RSC Chemical Biology最新文献

{"title":"Peptide-mediated display of Tau-derived peptide for construction of microtubule superstructures†","authors":"Hiroshi Inaba, Daichi Kageyama, Soei Watari, Mahoko Tateishi, Akira Kakugo and Kazunori Matsuura","doi":"10.1039/D4CB00290C","DOIUrl":"10.1039/D4CB00290C","url":null,"abstract":"<p >Microtubules are major cytoskeletons involved in various cellular functions, such as regulating cell shape and division and cargo transport <em>via</em> motor proteins. In addition to widely studied singlet microtubules, complex microtubule superstructures, including doublets and bundles, provide unique mechanical and functional properties <em>in vivo</em>. However, a method to construct such superstructures <em>in vitro</em> remains unresolved. This study presents a peptide-based approach for constructing microtubule superstructures by displaying Tau-derived peptides (TP) on the outer surface of microtubules using KA7 peptides as binding units. The KA7-connected TP (KA7–TP) bound to the <em>C</em>-terminal tail on the outer surface of microtubules and induced doublets and bundles by recruiting tubulin. Notably, the outer layers of the doublet microtubules generated by KA7–TP dissociated, highlighting the utility of this approach for studying the formation/dissociation mechanisms of microtubule superstructures. The simple peptide-based approach facilitates our understanding of microtubule superstructures and offers new opportunities for applying microtubule superstructures to nanotechnology.</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" 5","pages":" 737-745"},"PeriodicalIF":4.2,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11951922/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143755031","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":"Epichaperomes: redefining chaperone biology and therapeutic strategies in complex diseases","authors":"Chiranjeevi Pasala, Chander S. Digwal, Sahil Sharma, Shujuan Wang, Alessia Bubula and Gabriela Chiosis","doi":"10.1039/D5CB00010F","DOIUrl":"10.1039/D5CB00010F","url":null,"abstract":"<p >The complexity of disease biology extends beyond mutations or overexpression, encompassing stress-induced mechanisms that reshape proteins into pathological assemblies. Epichaperomes, stable and disease-specific assemblies of chaperones and co-chaperones, exemplify this phenomenon. This review emphasizes the critical structural and functional distinctions between epichaperomes and canonical chaperones, highlighting their role in redefining therapeutic strategies. Epichaperomes arise under stress conditions through post-translational modifications that stabilize these assemblies, enabling them to act as scaffolding platforms that rewire protein–protein interaction networks and drive the pathological phenotypes of complex diseases such as cancer and neurodegeneration. Chemical biology has been instrumental in uncovering the unique nature of epichaperomes, with small molecules like PU-H71 elucidating their biology and demonstrating their therapeutic potential by dismantling pathological scaffolds and restoring normal protein–protein interaction networks. By targeting epichaperomes, we unlock the potential for network-level interventions and personalized medicine, offering transformative possibilities for diseases driven by protein–protein interaction network dysregulation.</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" 5","pages":" 678-698"},"PeriodicalIF":4.2,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11933791/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143721838","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":"Development of a fluorescence-based assay for RecBCD activity using functional data analysis and design of experiments†","authors":"Adam Winnifrith, Steven R. Brown, Piotr Jedryszek, C. Grant, Philip E. Kay, Adam M. Thomas, Jacob D. Bradbury and Thomas Lanyon-Hogg","doi":"10.1039/D4CB00291A","DOIUrl":"10.1039/D4CB00291A","url":null,"abstract":"<p >Biochemical assays are essential tools in biological research and drug discovery, but optimisation of these assays is often a challenging and lengthy process due to the wide range of input variables and the complex effects of these variables on one another. Traditional ‘one-factor-at-a-time’ optimisation is both time-consuming and fails to explore the full range of input combinations. In contrast, the modern ‘design of experiments’ (DoE) approach enables simultaneous investigation of multiple input variables and their interactions, leading to more information-rich and efficient experimentation. We therefore sought to apply DoE to the optimisation of a new fluorescence-based assay for the enzyme RecBCD, a helicase–nuclease–ATPase complex involved in bacterial stress responses. A novel ‘functional data analysis’ (FDA) approach was used to predict the shape of RecBCD reaction curves in response to different combinations of input variables, which successfully identified assay conditions suitable for drug screening. Collectively, this work delivers a new assay for the antibiotic target RecBCD and demonstrates the potential of DoE and FDA to accelerate biochemical assay development.</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" 5","pages":" 772-779"},"PeriodicalIF":4.2,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11955833/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143765401","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":"Real-time bioluminescence imaging of nitroreductase in breast cancer bone metastasis†","authors":"Kang Lu, Mengxi Zhang, Zuotong Tian and Han Xiao","doi":"10.1039/D4CB00310A","DOIUrl":"10.1039/D4CB00310A","url":null,"abstract":"<p >Bone metastasis is a leading cause of mortality in breast cancer patients. Monitoring biomarkers for bone metastasis in breast cancer is crucial for the development of effective interventional treatments. Despite being a highly vascularized tissue, the bone presents a particularly hypoxic environment. Tumor hypoxia is closely linked to increased levels of various reductases, including nitroreductase (NTR). Currently, there are few probes available to detect NTR levels in breast cancer bone metastases. Although bioluminescent imaging is promising due to its specificity and high signal-to-noise ratio, many probes face challenges such as short emission wavelengths, reliance on complex conditions like external adenosine triphosphate, or lack of tissue specificity. In this study, through “caging” the luciferase substrate with an NTR-responsive aromatic nitro recognition group, we developed a highly sensitive and selective NTR-sensitive bioluminescent probe. The resulting probe effectively detects NTR in breast cancer cells and enables real-time monitoring of NTR in a mouse model of breast cancer bone metastasis. Additionally, it can differentiate between primary and bone tumors, and allow continuous monitoring of NTR levels, thus providing valuable insights into bone tumor progression. This work provides a powerful tool for further understanding the biological functions of NTR in breast cancer bone metastasis.</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" 5","pages":" 754-760"},"PeriodicalIF":4.2,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11934263/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143721839","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":"The role of water in mediating DNA structures with epigenetic modifications, higher-order conformations and drug–DNA interactions","authors":"Roshan Satange and Ming-Hon Hou","doi":"10.1039/D4CB00308J","DOIUrl":"10.1039/D4CB00308J","url":null,"abstract":"<p >Water is arguably one of the most important chemicals essential for the functioning of biological molecules. In the context of DNA, it plays a crucial role in stabilizing and modulating its structure and function. The discovery of water-bound motifs in crystal structures has greatly improved our understanding of the interactions between structured water molecules and DNA. In this manuscript, we review the role of water in mediating biologically relevant DNA structures, in particular those arising from epigenetic modifications and higher-order structures such as G-quadruplexes and i-motifs. We also examine water-mediated interactions between DNA and various small molecules, including groove binders and intercalators, and emphasize their importance for DNA function and therapeutic development. Finally, we discuss recent advances in tools and techniques for predicting water interactions in nucleic acid structures. By offering a fresh perspective on the role of water, this review underscores its importance as a molecular modulator of DNA structure and function.</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" 5","pages":" 699-720"},"PeriodicalIF":4.2,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11955920/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143764368","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":"Ganglioside lipids inhibit the aggregation of the Alzheimer's amyloid-β peptide†","authors":"Zenon Toprakcioglu, Akhila K. Jayaram and Tuomas P. J. Knowles","doi":"10.1039/D4CB00189C","DOIUrl":"10.1039/D4CB00189C","url":null,"abstract":"<p >The aggregation of the amyloid-β (Aβ) peptides (Aβ42/Aβ40) into amyloid fibrils and plaques is one of the molecular hallmarks in dementia and Alzheimer's disease (AD). While the molecular mechanisms behind this aggregation process are not fully known, it has been shown that some biomolecules can accelerate this process whereas others can inhibit amyloid formation. Lipids, which are ubiquitously found in cell membranes, play a pivotal role in protein aggregation. Here, we investigate how ganglioside lipids, which are abundant in the brain and in neurons, can influence the aggregation kinetics of both Aβ42 and Aβ40. We employ a variety of biophysical assays to characterise the effect ganglioside lipids have on the aggregation of Aβ. Through kinetic analysis, we show that the primary nucleation rate is greatly affected by the addition of gangliosides and that these lipids impair Aβ42 aggregation, while completely inhibiting Aβ40 aggregation. Furthermore, we find that an Aβ-ganglioside complex is formed, which potentially disrupts the aggregation pathway and results in delayed kinetics. Taken together, our results provide a quantitative description of how lipid molecules such as gangliosides can inhibit the aggregation of Aβ and shed light on the key factors that control these processes. In view of the fact that declining levels of gangliosides in neurons have been associated with ageing, our findings could be instrumental towards establishing new approaches in the prevention of amyloid-β aggregation.</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" 5","pages":" 809-822"},"PeriodicalIF":4.2,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11915136/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143664984","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":"Novel Tet3 enzymes for next-generation epigenetic sequencing†","authors":"Özge Simsir, Tobias Walter, Hanife Sahin, Thomas Carell and Sabine Schneider","doi":"10.1039/D4CB00315B","DOIUrl":"10.1039/D4CB00315B","url":null,"abstract":"<p >Epigenetic regulation of gene expression is essential for cellular development and differentiation processes in higher eukaryotes. Modifications of cytosine, in particular 5-methylcytosine (5mdC), in DNA play a central role through impacting chromatin structure, repressing transposons, and regulating transcription. DNA methylation is actively installed by DNA methyltransferases and reversed through Tet-dioxygenase-mediated oxidation of 5mdC to 5-hydroxylmethylcytosine (5hmdC), 5-formylcytosine (5fdC), and 5-carboxycytosine (5cadC). It is crucial to understand the role of these epigenetic DNA modifications in cellular differentiation and developmental processes, as well as in disease state mapping and tracing of 5mdC and its oxidized forms. In bisulfite sequencing, which has been the benchmark for mapping 5mdC for the last few decades, degradation of the majority of genetic material occurs through harsh chemical treatment. Alternative sequencing methods often utilize Tet-enzyme-mediated oxidation of 5mdC to locate 5mdC and 5hmdC in genomic DNA. Herein, we report the development of novel Tet3-variants for oxidation-based bisulfite-free 5mdC- sequencing.</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" 5","pages":" 731-736"},"PeriodicalIF":4.2,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11915426/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143664987","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":"Identification and characterization of ternary complexes consisting of FKBP12, MAPRE1 and macrocyclic molecular glues†","authors":"Michael Salcius, Antonin Tutter, Marianne Fouché, Halil Koc, Dan King, Anxhela Dhembi, Andrei Golosov, Wolfgang Jahnke, Chrystèle Henry, Dayana Argoti, Weiping Jia, Liliana Pedro, Lauren Connor, Philippe Piechon, Francesca Fabbiani, Regis Denay, Emine Sager, Juergen Kuehnoel, Marie-Anne Lozach, Fabio Lima, Angela Vitrey, Shu-Yu Chen, Gregory Michaud and Hans-Joerg Roth","doi":"10.1039/D4CB00279B","DOIUrl":"10.1039/D4CB00279B","url":null,"abstract":"<p >Many disease-relevant and functionally well-validated targets are difficult to drug. Their poorly defined 3D structure without deep hydrophobic pockets makes the development of ligands with low molecular weight and high affinity almost impossible. For these targets, incorporation into a ternary complex may be a viable alternative to modulate and in most cases inhibit their function. Therefore, we are interested in methods to identify and characterize molecular glues. In a protein array screen of 50 different macrocyclic FKBP12 ligands against 2500 different randomly selected proteins, a molecular glue compound was found to recruit a dimeric protein called MAPRE1 to FKBP12 in a compound-dependent manner. The corresponding ternary complex was characterized by TR-FRET proximity assay and native MS spectroscopy. Insights into the 3D structure of the ternary complex were obtained by 2D protein NMR spectroscopy and finally by an X-ray structure, which revealed the ternary complex as a 2 : 2 : 2 FKBP12 : molecular glue : MAPRE1 complex exhibiting multiple interactions that occur exclusively in the ternary complex and lead to significant cooperativity <em>α</em>. Using the X-ray structure, rationally guided synthesis of a series of analogues led to the cooperativity driven improvement in the stability of the ternary complex. Furthermore, the ternary complex formation of the series was confirmed by cellular NanoBiT assays, whose <em>A</em><small>_max</small> values correlate with those from the TR-FRET proximity assay. Furthermore, NanoBiT experiments showed the functional impact (inhibition) of these molecular glues on the interaction of MAPRE1 with its intracellular native partners.</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" 5","pages":" 788-799"},"PeriodicalIF":4.2,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11883961/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143587568","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":"Identification of microproteins with transactivation activity by polyalanine motif selection†","authors":"Archita Agrawal and Alan Saghatelian","doi":"10.1039/D4CB00277F","DOIUrl":"10.1039/D4CB00277F","url":null,"abstract":"<p >Microproteins are an emerging class of proteins that are encoded by small open reading frames (smORFs) less than or equal to 100 amino acids. The functions of several microproteins have been illuminated through phenotypic screening or protein–protein interaction studies, but thousands of microproteins remain uncharacterized. The functional characterization of microproteins is challenging due to a lack of sequence homology. Here, we demonstrate a strategy to enrich microproteins that contain specific motifs as a means to more rapidly characterize microproteins. Specifically, we used the fact that polyalanine motifs are associated with nuclear proteins to select 58 candidate microproteins to screen for transactivation function. We identified three microproteins with transactivation activity when tested as GAL4-fusions in a cell-based luciferase assay. The results support the continued use of the motif selection strategy for the discovery of microprotein function.</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" 5","pages":" 800-808"},"PeriodicalIF":4.2,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11898273/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143626410","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":"Peptides: potential delivery systems for mRNA","authors":"Huiting Liang, Yun Xing, Kexin Wang, Yaping Zhang, Feng Yin and Zigang Li","doi":"10.1039/D4CB00295D","DOIUrl":"10.1039/D4CB00295D","url":null,"abstract":"<p >mRNA-based therapies have broad applications in various disease treatments and have been applied in protein replacement therapy, gene editing, and vaccine development. Numerous research studies have been carried out aiming to increase the stability of mRNA, improve its translational efficiency, and reduce its immunogenicity. However, given mRNA's large molecular size and strong electronegativity, the safety and efficient delivery of mRNA into the target cells remains the critical rate-limiting step in current mRNA drug development. Various nanocarriers, such as liposomes, lipid nanoparticles, polyetherimide, and mesoporous silica nanoparticles, have been employed for mRNA delivery in the past few decades. Among them, peptides have demonstrated great potential as promising carrier candidates for mRNA delivery due to their high cell membrane permeability, good biocompatibility, definite chemical structure, and ease of preparation. Here, peptide-based mRNA delivery systems are systematically analyzed, including their construction strategies, mechanisms of action in mRNA delivery, and the application limitations or challenges. It is hoped that this review will guide the design, optimization, and applications of peptide carriers in mRNA-based drug development.</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" 5","pages":" 666-677"},"PeriodicalIF":4.2,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11891934/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143606635","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}