Computational and Experimental Druggability Assessment of Human DNA Glycosylases

Michel, Maurice; Visnes, Torkild; Homan, Evert; Seashore‐Ludlow, Brinton; Hedenström, Mattias; Wiita, Elisée; Vallin, Karl S. A.; Paulin, Cynthia B.J.; Zhang, Jiaxi; Wallner, Olov; Scobie, Martin; Schmidt, Andreas; Jenmalm-Jensen, Annika; Helleday, Thomas

doi:10.1021/acsomega.9b00162

Cited by 24 publications

(25 citation statements)

References 114 publications

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“…Yet this situation is ideal in the case of a synthetic lethality interaction between the pathologic context and DNA glycosylase [58,59]. Over the last few years, the search for inhibitors of DNA glycosylases hNeil1 (hNeil2) and hOgg1 has become a very active field [18][19][20][21]56,60,61]. We started this research in 2014 by discovering that 2-thioxanthine is an irreversible inhibitor of the bacterial enzymes Fpg and Nei and the human enzyme hNeil2, three enzymes belonging to the Fpg/Nei DNA glycosylase structural superfamily having a zinc finger (ZnF) [18].…”

Section: Discussionmentioning

confidence: 99%

Thiopurine Derivative-Induced Fpg/Nei DNA Glycosylase Inhibition: Structural, Dynamic and Functional Insights

Rieux

Goffinont

Coste

et al. 2020

IJMS

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DNA glycosylases are emerging as relevant pharmacological targets in inflammation, cancer and neurodegenerative diseases. Consequently, the search for inhibitors of these enzymes has become a very active research field. As a continuation of previous work that showed that 2-thioxanthine (2TX) is an irreversible inhibitor of zinc finger (ZnF)-containing Fpg/Nei DNA glycosylases, we designed and synthesized a mini-library of 2TX-derivatives (TXn) and evaluated their ability to inhibit Fpg/Nei enzymes. Among forty compounds, four TXn were better inhibitors than 2TX for Fpg. Unexpectedly, but very interestingly, two dithiolated derivatives more selectively and efficiently inhibit the zincless finger (ZnLF)-containing enzymes (human and mimivirus Neil1 DNA glycosylases hNeil1 and MvNei1, respectively). By combining chemistry, biochemistry, mass spectrometry, blind and flexible docking and X-ray structure analysis, we localized new TXn binding sites on Fpg/Nei enzymes. This endeavor allowed us to decipher at the atomic level the mode of action for the best TXn inhibitors on the ZnF-containing enzymes. We discovered an original inhibition mechanism for the ZnLF-containing Fpg/Nei DNA glycosylases by disulfide cyclic trimeric forms of dithiopurines. This work paves the way for the design and synthesis of a new structural class of inhibitors for selective pharmacological targeting of hNeil1 in cancer and neurodegenerative diseases.

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Section: Discussionmentioning

confidence: 99%

Thiopurine Derivative-Induced Fpg/Nei DNA Glycosylase Inhibition: Structural, Dynamic and Functional Insights

Rieux

Goffinont

Coste

et al. 2020

IJMS

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“…Druggability predictions using DoGSite are based on rigid protein structures, not allowing for flexibility typically induced by larger natural substrates or specifically designed small molecules (Michel et al, 2019). Another aspect is the potential existence of allosteric sites.…”

Section: Automated Arm -Step 2: Cryptosite and Ftmap Confirm Druggablmentioning

confidence: 99%

“…In case of the NUDIX proteins, NUDT22 for example showed to have high scores in DogSite and FTMap with CryptoSite confirming flexibility around two closely related sites. Further, in the past we have shown that comparing different crystals structures of the same protein can allow for the observation of targetable conformations more suitable smallmolecule development (Michel et al, 2019). With the open access deposition of all screening data by the SGC, a similar albeit more time consuming approach is possible for a number of NUDIX proteins 1 .…”

Section: Conclusion and Summarymentioning

confidence: 99%

In silico Druggability Assessment of the NUDIX Hydrolase Protein Family as a Workflow for Target Prioritization

et al. 2020

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Computational chemistry has now been widely accepted as a useful tool for shortening lead times in early drug discovery. When selecting new potential drug targets, it is important to assess the likelihood of finding suitable starting points for lead generation before pursuing costly high-throughput screening campaigns. By exploiting available high-resolution crystal structures, an in silico druggability assessment can facilitate the decision of whether, and in cases where several protein family members exist, which of these to pursue experimentally. Many of the algorithms and software suites commonly applied for in silico druggability assessment are complex, technically challenging and not always user-friendly. Here we applied the intuitive open access servers of DoGSite, FTMap and CryptoSite to comprehensively predict ligand binding pockets, druggability scores and conformationally active regions of the NUDIX protein family. In parallel we analyzed potential ligand binding sites, their druggability and pocket parameter using Schrödinger's SiteMap. Then an in silico docking cascade of a subset of the ZINC FragNow library using the Glide docking program was performed to assess identified pockets for large-scale small-molecule binding. Subsequently, this initial dual ranking of druggable sites within the NUDIX protein family was benchmarked against experimental hit rates obtained both in-house and by others from traditional biochemical and fragment screening campaigns. The observed correlation suggests that the presented user-friendly workflow of a dual parallel in silico druggability assessment is applicable as a standalone method for decision on target prioritization and exclusion in future screening campaigns.

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“…The DSF assay was done according to the protocol previously described by Michel et al [ 46 ]. In Brief, 0.2 μL triplicates in a 2:1 dilution of a 10 mM TH5487 solution and a DMSO control were spotted in White BioRad 384-well plates.…”

Section: Methodsmentioning

confidence: 99%

NEIL1 and NEIL2 Are Recruited as Potential Backup for OGG1 upon OGG1 Depletion or Inhibition by TH5487

Hanna

Michel

Helleday

et al. 2021

IJMS

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DNA damage caused by reactive oxygen species may result in genetic mutations or cell death. Base excision repair (BER) is the major pathway that repairs DNA oxidative damage in order to maintain genomic integrity. In mammals, eleven DNA glycosylases have been reported to initiate BER, where each recognizes a few related DNA substrate lesions with some degree of overlapping specificity. 7,8-dihydro-8-oxoguanine (8-oxoG), one of the most abundant DNA oxidative lesions, is recognized and excised mainly by 8-oxoguanine DNA glycosylase 1 (OGG1). Further oxidation of 8-oxoG generates hydantoin lesions, which are recognized by NEIL glycosylases. Here, we demonstrate that NEIL1, and to a lesser extent NEIL2, can potentially function as backup BER enzymes for OGG1 upon pharmacological inhibition or depletion of OGG1. NEIL1 recruitment kinetics and chromatin binding after DNA damage induction increase in cells treated with OGG1 inhibitor TH5487 in a dose-dependent manner, whereas NEIL2 accumulation at DNA damage sites is prolonged following OGG1 inhibition. Furthermore, depletion of OGG1 results in increased retention of NEIL1 and NEIL2 at damaged chromatin. Importantly, oxidatively stressed NEIL1- or NEIL2-depleted cells show excessive genomic 8-oxoG lesions accumulation upon OGG1 inhibition, suggesting a prospective compensatory role for NEIL1 and NEIL2. Our study thus exemplifies possible backup mechanisms within the base excision repair pathway.

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Computational and Experimental Druggability Assessment of Human DNA Glycosylases

Cited by 24 publications

References 114 publications

Thiopurine Derivative-Induced Fpg/Nei DNA Glycosylase Inhibition: Structural, Dynamic and Functional Insights

Thiopurine Derivative-Induced Fpg/Nei DNA Glycosylase Inhibition: Structural, Dynamic and Functional Insights

In silico Druggability Assessment of the NUDIX Hydrolase Protein Family as a Workflow for Target Prioritization

NEIL1 and NEIL2 Are Recruited as Potential Backup for OGG1 upon OGG1 Depletion or Inhibition by TH5487

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