Optimization of N‐Piperidinyl‐Benzimidazolone Derivatives as Potent and Selective Inhibitors of 8‐Oxo‐Guanine DNA Glycosylase 1

Abstract

8‐oxo Guanine DNA Glycosylase 1 is the initiating enzyme within base excision repair and removes oxidized guanines from damaged DNA. Since unrepaired 8‐oxoG could lead to G : C→T : A transversion, base removal is of utmost importance for cells to ensure genomic integrity. For cells with elevated levels of reactive oxygen species this dependency is further increased. In the past we and others have validated OGG1 as a target for inhibitors to treat cancer and inflammation. Here, we present the optimization campaign that led to the broadly used tool compound TH5487. Based on results from a small molecule screening campaign, we performed hit to lead expansion and arrived at potent and selective substituted N‐piperidinyl‐benzimidazolones. Using X‐ray crystallography data, we describe the surprising binding mode of the most potent member of the class, TH8535. Here, the N‐Piperidinyl‐linker adopts a chair instead of a boat conformation which was found for weaker analogues. We further demonstrate cellular target engagement and efficacy of TH8535 against a number of cancer cell lines.

Distinctive Formation of a DNA–Protein Cross-Link during the Repair of DNA Oxidative Damage: Insights into Human Disease from MD Simulations and QM/MM Calculations

“…MUTYH inherited biallelic variations can result in a condition known as MUTYH-associated polyposis (MAP), which has symptoms including the development of colon polyps and an increased risk of colorectal cancer. − Indeed, an N224S MUTYH variant associated with MAP alters a residue close to the active site, which could cause the reduced catalytic rates that have been linked with the disease . However, this is just one example among over 80 MUTYH missense and truncating variants whose functions are unclear. , There is also evidence that designing novel pharmaceuticals to target enzymes involved in DNA repair pathways may afford successful cancer treatments by increasing the efficacy of anticancer drugs or targeting DNA-repair defective cancers, − and highly specific and potent small molecule inhibitors have already been designed for enzymes that share mechanistic features with DNA glycosylases like MUTYH. − However, to aid the prediction of the dysfunction of MAP-related MUTYH variants in humans and develop possible cancer treatment strategies, the atomic level details of the chemistry facilitated by MUTYH are required. Indeed, structural information has proven essential for the rational development of small-molecule (transition state analogue) inhibitors. − …”

Nucleobase catalysts for the enzymatic activation of 8-oxoguanine DNA glycosylase 1

“…Interestingly, only small substituents like methyl (3), propyl (10) and S-methyl (12) were tolerated in the 8position. We observed a decrease in potency upon extension of the synthetic system via propyl (10), methylamino (13) and inactivity for more extended substituents (15)(16)(17). Next, we explored the apparent necessity of an unsubstituted 6-thio modification by generating analogues with thioether or sulfone modification (Table 1b).…”

“…Thus, as a qualitative readout to compare compound activity, we determined AC50 for all screened compounds on the substrate 8-oxoA:C through kinetic readout instead of a single point read for inhibitors. [16] We then counter-screened all actives for DNA intercalation, auto-fluorescence and APE1 interaction. Interestingly, among the primary hits (Figure 1, Figure S1) were compounds combining guanine with amines in the 6-position, generating structures similar to TH10785.…”

“…[14,15] Thus, depending on the desired effect, it may be beneficial to either increase or suppress the enzymatic activity of OGG1. While competitive inhibition of OGG1 [16,17] may also influence protein levels through NEDD4Lmediated protein degradation, [18] pharmacological 2 OGG1 activation has so far only been reported through enhancement of an otherwise rudimentary AP-lyase activity. [19][20][21] This AP-lyase activity is most likely controlled via product-assisted catalysis, [22] although an allosteric mechanism appears to be an additional possibility.…”

Nucleobase catalysts for the enzymatic activation of 8-oxoguanine DNA glycosylase 1

“…These results suggest that a series of OGG1 organocatalytic switches derived from nucleobases may be informed by previously observed OGG1 inhibitor chemical space to optimize the affinity handle of the molecules. [13] At the same time, the polar and nitrogen-rich scaffold of nucleobases appears suitable to stimulate proton abstraction during OGG1 catalysis.…”