RSC Chemical Biology最新文献

{"title":"Contributors to the RSC Chemical Biology Emerging Investigators Collection 2023","authors":"","doi":"10.1039/D4CB90013H","DOIUrl":"10.1039/D4CB90013H","url":null,"abstract":"<p >A graphical abstract is available for this content</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" 5","pages":" 397-400"},"PeriodicalIF":4.1,"publicationDate":"2024-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2024/cb/d4cb90013h?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140169976","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":"Pseudouridine and N1-methylpseudouridine as potent nucleotide analogues for RNA therapy and vaccine development","authors":"Lyana L. Y. Ho, Gabriel H. A. Schiess, Pâmella Miranda, Gerald Weber and Kira Astakhova","doi":"10.1039/D4CB00022F","DOIUrl":"10.1039/D4CB00022F","url":null,"abstract":"<p >Modified nucleosides are integral to modern drug development, serving as crucial building blocks for creating safer, more potent, and more precisely targeted therapeutic interventions. Nucleobase modifications often confer antiviral and anti-cancer activity as monomers. When incorporated into nucleic acid oligomers, they increase stability against degradation by enzymes, enhancing the drugs’ lifespan within the body. Moreover, modification strategies can mitigate potential toxic effects and reduce immunogenicity, making drugs safer and better tolerated. Particularly, <em>N</em>1-methylpseudouridine modification improved the efficacy of the mRNA coding for spike protein of COVID-19. This became a crucial step for developing COVID-19 vaccine applied during the 2020 pandemic. This makes <em>N</em>1-methylpseudouridine, and its “parent” analogue pseudouridine, potent nucleotide analogues for future RNA therapy and vaccine development. This review focuses on the structure and properties of pseudouridine and <em>N</em>1-methylpseudouridine. RNA has a greater structural versatility, different conformation, and chemical reactivity than DNA. Watson–Crick pairing is not strictly followed by RNA that has more unusual base pairs and base-triplets. This requires detailed structural studies and structure–activity relationship analyses for RNA, also when modifications are incorporated. Recent successes in this direction are revised in this review. We describe recent successes with using pseudouridine and <em>N</em>1-methylpseudouridine in mRNA drug candidates. We also highlight remaining challenges that need to be solved to develop new mRNA vaccines and therapies.</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" 5","pages":" 418-425"},"PeriodicalIF":4.1,"publicationDate":"2024-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2024/cb/d4cb00022f?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140169973","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":"Molecularly imprinted nanoparticles reveal regulatory scaffolding features in Pyk2 tyrosine kinase†","authors":"Tania M. Palhano Zanela, Milad Zangiabadi, Yan Zhao and Eric S. Underbakke","doi":"10.1039/D3CB00228D","DOIUrl":"10.1039/D3CB00228D","url":null,"abstract":"<p >Pyk2 is a multi-domain non-receptor tyrosine kinase that serves dual roles as a signaling enzyme and scaffold. Pyk2 activation involves a multi-stage cascade of conformational rearrangements and protein interactions initiated by autophosphorylation of a linker site. Linker phosphorylation recruits Src kinase, and Src-mediated phosphorylation of the Pyk2 activation loop confers full activation. The regulation and accessibility of the initial Pyk2 autophosphorylation site remains unclear. We employed peptide-binding molecularly imprinted nanoparticles (MINPs) to probe the regulatory conformations controlling Pyk2 activation. MINPs differentiating local structure and phosphorylation state revealed that the Pyk2 autophosphorylation site is protected in the autoinhibited state. Activity profiling of Pyk2 variants implicated FERM and linker residues responsible for constraining the autophosphorylation site. MINPs targeting each Src docking site disrupt the higher-order kinase interactions critical for activation complex maturation. Ultimately, MINPs targeting key regulatory motifs establish a useful toolkit for probing successive activational stages in the higher-order Pyk2 signaling complex.</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" 5","pages":" 447-453"},"PeriodicalIF":4.1,"publicationDate":"2024-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2024/cb/d3cb00228d?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140124598","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":"Discovery of potent and selective activity-based probes (ABPs) for the deubiquitinating enzyme USP30†","authors":"Milon Mondal, Fangyuan Cao, Daniel Conole, Holger W. Auner and Edward W. Tate","doi":"10.1039/D4CB00029C","DOIUrl":"10.1039/D4CB00029C","url":null,"abstract":"<p >Ubiquitin-specific protease 30 (USP30) is a deubiquitinating enzyme (DUB) localized at the mitochondrial outer membrane and involved in PINK1/Parkin-mediated mitophagy, pexophagy, BAX/BAK-dependent apoptosis, and IKKβ-USP30-ACLY-regulated lipogenesis/tumorigenesis. A USP30 inhibitor, <strong>MTX652</strong>, has recently entered clinical trials as a potential treatment for mitochondrial dysfunction. Small molecule activity-based probes (ABPs) for DUBs have recently emerged as powerful tools for in-cell inhibitor screening and DUB activity analysis, and here, we report the first small molecule ABPs (<strong>IMP-2587</strong> and <strong>IMP-2586</strong>) which can profile USP30 activity in cells. Target engagement studies demonstrate that <strong>IMP-2587</strong> and <strong>IMP-2586</strong> engage active USP30 at nanomolar concentration after only 10 min incubation time in intact cells, dependent on the presence of the USP30 catalytic cysteine. Interestingly, proteomics analyses revealed that DESI1 and DESI2, small ubiquitin-related modifier (SUMO) proteases, can also be engaged by these probes, further suggesting a novel approach to develop DESI ABPs.</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" 5","pages":" 439-446"},"PeriodicalIF":4.1,"publicationDate":"2024-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2024/cb/d4cb00029c?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140129753","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":"Leveraging machine learning models for peptide–protein interaction prediction","authors":"Song Yin, Xuenan Mi and Diwakar Shukla","doi":"10.1039/D3CB00208J","DOIUrl":"10.1039/D3CB00208J","url":null,"abstract":"<p >Peptides play a pivotal role in a wide range of biological activities through participating in up to 40% protein–protein interactions in cellular processes. They also demonstrate remarkable specificity and efficacy, making them promising candidates for drug development. However, predicting peptide–protein complexes by traditional computational approaches, such as docking and molecular dynamics simulations, still remains a challenge due to high computational cost, flexible nature of peptides, and limited structural information of peptide–protein complexes. In recent years, the surge of available biological data has given rise to the development of an increasing number of machine learning models for predicting peptide–protein interactions. These models offer efficient solutions to address the challenges associated with traditional computational approaches. Furthermore, they offer enhanced accuracy, robustness, and interpretability in their predictive outcomes. This review presents a comprehensive overview of machine learning and deep learning models that have emerged in recent years for the prediction of peptide–protein interactions.</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" 5","pages":" 401-417"},"PeriodicalIF":4.1,"publicationDate":"2024-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2024/cb/d3cb00208j?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140124711","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":"Engineering cell-free systems by chemoproteomic-assisted phenotypic screening†","authors":"Zarina Levitskaya, Zheng Ser, Hiromi Koh, Wang Shi Mei, Sharon Chee, Radoslaw Mikolaj Sobota and John F. Ghadessy","doi":"10.1039/D4CB00004H","DOIUrl":"10.1039/D4CB00004H","url":null,"abstract":"<p >Phenotypic screening is a valuable tool to both understand and engineer complex biological systems. We demonstrate the functionality of this approach in the development of cell-free protein synthesis (CFPS) technology. Phenotypic screening identified numerous compounds that enhanced protein production in yeast lysate CFPS reactions. Notably, many of these were competitive ATP kinase inhibitors, with the exploitation of their inherent substrate promiscuity redirecting ATP flux towards heterologous protein expression. Chemoproteomic-guided strain engineering partially phenocopied drug effects, with a 30% increase in protein yield observed upon deletion of the ATP-consuming SSA1 component of the HSP70 chaperone. Moreover, drug-mediated metabolic rewiring coupled with template optimization generated the highest protein yields in yeast CFPS to date using a hitherto less efficient, but more cost-effective glucose energy regeneration system. Our approach highlights the utility of target-agnostic phenotypic screening and target identification to deconvolute cell-lysate complexity, adding to the expanding repertoire of strategies for improving CFPS.</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" 4","pages":" 372-385"},"PeriodicalIF":4.1,"publicationDate":"2024-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2024/cb/d4cb00004h?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140046603","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":"Introduction to ‘The Epitranscriptome’","authors":"Ralph E. Kleiner, Claudia Höbartner and Guifang Jia","doi":"10.1039/D4CB90006E","DOIUrl":"10.1039/D4CB90006E","url":null,"abstract":"<p >A graphical abstract is available for this content</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" 4","pages":" 271-272"},"PeriodicalIF":4.1,"publicationDate":"2024-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2024/cb/d4cb90006e?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140046694","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 PCR primers enabling the design of flexible sticky ends for efficient concatenation of long DNA fragments†","authors":"Kohei Nomura, Kaoru Onda, Hirotaka Murase, Fumitaka Hashiya, Yukiteru Ono, Goro Terai, Natsuhisa Oka, Kiyoshi Asai, Daisuke Suzuki, Naho Takahashi, Haruka Hiraoka, Masahito Inagaki, Yasuaki Kimura, Yoshihiro Shimizu, Naoko Abe and Hiroshi Abe","doi":"10.1039/D3CB00212H","DOIUrl":"10.1039/D3CB00212H","url":null,"abstract":"<p >We developed chemically modified PCR primers that allow the design of flexible sticky ends by introducing a photo-cleavable group at the phosphate moiety. Nucleic acid derivatives containing <em>o</em>-nitrobenzyl photo-cleavable groups with a <em>tert</em>-butyl group at the benzyl position were stable during strong base treatment for oligonucleotide synthesis and thermal cycling in PCR reactions. PCR using primers incorporating these nucleic acid derivatives confirmed that chain extension reactions completely stopped at position 1 before and after the site of the photo-cleavable group was introduced. DNA fragments of 2 and 3 kbp, with sticky ends of 50 bases, were successfully concatenated with a high yield of 77%. A plasmid was constructed using this method. Finally, we applied this approach to construct a 48.5 kbp lambda phage DNA, which is difficult to achieve using restriction enzyme-based methods. After 7 days, we were able to confirm the generation of DNA of the desired length. Although the efficiency is yet to be improved, the chemically modified PCR primer offers potential to complement enzymatic methods and serve as a DNA concatenation technique.</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" 4","pages":" 360-371"},"PeriodicalIF":4.1,"publicationDate":"2024-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2024/cb/d3cb00212h?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140010884","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":"Tracking the cellular uptake and phototoxicity of Ru(ii)-polypyridyl-1,8-naphthalimide Tröger's base conjugates†","authors":"Sandra A. Bright, MariaLuisa Erby, Fergus E. Poynton, Daniel Monteyne, David Pérez-Morga, Thorfinnur Gunnlaugsson, D. Clive Williams and Robert B. P. Elmes","doi":"10.1039/D3CB00206C","DOIUrl":"10.1039/D3CB00206C","url":null,"abstract":"<p >Ruthenium(<small>II</small>) complexes are attracting significant research attention as a promising class of photosensitizers (PSs) in photodynamic therapy (PDT). Having previously reported the synthesis of two novel Ru(<small>II</small>)-polypyridyl-1,8-naphthalimide Tröger's base compounds <strong>1</strong> and <strong>2</strong> with interesting photophysical properties, where the emission from either the Ru(<small>II</small>) polypyridyl centres or the naphthalimide moieties could be used to monitor binding to nucleic acids, we sought to use these compounds to investigate further and in more detail their biological profiling, which included unravelling their mechanism of cellular uptake, cellular trafficking and cellular responses to photoexcitation. Here we demonstrate that these compounds undergo rapid time dependent uptake in HeLa cells that involved energy dependent, caveolae and lipid raft-dependent mediated endocytosis, as demonstrated by confocal imaging, and transmission and scanning electron microscopy. Following endocytosis, both compounds were shown to localise to mostly lysosomal and Golgi apparatus compartments with some accumulation in mitochondria but no localisation was found to the nucleus. Upon photoactivation, the compounds increased ROS production and induced ROS-dependent apoptotic cell death. The photo-activated compounds subsequently induced DNA damage and altered tubulin, but not actin structures, which was likely to be an indirect effect of ROS production and induced apoptosis. Furthermore, by changing the concentration of the compounds or the laser used to illuminate the cells, the mechanism of cell death could be changed from apoptosis to necrosis. This is the first detailed biological study of Ru(<small>II</small>)-polypyridyl Tröger's bases and clearly suggests caveolae-dependent endocytosis is responsible for cell uptake – this may also explain the lack of nuclear uptake for these compounds and similar results observed for other Ru(<small>II</small>)-polypyridyl complexes. These conjugates are potential candidates for further development as PDT agents and may also be useful in mechanistic studies on cell uptake and trafficking.</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" 4","pages":" 344-359"},"PeriodicalIF":4.1,"publicationDate":"2024-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2024/cb/d3cb00206c?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139923941","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 covalent compound selectively inhibits RNA demethylase ALKBH5 rather than FTO†","authors":"Gan-Qiang Lai, Yali Li, Heping Zhu, Tao Zhang, Jing Gao, Hu Zhou and Cai-Guang Yang","doi":"10.1039/D3CB00230F","DOIUrl":"10.1039/D3CB00230F","url":null,"abstract":"<p > <em>N</em> <small>⁶</small>-Methyladenosine (m<small>⁶</small>A) is the most prevalent mRNA modification and is required for gene regulation in eukaryotes. ALKBH5, an m<small>⁶</small>A demethylase, is a promising target, particularly for anticancer drug discovery. However, the development of selective and potent inhibitors of ALKBH5 rather than FTO remains challenging. Herein, we used a targeted covalent inhibition strategy and identified a covalent inhibitor, <strong>TD19</strong>, which selectively inhibits ALKBH5 compared with FTO demethylase in protein-based and tumor cell-based assays. <strong>TD19</strong> irreversibly modifies the residues C100 and C267, preventing ALKBH5 from binding to m<small>⁶</small>A-containing RNA. Moreover, <strong>TD19</strong> displays good anticancer efficacy in acute myeloid leukemia and glioblastoma multiforme cell lines. Thus, the ALKBH5 inhibitor developed in this study, which selectively targets ALKBH5 compared with FTO, can potentially be used as a probe for investigating the biological functions of RNA demethylase and as a lead compound in anticancer research.</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" 4","pages":" 335-343"},"PeriodicalIF":4.1,"publicationDate":"2024-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2024/cb/d3cb00230f?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139901963","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}