Biochemical Journal最新文献

{"title":"Methods to accelerate PROTAC drug discovery.","authors":"Jeyan Osman,Philip E Thompson,Manuela Jörg,Martin J Scanlon","doi":"10.1042/bcj20243018","DOIUrl":"https://doi.org/10.1042/bcj20243018","url":null,"abstract":"Proteolysis-targeting chimeras (PROTACs) represent a novel and promising modality for probing biological systems, elucidating pharmacological mechanisms, and identifying potential therapeutic leads. The field has made significant strides, as demonstrated by the growing number of PROTACs advancing to clinical trials. Despite this progress, the development of PROTACs faces significant challenges, which is partially due to the heterobivalent nature of this class of molecules. PROTACs must simultaneously bind to a protein of interest and an E3 ubiquitin ligase. This means PROTACs are significantly larger and more complex than conventional small molecules. This complexity impacts their design and synthesis, requiring strategic approaches to create libraries of PROTACs with various combinations of target ligands, linkers, and E3 ligase-recruiting elements. To fully realise the potential of this innovative technology, there is a need for novel approaches to accelerate the development of PROTACs. This review focuses on three critical areas to accelerate PROTAC development: appropriate target selection, modular chemical synthesis, and high-throughput biological evaluation. By appropriate selection of target proteins for degradation, optimizing synthesis methods to handle the complexity of PROTAC molecules, and employing robust high-throughput biological assays to evaluate PROTAC activity, researchers in academia and industry have streamlined the development and increased the success rate of PROTAC-based discovery programmes.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"18 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144504547","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Role of LRRK2 in axonal transport and Parkinson's disease.","authors":"Björn Twellsieck,C Alexander Boecker","doi":"10.1042/bcj20253133","DOIUrl":"https://doi.org/10.1042/bcj20253133","url":null,"abstract":"Axonal transport is crucial for neuronal health and function, facilitating the delivery of newly synthesized material from the soma via anterograde transport and the removal of aged proteins and damaged organelles for degradation via retrograde transport. Emerging evidence links Parkinson's disease (PD)-causing mutations in the leucine-rich repeat kinase 2 (LRRK2) gene to dysfunctional axonal transport. Pathogenic LRRK2 mutations induce increased LRRK2 kinase activity, leading to the hyperphosphorylation of RAB proteins, which are key regulators of intracellular trafficking and transport. Here, we review the current literature on how LRRK2 affects the axonal transport of different cargoes, focusing on synaptic vesicle precursors, mitochondria, and autophagosomes. We further discuss how LRRK2 influences cytoskeletal dynamics and how it affects vesicle trafficking at the Golgi, which may indirectly contribute to its effect on axonal transport. This review summarizes our current understanding of how pathogenic LRRK2 hyperactivation disrupts axonal transport and how this may be linked to the neurodegeneration of PD.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"91 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144504548","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Methods to accelerate PROTAC drug discovery.","authors":"Jeyan Osman, Philip E Thompson, Manuela Jörg, Martin J Scanlon","doi":"10.1042/BCJ20243018","DOIUrl":"10.1042/BCJ20243018","url":null,"abstract":"<p><p>Proteolysis-targeting chimeras (PROTACs) represent a novel and promising modality for probing biological systems, elucidating pharmacological mechanisms, and identifying potential therapeutic leads. The field has made significant strides, as demonstrated by the growing number of PROTACs advancing to clinical trials. Despite this progress, the development of PROTACs faces significant challenges, which is partially due to the heterobivalent nature of this class of molecules. PROTACs must simultaneously bind to a protein of interest and an E3 ubiquitin ligase. This means PROTACs are significantly larger and more complex than conventional small molecules. This complexity impacts their design and synthesis, requiring strategic approaches to create libraries of PROTACs with various combinations of target ligands, linkers, and E3 ligase-recruiting elements. To fully realise the potential of this innovative technology, there is a need for novel approaches to accelerate the development of PROTACs. This review focuses on three critical areas to accelerate PROTAC development: appropriate target selection, modular chemical synthesis, and high-throughput biological evaluation. By appropriate selection of target proteins for degradation, optimizing synthesis methods to handle the complexity of PROTAC molecules, and employing robust high-throughput biological assays to evaluate PROTAC activity, researchers in academia and industry have streamlined the development and increased the success rate of PROTAC-based discovery programmes.</p>","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"482 13","pages":""},"PeriodicalIF":4.3,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12312393/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144504754","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction: Roles for TAB1 in regulating the IL-1-dependent phosphorylation of the TAB3 regulatory subunit and activity of the TAK1 complex.","authors":"","doi":"10.1042/BJ20071149_COR","DOIUrl":"10.1042/BJ20071149_COR","url":null,"abstract":"","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"482 12","pages":"903-904"},"PeriodicalIF":4.4,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12235664/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144324396","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction: 14-3-3 binding to LRRK2 is disrupted by multiple Parkinson's disease-associated mutations and regulates cytoplasmic localization.","authors":"","doi":"10.1042/BJ20100483_COR","DOIUrl":"10.1042/BJ20100483_COR","url":null,"abstract":"","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"482 12","pages":"901-902"},"PeriodicalIF":4.4,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12235665/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144324395","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A new naphthalene-based fluorogenic substrate for cytochrome P450 4A11.","authors":"Dmitri R Davydov, Kannapiran Ponraj, Nadezhda Davydova, Dilip Kumar Singh, Bhagwat Prasad","doi":"10.1042/BCJ20253130","DOIUrl":"10.1042/BCJ20253130","url":null,"abstract":"<p><p>We aimed to create a high-throughput fluorimetric assay for the activity of CYP4A11, the major 20-HETE-producing enzyme. To this end, we probed 3-(6-methoxynaphthalen-2-yl)acrylic acid (MONACRA) as a potential CYP4A11 substrate. We studied its metabolism using human liver microsomes (HLM) and recombinant P450 enzymes. O-demethylation of MONACRA by cytochromes P450 creates 3-(6-hydroxynaphthalen-2-yl)acrylic acid. The bright fluorescence of the product and its clear spectral resolution from the substrate allowed us to create a fluorimetric assay of MONACRA metabolism. We tested 16 recombinant human P450 enzymes and found noticeable demethylation activity only with CYP4A11 and CYP1A2. The KM for CYP4A11 is 189±37 μM, and the kcat accounts for 67±18 min-1. CYP1A2 exhibits a KM of 161±34 μM, with a kcat value of 44±6 min-1, although this enzyme also exhibited a decreased rate of turnover at high substrate concentrations, evidencing substrate inhibition with Ksi=650±200 μM. The studies with fluvoxamine and epalrestat, specific inhibitors of CYP1A2 and CYP4A11, respectively, showed that despite the activity of recombinant CYP1A2 with MONACRA, it does not take part in its metabolism in HLM. Thus, MONACRA can be utilized as a specific fluorogenic substrate of CYP4A11. We developed a robust and sensitive automated fluorimetric assay of MONACRA demethylation and used it to compare the substrate saturation profiles in seven pooled HLM preparations with the known composition of the P450 pool. These studies demonstrated a close correlation between the rate of the main kinetic phase of MONACRA metabolism and the fractional content of CYP4A11 in the P450 pool.</p>","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12191924/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144198217","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structural insights into allosteric inhibition of HRI kinase by heme binding via HDX-MS.","authors":"Shivani Kanta, Vanesa Vinciauskaite, Graham Neill, Miratul M K Muqit, Glenn R Masson","doi":"10.1042/BCJ20253072","DOIUrl":"10.1042/BCJ20253072","url":null,"abstract":"<p><p>Heme-regulated inhibitor (HRI) is one of the four mammalian kinases that phosphorylate eIF2α, facilitating a cellular response to stress through the regulation of mRNA translation. Originally identified as a heme sensor in erythroid progenitor cells, HRI has since emerged as a potential therapeutic target in both cancer and neurodegeneration. Here, we characterise two modes of HRI inhibition using structural mass spectrometry, biochemistry, and biophysics. We examined several competitive ATP-mimetic inhibitors - dabrafenib, encorafenib, and GCN2iB - and compared them with the heme-mimetic allosteric inhibitor, hemin. By combining hydrogen-deuterium exchange mass spectrometry with protein models generated by AlphaFold 3, we investigated the structural basis of inhibition by dabrafenib and hemin. Our analysis revealed that hemin inhibition induces large-scale structural rearrangements in HRI, which are not observed with ATP-mimetic inhibitors. Our results suggest that HRI may be inhibited using two distinctly different modalities, which may guide future drug development.</p>","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12235045/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144224179","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Arginine promotes the activation of human lung fibroblasts independent of its metabolism.","authors":"Robert B Hamanaka, Kun Woo D Shin, M Volkan Atalay, Rengul Cetin-Atalay, Hardik Shah, Jennifer C Houpy Szafran, Parker S Woods, Angelo Y Meliton, Obada R Shamaa, Yufeng Tian, Takugo Cho, Gökhan M Mutlu","doi":"10.1042/BCJ20253033","DOIUrl":"10.1042/BCJ20253033","url":null,"abstract":"<p><p>Arginine is a conditionally essential amino acid with known roles in protein production, nitric oxide synthesis, biosynthesis of proline and polyamines, and regulation of intracellular signaling pathways. Arginine biosynthesis and catabolism have been linked to transforming growth factor-β (TGF-β)-induced activation of fibroblasts in the context of pulmonary fibrosis; however, a thorough study on the metabolic and signaling roles of arginine in the process of fibroblast activation has not been conducted. Here, we examined the role and regulation of arginine metabolism in lung fibroblasts activated with TGF-β. We found that TGF-β increases the expression of arginine biosynthetic and catabolic enzymes in lung fibroblasts. Surprisingly, using metabolic tracers of arginine and its precursors, we found little evidence of arginine synthesis or catabolism in lung fibroblasts treated with TGF-β. Despite this, arginine remained crucial for TGF-β-induced expression of collagen and α-smooth muscle actin. We found that arginine limitation leads to the activation of general control nonderepressible 2 (GCN2), while inhibiting TGF-β-induced mechanistic target of rapamycin complex 1 activation and collagen protein production. Extracellular citrulline could rescue the effect of arginine deprivation in an argininosuccinate synthase-dependent manner. Our findings suggest that the major role of arginine in lung fibroblasts is for charging of arginyl-tRNAs and promotion of signaling events which are required for fibroblast activation.</p>","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":" ","pages":""},"PeriodicalIF":4.3,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12235046/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144198218","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multiple transactivation domains of EZH2 bind to the TAZ2 domain of p300 and stimulate acetyltransferase function of p300.","authors":"Dustin Becht,Soumi Biswas,Chenxi Xu,Hongwen Xuan,Moustafa Khalil,Ling Cai,Catherine Musselman,Xin Liu,El Bachir Affar,Xiaobing Shi,Gang Wang,Tatiana Kutateladze","doi":"10.1042/bcj20253037","DOIUrl":"https://doi.org/10.1042/bcj20253037","url":null,"abstract":"The H3K27me-specific methyltransferase EZH2 is the catalytic subunit of the repressive complex PRC2. EZH2 is typically implicated in transcriptional silencing but can also activate gene expression. Here, we show that EZH2 contains three adjacent transactivation domains (EZH2TAD) that are recognized by the TAZ2 domain of the transcriptional coactivator and acetyltransferase p300 (p300TAZ2). Binding interfaces identified by chemical shift perturbations in NMR experiments, measurements of binding affinities, and analysis of the complex formation by mass photometry demonstrate that each EZH2TAD can be concomitantly bound by a separate p300TAZ2. Interaction of EZH2TADs with p300TAZ2 stimulates H3K18- and H3K27-specific acetyltransferase activity of p300. We show that in 22Rv1 prostate cancer cells EZH2 occupies a large set of gene loci lacking H3K27me3, and these non-canonical genomic sites are instead co-occupied by p300, RNA Pol II and BRD4, and are rich in histone marks associated with transcriptional activation. Our findings shed light on the potential basis for such a high degree genetic co-localization through the direct association of p300TAZ2 with EZH2TADs.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"44 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144320322","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Interplay of constipation, intestinal barrier dysfunction and fungal exposome in aetiopathogenesis of Parkinson's disease: hypothesis with supportive data.","authors":"Chianna Umamahesan, Aleksandra Pilcicka, Jennifer Yick, Kieran Baker, Melvyn Smith, David Taylor, Yun Ma, Benjamin H Mullish, Julian R Marchesi, Steven Gilbert, Shervin D Sadeghi Nasab, David Moyes, Polychronis Pavlidis, Bu'Hussain Hayee, Sylvia M Dobbs, R John Dobbs, André Charlett","doi":"10.1042/BCJ20240621","DOIUrl":"10.1042/BCJ20240621","url":null,"abstract":"<p><p>Constipation is a forerunner to Parkinson's disease (PD) diagnosis, worsening thereafter. We explore the relationship of intestinal barrier dysfunction to constipation and whether intestinal fungal load is an aggravating factor. Fungal load was quantified by real-time PCR, using ITS1F-ITS2 primer set, on microbial DNA extract from stool in 68 participants with PD, 102 without. Fungal load was 60% higher per decade after age 60 years, with no PD status interaction with age. After age adjustment, it was associated inversely with dietary renal acid load. It was unrelated to the presence of constipation or barrier dysfunction. Neither consumption of antimicrobials nor of other targeted exogenous substances was associated. Enzyme-linked immunosorbent assays measured barrier dysfunction markers, faecal alpha-1 antitrypsin (AAT), zonulin and serum intestinal fatty acid-binding protein (I-FABP). Barrier dysfunction was associated with constipation and slower radiographic colonic transit. Functional constipation was 28% more frequent with a doubling of AAT concentration. More colonic-transit test markers were retained in the transverse colon, the higher the AAT and zonulin concentrations, anatomically spotlighting abnormality for the entire colon. In contrast, the concentration of the small intestinal barrier marker I-FABP was associated with looser stool consistency, which is consistent with secondary microbial overgrowth. By showing a relationship of intestinal barrier dysfunction to constipation, this study supports the hypothesis that dysfunction may be consequential. Dysfunction may be a necessary, but not sufficient, precursor to PD, in allowing inflammaging. Since ageing is the clearest risk for PD, a gut pathogen escalating in abundance from the sixth decade, integral to fungal load, and whose reproduction and virulence is favoured by alkalinity, tallies.</p>","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12235043/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144224101","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}