Taylor E. Gray, Kristin B. Labasan, Gour C. Daskhan, Duong T. Bui, Maju Joe, Dhanraj Kumawat, Edward N. Schmidt, John S. Klassen and Matthew S. Macauley
{"title":"Synthesis of 4-azido sialic acid for testing against Siglec-7 and in metabolic oligosaccharide engineering†","authors":"Taylor E. Gray, Kristin B. Labasan, Gour C. Daskhan, Duong T. Bui, Maju Joe, Dhanraj Kumawat, Edward N. Schmidt, John S. Klassen and Matthew S. Macauley","doi":"10.1039/D5CB00030K","DOIUrl":"10.1039/D5CB00030K","url":null,"abstract":"<p >An important approach for tracking and visualizing sialic acid-containing glycans involves using sialic acid reporters functionalized with bioorthogonal handles. More specifically, metabolic oligosaccharide engineering (MOE) commonly employs monosaccharides with an alkyne or azide handle for incorporation into cellular glycans, followed by a subsequent click reaction to elaborate with a biotin or fluorophore handle. For sialic acid, this has been carried out extensively, with an azide or alkyne appended to the C5 <em>N</em>-acetamido group being the most common location for the handle. However, circumstances may require the handle to be at different positions and, to date, the C7 and C9 positions have been shown to work to varying degrees. Herein, we synthesized protected 4AzNeu5Ac that could be incorporated into cellular glycans nearly as efficiently as Neu5Az and targeted with DBCO-biotin through strain promoted azide–alkyne cycloaddition. Owing to the good incorporation of 4AzNeu5Ac into cellular glycans, we followed up this ability by first synthesizing the deprotected form of 4AzNeu5Ac, using a thioglycoside to lock the anomeric center during deprotection of the acetyl groups. Activation of 4AzNeu5Ac to CMP-4AzNeu5Ac then enabled the use of this donor by human sialyltransferase ST3GAL1 to transfer CMP-4AzNeu5Ac to β-Gal<em>p</em>-(1→3)-α-Gal<em>p</em>NAc. With purified α-4AzNeu<em>p</em>5Ac-(2→3)-β-Gal<em>p</em>-(1→3)-α-Gal<em>p</em>NAc in hand, we tested it as a ligand for Siglec-7 and found that the C4-Az modification is tolerated, opening future possibilities to exploit this position to generate high affinity and selective ligands. These findings expand the repertoire of metabolic oligosaccharide engineering agents and show that azide modifications are tolerated at the C4 position of sialic acid.</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" 6","pages":" 869-881"},"PeriodicalIF":4.2,"publicationDate":"2025-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12038855/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144057161","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Wantae Kim, Ziyang Zheng, Kangsan Kim, Yu-Hsuan Lee, Hung-wen Liu and Y. Jessie Zhang
{"title":"Structural and mechanistic insights into KslB, a bacterial Pictet–Spenglerase in kitasetaline biosynthesis†","authors":"Wantae Kim, Ziyang Zheng, Kangsan Kim, Yu-Hsuan Lee, Hung-wen Liu and Y. Jessie Zhang","doi":"10.1039/D5CB00070J","DOIUrl":"10.1039/D5CB00070J","url":null,"abstract":"<p >KslB is one of the few bacterial Pictet–Spenglerases recently identified in the biosynthesis of the β-carboline compound kitasetaline. While previous <em>in vitro</em> studies established that KslB catalyzes the condensation between <small>L</small>-tryptophan and α-ketoglutarate, the reaction mechanism, particularly its stereochemistry, remains poorly understood. This study presents five crystal structures of KslB, capturing key stages of reaction, shedding light on its catalytic dynamics. Among these, alternative binding poses of substrate and reaction product highlighted two significant features: (1) an additional pocket that accommodates <small>L</small>-tryptophan, and (2) two positively charged residues, Lys264 and Arg256, which form salt bridges with the product C1′ and C5′ carboxylate groups derived from α-ketoglutarate, ensuring a stereoselective process. These structural insights elucidate how KslB governs the stereochemistry of the cyclization process. Accordingly, we propose the configurations for the cyclized intermediate that align with the reaction's stereochemical outcome. Together, these findings offer valuable structural and mechanistic insights into KslB, paving the way for its potential engineering as a Pictet–Spengler biocatalyst.</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" 6","pages":" 933-941"},"PeriodicalIF":4.2,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12012969/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144003356","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Contributors to the RSC Chemical Biology Emerging Investigators Collection 2024","authors":"","doi":"10.1039/D5CB90017D","DOIUrl":"10.1039/D5CB90017D","url":null,"abstract":"<p >A graphical abstract is available for this content</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" 6","pages":" 857-859"},"PeriodicalIF":4.2,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11988756/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144040683","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
RSC Chemical BiologyPub Date : 2025-04-11eCollection Date: 2025-06-04DOI: 10.1039/d5cb90017d
{"title":"Contributors to the <i>RSC Chemical Biology</i> Emerging Investigators Collection 2024.","authors":"","doi":"10.1039/d5cb90017d","DOIUrl":"https://doi.org/10.1039/d5cb90017d","url":null,"abstract":"<p><p>This article profiles the early career researchers whose work features in the <i>RSC Chemical Biology</i> Emerging Investigators Collection 2024.</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":"6 6","pages":"857-859"},"PeriodicalIF":4.2,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11988756/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144227070","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Shivangi Sharma, J. Trae Hampton, Tatiana G. Kutateladze and Wenshe Ray Liu
{"title":"Epigenetic reader chromodomain as a potential therapeutic target","authors":"Shivangi Sharma, J. Trae Hampton, Tatiana G. Kutateladze and Wenshe Ray Liu","doi":"10.1039/D4CB00324A","DOIUrl":"10.1039/D4CB00324A","url":null,"abstract":"<p >Epigenetic mechanisms involve cooperative actions of enzymes that produce or remove post-translational modifications in histones and ‘readers’, the protein domains that bind these modifications. Methylation of lysine residues represents one of the most common modifications and is recognized by a family of chromodomains. Chromodomain containing proteins are implicated in transcriptional regulation and chromatin remodeling, and aberrant functions of these proteins are linked to human diseases, such as cancer, neurodegenerative disorders and developmental abnormalities. In this work, we review biological and pathological activities of chromodomains, highlighting their potential as prognostic biomarkers and their attractiveness as therapeutic targets. In the past few years, significant progress has been made in the development of chromodomain inhibitors, however sequence similarity within this family of readers presents challenges in designing selective probes. We describe recent advances and new strategies that are employed to overcome these challenges, including structure-based drug design, high-throughput screening, the use of peptide and DNA encoded libraries, and summarize research underscoring the benefit of targeting chromodomains to combat diseases.</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" 6","pages":" 833-844"},"PeriodicalIF":4.2,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12035754/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144051721","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Raven Shah, Wanlin Yan, Joyce Rigal, Steve Mullin, Lin Fan, Lynn McGregor, Andrew Krueger, Nicole Renaud, Andrea Byrnes and Jason R. Thomas
{"title":"Photoaffinity enabled transcriptome-wide identification of splice modulating small molecule–RNA binding events in native cells†","authors":"Raven Shah, Wanlin Yan, Joyce Rigal, Steve Mullin, Lin Fan, Lynn McGregor, Andrew Krueger, Nicole Renaud, Andrea Byrnes and Jason R. Thomas","doi":"10.1039/D4CB00266K","DOIUrl":"10.1039/D4CB00266K","url":null,"abstract":"<p >Splice modulating small molecules have been developed to promote the U1 snRNP to engage with pre-mRNAs with strong and altered sequence preference. Transcriptomic profiling of bulk RNA from compound treated cells enables detection of RNAs impacted; however, it is difficult to delineate whether transcriptional changes are a consequence of direct compound treatment or <em>trans</em>-acting effects. To identify RNA targets that bind directly with splice modulating compounds, we deployed a photoaffinity labeling (PAL)-based Chem-CLIP approach. Through this workflow, we identify the telomerase lncRNA (TERC) as a previously unknown target of this class of clinically relevant small molecules. Using cellular ΔSHAPE-MaP, we orthogonally validate and further define the compound binding site as likely to be the conserved CR4/5 domain. Additionally, a thorough analysis of the PAL-based Chem-CLIP data reveals that considering competed RNAs, irrespective of magnitude of enrichment, adds a rich dimension of hit calling.</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" 6","pages":" 905-918"},"PeriodicalIF":4.2,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11986670/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144020256","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Florentine U. Rutaganira, Maxwell C. Coyle, Maria H. T. Nguyen, Iliana Hernandez, Alex P. Scopton, Arvin C. Dar and Nicole King
{"title":"A stress-responsive p38 signaling axis in choanoflagellates†","authors":"Florentine U. Rutaganira, Maxwell C. Coyle, Maria H. T. Nguyen, Iliana Hernandez, Alex P. Scopton, Arvin C. Dar and Nicole King","doi":"10.1039/D4CB00122B","DOIUrl":"10.1039/D4CB00122B","url":null,"abstract":"<p >Animal kinases regulate cellular responses to environmental stimuli, including cell differentiation, migration, survival, and response to stress, but the ancestry of these functions is poorly understood. Choanoflagellates, the closest living relatives of animals, encode homologs of diverse animal kinases and have emerged as model organisms for reconstructing animal origins. However, efforts to identify key kinase regulators in choanoflagellates have been constrained by the limitations of currently available genetic tools. Here, we report on a framework that combines small molecule-driven kinase discovery with targeted genetics to reveal kinase function in choanoflagellates. To study the physiological roles of choanoflagellate kinases, we established two high-throughput platforms to screen the model choanoflagellate <em>Salpingoeca rosetta</em> with a curated library of human kinase inhibitors. We identified 95 diverse kinase inhibitors that disrupt <em>S. rosetta</em> cell proliferation. By focusing on one inhibitor, sorafenib, we identified a p38 kinase as a regulator of the heat shock response in <em>S. rosetta</em>. This finding reveals a conserved p38 function between choanoflagellates, animals, and fungi. Moreover, this study demonstrates that existing kinase inhibitors can serve as powerful tools to examine the ancestral roles of kinases that regulate modern animal development.</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" 6","pages":" 891-904"},"PeriodicalIF":4.2,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11984502/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144037328","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Burcu Bestas, H. Yesid Estupiñán, Qing Wang, Shabnam Kharazi, Chenfei He, Dara K. Mohammad, Dhanu Gupta, Oscar P. B. Wiklander, Taavi Lehto, Karin E. Lundin, Anna Berglöf, Mikael C. I. Karlsson, Frank Abendroth, Samir El Andaloussi, Michael J. Gait, Matthew J. A. Wood, Christian J. Leumann, Dmitry A. Stetsenko, Robert Månsson, Jesper Wengel, Rula Zain and C. I. Edvard Smith
{"title":"Cell-penetrating peptide-conjugated, splice-switching oligonucleotides mitigate the phenotype in BTK/Tec double deficient X-linked agammaglobulinemia model†","authors":"Burcu Bestas, H. Yesid Estupiñán, Qing Wang, Shabnam Kharazi, Chenfei He, Dara K. Mohammad, Dhanu Gupta, Oscar P. B. Wiklander, Taavi Lehto, Karin E. Lundin, Anna Berglöf, Mikael C. I. Karlsson, Frank Abendroth, Samir El Andaloussi, Michael J. Gait, Matthew J. A. Wood, Christian J. Leumann, Dmitry A. Stetsenko, Robert Månsson, Jesper Wengel, Rula Zain and C. I. Edvard Smith","doi":"10.1039/D4CB00312H","DOIUrl":"10.1039/D4CB00312H","url":null,"abstract":"<p >Splice-switching oligonucleotides (SSOs) have been developed as a treatment for various disorders, including Duchenne muscular dystrophy and spinal muscular atrophy. Here, the activity of several different SSOs was investigated as potential treatments for B lymphocyte disorders with a focus on X-linked agammaglobulinemia (XLA), caused by defects in the gene encoding Bruton's tyrosine kinase (<em>BTK</em>). In this study, the activity of locked nucleic acid (LNA), tricyclo-DNA (tcDNA), phosphoryl guanidine oligonucleotides (PGO) and phosphorodiamidate morpholino oligomers (PMO) were compared, targeting the pseudoexon region of <em>BTK</em> pre-mRNA. We further investigated the effect of conjugating cell-penetrating peptides, including Pip6a, to the SSOs. The effect was measured as splice-switching <em>in vitro</em> as well as in a further developed, bacterial artificial chromosome transgenic mouse model of XLA. Therapy in the form of intravenous infusions 2 times a week during 3 weeks of PMO oligomers conjugated to Pip6a was sufficient to partly restore the <em>in vivo</em> B lineage phenotype. SSOs treatment also provides a unique opportunity to get insights into a restoration process, when B lymphocytes of different maturation stages are simultaneously splice-corrected.</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" 5","pages":" 761-771"},"PeriodicalIF":4.2,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11955834/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143765400","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Enzyme-mediated proximity labeling reveals the co-translational targeting of DLGAP5 mRNA to the centrosome during mitosis†","authors":"Gang Wang, Mo Li and Peng Zou","doi":"10.1039/D4CB00155A","DOIUrl":"10.1039/D4CB00155A","url":null,"abstract":"<p >Subcellular RNA localization is a conserved mechanism in eukaryotic cells and plays critical roles in diverse physiological processes including cell proliferation, differentiation, and embryo development. Nevertheless, the characterization of centrosome-localized mRNAs remains underexplored due to technical difficulties. In this study, we utilize APEX2-mediated proximity labeling to map the centrosome-proximal transcriptome, identifying <em>DLGAP5</em> mRNA as a novel centrosome-localized transcript during mitosis. Using a combination of drug perturbation, truncation, deletion, and mutagenesis, we demonstrate that microtubule binding of nascent MBD1 polypeptides is required for centrosomal transport of <em>DLGAP5</em> mRNA. Our data also reveal that mRNA targeting efficiency is tightly linked to the coding sequence (CDS) length. Thus, our study provides a transcriptomic resource for future investigation of centrosome-localized RNAs and sheds light on mechanisms underlying mRNA centrosomal localization.</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" 6","pages":" 919-932"},"PeriodicalIF":4.2,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12002336/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144029119","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jonathan P. Dolan, Tessa Keenan, Aisling Ní Cheallaigh, Martin A. Fascione and Gavin J. Miller
{"title":"3′-O-β-Glucosylation of nucleoside analogues using a promiscuous bacterial glycosyltransferase†","authors":"Jonathan P. Dolan, Tessa Keenan, Aisling Ní Cheallaigh, Martin A. Fascione and Gavin J. Miller","doi":"10.1039/D5CB00026B","DOIUrl":"10.1039/D5CB00026B","url":null,"abstract":"<p >Nucleoside analogue therapeutics have a proven capability within drug discovery as antiviral and antineoplastic agents. However, their efficacy can be limited by poor cellular uptake, off target toxicity and low bioavailability. Glycosylation of pharmaceutical agents/natural products represents a strategically simple method to modulate pharmacological profiles. Herein, we explore biocatalytic glycosylation of nucleoside analogues. The activity of the nucleoside-specific 3′-<em>O</em>-glycosyltransferase AvpGT from <em>Streptomyces</em> sp. AVP053U2 is investigated toward a panel of both natural and clinically relevant purine and pyrimidine nucleoside analogues. AvpGT demonstrates broad substrate promiscuity, with glycosylation observed by HILIC-MS for 15 of 21 nucleosides tested. Of these, 12 nucleosides were successfully glycosylated on ≥25 μmol scale in 39–91% isolated yields, including four current therapeutics.</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" 6","pages":" 845-850"},"PeriodicalIF":4.2,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11959488/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143774522","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}