Structural features and kinetic characterization of alanine racemase from Staphylococcus aureus (Mu50)

The tertiary structure and kinetic properties of alanine racemase from Staphylococcus aureus are described and compared to other related alanine racemase structures

Small-molecule activation of OGG1 increases oxidative DNA damage repair by gaining a new function

Oxidative DNA damage is recognised by 8-oxoguanine (8-oxoG) DNA glycosylase 1 (OGG1), which excises 8-oxoG, leaving a substrate for apurinic endonuclease 1 (APE1), initiating repair. Here, we describe a small molecule (TH10785) that interacts with the Phe319 and Gly42 amino acids of OGG1, increases the enzyme activity 10-fold and generates a novel 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 ageing.European Research Council TAROX-695376Swedish Research Council 2015-00162 and 2018-03406Ministry of Science and Innovation, Spain/State Research Agency, Spain/10.13039/501.100011033European Regional Development Fund (ERDF) BFU2017-83900-PCrafoord Foundation 20190532Alfred Osterlund FoundationSwedish Pain Relief FoundationSwedish Cancer Society CAN 2018/0658 and CAN 2017/716Torsten and Ragnar Soderberg foundationDr. Ake-Olsson Foundation for Hematological Research 2020-00306Thomas Helleday Foundation for medical research postdoctoral stipendsNTNU Enabling Technology Programme on BiotechnologyEMBO Short-Term Fellowship 9005FEBS Short-Term FellowshipScandinavian ExchangeGerman Research Foundation (DFG) 239748522Sonderforschungsbereich (SFB) 1127Leibniz AwardNorwegian Research Council 303369Karolinska Institutet Research Foundation 2020-02186Lars Hiertas Minne StiftelseAsociacion Espanola Contra Cancer grant Postdoctoral AECC 2020 POSTD20042BENIInstituto de Salud Carlos III CP19/00063, PI20/00329 and PI19/00640European Social Fund (ESF)Innovative Medicines Initiative 2 Joint Undertaking (JU) 875510European Union's Horizon 2020 research and innovation program, Marie Sklodowska-Curie 722729Accepte

Massively parallel variant characterization identifies NUDT15 alleles associated with thiopurine toxicity

As a prototype of genomics-guided precision medicine, individualized thiopurine dosing based on pharmacogenetics is a highly effective way to mitigate hematopoietic toxicity of this class of drugs. Recently, NUDT15 deficiency was identified as a genetic cause of thiopurine toxicity, and NUDT15-informed preemptive dose reduction was quickly adopted in clinical settings. To exhaustively identify pharmacogenetic variants in this gene, we developed massively parallel NUDT15 function assays to determine the variants' effect on protein abundance and thiopurine cytotoxicity. Of the 3,097 possible missense variants, we characterized the abundance of 2,922 variants and found 54 hotspot residues at which variants resulted in complete loss of protein stability. Analyzing 2,935 variants in the thiopurine cytotoxicity-based assay, we identified 17 additional residues where variants altered NUDT15 activity without affecting protein stability. We identified structural elements key to NUDT15 stability and/or catalytical activity with single amino acid resolution. Functional effects for NUDT15 variants accurately predicted toxicity risk alleles in patients treated with thiopurines with far superior sensitivity and specificity compared to bioinformatic prediction algorithms. In conclusion, our massively parallel variant function assays identified 1,152 deleterious NUDT15 variants, providing a comprehensive reference of variant function and vastly improving the ability to implement pharmacogenetics-guided thiopurine treatment individualization.This article is available to RD&E staff via NHS OpenAthens. Click on the Publisher URL, and log in with NHS OpenAthens if prompted.R01 CA096670/CA/NCI NIH HHS/United States R25 CA023944/CA/NCI NIH HHS/United States P30 CA021765/CA/NCI NIH HHS/United States U10 CA098543/CA/NCI NIH HHS/United States U10 CA180899/CA/NCI NIH HHS/United States R01 GM118578/GM/NIGMS NIH HHS/United States U10 CA180886/CA/NCI NIH HHS/United States P50 GM115279/GM/NIGMS NIH HHS/United States U10 CA098413/CA/NCI NIH HHS/United States U10 CA095861/CA/NCI NIH HHS/United Statespublished version, accepted version (6 month embargo)

Pharmacological targeting of MTHFD2 suppresses acute myeloid leukemia by inducing thymidine depletion and replication stress

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