1
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Tu KJ, Diplas BH, Regal JA, Waitkus MS, Pirozzi CJ, Reitman ZJ. Mining cancer genomes for change-of-metabolic-function mutations. Commun Biol 2023; 6:1143. [PMID: 37950065 PMCID: PMC10638295 DOI: 10.1038/s42003-023-05475-w] [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: 04/20/2023] [Accepted: 10/17/2023] [Indexed: 11/12/2023] Open
Abstract
Enzymes with novel functions are needed to enable new organic synthesis techniques. Drawing inspiration from gain-of-function cancer mutations that functionally alter proteins and affect cellular metabolism, we developed METIS (Mutated Enzymes from Tumors In silico Screen). METIS identifies metabolism-altering cancer mutations using mutation recurrence rates and protein structure. We used METIS to screen 298,517 cancer mutations and identify 48 candidate mutations, including those previously identified to alter enzymatic function. Unbiased metabolomic profiling of cells exogenously expressing a candidate mutant (OGDHLp.A400T) supports an altered phenotype that boosts in vitro production of xanthosine, a pharmacologically useful chemical that is currently produced using unsustainable, water-intensive methods. We then applied METIS to 49 million cancer mutations, yielding a refined set of candidates that may impart novel enzymatic functions or contribute to tumor progression. Thus, METIS can be used to identify and catalog potentially-useful cancer mutations for green chemistry and therapeutic applications.
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Affiliation(s)
- Kevin J Tu
- Department of Radiation Oncology, Duke University, Durham, NC, 27710, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 21044, USA
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, CB2 0RE, UK
| | - Bill H Diplas
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Joshua A Regal
- Department of Radiation Oncology, Duke University, Durham, NC, 27710, USA
| | | | | | - Zachary J Reitman
- Department of Radiation Oncology, Duke University, Durham, NC, 27710, USA.
- Department of Neurosurgery, Duke University, Durham, NC, 27710, USA.
- Department of Pathology, Duke University, Durham, NC, 27710, USA.
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2
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Liu M, He K, Bi H, Wang M, Chen B, Tan T, Zhang Y. Metabolic Engineering for Effective Synthesis of 2-Hydroxyadipate. ACS Synth Biol 2023; 12:2475-2486. [PMID: 37527188 DOI: 10.1021/acssynbio.3c00362] [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: 08/03/2023]
Abstract
Adipic acid is an important monomer in the synthesis of nylon-6,6. In recent years, the biosynthesis of adipic acid has received more and more attention. The pathway with l-lysine as a precursor has potential for adipic acid synthesis, and 2-hydroxyadipate is a key intermediate metabolite in this pathway. In this Letter, the biosynthesis pathway of 2-hydroxyadipate was constructed in Escherichia coli. Through enhancement of precursor synthesis and cofactors regulation, 7.11 g/L of 2-hydroxyadipate was produced in the 5 L bioreactor, which verified the scale-up potential of 2-hydroxyadipate production. Furthermore, 11.1 g/L of 2-hydroxyadipate was produced in the 5 L bioreactor on the basis of potential optimization strategies via transcriptome analysis. This is the first time for the biosynthesis of 2-hydroxyadipate. The results lay a solid foundation for the biosynthesis of adipic acid and the production of bionylon.
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Affiliation(s)
- Meng Liu
- National Energy R&D Center for Biorefinery, Beijing Key Laboratory of Bioprocess, Beijing University of Chemical Technology, Beijing, 15th Beisanhuan East Road, Beijing, 100029, PR China
| | - Keqin He
- National Energy R&D Center for Biorefinery, Beijing Key Laboratory of Bioprocess, Beijing University of Chemical Technology, Beijing, 15th Beisanhuan East Road, Beijing, 100029, PR China
| | - Haoran Bi
- National Energy R&D Center for Biorefinery, Beijing Key Laboratory of Bioprocess, Beijing University of Chemical Technology, Beijing, 15th Beisanhuan East Road, Beijing, 100029, PR China
| | - Meng Wang
- National Energy R&D Center for Biorefinery, Beijing Key Laboratory of Bioprocess, Beijing University of Chemical Technology, Beijing, 15th Beisanhuan East Road, Beijing, 100029, PR China
| | - Biqiang Chen
- National Energy R&D Center for Biorefinery, Beijing Key Laboratory of Bioprocess, Beijing University of Chemical Technology, Beijing, 15th Beisanhuan East Road, Beijing, 100029, PR China
| | - Tianwei Tan
- National Energy R&D Center for Biorefinery, Beijing Key Laboratory of Bioprocess, Beijing University of Chemical Technology, Beijing, 15th Beisanhuan East Road, Beijing, 100029, PR China
| | - Yang Zhang
- National Energy R&D Center for Biorefinery, Beijing Key Laboratory of Bioprocess, Beijing University of Chemical Technology, Beijing, 15th Beisanhuan East Road, Beijing, 100029, PR China
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3
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Tian W, Zhang W, Wang Y, Jin R, Wang Y, Guo H, Tang Y, Yao X. Recent advances of IDH1 mutant inhibitor in cancer therapy. Front Pharmacol 2022; 13:982424. [PMID: 36091829 PMCID: PMC9449373 DOI: 10.3389/fphar.2022.982424] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/02/2022] [Indexed: 11/23/2022] Open
Abstract
Isocitrate dehydrogenase (IDH) is the key metabolic enzyme that catalyzes the conversion of isocitrate to α-ketoglutarate (α-KG). Two main types of IDH1 and IDH2 are present in humans. In recent years, mutations in IDH have been observed in several tumors, including glioma, acute myeloid leukemia, and chondrosarcoma. Among them, the frequency of IDH1 mutations is higher than IDH2. IDH1 mutations have been shown to increase the conversion of α-KG to 2-hydroxyglutarate (2-HG). IDH1 mutation-mediated accumulation of 2-HG leads to epigenetic dysregulation, altering gene expression, and impairing cell differentiation. A rapidly emerging therapeutic approach is through the development of small molecule inhibitors targeting mutant IDH1 (mIDH1), as evidenced by the recently approved of the first selective IDH1 mutant inhibitor AG-120 (ivosidenib) for the treatment of IDH1-mutated AML. This review will focus on mIDH1 as a therapeutic target and provide an update on IDH1 mutant inhibitors in development and clinical trials.
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Affiliation(s)
- Wangqi Tian
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi, China
| | - Weitong Zhang
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi, China
| | - Yifan Wang
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi, China
| | - Ruyi Jin
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi, China
| | - Yuwei Wang
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi, China
| | - Hui Guo
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi, China
| | - Yuping Tang
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi, China
| | - Xiaojun Yao
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, China
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4
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Saez-Jimenez V, Scrima S, Lambrughi M, Papaleo E, Mapelli V, Engqvist MKM, Olsson L. Directed Evolution of ( R)-2-Hydroxyglutarate Dehydrogenase Improves 2-Oxoadipate Reduction by 2 Orders of Magnitude. ACS Synth Biol 2022; 11:2779-2790. [PMID: 35939387 PMCID: PMC9396657 DOI: 10.1021/acssynbio.2c00162] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Pathway engineering is commonly employed to improve the
production
of various metabolites but may incur in bottlenecks due to the low
catalytic activity of a particular reaction step. The reduction of
2-oxoadipate to (R)-2-hydroxyadipate is a key reaction
in metabolic pathways that exploit 2-oxoadipate conversion via α-reduction
to produce adipic acid, an industrially important platform chemical.
Here, we engineered (R)-2-hydroxyglutarate dehydrogenase
from Acidaminococcus fermentans (Hgdh)
with the aim of improving 2-oxoadipate reduction. Using a combination
of computational analysis, saturation mutagenesis, and random mutagenesis,
three mutant variants with a 100-fold higher catalytic efficiency
were obtained. As revealed by rational analysis of the mutations found
in the variants, this improvement could be ascribed to a general synergistic
effect where mutation A206V played a key role since it boosted the
enzyme’s activity by 4.8-fold. The Hgdh variants with increased
activity toward 2-oxoadipate generated within this study pave the
way for the bio-based production of adipic acid.
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Affiliation(s)
- Veronica Saez-Jimenez
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Simone Scrima
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark.,Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Matteo Lambrughi
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
| | - Elena Papaleo
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark.,Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Valeria Mapelli
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Martin K M Engqvist
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Lisbeth Olsson
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
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Skoog E, Shin JH, Saez-Jimenez V, Mapelli V, Olsson L. Biobased adipic acid – The challenge of developing the production host. Biotechnol Adv 2018; 36:2248-2263. [DOI: 10.1016/j.biotechadv.2018.10.012] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 10/18/2018] [Accepted: 10/27/2018] [Indexed: 11/28/2022]
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Inhibition of mitochondrial 2-oxoglutarate dehydrogenase impairs viability of cancer cells in a cell-specific metabolism-dependent manner. Oncotarget 2018; 7:26400-21. [PMID: 27027236 PMCID: PMC5041988 DOI: 10.18632/oncotarget.8387] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 03/11/2016] [Indexed: 12/31/2022] Open
Abstract
2-Oxoglutarate dehydrogenase (OGDH) of the tricarboxylic acid (TCA) cycle is often implied to be inactive in cancer, but this was not experimentally tested. We addressed the question through specific inhibition of OGDH by succinyl phosphonate (SP). SP action on different cancer cells was investigated using indicators of cellular viability and reactive oxygen species (ROS), metabolic profiling and transcriptomics. Relative sensitivity of various cancer cells to SP changed with increasing SP exposure and could differ in the ATP- and NAD(P)H-based assays. Glioblastoma responses to SP revealed metabolic sub-types increasing or decreasing cellular ATP/NAD(P)H ratio under OGDH inhibition. Cancer cell homeostasis was perturbed also when viability indicators were SP-resistant, e.g. in U87 and N2A cells. The transcriptomics database analysis showed that the SP-sensitive cells, such as A549 and T98G, exhibit the lowest expression of OGDH compared to other TCA cycle enzymes, associated with higher expression of affiliated pathways utilizing 2-oxoglutarate. Metabolic profiling confirmed the dependence of cellular SP reactivity on cell-specific expression of the pathways. Thus, oxidative decarboxylation of 2-oxoglutarate is significant for the interdependent homeostasis of NAD(P)H, ATP, ROS and key metabolites in various cancer cells. Assessment of cell-specific responses to OGDH inhibition is of diagnostic value for anticancer strategies.
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8
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Narcross L, Bourgeois L, Fossati E, Burton E, Martin VJJ. Mining Enzyme Diversity of Transcriptome Libraries through DNA Synthesis for Benzylisoquinoline Alkaloid Pathway Optimization in Yeast. ACS Synth Biol 2016; 5:1505-1518. [PMID: 27442619 DOI: 10.1021/acssynbio.6b00119] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The ever-increasing quantity of data deposited to GenBank is a valuable resource for mining new enzyme activities. Falling costs of DNA synthesis enables metabolic engineers to take advantage of this resource for identifying superior or novel enzymes for pathway optimization. Previously, we reported synthesis of the benzylisoquinoline alkaloid dihydrosanguinarine in yeast from norlaudanosoline at a molar conversion of 1.5%. Molar conversion could be improved by reduction of the side-product N-methylcheilanthifoline, a key bottleneck in dihydrosanguinarine biosynthesis. Two pathway enzymes, an N-methyltransferase and a cytochrome P450 of the CYP719A subfamily, were implicated in the synthesis of the side-product. Here, we conducted an extensive screen to identify enzyme homologues whose coexpression reduces side-product synthesis. Phylogenetic trees were generated from multiple sources of sequence data to identify a library of candidate enzymes that were purchased codon-optimized and precloned into expression vectors designed to facilitate high-throughput analysis of gene expression as well as activity assay. Simple in vivo assays were sufficient to guide the selection of superior enzyme homologues that ablated the synthesis of the side-product, and improved molar conversion of norlaudanosoline to dihydrosanguinarine to 10%.
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Affiliation(s)
- Lauren Narcross
- Department
of Biology, Concordia University, Montréal, Québec H4B 1R6, Canada
- Centre
for Structural and Functional Genomics, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Leanne Bourgeois
- Department
of Biology, Concordia University, Montréal, Québec H4B 1R6, Canada
- Centre
for Structural and Functional Genomics, Concordia University, Montréal, Québec H4B 1R6, Canada
| | | | - Euan Burton
- Department
of Biology, Concordia University, Montréal, Québec H4B 1R6, Canada
- Centre
for Structural and Functional Genomics, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Vincent J. J. Martin
- Department
of Biology, Concordia University, Montréal, Québec H4B 1R6, Canada
- Centre
for Structural and Functional Genomics, Concordia University, Montréal, Québec H4B 1R6, Canada
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9
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Waitkus MS, Diplas BH, Yan H. Isocitrate dehydrogenase mutations in gliomas. Neuro Oncol 2015; 18:16-26. [PMID: 26188014 DOI: 10.1093/neuonc/nov136] [Citation(s) in RCA: 200] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 06/16/2015] [Indexed: 12/19/2022] Open
Abstract
Over the last decade, extraordinary progress has been made in elucidating the underlying genetic causes of gliomas. In 2008, our understanding of glioma genetics was revolutionized when mutations in isocitrate dehydrogenase 1 and 2 (IDH1/2) were identified in the vast majority of progressive gliomas and secondary glioblastomas (GBMs). IDH enzymes normally catalyze the decarboxylation of isocitrate to generate α-ketoglutarate (αKG), but recurrent mutations at Arg(132) of IDH1 and Arg(172) of IDH2 confer a neomorphic enzyme activity that catalyzes reduction of αKG into the putative oncometabolite D-2-hydroxyglutate (D2HG). D2HG inhibits αKG-dependent dioxygenases and is thought to create a cellular state permissive to malignant transformation by altering cellular epigenetics and blocking normal differentiation processes. Herein, we discuss the relevant literature on mechanistic studies of IDH1/2 mutations in gliomas, and we review the potential impact of IDH1/2 mutations on molecular classification and glioma therapy.
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Affiliation(s)
- Matthew S Waitkus
- The Preston Robert Tisch Brain Tumor Center at Duke, Pediatric Brain Tumor Foundation Institute at Duke, and Department of Pathology, Duke University Medical Center, Durham, North Carolina (M.S.W., B.H.D., H.Y.)
| | - Bill H Diplas
- The Preston Robert Tisch Brain Tumor Center at Duke, Pediatric Brain Tumor Foundation Institute at Duke, and Department of Pathology, Duke University Medical Center, Durham, North Carolina (M.S.W., B.H.D., H.Y.)
| | - Hai Yan
- The Preston Robert Tisch Brain Tumor Center at Duke, Pediatric Brain Tumor Foundation Institute at Duke, and Department of Pathology, Duke University Medical Center, Durham, North Carolina (M.S.W., B.H.D., H.Y.)
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10
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Bart JCJ, Cavallaro S. Transiting from Adipic Acid to Bioadipic Acid. Part II. Biosynthetic Pathways. Ind Eng Chem Res 2015. [DOI: 10.1021/ie502074d] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jan C. J. Bart
- Dipartimento di Ingegneria
Elettronica, Chimica e Ingegneria Industriale dell’Università di Messina, Viale F. Stagno D’Alcontres, 31-98166 Sant’Agata di
Messina, Italy
| | - Stefano Cavallaro
- Dipartimento di Ingegneria
Elettronica, Chimica e Ingegneria Industriale dell’Università di Messina, Viale F. Stagno D’Alcontres, 31-98166 Sant’Agata di
Messina, Italy
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11
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Change, exchange, and rearrange: protein engineering for the biotechnological production of fuels, pharmaceuticals, and other chemicals. Curr Opin Biotechnol 2013; 24:1010-6. [DOI: 10.1016/j.copbio.2013.02.027] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 02/25/2013] [Accepted: 02/26/2013] [Indexed: 01/07/2023]
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12
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Yang X, Zhang Y. Effect of temperature and sorbitol in improving the solubility of carboxylesterases protein CpCE-1 from Cydia pomonella and biochemical characterization. Appl Microbiol Biotechnol 2013; 97:10423-33. [DOI: 10.1007/s00253-013-5236-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 09/09/2013] [Indexed: 11/29/2022]
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13
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Cairns RA, Mak TW. Oncogenic isocitrate dehydrogenase mutations: mechanisms, models, and clinical opportunities. Cancer Discov 2013; 3:730-41. [PMID: 23796461 DOI: 10.1158/2159-8290.cd-13-0083] [Citation(s) in RCA: 325] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Heterozygous mutations in catalytic arginine residues of isocitrate dehydrogenases 1 and 2 (IDH1 and IDH2) are common in glioma, acute myeloid leukemia, chondrosarcoma, cholangiocarcinoma, and angioimmunoblastic T-cell lymphoma. The mutant enzymes acquire a neomorphic activity that converts α-ketoglutarate (α-KG) to D-2-hydroxyglutarate (D2HG), a rare metabolite. In cells and tissues expressing mutant IDH, D2HG concentrations are highly elevated. D2HG may act as an "oncometabolite" by inhibiting a class of α-KG-dependent enzymes involved in epigenetic regulation, collagen synthesis, and cell signaling. Knock-in mouse models of IDH1 mutations have shed light on these mechanisms and will provide valuable animal models for further investigation.
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Affiliation(s)
- Rob A Cairns
- Campbell Family Cancer Research Institute at Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
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15
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Hodges TR, Choi BD, Bigner DD, Yan H, Sampson JH. Isocitrate dehydrogenase 1: what it means to the neurosurgeon: a review. J Neurosurg 2013; 118:1176-80. [PMID: 23581583 DOI: 10.3171/2013.3.jns122282] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Isocitrate dehydrogenase 1 (IDH1) mutations have been discovered to be frequent and highly conserved in secondary glioblastoma multiforme and lower-grade gliomas. Although IDH1 mutations confer a unique genotype that has been associated with a favorable prognosis, the role of the mutated IDH1 enzyme and its metabolites in tumor initiation and maintenance remains unresolved. However, given that IDH1 mutations are homogeneously expressed and are limited solely to tumor tissue, targeting this mutation could potentially yield novel treatment strategies for patients with glioblastoma multiforme.
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Affiliation(s)
- Tiffany R Hodges
- Duke Brain Tumor Immunotherapy Program, Division of Neurosurgery, Department of Surgery, Duke University Medical Center, Durham, North Carolina 27710, USA
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16
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Van de Vyver S, Román-Leshkov Y. Emerging catalytic processes for the production of adipic acid. Catal Sci Technol 2013. [DOI: 10.1039/c3cy20728e] [Citation(s) in RCA: 231] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Auld D, Lea W, Davis MI, Simeonov A. Literature Search and Review. Assay Drug Dev Technol 2012. [DOI: 10.1089/adt.2012.1006.lr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Doug Auld
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
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19
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Chemitrends. INDIAN CHEMICAL ENGINEER 2012. [DOI: 10.1080/00194506.2012.758911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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