In silico design of the first DNA-independent mechanism-based inhibitor of mammalian DNA methyltransferase Dnmt1

Miletić, Vedran; Odorčić, Ivica; Nikolić, Patrik; Svedružić, Željko M.

doi:10.1371/journal.pone.0174410

Cited by 23 publications

(20 citation statements)

References 43 publications

(129 reference statements)

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Section: Introductionmentioning

confidence: 99%

“…27 Hence, further understanding of the precise DNMT-mediated oncogenic mechanisms in AML is required to select for specific and potent novel DNMT inhibitors which is currently under intense investigation and discovery. [28][29][30] In this review, we describe and discuss the oncogenic properties of DNMT1, DNMT3A, and DNMT3B in AML. We also describe the prognostic and predictive roles of DNMTs in clinical trials of AML patients with hypomethylating agents, as well as novel DNMT inhibitors that have been tested experimentally in AML cells.…”

Section: Introductionmentioning

confidence: 99%

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Oncogenic Roles and Inhibitors of DNMT1, DNMT3A, and DNMT3B in Acute Myeloid Leukaemia

2019

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Epigenetic alteration has been proposed to give rise to numerous classic hallmarks of cancer. Impaired DNA methylation plays a central role in the onset and progression of several types of malignancies, and DNA methylation is mediated by DNA methyltransferases (DNMTs) consisting of DNMT1, DNMT3A, and DNMT3B. DNMTs are frequently implicated in the pathogenesis and aggressiveness of acute myeloid leukaemia (AML) patients. In this review, we describe and discuss the oncogenic roles of DNMT1, DNMT3A, and DNMT3B in AML. The clinical response predictive roles of DNMTs in clinical trials utilising hypomethylating agents (azacitidine and decitabine) in AML patients are presented. Novel hypomethylating agent (guadecitabine) and experimental DNMT inhibitors in AML are also discussed. In summary, hypermethylation of tumour suppressors mediated by DNMT1 or DNMT3B contributes to the progression and severity of AML (except MLL-AF9 and inv(16)(p13;q22) AML for DNMT3B), while mutation affecting DNMT3A represents an early genetic lesion in the pathogenesis of AML. In clinical trials of AML patients, expression of DNMTs is downregulated by hypomethylating agents while the clinical response predictive roles of DNMT biomarkers remain unresolved. Finally, nucleoside hypomethylating agents have continued to show enhanced responses in clinical trials of AML patients, and novel non-nucleoside DNMT inhibitors have demonstrated cytotoxicity against AML cells in pre-clinical settings.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Oncogenic Roles and Inhibitors of DNMT1, DNMT3A, and DNMT3B in Acute Myeloid Leukaemia

2019

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“…Due to the structural similarity of the N‐ mustard analogues to SAM, it is feasible that they could function as inhibitors of DNMT1 and directly impact catalysis. Such a hypothesis is supported by recent efforts by Svedruzic et.al ., who designed transition‐state inhibitors of DNMT1 in silico which are predicted to form a covalent adduct with the active site cysteine . While such a hypothesis is reasonable, the unsubstituted analogue 1 would also be expected to demonstrate concentration‐dependent inhibition as well (which is not observed).…”

Section: Resultsmentioning

confidence: 99%

Evaluation of N‐Mustard Analogues of S‐Adenosyl‐L‐methionine with Eukaryotic DNA Methyltransferase 1

et al. 2019

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DNA methylation, which requires the universal methyl donor Sadenosyl-L-methionine (SAM), plays a pivotal role in eukaryotic gene regulation and when dysregulated, can result in severe alterations in cellular function. An emerging approach to further understand DNA methylation utilizes azide-and alkynefunctionalized N-mustard SAM analogues as biochemical tools to probe sites of DNA methylation. While the successful utility of these substituted analogues has been demonstrated with prokaryotic DNA methyltransferases, their utility with physio-logically-relevant eukaryotic DNA methyltransferase 1 (DNMT1) is examined for the first time here. A fluorescence-based magnetic bead assay was validated in initial experiments to measure the extent of DNA modification by the N-mustard analogues using Spiroplasma methylase, M.SssI, a prokaryotic model of DNMT1. Subsequent analysis with DNMT1 revealed limited utility of the analogues, as added azide-and alkynefunctionality appears to directly impact binding to DNMT1.[a] Dr.

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“…All-atom molecular dynamics calculations used the GROMACS 5.1.4 program package 49 as we have previously described 50,51 . Briefly, NAD(H) molecules from PDB files were processed using ACPYPE10, an interface for Antechamber (part of AmberTools11) that can generate topology types for GAFF force fields 52 .…”

Section: Methodsmentioning

confidence: 99%

Substrate Channelingviaa Transient Protein-Protein Complex: The case of D-Glyceraldehyde-3-Phosphate Dehydrogenase and L-Lactate Dehydrogenase

Svedružić

Odorčić

Chang

et al. 2020

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Background: D-Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and L-lactate dehydrogenase (LDH) can form a complex that can regulate the major metabolic pathways, however, the exact mechanism remains unknown. We analyzed a possibility of NADHchanneling from GAPDH-NADH complex to LDH isozymes using enzymes from different cells. Results: Enzyme-kinetics and NADH-binding studies showed that LDH can use GAPDH-NADH complex as a substrate. LDH activity with GAPDH-NADH complex was challenged with anti-LDH antibodies to show that the channeled and the diffusive reactions always take place in parallel. The channeling path is dominant only in assays with limiting free-NADH concertation that mimic cytosolic conditions. Analytical ultracentrifugation showed that the channeling does not require a high affinity complex. Molecular dynamics calculations and protein-protein interaction studies showed that LDH and GAPDH can form a leaky channeling complex only at subsaturating NADH concentrations. The interaction sites are conserved between LDH isozymes from heart and muscle, and between GAPDH molecules from rabbit and yeast cells. Positive electric fields between the NAD(H) binding sites on LDH and GAPDH tetramers, showed that NAD(H)-channeling within the LDH-GAPDH complex, can be an extension of NAD(H)channeling between the adjacent subunits in each tetramer. Conclusions: In the case of a transient (GAPDH-NADH)-LDH complex, the relative contribution from the channeled and the diffusive paths depends on the overlap between off-rates for the transient (GAPDH-NADH)-LDH complex and off-rates for the GAPDH-NADH complex. Molecular evolution or metabolic engineering protocols can exploit substrate channeling for metabolic flux control by fine-tuning substrate-binding affinity for the key enzymes in the competing reaction paths. Highlights-Substrate channeling molecular mechanism can regulate energy production and aerobic and anaerobic metabolism in cells -LDH and GAPDH can form a channeling complex only at sub-saturating NADH concentration -Channeled and diffusive paths always compete and take place in parallel -NADH channeling does not require a high-affinity complex -NADH channeling within GAPDH-LDH complex is an extension of NAD(H) channeling within each tetramer -Allosteric modulation of NADH binding affinity in GAPDH tetramer can regulate NAD(H) channeling Introduction D-glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and L-lactate dehydrogenases (LDH) are two NAD(H) dependent dehydrogenases that participate in glycolytic and gluconeogenic pathways 1,2 . Glycolysis and gluconeogenesis are the two major metabolic pathways that provide cells with metabolic precursors and a rapid source of energy. Parallel to glycolysis GAPDH participates in microtubule bundling, DNA replication and repair, apoptosis, the export of nuclear RNA, membrane fusion, and phosphotransferase activity 1,2 . GAPDH is implicated in Huntington's disease 3 , prostate cancer, and viral pathogenesis 1,2 . GAPDH could be a target of nitric oxide 4 and a target of ...

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In silico design of the first DNA-independent mechanism-based inhibitor of mammalian DNA methyltransferase Dnmt1

Cited by 23 publications

References 43 publications

Oncogenic Roles and Inhibitors of DNMT1, DNMT3A, and DNMT3B in Acute Myeloid Leukaemia

Oncogenic Roles and Inhibitors of DNMT1, DNMT3A, and DNMT3B in Acute Myeloid Leukaemia

Evaluation of N‐Mustard Analogues of S‐Adenosyl‐L‐methionine with Eukaryotic DNA Methyltransferase 1

Substrate Channelingviaa Transient Protein-Protein Complex: The case of D-Glyceraldehyde-3-Phosphate Dehydrogenase and L-Lactate Dehydrogenase

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