Studies on: roles and therapeutic potential of isocitrate dehydrogenase mutations in cancer and inhibition of the SARS-CoV-2 main protease

Thesis

Altered metabolism is a hallmark of cancer. Mutations in the metabolic enzymes human isocitrate dehydrogenase 1 and 2 (IDH1/2) are common in various cancers, with significant prevalence in glioma. Small-molecule inhibitors targeting IDH1 and IDH2 variants have been approved for treatment of haematological malignancies, and, recently for glioma treatment. Resistance to these inhibitors has been observed and is associated with disease relapse. The precise metabolic mechanisms linking IDH1 mutations to oncogenic drivers in glioma remain unclear. This thesis describes studies investigating the role of IDH1/2 WT and IDH1 R132H in glioma and studies seeking to identify new treatment strategies exploiting the resulting metabolic dysfunction. Work carried out to meet the urgent need for COVID-19 therapeutics is also described, that is, structure-activity studies aiming to develop a small-molecule inhibitor targeting the SARS-CoV-2 main protease.

Chapter 1 reviews the effects of the IDH1/2 mutation gain-of-function in cancer and existing therapeutic avenues. Chapter 2 describes the synthesis of inhibitors of IDH1 WT and IDH2 WT, inhibition studies on the binding kinetics of IDH1 WT, and the investigation of a novel potential scaffold for IDH1 R132H inhibitors. Chapter 3 describes metabolomic studies on the effects of the IDH1 R132H mutation on LN18 GBM cells, and the effects of IDH1 WT and IDH2 WT inhibitors on LN18 GBM cells, with and without the IDH1 R132H mutation. Chapter 4 describes the development of ebselen-type inhibitors against the SARS-CoV-2 main protease. This thesis tentatively proposes a link between IDH1 R132H and an oncogenic driver in glioma, and proposes novel therapeutic avenues against IDH1 R132H glioma.

Authors: Graf Thun-Hohenstein, S

• DOI: 10.5287/ora-yeog5gamj
• Type of award: DPhil
• Awarding institution: University of Oxford
• Language: English
• Keywords: LOOCV; Kdpre; pseudohypoxia; BCAT1; NAG; Protein Kinase C delta; antimicrobial activity; GHB; chemical biology; protein kinase C; peroxisomal metabolism; NADPH absorbance assay; open-inactive conformation; NMR spectroscopy; glutaconate; FNR; PROTAC; branched-chain aminotransferase; FRET; univariate statistical analysis; AG-881; citramalic acid; neomorphic gain-of-function; β-Citryl glutamate; covalent inhibitor; 3-pyrimidin-4-yl-oxazolidin-2-one scaffold; cell culture; hallmarks of cancer; 2-OG; RIMKLA; therapeutics; gain-of-function mutation; dimer-interface binding; IDH inhibitor class; IDH2 wild-type; 2-hydroxyglutaric acid; SPE-MS; blood–brain barrier penetration; pre-equilibrium dissociation constant; electrochemical leaf; flash chromatography; prolyl hydroxylase domain; PLpro; glutamine-glutamate cycle; HOT; PCA; slow-binding inhibitor kinetics; NADP+; N-acetylaspartylglutamate; proteolysis-targeting chimera; TET2; oncology; untargeted metabolomics; blood–brain barrier; 2-oxoglutaric acid; metabolomics; beta-citryl-L-glutamate; peroxisome; 2-OG-dependent oxygenases; GLUD1; PHD2; AG-120; false discovery rate; β-CG; brain tumours; POMS; organic synthesis; glutarate; principal component analysis; γ-Hydroxybutyric acid; ribosomal modification protein rimK-like family member A; GBM; e-Leaf; IDH2; Krebs cycle; FRET assay; diacylglycerol; 2-hydroxyglutarate; glioblastoma multiforme; biochemistry; electron carriers; KDM4A; GLS; warburg effect; metabolism; cereblon E3 ligase; Protein Kinase C δ; tumorigenesis; glutaconic acid; GLUD2; VLCFA; PKCδ; lysine degradation; nanoconfined enzyme cascade; Mpro; hypoxia-inducible factor; mycobacterium tuberculosis; IDH; LdtMt2; solid-phase extraction mass spectrometry; Ullmann coupling; inhibition assays; ribosomal modification protein rimK-like family member B; protein-observed mass spectrometry; SARS-CoV-2; citramalate; 2-HG; BBB penetration; altered metabolism; glutaric acid; beta-citryl glutamate; COVID-19; partial least squares-discriminant analysis; isocitrate dehydrogenase; FT-2102; oxidative stress; hydroxyacid-oxoacid transhydrogenase; glutaminase; L; HIF stabilisation; benzisothiazolinone; enzyme inhibition; oncometabolite; tricarboxylic acid cycle; 2-oxoglutarate; AML; IDH2 R140Q; Class II IDH inhibitor; IC-MS; acute myeloid leukaemia; enasidenib; Suzuki–Miyaura cross-coupling; Ellman's chiral auxiliary; FC analysis; multivariate statistical analysis; IDH1 R132H; alpha-ketoglutaric acid; RIMKLB; Beta-Oxidation; structure-activity relationship; glutamate dehdyrogenase; apoptosis; alpha-ketoglutarate; ebsulfur; Ebselen; glutathione; SARS-CoV-2 main protease; NADPH; cancer; thalidomide-based degrader; leave-one-out-cross-validation; BBB; lipolysis; tissue culture; drug discovery; ion-exchange chromatography mass spectrometry; FDR; PLS-DA; cellular redox homeostasis; AG-221; E3 Ligase; IDH1 R132C; D-transpeptidase; succinic semialdehyde; DAG; gamma-hydroxybutyric acid; glycolysis; β-Citryl-L-glutamate; IDH2 R172K; pentose phosphate pathway; very-long-chain fatty acids; vorasidenib; SAR; BIT; mass spectrometry; medicinal chemistry; c-Abl; redox homeostasis; olutasidenib; IDH305; ivosidenib; papain-like protease; tryptophan degradation; glioma; N-acetylglutamate; fluorescence-based assay; fold-change analysis; IDH1; Ferredoxin NADP+ reductase; PPP; β-Oxidation; dominant-negative phenotype; cell viability; NAAG; allosteric inhibitor; IDH1 wild-type; covalent cysteine-reactive inhibitor; glutathione biosynthesis; lipid metabolism; hydroxylysine degradation; TCA cycle
• Subjects: Peroxisomes; Polyamines; Antibiotics; Medicinal chemistry; Cancer; Protein kinase C; Synthetic drugs; Biological chemistry; Targeted protein degradation; Biochemistry; Chemical biology; Organic compounds; Cancer cells; Metabolomics; Isocitrate dehydrogenase; Astrocytomas; Electrochemical apparatus; PROTACs; Lipids--Metabolism; Glutathione; Drug resistance in cancer cells; Physical organic chemistry; Drug resistance in microorganisms; COVID-19 Pandemic, 2020-2023; Krebs cycle; Bioorganic chemistry; Organic reaction mechanisms; Glioblastoma multiforme; Cell metabolism; Organic chemistry; Brain--Cancer; Pentose phosphate pathway; COVID-19 (Disease); Antibacterial agents; Oxidative stress; Enzyme kinetics