RSC Chemical Biology最新文献

{"title":"An artesunate-modified half-sandwich iridium(iii) complex inhibits colon cancer cell proliferation and metastasis through the STAT3 pathway†","authors":"Dongping Deng, Na Xu, Mengmeng Wang, Guandong Zhang, Yan Su, Hongbao Fang and Zhi Su","doi":"10.1039/D4CB00114A","DOIUrl":"10.1039/D4CB00114A","url":null,"abstract":"<p >Colon cancer is one of the most commonly diagnosed cancers and is recognized as the most aggressive tumor of the digestive system. Aberrant activation of signal transducer and activator of transcription 3 (STAT3) is associated with proliferation, metastasis and immunosuppression of the tumor cells. Here, to inhibit the STAT3 pathway and suppress metastasis in colon cancer cells, the half-sandwich iridium complex <strong>Ir-ART</strong> containing an artesunate-derived ligand was synthesized. The complex showed remarkable antiproliferative activity against human colon cancer HCT-116 cells and exhibited a concentration-dependent reduction in STAT3 protein expression. Mechanism study demonstrates that <strong>Ir-ART</strong> is located mainly in the nucleus and mitochondria, causing γ-H2AX and cyclin B1 reduction and reactive oxygen species accumulation and mitochondrial membrane potential loss, ultimately leading to autophagic cell death. The migration of cancer cells was also inhibited <em>via</em> metalloproteinase 9 downregulation. Furthermore, <strong>Ir-ART</strong> could initiate antitumor immune responses by eliciting immunogenic cell death and downregulating immunosuppressive cytokine cyclooxygenase-2. Taken together, <strong>Ir-ART</strong> is expected to be further applied to chemotherapy and immunotherapy for colon cancer.</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" 2","pages":" 218-226"},"PeriodicalIF":4.2,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11651070/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142855947","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":"Induced cell phenotype activity recording of DNA-tagged ligands†","authors":"Philipp N. Sander, Jared T. Gillen Miller and Luke L. Lairson","doi":"10.1039/D4CB00137K","DOIUrl":"10.1039/D4CB00137K","url":null,"abstract":"<p >Based on their ability to canvas vast genetic or chemical space at low cost and high speed, DNA-encoded libraries (DEL) have served to enable both genomic and small molecule discovery. Current DEL chemical library screening approaches focus primarily on <em>in vitro</em> target-based affinity or activity. Here we describe an approach to record the phenotype-based activity of DNA-encoded small molecules on their cognate barcode in living cells. We transfected chloroalkane-derivatized DNA barcodes carrying photoreleasable small molecules into cells. Following photorelease, bioactive compounds induced expression of a reporter gene cassette containing self-labeling HaloTag protein that becomes covalently modified by encoding barcodes. We demonstrate that we can recover activity information from cells that received active compound following immunoprecipitation-based enrichment. This generalizable approach should enable future strategies that facilitate phenotype-based screens of DNA-encoded chemical libraries in complex cellular or organism level systems.</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" 2","pages":" 273-280"},"PeriodicalIF":4.2,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11701724/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142956491","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":"Investigating protein degradability through site-specific ubiquitin ligase recruitment†","authors":"Olivia Shade, Amy Ryan, Gabriella Belsito and Alexander Deiters","doi":"10.1039/D4CB00273C","DOIUrl":"10.1039/D4CB00273C","url":null,"abstract":"<p >We report targeted protein degradation through the site-specific recruitment of native ubiquitin ligases to a protein of interest <em>via</em> conjugation of E3 ligase ligands. Direct comparison of degradation ability of proteins displaying the corresponding bioconjugation handle at different regions of protein surfaces was explored. We demonstrate the benefit of proximal lysine residues and investigate flexibility in linker length for the design of optimal degraders. Two proteins without known small molecule ligands, EGFP and DUSP6, were differentially degraded when modified at different locations on their protein surfaces. Further, the cereblon-mediated degradation of the known PROTAC target ERRα was improved through the recruitment of the E3 ligase to regions different from the known ligand binding site. This new methodology will provide insight into overall protein degradability, even in the absence of a known small molecule ligand and inform the process of new ligand and PROTAC development to achieve optimal protein degradation. Furthermore, this approach represents a new, small molecule-based conditional OFF switch of protein function with complete genetic specificity. Importantly, the protein of interest is only modified with a minimal surface modification (&lt;200 Da) and does not require any protein domain fusions.</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" 2","pages":" 240-248"},"PeriodicalIF":4.2,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11657224/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142877774","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":"Advanced reactivity-based sequencing methods for mRNA epitranscriptome profiling†","authors":"Zhihe Cai, Peizhe Song, Kemiao Yu and Guifang Jia","doi":"10.1039/D4CB00215F","DOIUrl":"10.1039/D4CB00215F","url":null,"abstract":"<p >Currently, over 170 chemical modifications identified in RNA introduce an additional regulatory attribute to gene expression, known as the epitranscriptome. The development of detection methods to pinpoint the location and quantify these dynamic and reversible modifications has significantly expanded our understanding of their roles. This review goes deep into the latest progress in enzyme- and chemical-assisted sequencing methods, highlighting the opportunities presented by these reactivity-based techniques for detailed characterization of RNA modifications. Our survey provides a deeper understanding of the function and biological roles of RNA modification.</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" 2","pages":" 150-169"},"PeriodicalIF":4.2,"publicationDate":"2024-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11694185/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142932662","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":"Exploring the metabolic potential of Aeromonas to utilise the carbohydrate polymer chitin†","authors":"Claudia G. Tugui, Dimitry Y. Sorokin, Wim Hijnen, Julia Wunderer, Kaatje Bout, Mark C. M. van Loosdrecht and Martin Pabst","doi":"10.1039/D4CB00200H","DOIUrl":"10.1039/D4CB00200H","url":null,"abstract":"<p >Members of the <em>Aeromonas</em> genus are commonly found in natural aquatic ecosystems. However, they are also frequently present in non-chlorinated drinking water distribution systems. High densities of these bacteria indicate favorable conditions for microbial regrowth, which is considered undesirable. Studies have indicated that the presence of <em>Aeromonas</em> is associated with loose deposits and the presence of invertebrates, specifically <em>Asellus aquaticus</em>. Therefore, a potential source of energy in these nutrient poor environments is chitin, the structural shell component in these invertebrates. In this study, we demonstrate the ability of two <em>Aeromonas</em> strains, commonly encountered in drinking water distribution systems, to effectively degrade and utilize chitin as a sole carbon and nitrogen source. We conducted a quantitative proteomics study on the cell biomass and secretome from pure strain cultures when switching the nutrient source from glucose to chitin, uncovering a diverse array of hydrolytic enzymes and metabolic pathways specifically dedicated to the utilization of chitin. Additionally, a genomic analysis of different <em>Aeromonas</em> species suggests the general ability of this genus to degrade and utilize a variety of carbohydrate biopolymers. This study indicates the relation between the utilization of chitin by <em>Aeromonas</em> and their association with invertebrates such as <em>A. aquaticus</em> in loose deposits in drinking water distribution systems.</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" 2","pages":" 227-239"},"PeriodicalIF":4.2,"publicationDate":"2024-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11653859/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142865439","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":"Mechanistic insights into allosteric regulation of the reductase component of p-hydroxyphenylacetate 3-hydroxylase by p-hydroxyphenylacetate: a model for effector-controlled activity of redox enzymes†","authors":"Surawit Visitsatthawong, Piyanuch Anuwan, Narin Lawan, Pimchai Chaiyen and Thanyaporn Wongnate","doi":"10.1039/D4CB00213J","DOIUrl":"10.1039/D4CB00213J","url":null,"abstract":"<p >Understanding how an enzyme regulates its function through substrate or allosteric regulation is crucial for controlling metabolic pathways. Some flavin-dependent monooxygenases (FDMOs) have evolved an allosteric mechanism to produce reduced flavin while minimizing the use of NADH and the production of harmful hydrogen peroxide (H<small>₂</small>O<small>₂</small>). In this work, we investigated in-depth mechanisms of how the reductase component (C1) of <em>p</em>-hydroxyphenylacetate (HPA) 3-hydroxylase (HPAH) from <em>Acinetobacter baumanii</em> is allosterically controlled by the binding of HPA, which is a substrate of its monooxygenase counterpart (C2). The C1 structure can be divided into three regions: the N-terminal domain (flavin reductase); a flexible loop; and the C-terminal domain, which is homologous to NadR, a repressor protein having HPA as an effector. The binding of HPA to NadR induces a conformational change in the recognition helix, causing it to disengage from the NadA gene. The HPA binding site of C1 is located at the C-terminal domain, which can be divided into five helices. Molecular dynamics simulations performed on HPA-docked C1 elucidated the allosteric mechanism. The carboxylate group of HPA maintains the salt bridge between helix 2 and the flexible loop. This maintenance shortens the loop between helices 2 and 3, causing helix 3 to disengage from the N-terminal domain. The aromatic ring of HPA induces a conformational change in helices 1 and 5, pulling helix 4, analogous to the recognition helix in NadR, away from the N-terminal domain. A Y189A mutation, obtained from site-saturation mutagenesis, confirms that HPA with an unsuitable conformation cannot induce the conformational change of C1. Additionally, an HPA-independent effect is observed, in which Arg20, an NADH binding residue on the N-terminal domain, occasionally disengages from helix 4. This model provides valuable insights into the allosteric regulation of two-component FDMOs and aromatic effector systems.</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" 1","pages":" 81-93"},"PeriodicalIF":4.2,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11618861/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142795672","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":"A chemigenetic indicator based on a synthetic chelator and a green fluorescent protein for imaging of intracellular sodium ions†","authors":"Shiori Takeuchi, Shosei Imai, Takuya Terai and Robert E. Campbell","doi":"10.1039/D4CB00256C","DOIUrl":"10.1039/D4CB00256C","url":null,"abstract":"<p >A chemigenetic indicator with an affinity suitable for imaging of intracellular sodium ions (Na<small>⁺</small>) in mammalian cells was developed. The indicator, based on a chimera of green fluorescent protein (GFP) and HaloTag labeled with a synthetic crown ether chelator, was produced by a combination of rational design and directed evolution. In mammalian cells the indicator exhibited an approximately 100% increase in excitation ratio when the cells were treated with 20 mM Na<small>⁺</small> and an ionophore.</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" 2","pages":" 170-174"},"PeriodicalIF":4.2,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11638762/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142829566","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":"Yatakemycin biosynthesis requires two deoxyribonucleases for toxin self-resistance†","authors":"Jonathan Dorival, Hua Yuan, Allison S. Walker, Gong-Li Tang and Brandt F. Eichman","doi":"10.1039/D4CB00203B","DOIUrl":"10.1039/D4CB00203B","url":null,"abstract":"<p >The highly active natural product yatakemycin (YTM) from <em>Streptomyces</em> sp. TP-A0356 is a potent DNA damaging agent with antimicrobial and antitumor properties. The YTM biosynthesis gene cluster (<em>ytk</em>) contains several toxin self-resistance genes. Of these, <em>ytkR2</em> encodes a DNA glycosylase that is important for YTM production and host survival by excising lethal YTM-adenine lesions from the genome, presumably initiating a base excision repair (BER) pathway. However, the genes involved in repair of the resulting apurinic/apyrimidinic (AP) site as the second BER step have not been identified. Here, we show that <em>ytkR4</em> and <em>ytkR5</em> are essential for YTM production and encode deoxyribonucleases related to other known DNA repair nucleases. Purified YtkR4 and YtkR5 exhibit AP endonuclease activity specific for YtkR2-generated AP sites, providing a basis for BER of the toxic AP intermediate produced from YTM-adenine excision and consistent with co-evolution of <em>ytkR2</em>, <em>ytkR4</em>, and <em>ytkR5</em>. YtkR4 and YtkR5 also exhibit 3′–5′ exonuclease activity with differing substrate specificities. The YtkR5 exonuclease is capable of digesting through a YTM-DNA lesion and may represent an alternative repair mechanism to BER. We also show that <em>ytkR4</em> and <em>ytkR5</em> homologs are often clustered together in putative gene clusters related to natural product production, consistent with non-redundant roles in repair of other DNA adducts derived from genotoxic natural products.</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" 1","pages":" 94-105"},"PeriodicalIF":4.2,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11621827/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142795674","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":"Click-ready iridium(iii) complexes as versatile bioimaging probes for bioorthogonal metabolic labeling.","authors":"Vincent Rigolot, Clémence Simon, Aude Bouchet, Lucas Lancel, Veronica Di Battista, Dmitry Karpov, Boris Vauzeilles, Corentin Spriet, Michel Sliwa, Sylvain Bohic, Christophe Biot, Cédric Lion","doi":"10.1039/d4cb00255e","DOIUrl":"10.1039/d4cb00255e","url":null,"abstract":"<p><p>Herein, we report the synthesis, photophysical characterization and validation of iridium(iii)-polypyridine complexes functionalized for click chemistry and bioorthogonal chemistry, as well as their versatile applications as probes in bioimaging studies exploiting metabolic labeling. The designed dyes are conjugated to chemical reporters in a specific manner within cells by CuAAC ligation and display attractive photophysical properties in the UV-visible range. They are indeed highly photostable and emit in the far-red to near-IR region with long lifetimes and large Stokes shifts. We demonstrate that they can be efficiently used to monitor nascent intracellular sialylated glycoconjugates in bioorthogonal MOE studies with a varied panel of optical and non-optical techniques, namely conventional UV-vis laser scanning confocal microscopy (for routine purposes), UV-vis time-resolved luminescence imaging (for specificity and facilitated multiplexing with nano-environment sensitivity), synchrotron radiation based X-ray fluorescence nanoimaging (for high resolution, elemental mapping and quantification <i>in situ</i>) and inductively coupled plasma mass spectrometry (for routine quantification on cell populations with high statistical confidence). The synthesized Ir(iii) complexes were utilized in single labeling experiments, as well as in dual click-labeling experiments utilizing two distinct monosaccharide reporters relevant to the same metabolic pathway.</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11632520/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142819650","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 His-Tag-mediated pull-down and quantification assay for G-quadruplex containing DNA sequences†","authors":"Enrico Cadoni, Hanne Moerman and Annemieke Madder","doi":"10.1039/D4CB00185K","DOIUrl":"10.1039/D4CB00185K","url":null,"abstract":"<p >In this study, we developed a simple pull-down assay using peptide nucleic acids (PNAs) equipped with a His-Tag and a G-quadruplex (G4) ligand for the selective recognition and quantification of G4-forming DNA sequences. Efficient and specific target recovery was achieved using optimized buffer conditions and magnetic Ni–NTA beads, while quantification was realized by employing the enzyme-like properties of the G4/hemin complex. The assay was validated through HPLC analysis and adapted for a 96-well plate format. The results show that higher recovery can be achieved using His-Tag with Ni–NTA magnetic beads as compared to the more common biotin–streptavidin purification. The inclusion of the G4-ligand as an additional selectivity handle was shown to be beneficial for both recovery and selectivity.</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" 1","pages":" 56-64"},"PeriodicalIF":4.2,"publicationDate":"2024-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11613956/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142781605","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}