RSC Chemical Biology最新文献

Identification and characterization of ternary complexes consisting of FKBP12, MAPRE1 and macrocyclic molecular glues.

IF 4.2

RSC Chemical Biology Pub Date : 2025-03-06 DOI: 10.1039/d4cb00279b

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, Hans-Joerg Roth

{"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, Hans-Joerg Roth","doi":"10.1039/d4cb00279b","DOIUrl":"10.1039/d4cb00279b","url":null,"abstract":"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 α. 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 A max 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.","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" ","pages":""},"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}

引用次数: 0

Identification of microproteins with transactivation activity by polyalanine motif selection.

IF 4.2

RSC Chemical Biology Pub Date : 2025-03-06 DOI: 10.1039/d4cb00277f

Archita Agrawal, Alan Saghatelian

引用次数: 0

Peptides: potential delivery systems for mRNA.

IF 4.2

RSC Chemical Biology Pub Date : 2025-02-26 DOI: 10.1039/d4cb00295d

Huiting Liang, Yun Xing, Kexin Wang, Yaping Zhang, Feng Yin, Zigang Li

{"title":"Peptides: potential delivery systems for mRNA.","authors":"Huiting Liang, Yun Xing, Kexin Wang, Yaping Zhang, Feng Yin, Zigang Li","doi":"10.1039/d4cb00295d","DOIUrl":"10.1039/d4cb00295d","url":null,"abstract":"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.","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" ","pages":""},"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}

引用次数: 0

Identification of γ-butyrolactone signalling molecules in diverse actinomycetes using resin-assisted isolation and chemoenzymatic synthesis.

IF 4.2

RSC Chemical Biology Pub Date : 2025-02-25 DOI: 10.1039/d5cb00007f

Yuta Kudo, Keiichi Konoki, Mari Yotsu-Yamashita

{"title":"Identification of γ-butyrolactone signalling molecules in diverse actinomycetes using resin-assisted isolation and chemoenzymatic synthesis.","authors":"Yuta Kudo, Keiichi Konoki, Mari Yotsu-Yamashita","doi":"10.1039/d5cb00007f","DOIUrl":"10.1039/d5cb00007f","url":null,"abstract":"Actinomycetes are prolific producers of secondary metabolites with diverse bioactivities. Secondary metabolism in actinomycetes is regulated by signalling molecules, often termed \"bacterial hormones.\" In Streptomyces griseus, the γ-butyrolactone (GBL) A-factor (1) plays a key role in regulating secondary metabolism, including streptomycin production. The widespread presence of afsA, the gene encoding A-factor synthase, suggests that GBLs are a major class of signalling molecules in actinomycetes. However, their identification is hindered by the requirement for large-scale cultures. This study presents two methodologies for identifying natural GBLs. First, a resin-assisted culture method combined with MS-guided screening enabled the isolation and structural determination of GBLs (2-5) from smaller-scale cultures. Second, a chemoenzymatic synthesis method involving one-pot three enzymatic reactions was developed, allowing the production of GBL standards (10a-10l). Using these standards, HR-LCMS analysis of 31 strains across 10 actinomycetes genera identified GBLs in nearly half of the tested strains, including genera where GBLs were detected for the first time. Chiral HPLC analysis further revealed the presence of the (3S)-isomer of GBL (11), an enantiomer of known GBLs. This study uncovers the widespread distribution and structural diversity of GBLs among actinomycetes, providing insights into their regulatory roles and potential for activating secondary metabolism, which may facilitate the discovery of new natural products.","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11877004/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143568434","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}

引用次数: 0

Biochemical investigations using mass spectrometry to monitor JMJD6-catalysed hydroxylation of multi-lysine containing bromodomain-derived substrates.

IF 4.2

RSC Chemical Biology Pub Date : 2025-02-24 DOI: 10.1039/d4cb00311j

Thomas P Corner, Eidarus Salah, Anthony Tumber, Lennart Brewitz, Christopher J Schofield

{"title":"Biochemical investigations using mass spectrometry to monitor JMJD6-catalysed hydroxylation of multi-lysine containing bromodomain-derived substrates.","authors":"Thomas P Corner, Eidarus Salah, Anthony Tumber, Lennart Brewitz, Christopher J Schofield","doi":"10.1039/d4cb00311j","DOIUrl":"10.1039/d4cb00311j","url":null,"abstract":"Jumonji-C domain-containing protein 6 (JMJD6) is a human 2-oxoglutarate (2OG)/Fe(ii)-dependent oxygenase catalysing post-translational C5 hydroxylation of multiple lysine residues, including in the bromodomain-containing proteins BRD2, BRD3 and BRD4. The role(s) of JMJD6-catalysed substrate hydroxylation are unclear. JMJD6 is important in development and JMJD6 catalysis may promote cancer. We report solid-phase extraction coupled to mass spectrometry assays monitoring JMJD6-catalysed hydroxylation of BRD2-4 derived oligopeptides containing multiple lysyl residues. The assays enabled determination of apparent steady-state kinetic parameters for 2OG, Fe(ii), l-ascorbate, O2 and BRD substrates. The JMJD6 K app m for O2 was comparable to that reported for the structurally related 2OG oxygenase factor inhibiting hypoxia-inducible factor-α (FIH), suggesting potential for limitation of JMJD6 activity by O2 availability in cells, as proposed for FIH and some other 2OG oxygenases. The new assays will help development of small-molecule JMJD6 inhibitors for functional assignment studies and as potential cancer therapeutics.","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11878239/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143568429","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}

引用次数: 0

Design and application of a fluorescent probe for imaging of endogenous Bruton's tyrosine kinase with preserved enzymatic activity.

IF 4.2

RSC Chemical Biology Pub Date : 2025-02-20 DOI: 10.1039/d4cb00313f

Anna P Valaka, Hampus Nyström, Liliana Håversen, Carlos Benitez-Martin, Clara Schäfer, Woo Suk Jang, Alessandro Camponeschi, Joakim Andréasson, Jan Borén, Morten Grøtli

{"title":"Design and application of a fluorescent probe for imaging of endogenous Bruton's tyrosine kinase with preserved enzymatic activity.","authors":"Anna P Valaka, Hampus Nyström, Liliana Håversen, Carlos Benitez-Martin, Clara Schäfer, Woo Suk Jang, Alessandro Camponeschi, Joakim Andréasson, Jan Borén, Morten Grøtli","doi":"10.1039/d4cb00313f","DOIUrl":"https://doi.org/10.1039/d4cb00313f","url":null,"abstract":"Fluorophore integration into proteins within living cells is essential for exploring proteins in their natural environment. Bruton's tyrosine kinase (BTK), is a validated oncology target and is crucial for B cell proliferation and activation. Developing BTK-labelling probes is key to understand BTK's dynamic signalling pathway. In this work, we aimed to develop a novel fluorescent labelling probe for endogenous BTK imaging while preserving its enzymatic activity. Evobrutinib, a second-generation BTK inhibitor with high selectivity, was chosen as the scaffold. We designed two probes, Evo-1 and Evo-2, with a BODIPY fluorescent group, guided by molecular modelling. The synthesis was achieved using optimised Suzuki-Miyaura cross-coupling and amide coupling reactions. Biochemical assays confirmed covalent binding to Cys481 of BTK while preserving its enzymatic activity. Labelling of endogenous BTK with Evo-2 with reduced off-target effects in Ramos cells was validated in cellular assays. The dynamic signalling pathway of BTK in its native environment was investigated by confocal microscopy with Evo-2. This methodology is a valuable asset in the chemical biology toolbox for studying protein dynamics and interactions in real time without interfering with the protein activity.","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11867108/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143543872","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}

引用次数: 0

Three- and four-stranded nucleic acid structures and their ligands.

IF 4.2

RSC Chemical Biology Pub Date : 2025-02-19 DOI: 10.1039/d4cb00287c

Yoshiki Hashimoto, Sumit Shil, Mitsuki Tsuruta, Keiko Kawauchi, Daisuke Miyoshi

引用次数: 0

Functionalization of a versatile fluorescent sensor for detecting protease activity and temporally gated opioid sensing.

IF 4.2

RSC Chemical Biology Pub Date : 2025-02-18 DOI: 10.1039/d4cb00276h

Jennifer Sescil, Hailey Fiel, Steven M Havens, Emma Fu, Xingyu Li, Kayla E Kroning, Isabel Solowiej, Peng Li, Wenjing Wang

{"title":"Functionalization of a versatile fluorescent sensor for detecting protease activity and temporally gated opioid sensing.","authors":"Jennifer Sescil, Hailey Fiel, Steven M Havens, Emma Fu, Xingyu Li, Kayla E Kroning, Isabel Solowiej, Peng Li, Wenjing Wang","doi":"10.1039/d4cb00276h","DOIUrl":"10.1039/d4cb00276h","url":null,"abstract":"Genetically encoded fluorescent sensors have been widely applied to detect cell signaling molecules and events. We previously designed a fluorescent sensor motif suitable for detecting protease activity and opioids. In this manuscript, we demonstrated the motif's first use for reporting on protease activity in animal models, demonstrating a high signal-to-background ratio of 29. We further functionalized this sensor motif to detect the activity of the coronavirus main protease, Mpro, and demonstrated its utility in characterizing an Mpro inhibitor. The Mpro sensor will facilitate the study of coronaviral activity in cell cultures and potentially in animal models. Additionally, we developed an innovative method for engineering a protease-based time-gating mechanism using this versatile sensor motif, allowing the temporally controlled detection of opioids. This time-gating strategy for detecting opioids can be generalized to other similar sensors, enabling detection of G protein-coupled receptor ligands with improved temporal resolution.","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11835013/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143460115","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}

引用次数: 0

Covalent functionalization of G protein-coupled receptors by small molecular probes.

IF 4.2

RSC Chemical Biology Pub Date : 2025-02-14 DOI: 10.1039/d4cb00294f

Bert L H Beerkens, Adriaan P IJzerman, Laura H Heitman, Daan van der Es

{"title":"Covalent functionalization of G protein-coupled receptors by small molecular probes.","authors":"Bert L H Beerkens, Adriaan P IJzerman, Laura H Heitman, Daan van der Es","doi":"10.1039/d4cb00294f","DOIUrl":"10.1039/d4cb00294f","url":null,"abstract":"Roughly one-third of all marketed drugs act by binding to one or more of the >800 human GPCRs, primarily through activation or inhibition via the orthosteric binding site. In addition, novel strategies to alter GPCR functioning are being developed, including allosteric, biased and covalently binding ligands. Molecular probes play an important role in verifying such drug molecules with new modes of action and providing information on all factors involved in GPCR signalling. Various types of molecular probes have been developed, ranging from small molecules to antibodies, each bearing its own advantages and disadvantages. In this mini-review, a closer look is taken at small molecular probes that functionalize GPCRs in a covalent manner, such as through the conjugation of reporter groups like fluorophores or biotin. Covalently bound reporter groups allow the investigation of GPCRs across an increasing range of biochemical assay types, yielding new insights into GPCR signalling pathways. Here, a broad range of recently developed 'functionalized covalent probes' is summarized. Furthermore, the use of these probes in biochemical assays and their applications in the field of GPCR research are discussed. Lastly, a view on possible future applications of these types of small molecular probes is provided.","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11827490/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143434001","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}

引用次数: 0

Decoding allosteric landscapes: computational methodologies for enzyme modulation and drug discovery.

IF 4.2

RSC Chemical Biology Pub Date : 2025-02-14 DOI: 10.1039/d4cb00282b

Ruidi Zhu, Chengwei Wu, Jinyin Zha, Shaoyong Lu, Jian Zhang

{"title":"Decoding allosteric landscapes: computational methodologies for enzyme modulation and drug discovery.","authors":"Ruidi Zhu, Chengwei Wu, Jinyin Zha, Shaoyong Lu, Jian Zhang","doi":"10.1039/d4cb00282b","DOIUrl":"10.1039/d4cb00282b","url":null,"abstract":"Allosteric regulation is a fundamental mechanism in enzyme function, enabling dynamic modulation of activity through ligand binding at sites distal to the active site. Allosteric modulators have gained significant attention due to their unique advantages, including enhanced specificity, reduced off-target effects, and the potential for synergistic interaction with orthosteric agents. However, the inherent complexity of allosteric mechanisms has posed challenges to the systematic discovery and design of allosteric modulators. This review discusses recent advancements in computational methodologies for identifying and characterizing allosteric sites in enzymes, emphasizing techniques such as molecular dynamics (MD) simulations, enhanced sampling methods, normal mode analysis (NMA), evolutionary conservation analysis, and machine learning (ML) approaches. Advanced tools like PASSer, AlloReverse, and AlphaFold have further enhanced the understanding of allosteric mechanisms and facilitated the design of selective allosteric modulators. Case studies on enzymes such as Sirtuin 6 (SIRT6) and MAPK/ERK kinase (MEK) demonstrate the practical applications of these approaches in drug discovery. By integrating computational predictions with experimental validation, this review highlights the transformative potential of computational strategies in advancing allosteric drug discovery, offering innovative opportunities to regulate enzyme activity for therapeutic benefits.","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11836628/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143469649","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}

引用次数: 0