RSC Chemical Biology最新文献

{"title":"RNA-binding landscape of amiloride: large-scale profiling and structural basis of U-U mismatch recognition.","authors":"Kosuke Tsuzuki, Kazumitsu Onizuka, Momo Okada, Ryosuke Nagasawa, Emi Miyashita, Kaoru R Komatsu, Hirohide Saito, Jiro Kondo, Fumi Nagatsugi","doi":"10.1039/d6cb00055j","DOIUrl":"https://doi.org/10.1039/d6cb00055j","url":null,"abstract":"<p><p>Amiloride possesses a characteristic chemical scaffold capable of recognizing uracil (U) through three complementary hydrogen bonds; however, its binding selectivity toward naturally occurring RNA structural motifs has remained uncharacterized. In this study, we present a large-scale analysis of amiloride's RNA binding properties and structural characterization of the amiloride-RNA complex. Using folded RNA element profiling with structure library (FOREST), we evaluated the RNA-binding selectivity of amiloride across 3000 structured RNA motifs and uncovered pronounced binding preferences for G-quadruplexes and, notably, for a specific internal loop motif containing a U-U mismatch (<i>K</i> _Dapp = 0.31 µM). Furthermore, a motif extraction strategy was used to enable detailed structural investigation. The X-ray crystal structure of the amiloride-RNA complex provides the first structural evidence that amiloride recognizes a U residue within a naturally occurring RNA context <i>via</i> its signature complementary hydrogen bonding interactions.</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13147285/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147844391","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":"Structural and biochemical insights into the inhibition of <i>Mycobacterium tuberculosis</i> cyclic dinucleotide phosphodiesterase by a sulfur-modified cyclic dinucleotide analog.","authors":"Dagur Singh Hanuman, Singh Neeharika, Sinha Krishna Murari, Simpa K Yeboah, Herman O Sintim, Eerappa Rajakumara","doi":"10.1039/d6cb00006a","DOIUrl":"https://doi.org/10.1039/d6cb00006a","url":null,"abstract":"<p><p>Cyclic dinucleotide (CDN) signaling plays a pivotal role in bacterial physiology and host-pathogen interactions. <i>Mycobacterium tuberculosis</i> (Mtb) releases a cyclic dinucleotide phosphodiesterase (CdnP) in the macrophages, which hydrolyzes Mtb-derived 3'3'-c-di-AMP and 3'3'-c-di-GMP, and a host-derived 2'3'-cGAMP STING agonist, to evade the host's innate immune response mediated by the STING protein. Therefore, by inhibiting CdnP released into host cells, the STING pathway can be potentiated, leading to improved bacterial clearance, which represents a potential novel approach for anti-tuberculosis (anti-TB) therapy. Here we report ES-2'3'-cAAMP, an analog of the host-derived STING agonist 2'3'-cGAMP, in which the phosphodiester bond is modified and the base is replaced, binds to CdnP with a micromolar binding affinity and competes with CdnP's substrates - 3'3'-c-di-AMP and 3'3'-c-di-GMP - binding to CdnP. Significantly, CdnP's phosphodiesterase catalytic activity is inhibited by ES-2'3'-cAAMP. Furthermore, the CdnP-ES-2'3'-cAAMP complex structure reported here is the first structure of the CdnP complexed with CDN, revealing the unique pose of ES-2'3'-cAAMP in the catalytic pocket of CdnP that is inaccessible to catalytic residues and Mn²⁺ ions for its hydrolysis, and in parallel blocks the binding of the natural substrates of CdnP that explains the structural basis of CdnP's catalytic activity inhibition by the inhibitor. Additionally, 2'3'-cGAMP in the STING receptor and ES-2'3'-cAAMP in the CdnP adopted an identical horseshoe conformation, suggesting that ES-2'3'-cAAMP, or an analogue thereof, can bind to and stimulate STING, thus acting as a synthetic STING agonist. These combined structural and biochemical findings provide new mechanistic insights into the inhibition of Mtb CdnP and offer a novel approach to host-directed anti-TB therapies that aim to enhance the host's own immune responses rather than directly killing the pathogen, which may help to mitigate the problem of antibiotic resistance.</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13077336/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147693017","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 the lipoprotein trafficking pathway for the development of novel antimicrobials.","authors":"Haley B Gartrell, Taryn Trigler, Marcin Grabowicz, William M Wuest","doi":"10.1039/d6cb00009f","DOIUrl":"https://doi.org/10.1039/d6cb00009f","url":null,"abstract":"<p><p>Antimicrobial resistance continues to limit the number of effective antimicrobials to treat bacterial infections. The development of antimicrobials with unique mechanisms of action is crucial to overcoming this threat. By employing various methods of hit identification, such as artificial intelligence, whole-cell screening, and drug repurposing, small-molecules that display activity against bacterial pathogens can be identified. Herein, four molecules (abaucin, enterololin, lolamicin, and fendiline) that were found to have high potency against either <i>Escherichia coli</i> or <i>Acinetobacter baumannii</i> utilizing these drug discovery strategies are described. They were all found to target the lipoprotein trafficking pathway (Lol). Within Gram-negative species, lipoproteins are essential for cell viability, making the Lol pathway an interesting target to exploit for the discovery of antimicrobials. This review highlights the importance of lipoproteins as antibacterial targets and details four examples of the development of small-molecule inhibitors of Lol.</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13097052/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147784678","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 green enzymatic route for the biotransformation of naphthalene to phthalic acid.","authors":"Yang Huang, Maxine Yew, Suxin Huang, Haifeng Liu, Leilei Zhu","doi":"10.1039/d6cb00050a","DOIUrl":"https://doi.org/10.1039/d6cb00050a","url":null,"abstract":"<p><p>Naphthalene, an abundant polycyclic aromatic hydrocarbon (PAH) often emitted as an industrial byproduct, represents a significant yet underutilized carbon feedstock for chemical synthesis. Due to its high chemical stability and hydrophobicity, conventional physicochemical treatment methods are often energy-intensive, condition-dependent, and prone to causing secondary pollution. Biocatalysis offers a green strategy for the selective activation and cleavage of aromatic rings under mild conditions. In this study, we constructed a multi-enzyme cascade reaction for the continuous biocatalytic conversion of naphthalene to phthalic acid. The cascade begins with the oxyfunctionalization of naphthalene into 1-naphthol by using the unspecific peroxygenase AaeUPO, followed by a carboxylation-oxygenation coupling reaction to yield 2'-carboxybenzyl-pyruvic acid, and ultimately an NAD⁺-dependent oxidation to transform 2-carboxybenzaldehyde into phthalic acid. This work demonstrates a promising multi-enzyme strategy for the mild conversion of naphthalene and provides a methodological and conceptual basis for developing green and sustainable biotransformation routes for PAHs.</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13077335/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147692940","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 cysteine reactive chloroalkane probe enables HaloTag ligation for downstream chemical proteomics analysis.","authors":"Rubaba R Abanti, Dongqing Wu, Pavel Kielkowski","doi":"10.1039/d6cb00004e","DOIUrl":"https://doi.org/10.1039/d6cb00004e","url":null,"abstract":"<p><p>Chemical proteomics is a powerful method to track proteins labelled by reactive small molecules in living cells on a proteome-wide scale. The strategy relies on the reactivity and specificity of bioorthogonal 'click reactions'. Although a variety of bioorthogonal reactions have been developed to facilitate chemical proteomics, their reactivity and specificity might not be comparable with enzymatic reactions. Here, we describe an iodoacetamide chloroalkane cysteine reactive probe that is, upon reaction with the nucleophilic cysteine of thioredoxin (TrxA), efficiently and specifically conjugated with the HaloTag protein. The TrxA-HaloTag conjugate is utilized for downstream chemoproteomics analysis, including in-gel shift assay and mass spectrometry-based proteomics. The TrxA-HaloTag conjugation in whole cell lysate allows fast and efficient pull-down of labelled proteins on anti-HaloTag nanobeads, resulting in low background after mass spectrometric analysis. The main advantage of the system is its high efficiency and complete bioorthogonality due to enzymatic reactivity that is characteristic for HaloTag ligation. This study demonstrates the utility of chloroalkane small compound probes for chemoproteomics applications.</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13103961/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147784685","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":"Influence of linker design on the stability, folding, and assembly of tethered collagen-mimetic peptides.","authors":"Debasis Ghosh, Anthony R Perez, S M Mobin Sikder, Jesus R Vasquez, Claire Zhang, Anjan Maity, Tao Ye, Andrea D Merg","doi":"10.1039/d5cb00298b","DOIUrl":"10.1039/d5cb00298b","url":null,"abstract":"<p><p>Covalently tethered collagen-mimetic peptides (CMPs) serve as synthetically programmable molecules for studying the collagen triple helix fold. Tethered CMPs, which overcome limitations that are inherent to their untethered counterparts (<i>e.g.</i>, decreased stability, concentration-dependent folding, and slow folding kinetics), are constructed using a variety of templating strategies. Despite the plethora of reports of tethered CMPs in literature, there has been little exploration in determining the effects that the linker region, which connects the CMP sequence to the trivalent scaffold, has on the stability and assembly of tethered CMP triple helices. Here, we systematically study the influence of linker length and composition on the stability, folding, and assembly of covalently tethered CMPs. We synthesized a family of tethered CMPs comprising PEGylated linkers of different lengths (CTH-PEG2, CTH-PEG4, CTH-PEG6) to assess how linker length influences the properties of CMP triple helices. Moreover, we synthesized tethered CMPs comprising hydrophobic (CTH-HEX) and peptide-based linkers (CTH-GSG). All tethered CMPs possess a triblock sequence architecture that directs the assembly of resulting triple helices into nanostructures. Transmission electron microscopy (TEM) and atomic force microscopy (AFM) confirm that tethered CMPs assemble into nanosheets and nanoribbons. Circular dichroism (CD) spectroscopy reveals that increasing the length of the flexible linker systematically decreases the thermal stability of tethered CMP triple helices and alters their folding kinetics. Furthermore, CD data of CTH-HEX and CTH-GSG indicate that linker composition can play a role, though limited, in influencing the stability and folding properties of CMP triple helices. The presented work highlights how tuning the linker design - both length and composition - serves as a facile route towards fine-tuning the properties of CMP triple helices and their assemblies without perturbing the CMP sequence architecture, and will provide guidance to future researchers in choosing appropriate linkers for their own applications.</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13088989/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147724334","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":"Keap1-Kelch-targeting protein-protein interaction inhibitors, but not reversibly-binding electrophiles, increase the thermostability of Keap1 in the cellular environment.","authors":"Sharadha Dayalan Naidu, Dina Dikovskaya, Jasmine M Walker, Charlotte Lim Jia Yee, Annamarie J Cafferkey, Manaka Tatsuno, Jialin Feng, Terry W Moore, Tatum Johnson, Tadashi Honda, Geoff Wells, Takafumi Suzuki, Masayuki Yamamoto, Albena T Dinkova-Kostova","doi":"10.1039/d6cb00045b","DOIUrl":"https://doi.org/10.1039/d6cb00045b","url":null,"abstract":"<p><p>The Kelch-like ECH-associated protein 1/nuclear factor erythroid 2-p45-related factor 2 (Keap1/Nrf2) partnership orchestrates the cellular defence against oxidative, inflammatory and metabolic stress. Dysregulation of Nrf2 is involved in the pathogenesis of numerous chronic diseases. Under homeostatic conditions, Keap1 continuously targets Nrf2 for ubiquitination and degradation. When Keap1 is inactivated, Nrf2 accumulates and translocates to the nucleus, where it activates transcription of genes encoding cytoprotective proteins. There are two main types of Keap1 inhibitors, electrophiles and Keap1-Nrf2 protein-protein interaction (PPI) inhibitors. Using a quantitative fluorescence-based cellular thermal shift assay (CETSA), we investigated the ability of a panel of electrophilic Nrf2 activators and PPI inhibitors to bind to Keap1 in lysates and intact cells stably expressing Keap1-mCherry or free mCherry as controls. All PPI inhibitors tested caused an increase in the thermostability of Keap1-mCherry. Surprisingly however, electrophiles that bind covalently and reversibly to thiols did not. Moreover, treatment of intact cells with the double Michael acceptors bis(benzylidene)acetone and its hydroxylated derivative bis(2-hydroxybenzylidene)acetone caused a decrease in the thermostability of Keap1. Thus, in addition to confirming target engagement of Keap1-targeting PPI inhibitors in the cellular environment, the Keap1 fluorescence-based CETSA is capable of distinguishing between the mechanism of action of the two types of Nrf2 activators in the cellular environment, and has the potential for cost-effective, high-throughput applications.</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13093462/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147784694","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":"Intricacies in iron-sulfur cluster function and biogenesis: functional versatility, sulfur sources, and enzyme specificity.","authors":"Sarah M Spigelmyer, Patricia C Dos Santos","doi":"10.1039/d5cb00330j","DOIUrl":"https://doi.org/10.1039/d5cb00330j","url":null,"abstract":"<p><p>Iron-sulfur (Fe-S) clusters are ancient inorganic cofactors ubiquitous across all domains of life. These cofactors associate with proteins through constitutive or transient coordination, expanding their chemistries and versatility in biological processes. Thus, Fe-S proteins participate in intricate and multifaceted chemistries critical to life on Earth. The biosynthesis of these cofactors has evolved to require complex machinery to catalyze cluster formation and subsequent transfer to target apo-proteins. Five Fe-S cluster biogenesis systems have been identified in prokaryotes, with varying degrees of complexity, including: iron-sulfur cluster (ISC), nitrogen fixation (NIF), sulfur mobilization (SUF), minimal iron-sulfur system (MIS), and SUF-like minimal system (SMS). Sulfur mobilization in the biosynthesis of Fe-S clusters is initiated, in most cases, by cysteine sulfurtransferases, also known as cysteine desulfurases. These enzymes use the amino acid cysteine as a sulfur source and require specific interactions with a sulfur acceptor to promote sulfur transfer. Physical interactions and coordination among biosynthetic components restrict their functions and guarantee the trafficking of reactive intermediates to proper destinations. As recently reported, the occurrence of alternate biosynthetic schemes using sulfide as the sulfur source bypasses the requirement for sulfurtransferases and provides alternate evolutionary strategies to construct Fe-S clusters.</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13066941/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147677282","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":"Heck-type C-glycosylations in the synthesis of artificial nucleotides and functional nucleic acids.","authors":"Robert Dörrenhaus, Andre Zenz, Stephanie Kath-Schorr","doi":"10.1039/d6cb00078a","DOIUrl":"https://doi.org/10.1039/d6cb00078a","url":null,"abstract":"<p><p>Advances in nucleic acid chemistry have driven the development of a wide variety of artificial nucleobases. The synthesis of the glycosidic bond towards nucleosides still remains a major challenge in nucleic acid chemistry, particularly for C-glycosidic DNA nucleosides. This review highlights the Heck reaction as a central and versatile strategy for constructing diverse C-glycosidic DNA analogues. It discusses the underlying reaction mechanism, commonly employed catalyst and ligand systems and the scope of tolerated substituents. In addition, the review summarizes the subsequent applications of these artificial nucleobases with a particular emphasis on fluorescent nucleobase analogues.</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13059217/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147647033","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 \"Endocytosis and cellular delivery\".","authors":"Alexander Kros, Georgina Such, Vincent M Rotello","doi":"10.1039/d6cb90009g","DOIUrl":"10.1039/d6cb90009g","url":null,"abstract":"<p><p>Alexander Kros, Georgina Such, and Vincent Rotello introduce the <i>RSC Pharmaceutics</i> and <i>RSC Chemical Biology</i> themed collection on Endocytosis and cellular delivery.</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13019361/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147575746","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}