Mechanism of substrate hydrolysis by the human nucleotide pool sanitiser DNPH1

Transition State Analogs of Human DNPH1 Reveal Two Electrophile Migration Mechanisms

DNPH1 is responsible for eliminating the epigenetically modified nucleotide, 5-hydroxymethyl-2'-deoxyuridine 5'-monophosphate (hmdUMP), preventing formation of hmdUTP, a mutation-inducing nucleotide. Loss of DNPH1 activity sensitizes PARP inhibition-resistant BRCA-deficient cancers by causing incorporation of hmdUTP into DNA. Hydrolysis of hmdUMP by DNPH1 proceeds through a covalent intermediate between Glu104 and 2-deoxyribose 5-phosphate, followed by hydrolysis, a reaction cycle with two transition states. We describe synthesis and characterization of transition state mimics for both transition states of DNPH1. Both transition states prefer inhibitors with cationic charge at the anomeric center and provide a foundation for inhibitor design. Ground-state complexes show reaction coordinate nucleophiles poised 3.3-3.7 Å from the anomeric carbon while transition state analogs tighten the reaction coordinate to place the nucleophiles 2.7-2.8 Å from the anomeric carbon. Crystal structures of DNPH1 with transition state analogs reveal transition states where the electrophilic ribocation migrates between the leaving groups and attacking nucleophiles.

Degradation of the novel herbicide tiafenacil in aqueous solution: Kinetics, various influencing factors, hydrolysis products identification, and toxicity assessment

As new pesticides are continually introduced into agricultural systems, understanding their environmental behavior and potential toxicity effects is crucial for effective risk assessment. This study utilized QuEChERS and UPLC-QTOF-MS/MS techniques to analyze Tiafenacil (TFA) and its six hydrolysis products (HP1 to HP6) in water, marking the first comprehensive report on these degradation products. Calibration curves demonstrated strong linearity (R2 ≥ 0.9903) across concentrations ranging from 0.02 to 3.50 mg L-1. TFA's hydrolysis followed single first-order kinetic (SFOK) model, with rapid degradation observed under alkaline and high-temperature conditions, resulting in half-lives ranging from 0.22 to 84.82 days. The ECOSAR model predicts that TFA's hydrolysis products exhibit acute and chronic toxicity to fish, Daphnia, and green algae. Additionally, hydrolysis products HP1, HP5, and HP6 were detected in irrigation water from citrus orchards, posing higher predicted toxicity risks to fish and green algae. This highlights the necessity for further risk assessments considering transformation products. Overall, this study enhances our understanding of TFA's environmental fate and supports its safe agricultural application and monitoring practices.

Lower ratio of IMPDH1 to IMPDH2 sensitizes gliomas to chemotherapy

Gliomas are the most common primary tumors of the central nervous system, with approximately half of patients presenting with the most aggressive form of glioblastoma. Although several molecular markers for glioma have been identified, they are not sufficient to predict the prognosis due to the extensive genetic heterogeneity within glioma. Our study reveals that the ratio of IMPDH1 to IMPDH2 expression levels serves as a molecular indicator for glioma treatment prognosis. Patients with a higher IMPDH1/IMPDH2 ratio exhibit a worse prognosis, while those with a lower ratio display a more favorable prognosis. We further demonstrate that IMPDH1 plays a crucial role in maintaining cellular GTP/GDP levels following DNA damage compared to IMPDH2. In the absence of IMPDH1, cells experience an imbalance in the GTP/GDP ratio, impairing DNA damage repair capabilities and rendering them more sensitive to TMZ. This study not only introduces a novel prognostic indicator for glioma clinical diagnosis but also offers innovative insights for precise and stratified glioma treatment.

Human 2'-Deoxynucleoside 5'-Phosphate N-Hydrolase 1: The Catalytic Roles of Tyr24 and Asp80

The human enzyme 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 (HsDNPH1) catalyses the hydrolysis of 5-hydroxymethyl-2'-deoxyuridine 5'-phosphate to generate 5-hydroxymethyluracil and 2-deoxyribose-5-phosphate via a covalent 5-phospho-2-deoxyribosylated enzyme intermediate. HsDNPH1 is a promising target for inhibitor development towards anticancer drugs. Here, site-directed mutagenesis of conserved active-site residues, followed by HPLC analysis of the reaction and steady-state kinetics are employed to reveal the importance of each of these residues in catalysis, and the reaction pH-dependence is perturbed by each mutation. Solvent deuterium isotope effects indicate no rate-limiting proton transfers. Crystal structures of D80N-HsDNPH1 in unliganded and substrate-bound states, and of unliganded D80A- and Y24F-HsDNPH1 offer atomic level insights into substrate binding and catalysis. The results reveal a network of hydrogen bonds involving the substrate and the E104-Y24-D80 catalytic triad and are consistent with a proposed mechanism whereby D80 is important for substrate positioning, for helping modulate E104 nucleophilicity, and as the general acid in the first half-reaction. Y24 positions E104 for catalysis and prevents a catalytically disruptive close contact between E104 and D80.