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Oxidative DNA damage is recognized by 8-oxoguanine (8-oxoG) DNA glycosylase 1 (OGG1), which excises 8-oxoG, leaving a substrate for apurinic endonuclease 1 (APE1) and initiating repair. Here, we describe a small molecule (TH10785) that interacts with the phenylalanine-319 and glycine-42 amino acids of OGG1, increases the enzyme activity 10-fold, and generates a previously undescribed β,δ-lyase enzymatic function. TH10785 controls the catalytic activity mediated by a nitrogen base within its molecular structure. In cells, TH10785 increases OGG1 recruitment to and repair of oxidative DNA damage. This alters the repair process, which no longer requires APE1 but instead is dependent on polynucleotide kinase phosphatase (PNKP1) activity. The increased repair of oxidative DNA lesions with a small molecule may have therapeutic applications in various diseases and aging.

Acute myeloid leukemia (AML) is an aggressive hematologic malignancy, exhibiting high levels of reactive oxygen species (ROS). ROS levels have been suggested to drive leukemogenesis and is thus a potential novel target for treating AML. MTH1 prevents incorporation of oxidized nucleotides into the DNA to maintain genome integrity and is upregulated in many cancers. Here we demonstrate that hematologic cancers are highly sensitive to MTH1 inhibitor TH1579 (karonudib). A functional precision medicine ex vivo screen in primary AML bone marrow samples demonstrated a broad response profile of TH1579, independent of the genomic alteration of AML, resembling the response profile of the standard-of-care treatments cytarabine and doxorubicin. Furthermore, TH1579 killed primary human AML blast cells (CD45+) as well as chemotherapy resistance leukemic stem cells (CD45+Lin−CD34+CD38−), which are often responsible for AML progression. TH1579 killed AML cells by causing mitotic arrest, elevating intracellular ROS levels, and enhancing oxidative DNA damage. TH1579 showed a significant therapeutic window, was well tolerated in animals, and could be combined with standard-of-care treatments to further improve efficacy. TH1579 significantly improved survival in two different AML disease models in vivo. In conclusion, the preclinical data presented here support that TH1579 is a promising novel anticancer agent for AML, providing a rationale to investigate the clinical usefulness of TH1579 in AML in an ongoing clinical phase I trial.Significance:The MTH1 inhibitor TH1579 is a potential novel AML treatment, targeting both blasts and the pivotal leukemic stem cells while sparing normal bone marrow cells.

Supplementary figures and tables and material and methods

The folate metabolism enzyme MTHFD2 (methylenetetrahydrofolate dehydrogenase/cyclohydrolase) is consistently overexpressed in cancer but its roles are not fully characterized, and current candidate inhibitors have limited potency for clinical development. In the present study, we demonstrate a role for MTHFD2 in DNA replication and genomic stability in cancer cells, and perform a drug screen to identify potent and selective nanomolar MTHFD2 inhibitors; protein cocrystal structures demonstrated binding to the active site of MTHFD2 and target engagement. MTHFD2 inhibitors reduced replication fork speed and induced replication stress followed by S-phase arrest and apoptosis of acute myeloid leukemia cells in vitro and in vivo, with a therapeutic window spanning four orders of magnitude compared with nontumorigenic cells. Mechanistically, MTHFD2 inhibitors prevented thymidine production leading to misincorporation of uracil into DNA and replication stress. Overall, these results demonstrate a functional link between MTHFD2-dependent cancer metabolism and replication stress that can be exploited therapeutically with this new class of inhibitors. Helleday and colleagues describe a nanomolar MTHFD2 inhibitor that causes replication stress and DNA damage accumulation in cancer cells via thymidine depletion, demonstrating a potential therapeutic strategy in AML tumors in vivo.

Sterile alpha motif and histidine-aspartic acid domain containing protein-1 (SAMHD1) is a deoxynucleoside triphosphate (dNTP) triphosphohydrolase central to cellular nucleotide pool homeostasis. Recent literature has also demonstrated how SAMHD1 can detoxify chemotherapy metabolites thereby controlling their clinical responses. To further understand SAMHD1 biology and to investigate the potential of targeting this enzyme as a neoadjuvant to existing chemotherapies we set out to discover selective small molecule-based inhibitors of SAMHD1. Here we report a discovery pipeline encompassing a biochemical screening campaign and a set of complementary biochemical, biophysical, and cell-based readouts for further characterisation of the screen output. The identified hit compound TH6342 and its analogues, accompanied by their inactive negative control analogue TH7126, demonstrated specific, low μM potency in inhibiting the hydrolysis of both natural substrates and nucleotide analogue therapeutics, shown using complementary enzyme-coupled and direct enzymatic activity assays. Their mode of inhibition was subsequently detailed by coupling kinetic studies with thermal shift assays, where TH6342 and analogues were shown to engage with pre-tetrameric SAMHD1 and deter the oligomerisation and allosteric activation of SAMHD1 without occupying nucleotide binding pockets. We further outline the development and application of multiple cellular assays for assessing cellular target engagement and associated functional effects, including CETSA and an in-cell dNTP hydrolase activity assay, which highlighted future optimisation strategies of this chemotype. In summary, with a novel mode of inhibition, TH6342 and analogues broaden the set of tool compounds available in deciphering SAMHD1 enzymology and functions, and furthermore, the discovery pipeline reported herein represents a thorough framework for future SAMHD1 inhibitor development.Abstract Figure

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.

The NUDIX hydrolase NUDT15 was originally implicated in sanitizing oxidized nucleotides but was later shown to hydrolyze the active thiopurine metabolites, 6-thio-(d)GTP, thereby dictating the clinical response of this standard-of-care treatment for leukemia and inflammatory diseases. Nonetheless, its physiological roles remain elusive. Here, we sought to develop the first small-molecule NUDT15 inhibitors to elucidate its biological functions, and potentially for improving NUDT15-dependent chemotherapeutics. Lead compound TH1760, demonstrated low-nanomolar biochemical potency through direct and specific binding into the NUDT15 catalytic pocket and engaged cellular NUDT15 in the low-micromolar range. We further employed thiopurine potentiation as a proxy functional read-out and demonstrated that TH1760 sensitized cells to 6-thioguanine through enhanced accumulation of 6-thio-(d)GTP in nucleic acids. A biochemically validated, inactive structural analog, TH7285, confirmed that increased thiopurine toxicity is via direct NUDT15 inhibition. In conclusion, TH1760 represents the first chemical probe for interrogating NUDT15 biology and potential therapeutic avenues.

Supplementary methods for the article "Pharmacological targeting of MTHFD2 suppresses acute myeloid leukemia by inducing thymidine depletion and replication stress".

Purpose: Many cancers suffer from dysfunctional redox status. MTH1 protects cancer cells from oxidative DNA damage by preventing incorporation of oxidized nucleotides. OXC-101 (Karonudib) is a dual-action mitotic disruptor and MTH1 inhibitor, preventing exit from mitosis and sanitation of oxidative damage to DNA subunits in cancer cells. MASTIFF, (MTH1, A Phase I, Study on Tumors Inhibition, First in Human, First in Class), is a first- in- human phase 1 study, with the primary aim to assess safety, tolerability, and pharmacokinetics (PK) of OXC-101 in patients (pts) with advanced solid malignant tumors (NCT03036228). Methods: Phase 1a study with 3+3 design and intra-patient dose escalation. New cohorts were opened following review of safety and PK data by the safety data monitoring board after the first treatment cycle of 4 weeks (w). All patients had progressive stage IV disease with no treatment options in SOC at inclusion. Radiological tumor response evaluation (RECIST 1.1) was performed 8w of the first 24w, 12w thereafter. The first 29 patients (cohort 1-10) obtained an oral solution. From cohort 11 pts obtained 100mg tablets. Results: 50 subjects (50% female, 50% male) were enrolled at 16 dose levels of OXC-101 at varying posology: 25-900 mg BID, 800-1000mg QD; every second day, once or twice weekly. Mean age was 52 years (range:20-74). 92% of pts had received previous chemotherapy (mean: 5 lines, range:0-34), 18% endocrine therapy and 52% other therapies (incl immunotherapy). OXC-101 was generally well tolerated and with manageable toxicity for dose levels for an average of 121 days (range:2-513 days), and 43/50 subjects discontinued due to disease progression. A total of 20 SAEs were reported: 8 SAEs in 7 subjects were considered related/possibly related to OXC-101 and included pneumonia (3/8), febrile neutropenia (2/8), ileus (1/8), unspecified infection (1/8) and fever (1/8). There were 14 dose-limiting toxicities (DLTs) reported in 7 subjects. At 510mg every second day (1785mg weekly) 2/5 subjects reported G4 neutropenia; at 500mg BID/1000mg QD, twice per week (2000 mg weekly) 2/9 subjects reported G4 neutropenia; at 900mg BID, once weekly (1800 mg weekly) 3/3 subjects reported decrease in white blood count incl. neutropenia. PK was robust and predictable with good exposure correlation between solution and tablet formulation, with an average half-life of 10 hrs in plasma. 15/49 (31%) of the subjects showed stable disease at first radiological evaluation. One subject had stable disease during 73 weeks on OXC-101 treatment. IHC and western blot analysis on tumor biopsies confirmed mechanism of action. A dose of 900mg (500mg mane, 400mg nocte) twice a week (total weekly dose 1800mg) was determined as the Recommended Phase 2 Dose (RP2D). This will be further explored in tumor specific cohorts. Conclusion: OXC-101 has a favorable safety profile with an RP2D of 900mg twice a week. Citation Format: Jeffrey Yachnin, Lars Ny, Teresa Sandvall, Kumar Sanjiv, Martin Scobie, Björn Platzack, Pawel Barancewski, Olof Breuer, Vassilis Gorgoulis, Ioannis S. Pateras, Maria Klockare, Austin Smith, Ulrika Warpman Berglund, Thomas Helleday. OXC-101 shows favorable safety profile in first in human phase 1 trial in patients with advanced solid cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr CT182.

DNA-dependent protein kinase (DNA-PK) plays an important role in the repair of DNA double-strand breaks via the non-homologous end joining (NHEJ) pathway. In addition to its role in the NHEJ pathway, DNA-PK is also known to have an emerging role in cell cycle progression and mitosis. Some studies have shown that depletion or inhibition of DNA-PK inhibitors leads to a delay in the transition from metaphase to anaphase. The mitotic MTH1 inhibitor OXC-101(TH1579, karonudib) is a dual inhibitor that both targets MTH1 and disrupts tubulin polymerization in cancer cells, causing DNA damage and mitotic catastrophe in cancer cells. Based on the involvement of DNA-PK in mitosis, we hypothesized that depletion/inhibition of DNA-PK might enhance the DNA damage and mitotic catastrophic effect of OXC-101.To test our hypothesis, we performed an in vitro drug combination experiment using the DNA-PK inhibitor nedisertib with OXC-101 in non-small cell lung carcinoma NSCLC (H460,A549), uveal melanoma (MP -38, MP -41 and MP46), osteosarcoma (U2OS) and) and neuroblastoma (IMR32, Kelly, SKNFI) cancer cell lines and non-cancerous foreskin fibroblasts(VH-10, BjhTERT). We found cancer-specific synergistic drug interactions between nedisertib and OXC-101. Combined treatment of nedisertib and OXC-101 to H460 and MP46 increased expression of s10H3 (mitotic marker) and the apoptosis marker (cPARP) compared with single treatment. However, there was no additional increase in expression of the DNA damage markerγH2AX with combined treatment. We also performed annexin V staining by FACS on MP38 andMP48 cells and observed a significant increase in the apoptotic population with combination treatment compared with single treatment. Imaging live cells, we observed a significant delay or arrest in the mitotic phase followed by death of cancer cells in mitosis in response to combination treatment, whereas cells treated individually with nedisertib or OXC-101 continued to proliferate and progress to the next phase of the cell cycle. These data suggest that the DNA-PK inhibitor may enhance the cytotoxic effect of OXC-101specifically in cancer cells. In addition, we will conduct an in-depth mechanistic study of how depletion/inhibition of DNA-PK enhances the cytotoxicity of OXC-101 and validate the drug combination in an appropriate preclinical mouse model. Citation Format: Akhilesh Nagesh Danda, Helge Gad, Martin Scobie, Laura Martínez-López, Nuria Pastor Carrillo, Manuel Luis Orta, Thomas Helleday, Ulrika warpman berglund, Kumar Sanjiv. DNA-PK inhibition augment the cancer specific cytotoxicity of mitotic MTH1 inhibitor OXC-101 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6204.

The enzyme NUDT15 efficiently hydrolyzes the active metabolites of thiopurine drugs, which are routinely used for treating cancer and inflammatory diseases. Loss-of-function variants in NUDT15 are strongly associated with thiopurine intolerance, such as leukopenia, and preemptive NUDT15 genotyping has been clinically implemented to personalize thiopurine dosing. However, understanding the molecular consequences of these variants has been difficult, as no structural information was available for NUDT15 proteins encoded by clinically actionable pharmacogenetic variants because of their inherent instability. Recently, the small molecule NUDT15 inhibitor TH1760 has been shown to sensitize cells to thiopurines, through enhanced accumulation of 6-thio-guanine in DNA. Building upon this, we herein report the development of the potent and specific NUDT15 inhibitor, TH7755. TH7755 demonstrates a greatly improved cellular target engagement and 6-thioguanine potentiation compared with TH1760, while showing no cytotoxicity on its own. This potent inhibitor also stabilized NUDT15, enabling analysis by X-ray crystallography. We have determined high-resolution structures of the clinically relevant NUDT15 variants Arg139Cys, Arg139His, Val18Ile, and V18_V19insGlyVal. These structures provide clear insights into the structural basis for the thiopurine intolerance phenotype observed in patients carrying these pharmacogenetic variants. These findings will aid in predicting the effects of new NUDT15 sequence variations yet to be discovered in the clinic.

Inflammatory diseases, including psoriasis, are characterized by changes in redox regulation. The MTH1 prevents the incorporation of oxidized nucleotides during DNA replication. Using MTH1 small-molecule inhibitors, we found induced apoptosis through 8-oxodeoxyguanosine triphosphate accumulation and DNA double-strand breaks after oxidative stress in normal and malignant keratinocytes. In psoriasis, we detected increased MTH1 expression in lesional skin and PBMCs compared with that in the controls. Using the imiquimod psoriasis mouse model, we found that MTH1 inhibition diminished psoriatic histological characteristics and normalized the levels of neutrophils and T cells in the skin and skin-draining lymph nodes. The inhibition abolished the expression of T helper type 17-associated cytokines in the skin, which was in line with decreased levels of IL-17-producing gd T cells in lymph nodes. In human keratinocytes, MTH1 inhibition prevented the upregulation of IL-17-downstream genes, which was independent of ROS-induced apoptosis. In conclusion, our data support MTH1 inhibition using small molecules suitable for topical application as a promising therapeutic approach to psoriasis. Funding Agencies|Ingrid Asp Psoriasis Foundation; Welander Foundation; Swedish Psoriasis Association; Swedish Cancer SocietySwedish Cancer Society [CAN-18-0658]; Svenska Smartafonden; Swedish Foundation for Strategic ResearchSwedish Foundation for Strategic Research [RB130224]

Two screening campaigns using commercial (Chembridge DiverSET) and proprietary (Chemical Biology Consortium Sweden, CBCS) compound libraries, revealed a number of pyridone- and pyrimidinone-derived systems as inhibitors of the human dCTP pyrophosphatase 1 (dCTPase). In this letter, we present their preliminary structure-activity-relationships (SAR) and ligand efficiency scores (LE and LLE).

The dCTP pyrophosphatase 1 (dCTPase) is a nucleotide pool "housekeeping" enzyme responsible for the catabolism of canonical and noncanonical nucleoside triphosphates (dNTPs) and has been associated with cancer progression and cancer cell stemness. We have identified a series of piperazin-1-ylpyridazines as a new class of potent dCTPase inhibitors. Lead compounds increase dCTPase thermal and protease stability, display outstanding selectivity over related enzymes and synergize with a cytidine analogue against leukemic cells. This new class of dCTPase inhibitors lays the first stone toward the development of drug-like probes for the dCTPase enzyme.

The dCTP pyrophosphatase 1 (dCTPase) is involved in the regulation of the cellular dNTP pool and has been linked to cancer progression. Here we report on the discovery of a series of 3,6-disubstituted triazolothiadiazoles as potent dCTPase inhibitors. Compounds 16 and 18 display good correlation between enzymatic inhibition and target engagement, together with efficacy in a cellular synergy model, deeming them as a promising starting point for hit-to-lead development.

In this study, we provide insight into the metabolic profile of a series of piperazin-1-ylpyridazines suffering from rapid in vitro intrinsic clearance in a metabolic stability assay using liver microsomes (e.g. compound 1 MLM/HLM t1/2 = 2/3 min). Aided by empirical metabolite identification and computational predictive models, we designed the structural modifications required to improve in vitro intrinsic clearance by more than 50-fold (e.g. compound 29 MLM/HLM t1/2 = 113/105 min).

Background: Previously we showed cancer cells rely on the MTH1 protein to prevent incorporation of otherwise deadly oxidised nucleotides into DNA and we developed MTH1 inhibitors which selectively kill cancer cells. Recently several new and potent inhibitors of MTH1 were demonstrated to be non toxic to cancer cells challenging the utility of MTH1 inhibition as a target for cancer treatment. Material and methods: Human cancer cell lines were exposed in vitro to MTH1 inhibitors or depleted of MTH1 by siRNA or shRNA. 8 oxodG was measured by immunostaining and modified comet assay. Thermal Proteome profiling proteomics cellular thermal shift assays kinase and CEREP panel were used for target engagement mode of action and selectivity investigations of MTH1 inhibitors. Effect of MTH1 inhibition on tumour growth was explored in BRAF V600E mutated malignant melanoma patient derived xenograft and human colon cancer SW480 and HCT116 xenograft models. Results: Here we demonstrate that recently described MTH1 inhibitors which fail to kill cancer cells also fail to introduce the toxic oxidized nucleotides into DNA. We also describe a new MTH1 inhibitor TH1579 (Karonudib) an analogue of TH588 which is a potent selective MTH1 inhibitor with good oral availability and demonstrates excellent pharmacokinetic and anti cancer properties in vivo. Conclusion: We demonstrate that in order to kill cancer cells MTH1 inhibitors must also introduce oxidized nucleotides into DNA. Furthermore we describe TH1579 as a best in class MTH1 inhibitor which we expect to be useful in order to further validate the MTH1 inhibitor concept. Key words: MTH1 reactive oxygen species cancer small molecule inhibitors DNA damage

In liver, the prodrug proguanil metabolizes into active metabolite cycloguanil, which inhibit folic acid synthesis in plasmodium by inhibiting dihydrofolate reductase (DHFR) enzyme. Proguanil is mostly used in combination with atovaquone as anti-malarial therapy. Regarding repurposing of proguanil as anti-cancer drug, not much has been explored yet, except one recent study, where they showed that proguanil suppress breast cancer cell proliferation by generating ROS and disruption of mitochondrial membrane potential. OGG1 is a base excision repair (BER) enzyme involved in recognition and excision of lethal oxidized guanine (8-oxoG) from DNA, which forms due to oxidative stress in cancer cells. Presence of such toxic lesions in DNA leads to replication stress and cell death. In our recent study, we found that suppression of OGG1, either by shRNA or by using specific OGG1 inhibitor TH5487, significantly reduces proliferation of many different cancer cell types. This effect is due to a decrease in mitochondrial membrane potential and increased replication stress. In the present study, we have been exploring if OGG1 depleted cells became more sensitive to proguanil based on its property to induce ROS mediated oxidative stress in the cancer cells. OGG1 depleted AML cancer cell line A3 was more sensitive to proguanil treatment in comparison to non-target control. Furthermore, we also found synergistic drug-drug interaction between TH5487 and proguanil in AML cell lines, A3, HL60, THP1, colon cancer cell line HCT116, lung cancer cell line H460, bladder cancer NTUB1, osteosarcoma cell line U2OS, while less pronounced effect was observed in lymphoblastoid cell lines, suggesting cancer specificity of drug combination. Combination treatment of TH5487 with proguanil induced more ROS and DNA damage in cancer cells in comparison to DMSO control, TH5487 or proguanil alone. No target engagement or stabilization was observed with DHFR in human osteosarcoma cells, even after 24hrs of treatment with proguanil using by CESTA method. This implies DHFR independent inhibition of unknown target, which enhance the toxicity of OGG1 inhibitor in cancer cell or vice versa. In conclusion, our preliminary investigation suggests that proguanil in combination with OGG1 inhibitor synergistically kill cancer cells and in-depth studies are required to validate the unknow target of proguanil in cancer cells to use proguanil as anti-cancer drug either alone or in combination. Citation Format: Varshni Rajagopal, Karthick Marimuthu, Carlos Benitez-Buelga, Olov Wallner, Evert Homan, Martin Scobie, Christina Kalderén, Thomas Helleday, Ulrika Warpman Berglund, Kumar Sanjiv. OGG1 depleted cancer cells are sensitive to anti-malarial drug proguanil: Repurposing for cancer treatment [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4799.

Due to a polar or even charged binding interface, DNA-binding proteins are considered extraordinarily difficult targets for development of small-molecule ligands and only a handful of proteins have been targeted successfully to date. Recently, however, it has been shown that development of selective and efficient inhibitors of 8-oxoguanine DNA glycosylase is possible. Here, we describe the initial druggability assessment of DNA glycosylases in a computational setting and experimentally investigate several methods to target endonuclease VIII-like 1 (NEIL1) with small-molecule inhibitors. We find that DNA glycosylases exhibit good predicted druggability in both DNA-bound and -unbound states. Furthermore, we find catalytic sites to be highly flexible, allowing for a range of interactions and binding partners. One flexible catalytic site was rationalized for NEIL1 and further investigated experimentally using both a biochemical assay in the presence of DNA and a thermal shift assay in the absence of DNA.

Karonudib (TH1579) is a novel compound that exerts anti-tumor activities and has recently entered phase I clinical testing. The aim of this study was to conduct a pre-clinical trial in patient-derived xenografts to identify the possible biomarkers of response or resistance that could guide inclusion of patients suffering from metastatic melanoma in phase II clinical trials. Patient-derived xenografts from 31 melanoma patients with metastatic disease were treated with karonudib or a vehicle for 18 days. Treatment responses were followed by measuring tumor sizes, and the models were categorized in the response groups. Tumors were harvested and processed for RNA sequencing and protein analysis. To investigate the effect of karonudib on T-cell-mediated anti-tumor activities, tumor-infiltrating T cells were injected in mice carrying autologous tumors and the mice treated with karonudib. We show that karonudib has heterogeneous anti-tumor effect on metastatic melanoma. Thus, based on the treatment responses, we could divide the 31 patient-derived xenografts in three treatment groups: progression group (32%), suppression group (42%), and regression group (26%). Furthermore, we show that karonudib has anti-tumor effect, irrespective of major melanoma driver mutations. Also, we identify high expression of ABCB1, which codes for p-gp pumps as a resistance biomarker. Finally, we show that karonudib treatment does not hamper T-cell-mediated anti-tumor responses. These findings can be used to guide future use of karonudib in clinical use with a potential approach as precision medicine.

DNA binding as an anti-inflammatory Mice that lack the gene encoding 8-oxoguanine DNA glycosylase 1 (OGG1) show resistance to inflammation. This enzyme binds to sites of oxidative DNA damage and initiates DNA base excision repair. Visnes et al. developed a small-molecule drug that acts as a potent and selective active-site inhibitor that stops OGG1 from recognizing its DNA substrate (see the Perspective by Samson). The drug inhibited DNA repair and modified OGG1 chromatin dynamics, which resulted in the inhibition of proinflammatory pathway genes. The drug was well tolerated by mice and suppressed lipopolysaccharide- and tumor necrosis factor–α–mediated neutrophilic inflammation in the lungs. Science , this issue p. 834 ; see also p. 748

With a diverse network of substrates, NUDIX hydrolases have emerged as a key family of nucleotide-metabolizing enzymes. NUDT5 (also called NUDIX5) has been implicated in ADP-ribose and 8-oxo-guanine metabolism and was recently identified as a rheostat of hormone-dependent gene regulation and proliferation in breast cancer cells. Here, we further elucidate the physiological relevance of known NUDT5 substrates and underscore the biological requirement for NUDT5 in gene regulation and proliferation of breast cancer cells. We confirm the involvement of NUDT5 in ADP-ribose metabolism and dissociate a relationship to oxidized nucleotide sanitation. Furthermore, we identify potent NUDT5 inhibitors, which are optimized to promote maximal NUDT5 cellular target engagement by CETSA. Lead compound, TH5427, blocks progestin-dependent, PAR-derived nuclear ATP synthesis and subsequent chromatin remodeling, gene regulation and proliferation in breast cancer cells. We herein present TH5427 as a promising, targeted inhibitor that can be used to further study NUDT5 activity and ADP-ribose metabolism., NUDIX hydrolases are an important family of nucleotide-metabolizing enzymes. Here, the authors identify potent, small molecule inhibitors of NUDT5, which is implicated in ADP-ribose and 8-oxo-guanine metabolism, and confirm its role in gene regulation and proliferation in breast cancer cells.

Fragment-based lead discovery has emerged as a leading drug development strategy for novel therapeutic targets. Although fragment-based drug discovery benefits immensely from access to atomic-resolution information, structure-based virtual screening has rarely been used to drive fragment discovery and optimization. Here, molecular docking of 0.3 million fragments to a crystal structure of cancer target MTH1 was performed. Twenty-two predicted fragment ligands, for which analogs could be acquired commercially, were experimentally evaluated. Five fragments inhibited MTH1 with IC50 values ranging from 6 to 79 μM. Structure-based optimization guided by predicted binding modes and analogs from commercial chemical libraries yielded nanomolar inhibitors. Subsequently solved crystal structures confirmed binding modes predicted by docking for three scaffolds. Structure-guided exploration of commercial chemical space using molecular docking gives access to fragment libraries that are several orders of magnitude lar...

// Anna Hagenkort 1, * , Cynthia B.J. Paulin 1, * , Matthieu Desroses 1, * , Antonio Sarno 2 , Elisee Wiita 1 , Oliver Mortusewicz 1 , Tobias Koolmeister 1 , Olga Loseva 1 , Ann-Sofie Jemth 1 , Ingrid Almlof 1 , Evert Homan 1 , Thomas Lundback 3 , Anna-Lena Gustavsson 3 , Martin Scobie 1 , Thomas Helleday 1 1 Division of Translational Medicine and Chemical Biology, Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden 2 Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway 3 Chemical Biology Consortium Sweden, Division of Translational Medicine and Chemical Biology, Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden * These authors have contributed equally to this work Correspondence to: Thomas Helleday, email: thomas.helleday@scilifelab.se Keywords: dUTPase, 5-Fluorouracil, DNA replication, combination therapy Received: July 07, 2016 Accepted: February 06, 2017 Published: February 28, 2017 ABSTRACT The antimetabolite 5-Fluorouracil (5-FU) is used in the treatment of various forms of cancer and has a complex mode of action. Despite 6 decades in clinical application the contribution of 5-FdUTP and dUTP [(5-F)dUTP] and 5-FUTP misincorporation into DNA and RNA respectively, for 5-FU-induced toxicity is still under debate. This study investigates DNA replication defects induced by 5-FU treatment and how (5-F)dUTP accumulation contributes to this effect. We reveal that 5-FU treatment leads to extensive problems in DNA replication fork progression, causing accumulation of cells in S-phase, DNA damage and ultimately cell death. Interestingly, these effects can be reinforced by either depletion or inhibition of the deoxyuridine triphosphatase (dUTPase, also known as DUT), highlighting the importance of (5-F)dUTP accumulation for cytotoxicity. With this study, we not only extend the current understanding of the mechanism of action of 5-FU, but also contribute to the characterization of dUTPase inhibitors. We demonstrate that pharmacological inhibition of dUTPase is a promising approach that may improve the efficacy of 5-FU treatment in the clinic.

MTH1 prevents incorporation of oxidized deoxynucleoside triphosphates (e.g., 8-oxodGTP) into DNA. Earlier we demonstrated that MTH1 inhibitors TH588 and TH1579 possesses anti-cancer activity in various tumour types, while other structurally distinct MTH1 inhibitors failed to kill cancer cells or elevate the levels of oxidized nucleotides in DNA. In our current study, we found a novel function of MTH1 in mitosis, as it plays an important role in correct spindle assembly in cancer cells and progression through mitosis, and furthermore, we demonstrate MTH1 binds tubulin in vivo. We also observed that structurally distinct MTH1 inhibitors display differential abilities to break the MTH1 tubulin interaction, and also demonstrate that TH588 and TH1579 can directly inhibit tubulin polymerisation in vitro. Consistent with our results, we establish that TH588 and TH1579 kill cancer cells by a mitosis-dependent mechanism and implicate reactive oxygen species (ROS) accumulation and incorporation of oxidised nucleotides into DNA in this process. Furthermore, we found that non-cytotoxic MTH1 inhibitors can become cytotoxic and increase incorporation of oxidised nucleotides into DNA when they are combined with sub-therapeutic concentrations of mitotic inhibitors. In conclusion, MTH1 inhibitors killing cancer cells have a unique and complex mechanism of action: (1) causing a mitotic arrest, induced by targeting MTH1 which is required for mitotic progression, but also through direct inhibition of microtubule polymerisation, in-turn leading to an increase in ROS and likely 8-oxodGTP and (2) MTH1-dependent 8-oxodGTPase inhibitory activity causing incorporation of damaged nucleotides into DNA to kill cancer cells. Citation Format: Kumar Sanjiv, Helge gad, Sean G. Rudd, Oliver Mortusewicz, Ailine Stolz, Nuno Amaral, Lars Brautigham, Linda Pudelko, Christina Kaldéren, Ann-Sofie Jemth, Ingrid Almlöf, Torkild Visnes, Niklas Schultz, Johan Boström, José Manuel Calderon Montano1, Anna Hagenkort, Petra Groth, Camilla Gokturk, Tobias Koolmeister, Prasad Wakchaure, Evert Homan, Mikael Altun, Cecilia Ström, Martin Scobie, Holger Bastians, Ulrika Warpman Berglund, Thomas Helleday. MTH1 promotes mitotic progression to avoid oxidative DNA damage in cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 105.

This paper describes a facile, efficient, and clean synthesis of various pyrazolones by employing T3P® as a catalyst and performing the reaction under microwave irradiation. This two-step, one-pot reaction proceeded readily and tolerated a variety of functional groups. A wide range of pyrazolone derivatives were obtained in good to excellent yields.

This Letter describes a convenient, efficient, and clean synthesis of various tetrahydro-β-carbolines catalyzed by propane phosphonic acid anhydride T3P® under microwave irradiation.

The dCTPase pyrophosphatase 1 (dCTPase) regulates the intracellular nucleotide pool through hydrolytic degradation of canonical and noncanonical nucleotide triphosphates (dNTPs). dCTPase is highly expressed in multiple carcinomas and is associated with cancer cell stemness. Here we report on the development of the first potent and selective dCTPase inhibitors that enhance the cytotoxic effect of cytidine analogues in leukemia cells. Boronate 30 displays a promising in vitro ADME profile, including plasma and mouse microsomal half-lives, aqueous solubility, cell permeability and CYP inhibition, deeming it a suitable compound for in vivo studies.

Starting from o-nitro-aryl and -heteroaryl halides a two-step sequence of Suzuki coupling and Cadogan—Sundberg cyclization yields indoles and pyrrolo-annelated heteroarenes.

A method for synthesizing combinatorial libraries of unsymmetrically substituted tetra-meso-phenyl porphyrins on polystyrene based resin is described. Attachment of 5,15-dibromo-10-(4-hydroxyphenyl)-20-(4-nitrophenyl)porphyrin onto brominated Wang resin gave a convenient scaffold for the synthesis of photoactive porphyrin libraries with three points for generating diversity. An array of nine TPP derivatives was prepared by sequential Suzuki coupling/nitro-reduction and acylation protocols.

Summary ATR and CHK1 maintain cancer cell survival under replication stress and inhibitors of both kinases are currently undergoing clinical trials. As ATR activity is increased after CHK1 inhibition, we hypothesized that this may indicate an increased reliance on ATR for survival. Indeed, we observe that replication stress induced by the CHK1 inhibitor AZD7762 results in replication catastrophe and apoptosis, when combined with the ATR inhibitor VE-821 specifically in cancer cells. Combined treatment with ATR and CHK1 inhibitors leads to replication fork arrest, ssDNA accumulation, replication collapse, and synergistic cell death in cancer cells in vitro and in vivo. Inhibition of CDK reversed replication stress and synthetic lethality, demonstrating that regulation of origin firing by ATR and CHK1 explains the synthetic lethality. In conclusion, this study exemplifies cancer-specific synthetic lethality between two proteins in the same pathway and raises the prospect of combining ATR and CHK1 inhibitors as promising cancer therapy., Graphical Abstract, Highlights • Synthetic lethality within the same pathway is via the induction of replication catastrophe • New origin firing and replication stress induced by CHK1 inhibitor reliance on ATR • ATR and CHK1 inhibitor combination results in cancer-specific cytotoxicity • ATR and CHK1 inhibitor combination could be used broadly across cancer indications, Sanjiv et al. report synthetic lethality in cancer cells induced by the inhibition of two kinases, ATR and CHK1, operating in the same signaling pathway. This combination therapy could potentially be used for the treatment of various cancer types due to cancer-specific cytotoxicity.

The multicomponent reaction of boronic esters with imine or iminium species (generated in situ by reaction of amines with glyoxylic acid) has received little attention in the literature despite the current interest in the corresponding reactions of boronic acids (Petasis reaction). Moreover, the use of boronic esters in this reaction is particularly attractive since chiral esters could act as auxiliaries in a novel enantioselective process. We set out to establish whether boronic esters were general substrates in the Petasis reaction. Pinacolyl boronic esters were selected for study as a model substrate for more complex homochiral boronic esters because of their ease of synthesis and chemical stability. We found that pinacolyl boronic esters do not react with imines derived from primary amines and glyoxylic acid under standard conditions. By contrast, imines derived from secondary amines and glyoxylic acid react readily with vinylboronic esters but less readily with heteroaryl- or arylboronic esters.

Nature 508, 215–221 (2014); doi:10.1038/nature13181 In this Article, the structure of compound TH650 (4) in Fig. 4a was drawn incorrectly; the correct structure is shown as Fig. 1 to this Corrigendum. Preparative, spectroscopic and biological data associated with this compound are as reported in theArticle, and the error does not influence any of the reported data or interpretations.

A two-step synthesis of structurally diverse pyrrole-containing bicyclic systems is reported. ortho-Nitro-haloarenes coupled with vinylic N-methyliminodiacetic acid (MIDA) boronates generate ortho-vinyl-nitroarenes, which undergo a "metal-free" nitrene insertion, resulting in a new pyrrole ring. This novel synthetic approach has a wide substrate tolerance and it is applicable in the preparation of more complex "drug-like" molecules. Interestingly, an ortho-nitro-allylarene derivative furnished a cyclic β-aminophosphonate motif.

Histone acetylation is required for many aspects of gene regulation, genome maintenance and metabolism and dysfunctional acetylation is implicated in numerous diseases, including cancer. Acetylation is regulated by histone acetyltransferases (HATs) and histone deacetylases and currently, few general HAT inhibitors have been described. We identified the HAT Tip60 as an excellent candidate for targeted drug development, as Tip60 is a key mediator of the DNA damage response and transcriptional co-activator. Our modeling of Tip60 indicated that the active binding pocket possesses opposite charges at each end, with the positive charges attributed to two specific side chains. We used structure based drug design to develop a novel Tip60 inhibitor, TH1834, to fit this specific pocket. We demonstrate that TH1834 significantly inhibits Tip60 activity in vitro and treating cells with TH1834 results in apoptosis and increased unrepaired DNA damage (following ionizing radiation treatment) in breast cancer but not control cell lines. Furthermore, TH1834 did not affect the activity of related HAT MOF, as indicated by H4K16Ac, demonstrating specificity. The modeling and validation of the small molecule inhibitor TH1834 represents a first step towards developing additional specific, targeted inhibitors of Tip60 that may lead to further improvements in the treatment of breast cancer.

A new T3P®-assisted, convenient and efficient procedure for the synthesis of dihydroquinazolinones is described. The main advantages of this protocol include its practical simplicity, short reaction times and particularly the ease with which products are isolated.

Four new ligands that bind to the minor groove of DNA have been designed, synthesized, and evaluated by DNA footprinting. Two of the ligands are polyamides containing central regions with five or six N-methylpyrrole units, conferring hydrophobicity and good binding affinity but without retaining the correct spacing for hydrogen bonding in the base of the minor groove. The two remaining ligands have central regions which are head-to-head-linked polyamides, in which the linker is designed to improve the phasing of hydrogen bonding of the ligand with the floor of the minor groove. The highest affinity was obtained with the two polypyrroles without headgroup spacers, indicating that H-bond phasing is secondary in determining affinity compared to the major hydrophobic driving force. With a dimethylaminoalkyl group, representing a moiety with modest base strength, at both ends, water solubility is good and pH-partition theory predicts that penetration through lipid membranes will be enhanced, compared to strongly basic amidine analogues of the alkaloid precursors. All four compounds bind to DNA, with strong selectivity for AT sequences but some tolerance of GC base pairs and subtle individual preferences. The data show that very high affinities can be anticipated for future compounds in this series, but drug design must take account of overall physicochemical properties as well as the details of hydrogen bonding between ligands and the floor of the minor groove.

A series of head to head linked dimers of heterocyclic amino acids has been prepared for investigation of affinity and selectivity in binding to the minor groove of DNA. The selection of targets for synthesis was led by computer based design. Several novel dicarboxylic acid linkers including indoles, phenanthrenes, a fluorenone, and a bisbenzothiophene have been included. Analysis of binding to DNA by footprinting showed high affinity for compounds derived from 2,7-dihydrophenanthrene dicarboxylic acid and a predominant selectivity for AT rich regions containing at least 4 AT pairs but with the ability to span up to two CG base pairs.

Combinatorial techniques, both solid and solution phase, have been applied to the synthesis of unsymmetrically substituted 5,15-diphenylporphyrins. 5-(4-Hydroxyphenyl)-15-pentafluorophenylporphyrin can be loaded onto solid supports and substituted on the pentafluorophenyl ring with thiols. Diversity is then expanded by cleavage and solution phase substitution of the second phenyl ring using a solid supported base.

Microwave-assisted reductive alkylation of methyl carbamate with a range of aldehydes provides, after basic work-up, an experimentally simple, one-pot method for rapid functional group interconversion of structurally diverse aldehydes into primary amines. The method has several advantages over more traditional methods of carrying out this transformation and is particularly amenable- to high-throughput synthesis.

This paper describes a facile, efficient, and clean synthesis of various pyrazolones by employing T3P® as a catalyst and performing the reaction under microwave irradiation. This two-step, one-pot reaction proceeded readily and tolerated a variety of functional groups. A wide range of pyrazolone derivatives were obtained in good to excellent yields.

A novel general protocol for the construction of hydantoins and thiohydantoins on a solid support has been developed. Using this novel methodology, the synthesis of a diverse 96-compound library has been achieved. Resin-bound dipeptides are cyclised via the formation of an intermediate isocyanate or isothiocyanate on resin as the key step in the strategy.