title: Oncometabolites d- and l-2-Hydroxyglutarate Inhibit the AlkB Family DNA Repair Enzymes under Physiological Conditions.
abstract: Cancer-associated mutations often lead to perturbed cellular energy metabolism and accumulation of potentially harmful oncometabolites. One example is the chiral molecule 2-hydroxyglutarate (2HG); its two stereoisomers (d- and l-2HG) have been found at abnormally high concentrations in tumors featuring anomalous metabolic pathways. 2HG has been demonstrated to competitively inhibit several α-ketoglutarate (αKG)- and non-heme iron-dependent dioxygenases, including some of the AlkB family DNA repair enzymes, such as ALKBH2 and ALKBH3. However, previous studies have only provided the IC50values of d-2HG on the enzymes, and the results have not been correlated to physiologically relevant concentrations of 2HG and αKG in cancer cells. In this work, we performed detailed kinetic analyses of DNA repair reactions catalyzed by ALKBH2, ALKBH3, and the bacterial AlkB in the presence of d- and l-2HG in both double- and single-stranded DNA contexts. We determined the kinetic parameters of inhibition, including kcat, KM, and Ki. We also correlated the relative concentrations of 2HG and αKG previously measured in tumor cells with the inhibitory effect of 2HG on the AlkB family enzymes. Both d- and l-2HG significantly inhibited the human DNA repair enzymes ALKBH2 and ALKBH3 at pathologically relevant concentrations (73-88% for d-2HG and 31-58% for l-2HG inhibition). This work provides a new perspective that the elevation of the d- or l-2HG concentration in cancer cells may contribute to an increased mutation rate by inhibiting the DNA repair performed by the AlkB family enzymes and thus exacerbate the genesis and progression of tumors.
authors.affiliation: Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island , Kingston, Rhode Island 02881, United States.
authors.forename: Fangyi
authors.initials: F
authors.lastname: Chen
authors.affiliation: Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island , Kingston, Rhode Island 02881, United States.
authors.forename: Ke
authors.initials: K
authors.lastname: Bian
authors.affiliation: Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island , Kingston, Rhode Island 02881, United States.
authors.forename: Qi
authors.initials: Q
authors.lastname: Tang
authors.affiliation: Department of Biological Engineering, Department of Chemistry, and Center for Environmental Health Sciences, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States.
authors.forename: Bogdan I
authors.initials: BI
authors.lastname: Fedeles
authors.affiliation: Department of Biological Engineering, Department of Chemistry, and Center for Environmental Health Sciences, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States.
authors.forename: Vipender
authors.initials: V
authors.lastname: Singh
authors.affiliation: Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island , Kingston, Rhode Island 02881, United States.
authors.forename: Zachary T
authors.initials: ZT
authors.lastname: Humulock
authors.affiliation: Department of Biological Engineering, Department of Chemistry, and Center for Environmental Health Sciences, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States.
authors.forename: John M
authors.initials: JM
authors.lastname: Essigmann
authors.affiliation: Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island , Kingston, Rhode Island 02881, United States.
authors.forename: Deyu
authors.identifier: 0000-0002-1082-0569
authors.initials: D
authors.lastname: Li
mesh_terms: D000071499:AlkB Homolog 2, Alpha-Ketoglutarate-Dependent Dioxygenase / Q000037:antagonists & inhibitors / Q000235:genetics / Q000378:metabolism*; D000071500:AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase / Q000037:antagonists & inhibitors / Q000235:genetics / Q000378:metabolism*; D001483:Base Sequence; D002851:Chromatography, High Pressure Liquid; D004260:DNA Repair; D057075:Enzyme Assays; D005977:Glutarates / Q000032:analysis / Q000737:chemistry / Q000378:metabolism*; D006801:Humans; D020128:Inhibitory Concentration 50; D007656:Ketoglutaric Acids / Q000032:analysis / Q000737:chemistry / Q000378:metabolism; D007700:Kinetics; D011485:Protein Binding; D011994:Recombinant Proteins / Q000096:biosynthesis / Q000737:chemistry / Q000302:isolation & purification; D013237:Stereoisomerism
chemical_list: D005977:Glutarates; D007656:Ketoglutaric Acids; D011994:Recombinant Proteins; C019417:alpha-hydroxyglutarate; C486439:ALKBH3 protein, human; D000071500:AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase; C486440:ALKBH2 protein, human; D000071499:AlkB Homolog 2, Alpha-Ketoglutarate-Dependent Dioxygenase