5'-Phosphorylation Increases the Efficacy of Nucleoside Inhibitors of the DNA Repair Enzyme SNM1A

Function and inhibition of the DNA repair enzyme SNM1A

SNM1A is an enzyme involved in several important biological pathways. To date, most investigations have focused on its role in repairing interstrand crosslinks, a highly cytotoxic form of DNA damage. SNM1A acts as a 5'-3' exonuclease, displaying an unusual capability to digest DNA past the site of a crosslink lesion. Recently, additional functions of this enzyme in the repair of DNA double-strand breaks and critically shortened telomeres have been uncovered. Furthermore, SNM1A is involved in two cell cycle checkpoints that arrest cell division in response to DNA damage. Inhibition of both DNA repair enzymes and cell cycle checkpoint proteins are effective strategies for cancer treatment, and SNM1A is therefore of significant interest as a potential therapeutic target. As a member of the metallo-β-lactamase superfamily, SNM1A is postulated to contain two metal ions in the active site that catalyse hydrolysis of the phosphodiester backbone of DNA. Substrate-mimic probes based on a nucleoside or oligonucleotide scaffold appended with a metal-binding group have proven effective in vitro. High-throughput screening campaigns have identified potent inhibitors, some of which were successful in sensitising cells to DNA-damaging cancer drugs. This review discusses the biological role, structure, and mechanism of action of SNM1A, and the development of SNM1A inhibitors for cancer therapy.

Potentiality of Nucleoside as Antioxidant by Analysis on Oxidative Susceptibility, Drug Discovery, and Synthesis

Nucleosides are sensitive sites towards oxidations caused by endogenous and exogenous oxidative resources, and a large number of the produced DNA lesions behave as pathogenesis eventually. We herein analyze oxidative modes of nucleosides and structure- activity relationships of some clinical nucleoside drugs. Together with our previous findings on the inhibitory effects of nucleoside derivatives against DNA oxidation, all these results imply a possibility for nucleoside to be a new member in the family of antioxidants. Then, some novel synthetic routines of nucleoside analogs are collected to reveal the applicability in the construction of nucleoside antioxidants. Therefore, it is reasonable to envision that the nucleoside antioxidant will be a novel topic in the research of both nucleosides and antioxidants.

Zinc-Binding Oligonucleotide Backbone Modifications for Targeting a DNA-Processing Metalloenzyme

A series of chemically-modified oligonucleotides for targeting the DNA repair nuclease SNM1A have been designed and synthesised. Each oligonucleotide contains a modified internucleotide linkage designed to both mimic the native phosphodiester backbone and chelate to the catalytic zinc ion(s) in the SNM1A active site. Dinucleoside phosphoramidites containing urea, squaramide, sulfanylacetamide, and sulfinylacetamide linkages were prepared and employed successfully in solid-phase oligonucleotide synthesis. All the modified oligonucleotides were found to interact with SNM1A in a gel electrophoresis-based assay, demonstrating the first examples of inhibition of DNA damage repair enzymes for many of these groups in oligonucleotides. One strand containing a sulfinylacetamide-linkage was found to have the strongest interaction with SNM1A and was further tested in a real-time fluorescence assay. This allowed an IC50 value of 231 nM to be determined, significantly lower than previously reported substrate-mimics targeting this enzyme. It is expected that these modified oligonucleotides will serve as a scaffold for the future development of fluorescent or biotin-labelled probes for the in vivo study of DNA repair processes.

Cell-active small molecule inhibitors validate the SNM1A DNA repair nuclease as a cancer target

The three human SNM1 metallo-β-lactamase fold nucleases (SNM1A-C) play key roles in DNA damage repair and in maintaining telomere integrity. Genetic studies indicate that they are attractive targets for cancer treatment and to potentiate chemo- and radiation-therapy. A high-throughput screen for SNM1A inhibitors identified diverse pharmacophores, some of which were shown by crystallography to coordinate to the di-metal ion centre at the SNM1A active site. Structure and turnover assay-guided optimization enabled the identification of potent quinazoline-hydroxamic acid containing inhibitors, which bind in a manner where the hydroxamic acid displaces the hydrolytic water and the quinazoline ring occupies a substrate nucleobase binding site. Cellular assays reveal that SNM1A inhibitors cause sensitisation to, and defects in the resolution of, cisplatin-induced DNA damage, validating the tractability of MBL fold nucleases as cancer drug targets.

Deploying solid-phase synthesis to access thymine-containing nucleoside analogs that inhibit DNA repair nuclease SNM1A

Nucleoside analogs show useful bioactive properties. A versatile solid-phase synthesis that readily enables the diversification of thymine-containing nucleoside analogs is presented. The utility of the approach is demonstrated with the preparation of a library of compounds for analysis with SNM1A, a DNA damage repair enzyme that contributes to cytotoxicity. This exploration provided the most promising nucleoside-derived inhibitor of SNM1A to date with an IC50 of 12.3 μM.

Two-Step Validation Approach for Tools To Study the DNA Repair Enzyme SNM1A

We report a two-step validation approach to evaluate the suitability of metal-binding groups for targeting DNA damage-repair metalloenzymes using model enzyme SNM1A. A fragment-based screening approach was first used to identify metal-binding fragments suitable for targeting the enzyme. Effective fragments were then incorporated into oligonucleotides using the copper-catalysed azide-alkyne cycloaddition reaction. These modified oligonucleotides were recognised by SNM1A at >1000-fold lower concentrations than their fragment counterparts. The exonuclease SNM1A is a key enzyme involved in the repair of interstrand crosslinks, a highly cytotoxic form of DNA damage. However, SNM1A and other enzymes of this class are poorly understood, as there is a lack of tools available to facilitate their study. Our novel approach of incorporating functional fragments into oligonucleotides is broadly applicable to generating modified oligonucleotide structures with high affinity for DNA damage-repair enzymes.

The 5′-phosphate enhances the DNA-binding and exonuclease activities of human mitochondrial genome maintenance nuclease 1 (MGME1)

In higher eukaryotes, mitochondria play multiple roles in energy production, signaling, and biosynthesis. Mitochondria possess multiple copies of mitochondrial DNA (mtDNA), which encodes 37 genes that are essential for mitochondrial and cellular function. When mtDNA is challenged by endogenous and exogenous factors, mtDNA undergoes repair, degradation, and compensatory synthesis. mtDNA degradation is an emerging pathway in mtDNA damage response and maintenance. A key factor involved is the human mitochondrial genome maintenance exonuclease 1 (MGME1). Despite previous biochemical and functional studies, controversies exist regarding the polarity of MGME1-mediated DNA cleavage. Also, how DNA sequence may affect the activities of MGME1 remains elusive. Such information is not only fundamental to the understanding of MGME1 but critical for deciphering the mechanism of mtDNA degradation. Herein, we use quantitative assays to examine the effects of substrate structure and sequence on the DNA-binding and enzymatic activities of MGME1. We demonstrate that MGME1 binds to and cleaves from the 5′-end of single-stranded DNA substrates, especially in the presence of 5′-phosphate, which plays an important role in DNA binding and optimal cleavage by MGME1. In addition, MGME1 tolerates certain modifications at the terminal end, such as a 5′-deoxyribosephosphate intermediate formed in base excision repair. We show that MGME1 processes different sequences with varying efficiencies, with dT and dC sequences being the most and least efficiently digested, respectively. Our results provide insights into the enzymatic properties of MGME1 and a rationale for the coordination of MGME1 with the 3′–5′ exonuclease activity of DNA polymerase γ in mtDNA degradation.