Biochemical Journal最新文献

Activity-based probes for dynamic characterisation of polysaccharide-degrading enzymes. 基于活性的多糖降解酶动态表征探针。

IF 4.1 3区生物学

Biochemical Journal Pub Date : 2025-07-01 DOI: 10.1042/bcj20253060

Isabelle B Pickles,Thamy L R Corrêa,Herman S Overkleeft,Gideon J Davies

{"title":"Activity-based probes for dynamic characterisation of polysaccharide-degrading enzymes.","authors":"Isabelle B Pickles,Thamy L R Corrêa,Herman S Overkleeft,Gideon J Davies","doi":"10.1042/bcj20253060","DOIUrl":"https://doi.org/10.1042/bcj20253060","url":null,"abstract":"Carbohydrate-active enzymes play essential roles in polysaccharide degradation, yet their biochemical characterisation remains challenging - especially in the face of rapidly expanding genomic and structural data. Standard annotations often overlook critical properties such as expression patterns, enzyme stability and substrate specificity, which are key to understanding function in biological and industrial contexts. Activity-based probes (ABPs) offer a direct solution by enabling selective detection of active enzymes within complex systems. This review focuses on ABPs for retaining glycosidases, tracing their development from early applications in medical diagnostics to emerging uses in biomass degradation. We examine recent advances in scaffold design - including fluorosugars, epoxides, aziridines and cyclic sulphates - and their utility in enzyme profiling, inhibitor discovery and biotechnology. Current ABPs remain limited: they cannot yet target inverting enzymes and other classes lacking nucleophilic residues, a gap that may be bridged through computational modelling and AI-guided probe development. Looking forward, integration of ABPs with enzyme engineering and design holds promise for unlocking new classes of biocatalysts tailored for industrial and biomedical use.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"6 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144533367","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}

引用次数: 0

Characterisation of an Influenza B virus-derived peptide presented by HLA-B*18:01. HLA-B*18:01表达的乙型流感病毒衍生肽的特征

IF 4.1 3区生物学

Biochemical Journal Pub Date : 2025-06-26 DOI: 10.1042/bcj20240739

Lawton D Murdolo,Samuel Liwei Leong,Janesha C Maddumage,Nicole Mifsud,Demetra Sm Chatzileontiadou,Emma J Grant,Stephanie Gras

{"title":"Characterisation of an Influenza B virus-derived peptide presented by HLA-B*18:01.","authors":"Lawton D Murdolo,Samuel Liwei Leong,Janesha C Maddumage,Nicole Mifsud,Demetra Sm Chatzileontiadou,Emma J Grant,Stephanie Gras","doi":"10.1042/bcj20240739","DOIUrl":"https://doi.org/10.1042/bcj20240739","url":null,"abstract":"The Influenza B virus (IBV) can pose a significant threat to global health. Despite this, IBV is understudied compared to Influenza A virus (IAV). CD8+ T cells have proven highly effective in reducing influenza disease severity. In addition, pre-existing immune responses towards IAV epitopes may provide protection against homologous IBV-derived peptides due to T cell cross-reactivity. To exploit the advantages of T cells for future vaccine developments, a better understanding of the IBV-derived peptide presentation by the highly polymorphic Human Leukocyte Antigen (HLA) is required. We previously determined that the IAV-derived PB1177-A peptide was presented by the HLA-B*18:01 molecule and induced CD8+ T cell responses. Here we assessed the PB1177-A IBV homologue (PB1177-B). Intracellular cytokine staining assays showed that PB1177-B was unable to activate CD8+ T cells from several HLA-B*18:01+ samples tested. We determined that the IAV- and IBV-derived PB1177 adopted different stability and conformation in the cleft of HLA-B*18:01. Molecular dynamics analysis on the crystal structure showed that PB1177-B had a central flexible region with a large hydrophobic patch formed by two phenylalanine residues, not present in PB1177-A. The flexibility and the lower stability of the HLA-B*18:01-PB1177-B complex may hinder CD8+ T cell receptor binding, underpinning the lack of CD8+ T cell activation observed. This provides additional insights into the differences between IAV- and IBV-specific CD8+ T cell responses.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"49 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144521431","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}

引用次数: 0

Role of LRRK2 in axonal transport and Parkinson's disease. LRRK2在轴突转运和帕金森病中的作用。

IF 4.4 3区生物学

Biochemical Journal Pub Date : 2025-06-25 DOI: 10.1042/BCJ20253133

Björn Twellsieck, C Alexander Boecker

引用次数: 0

Methods to accelerate PROTAC drug discovery. 加速PROTAC药物发现的方法。

IF 4.1 3区生物学

Biochemical Journal Pub Date : 2025-06-25 DOI: 10.1042/bcj20243018

Jeyan Osman,Philip E Thompson,Manuela Jörg,Martin J Scanlon

{"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}

引用次数: 0

Role of LRRK2 in axonal transport and Parkinson's disease. LRRK2在轴突转运和帕金森病中的作用。

IF 4.1 3区生物学

Biochemical Journal Pub Date : 2025-06-25 DOI: 10.1042/bcj20253133

Björn Twellsieck,C Alexander Boecker

引用次数: 0

Methods to accelerate PROTAC drug discovery. 加速PROTAC药物发现的方法。

IF 4.4 3区生物学

Biochemical Journal Pub Date : 2025-06-25 DOI: 10.1042/BCJ20243018

Jeyan Osman, Philip E Thompson, Manuela Jörg, Martin J Scanlon

{"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":"482 13","pages":""},"PeriodicalIF":4.4,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Structure and activity of the essential UCH family deubiquitinase DUB16 from Leishmania donovani. 多诺瓦利什曼原虫UCH家族去泛素酶DUB16的结构和活性。

IF 4.4 3区生物学

Biochemical Journal Pub Date : 2025-06-23 DOI: 10.1042/BCJ20253107

James A Brannigan, Mohd Kamran, Nathaniel G Jones, Elisa M Nightingale, Eleanor J Dodson, Sarfaraz A Ejazi, Jeremy C Mottram, Nahid Ali, Anthony J Wilkinson

{"title":"Structure and activity of the essential UCH family deubiquitinase DUB16 from Leishmania donovani.","authors":"James A Brannigan, Mohd Kamran, Nathaniel G Jones, Elisa M Nightingale, Eleanor J Dodson, Sarfaraz A Ejazi, Jeremy C Mottram, Nahid Ali, Anthony J Wilkinson","doi":"10.1042/BCJ20253107","DOIUrl":"https://doi.org/10.1042/BCJ20253107","url":null,"abstract":"In Leishmania parasites, as for their hosts, the ubiquitin proteasome system is important for cell viability. As part of a systematic gene deletion study, it was discovered that four cysteine protease type deubiquitinases (DUBs) are essential for parasite survival in the promastigote stage, including DUB16. Here we have purified and characterised recombinant DUB16 from Leishmania donovani, which belongs to the ubiquitin C-terminal hydrolase (UCH) family. DUB16 efficiently hydrolyses C-terminal aminocoumarin and rhodamine conjugates of ubiquitin consistent with proposed cellular roles of UCH-type DUBs in regenerating free monomeric ubiquitin from small molecule ubiquitin adducts arising from adventitious metabolic processes. The crystal structure of DUB16 reveals a typical UCH-type deubiquitinase fold, and a relatively short and disordered crossover loop that appears to restrict access to the catalytic cysteine. At close to stoichiometric enzyme to substrate ratios, DUB16 exhibits deubiquitinase activity towards diubiquitins linked through isopeptide bonds between Lys11, Lys48 or Lys63 residues of the proximal ubiquitin and the C-terminus of the distal ubiquitin. With 100-1000-fold higher turnover rates, DUB16 cleaves the ubiquitin-ribosomal L40 fusion protein to give the mature products. A DUB-targeting cysteine-reactive cyanopyrrolidine compound, IMP-1710, inhibits DUB16 activity. IMP-1710 was shown in promastigote cell viability assays to have parasite killing activity with EC50 values of 1-2 M, comparable to the anti-leishmanial drug, miltefosine. L. mexicana parasites engineered to overproduce DUB16 showed a modest increase in resistance to IMP-1710, providing evidence that IMP-1710 inhibits DUB16 in vivo. While it is highly likely that IMP-1710 has additional targets, these results suggest that DUB16 is a potential target for the development of new anti-leishmanial compounds.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144504721","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}

引用次数: 0

Correction: Roles for TAB1 in regulating the IL-1-dependent phosphorylation of the TAB3 regulatory subunit and activity of the TAK1 complex. 更正：TAB1在调节il -1依赖性的TAB3调节亚基磷酸化和TAK1复合物活性中的作用。

IF 4.4 3区生物学

Biochemical Journal Pub Date : 2025-06-18 DOI: 10.1042/BJ20071149_COR

引用次数: 0

Correction: 14-3-3 binding to LRRK2 is disrupted by multiple Parkinson's disease-associated mutations and regulates cytoplasmic localization. 更正：14-3-3与LRRK2的结合被多种帕金森病相关突变破坏并调节细胞质定位。

IF 4.4 3区生物学

Biochemical Journal Pub Date : 2025-06-18 DOI: 10.1042/BJ20100483_COR

引用次数: 0

A new naphthalene-based fluorogenic substrate for cytochrome P450 4A11. 细胞色素P450 4A11的新型萘基荧光底物。

IF 4.4 3区生物学

Biochemical Journal Pub Date : 2025-06-17 DOI: 10.1042/BCJ20253130

Dmitri R Davydov, Kannapiran Ponraj, Nadezhda Davydova, Dilip Kumar Singh, Bhagwat Prasad

{"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":"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.","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}

引用次数: 0