Activity-based protein profiling reveals deubiquitinase and aldehyde dehydrogenase targets of a cyanopyrrolidine probe

Ubiquitin carboxy-terminal hydrolase L1 (UCHL1), a deubiquitinating enzyme (DUB), is a potential drug target in various cancers, and liver and lung fibrosis. However, bona fide functions and substrates of UCHL1 remain poorly understood. Herein, we report the characterization of UCHL1 covalent inhibitor MT16-001 based on a thiazole cyanopyrrolidine scaffold. In combination with chemical proteomics, a closely related activity-based probe (MT16-205) was used to generate a comprehensive quantitative profile for on- and off-targets at endogenous cellular abundance. Both compounds are selective for UCHL1 over other DUBs in intact cells but also engage a range of other targets with good selectivity over the wider proteome, including aldehyde dehydrogenases, redox-sensitive Parkinson’s disease related protein PARK7, and glutamine amidotransferase. Taken together, these results underline the importance of robust profiling of activity-based probes as chemical tools and highlight the cyanopyrrolidine warhead as a versatile platform for liganding diverse classes of protein with reactive cysteine residues which can be used for further inhibitor screening, and as a starting point for inhibitor development

Neddylation inhibition prevents acetaminophen-induced liver damage by enhancing the anabolic cardiolipin pathway

\ua9 2024 The AuthorsDrug-induced liver injury (DILI) is a significant cause of acute liver failure (ALF) and liver transplantation in the Western world. Acetaminophen (APAP) overdose is a main contributor of DILI, leading to hepatocyte cell death through necrosis. Here, we identified that neddylation, an essential post-translational modification involved in the mitochondria function, was upregulated in liver biopsies from patients with APAP-induced liver injury (AILI) and in mice treated with an APAP overdose. MLN4924, an inhibitor of the neuronal precursor cell-expressed developmentally downregulated protein 8 (NEDD8)-activating enzyme (NAE-1), ameliorated necrosis and boosted liver regeneration in AILI. To understand how neddylation interferes in AILI, whole-body biotinylated NEDD8 (bioNEDD8) and ubiquitin (bioUB) transgenic mice were investigated under APAP overdose with and without MLN4924. The cytidine diphosphate diacylglycerol (CDP-DAG) synthase TAM41, responsible for producing cardiolipin essential for mitochondrial activity, was found modulated under AILI and restored its levels by inhibiting neddylation. Understanding this ubiquitin-like crosstalk in AILI is essential for developing promising targeted inhibitors for DILI treatment

SUMOylation controls Hu antigen R posttranscriptional activity in liver cancer

© 2024 The Author(s). This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).The posttranslational modification of proteins critically influences many biological processes and is a key mechanism that regulates the function of the RNA-binding protein Hu antigen R (HuR), a hub in liver cancer. Here, we show that HuR is SUMOylated in the tumor sections of patients with hepatocellular carcinoma in contrast to the surrounding tissue, as well as in human cell line and mouse models of the disease. SUMOylation of HuR promotes major cancer hallmarks, namely proliferation and invasion, whereas the absence of HuR SUMOylation results in a senescent phenotype with dysfunctional mitochondria and endoplasmic reticulum. Mechanistically, SUMOylation induces a structural rearrangement of the RNA recognition motifs that modulates HuR binding affinity to its target RNAs, further modifying the transcriptomic profile toward hepatic tumor progression. Overall, SUMOylation constitutes a mechanism of HuR regulation that could be potentially exploited as a therapeutic strategy for liver cancer.This work was supported by grants to M.L.M.-C. from Departamento de Industria del Gobierno Vasco, Spain; Ministerio de Ciencia e Innovación, Spain (grant no. PID2020-117116RB-I00); European Regional Development Fund (ERDF), EU; and CIBERehd, which is funded by Instituto de Salud Carlos III (ISCIII), Spain. M.L.M.-C. and J.S. received funding from Ministerio de Ciencia e Innovación (grant no. RTC2019-007125-1) and ISCIII (grant no. DTS20/00138). M.L.M.-C. and R.M.L. acknowledge Ministerio de Ciencia e Innovación (grant no. RED2022-134397-T). M.L.M.-C. and J.M.B. were awarded with a grant from Fundación la Caixa, Spain (grant no. HR17-00601). M.L.M.-C., J.M.B., M.A.A., and J.J.G.M. acknowledge financial support from Fundación Científica de la Asociación Española Contra el Cáncer (AECC), Spain. M.S.R. recognizes funding from Fondo Sectorial de Investigación SRE - CONACYT, Mexico (grant no. 0280365); Horizon 2020 Research and Innovation Program funded under Marie Skłodowska-Curie Actions, EU (grant no. 765445); and REPÈRE and Programme de Prématuration from Région Occitanie, France. M.G., S.D., and K.M.-M. were supported by the National Institute on Aging (NIA), National Institutes of Health (NIH), US (grant no. Z01-AG000511-23). I.D.-M. is grateful for the grants received from Junta de Andalucía, Spain (grant no. BIO-198, US-1254317, P18-FR-3487, and P18-HO-4091); Ministerio de Ciencia, Innovación y Universidades, Spain (grant no. PGC2018-096049-BI00); and Fundación Ramón Areces, Spain. T.D. acknowledges Fondation ARC, France (grant no. 208084). J.J.G.M. was supported by Junta de Castilla y León, Spain (grant no. SA063P17); Fundación La Marató TV3, Spain (grant no. 201916-31); ISCIII (grant no. PI19/00819); CIBERehd; and ERDF (grant no. OLD-HEPAMARKER). M.A.A. recognizes Gobierno de Navarra, Spain (grant no. GºNa 42/21); Eurorregión Nueva Aquitania-Euskadi-Navarra, Spain; Ministerio de Ciencia e Innovación (grant no. PID2019-104878RB-I00); and CIBERehd. A.P. expresses gratitude to the European Research Council (ERC), EU (grant no. 804236) for their support. M.D.G. received financial support from Junta de Andalucía (grant no. PEMP-0036-2020 and BIO-0139); Ministerio de Universidades, Spain (grant no. FPU20/03957); ISCIII (grant no. PI20/01301), Fundación Sociedad Española de Endocrinología y Nutrición (FSEEN), Spain; CIBERehd; and CIBERobn, which is also funded by ISCIII. J.M.B. acknowledges Euskadi RIS3 (grant no. 2019222054, 2020333010, and 2021333003) and Elkartek programs from Gobierno Vasco (grant no. KK-2020/00008); ISCIII (grant no. PI18/01075, CPII19/00008, and PI21/00922); CIBERehd; PSC Support, UK; AMMF The Cholangiocarcinoma Charity, UK (grant no. EU/2019/AMMFt/001); Horizon 2020 Research and Innovation Program (grant no. 825510); ERDF; and PSC Partners Seeking a Cure, US. A.L. received financial support from the Damon Runyon-Rachleff Innovation Award, US (grant no. DR52-18) and the MERIT Award (R37) from the National Cancer Institute (NCI), NIH (grant no. R37CA230636). F.E. expresses his gratitude to ProteoRed from ISCIII (grant no. PT13/0001/0027) and CIBERehd. N.G.A.A. was funded by Ministerio de Ciencia, Innovación y Universidades (grant no. RTI2018-095700-B-I00). R.B. acknowledges financial support from Gobierno Vasco (grant no. IT1165-19); Ministerio de Economía, Industria y Competitividad, Spain (grant no. SAF2017-90900-REDT); Ministerio de Economía, Industria y Competitividad, ERDF (grant no. BFU2017-84653-P); Ministerio de Ciencia e Innovación (grant no. PID2020-114178GB-I00); and Horizon 2020 funded under Marie Skłodowska-Curie Actions (grant no. 765445-EU). A.M.A. acknowledges CIBERehd. L.A.M.-C. obtained grants from Ministerio de Economía y Competitividad (grant no. CSD2008-00005); Ministerio de Economía, Industria y Competitividad (grant no. BFU2016-77408-R); ISCIII; and EJP RD, EU (grant no. EJPRD19-040). I.G.-R. was supported by Ministerio de Economía, Industria y Competitividad (grant no. BES-2017-080435 ). M.S.-M. is grateful to the AECC, Sede de Bizkaia, Spain for the financial support. J.D.Z. was awarded with a grant from Ministerio de Economía, Industria y Competitividad (grant no. SEV-2016-0644-18-2). C.M. acknowledges Gobierno Vasco (grant no. IT-1264-19) and Ministerio de Ciencia e Innovación (grant no. PID2022-136788OB-I00). A.V.-C. was supported by Ministerio de Educación, Cultura y Deporte, Spain (grant no. FPU016/01513). C.F.-R. thanks Tekniker, Spain and CIC bioGUNE, Spain for financial support. A.G.-d.R. was funded by Bikaintek program from Gobierno Vasco (grant no. 48-AF-W1-2019-00012). N.G.-U. obtained a grant from Gobierno Vasco. T.C.D. expresses gratitude to AECC. J.S. received financial support from CIBERehd. C.M.R.-G. was supported by Ayudas a la Recualificación Margarita Salas from Universidad de Extremadura, Ministerio de Universidades financed by NextGenerationEU.Peer reviewe

Correction to “Discovery of a Potent and Selective Covalent Inhibitor and Activity-Based Probe for the Deubiquitylating Enzyme UCHL1, with Antifibrotic Activity”

Supporting Information, pages S38 and S44. In the PDF Supporting Information, Schemes S1 and S3 contained errors in the synthetic conditions. The conditions for the steps 5 → 6 and 12 → 13 in the respective schemes should be “TFA, DCM, rt” (not “TMSI, K2CO3, CH2Cl2”)

Discovery of a potent and selective covalent inhibitor and activity-based probe for the deubiquitylating enzyme UCHL1, with anti-fibrotic activity

Ubiquitin carboxy-terminal hydrolase L1 (UCHL1) is a deubiquitylating enzyme which is proposed as a potential therapeutic target in neurodegeneration, cancer, and liver and lung fibrosis. Herein we report the discovery of the most potent and selective UCHL1 probe (IMP-1710) to date based on a covalent inhibitor scaffold and apply this probe to identify and quantify target proteins in intact human cells. IMP-1710 stereoselectively labels the catalytic cysteine of UCHL1 at low nanomolar concentration in cells. We further demonstrate that potent and selective UCHL1 inhibitors block pro-fibrotic responses in a cellular model of idiopathic pulmonary fibrosis, supporting the potential of UCHL1 as a potential therapeutic target in fibrotic diseases

Anti-miR-518d-5p overcomes liver tumor cell death resistance through mitochondrial activity

Dysregulation of miRNAs is a hallmark of cancer, modulating oncogenes, tumor suppressors, and drug responsiveness. The multi-kinase inhibitor sorafenib is one of the first-line drugs for advanced hepatocellular carcinoma (HCC), although the outcome for treated patients is heterogeneous. The identification of predictive biomarkers and targets of sorafenib efficacy are sorely needed. Thus, selected top upregulated miRNAs from the C19MC cluster were analyzed in different hepatoma cell lines compared to immortalized liver human cells, THLE-2 as control. MiR-518d-5p showed the most consistent upregulation among them. Thus, miR-518d-5p was measured in liver tumor/non-tumor samples of two distinct cohorts of HCC patients (n = 16 and n = 20, respectively). Circulating miR-518d-5p was measured in an independent cohort of HCC patients receiving sorafenib treatment (n = 100), where miR-518d-5p was analyzed in relation to treatment duration and patient’s overall survival. In vitro and in vivo studies were performed in human hepatoma BCLC3 and Huh7 cells to analyze the effect of miR-518d-5p inhibition/overexpression during the response to sorafenib. Compared with healthy individuals, miR-518d-5p levels were higher in hepatic and serum samples from HCC patients (n = 16) and in an additional cohort of tumor/non-tumor paired samples (n = 20). MiR-518d-5p, through the inhibition of c-Jun and its mitochondrial target PUMA, desensitized human hepatoma cells and mouse xenograft to sorafenib-induced apoptosis. Finally, serum miR-518d-5p was assessed in 100 patients with HCC of different etiologies and BCLC-stage treated with sorafenib. In BCLC-C patients, higher serum miR-518d-5p at diagnosis was associated with shorter sorafenib treatment duration and survival. Hence, hepatic miR-518d-5p modulates sorafenib resistance in HCC through inhibition of c-Jun/PUMA-induced apoptosis. Circulating miR-518d-5p emerges as a potential lack of response biomarker to sorafenib in BCLC-C HCC patients