
- From the Department of Food Science and the Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, New Jersey 08901 and
| | - Mitchell E Granade
- the Department of Pharmacology, University of Virginia, Charlottesville, Virginia 22908
| | - Azam Hassaninasab
- From the Department of Food Science and the Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, New Jersey 08901 and
| | - Dana Wang
- the Department of Pharmacology, University of Virginia, Charlottesville, Virginia 22908
| | - Joanna M Kwiatek
- From the Department of Food Science and the Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, New Jersey 08901 and
| | - Gil-Soo Han
- From the Department of Food Science and the Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, New Jersey 08901 and
| | - Thurl E Harris
- the Department of Pharmacology, University of Virginia, Charlottesville, Virginia 22908
| | - George M Carman
- From the Department of Food Science and the Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, New Jersey 08901 and
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