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Recent advances in proximity labeling for chemical proteomics: Paving the way for in vivo applications 化学蛋白质组学近距离标记的最新进展：为体内应用铺平道路
IF 6.9 2区 生物学
Current Opinion in Chemical Biology Pub Date : 2025-07-04 DOI: 10.1016/j.cbpa.2025.102620
Fátima Yuri Tanimura Valor, Tomonori Tamura, Itaru Hamachi
{"title":"Recent advances in proximity labeling for chemical proteomics: Paving the way for in vivo applications","authors":"Fátima Yuri Tanimura Valor,&nbsp;Tomonori Tamura,&nbsp;Itaru Hamachi","doi":"10.1016/j.cbpa.2025.102620","DOIUrl":"10.1016/j.cbpa.2025.102620","url":null,"abstract":"<div><div>The integration of proximity labeling (PL) and advanced mass spectrometry-based proteomics is a robust framework for mapping protein–protein interaction (PPI) networks and local protein inventories in the crowded multimolecular environment of live cells. Over the last decade, numerous PL technologies such as biotin identification (BioID), ascorbate peroxidase (APEX) etc. using engineered enzymes or synthetic photocatalysts have been developed and successfully used in cell-based experiments. However, the application of such technologies beyond cultured cells, (i.e. in more complicated tissues or <em>in vivo</em>) remains challenging. In this review, we summarize the current issues in applying PL methods <em>in vivo</em> and highlight recent studies that could provide breakthroughs to overcome the existing limitations and expand the application of PL to tissues and <em>in vivo</em>.</div></div>","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":"87 ","pages":"Article 102620"},"PeriodicalIF":6.9,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144548597","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Editorial overview: Glycobiology (2024) 编辑概述：糖生物学（2024）
IF 6.9 2区 生物学
Current Opinion in Chemical Biology Pub Date : 2025-06-28 DOI: 10.1016/j.cbpa.2025.102619
Mia L. Huang, Peng Wu
{"title":"Editorial overview: Glycobiology (2024)","authors":"Mia L. Huang,&nbsp;Peng Wu","doi":"10.1016/j.cbpa.2025.102619","DOIUrl":"10.1016/j.cbpa.2025.102619","url":null,"abstract":"","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":"87 ","pages":"Article 102619"},"PeriodicalIF":6.9,"publicationDate":"2025-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144502448","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Editorial overview: Editorial of molecular imaging 编辑概述：分子成像编辑
IF 6.9 2区 生物学
Current Opinion in Chemical Biology Pub Date : 2025-06-27 DOI: 10.1016/j.cbpa.2025.102618
Jefferson Chan, Martin J. Schnermann
{"title":"Editorial overview: Editorial of molecular imaging","authors":"Jefferson Chan,&nbsp;Martin J. Schnermann","doi":"10.1016/j.cbpa.2025.102618","DOIUrl":"10.1016/j.cbpa.2025.102618","url":null,"abstract":"","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":"87 ","pages":"Article 102618"},"PeriodicalIF":6.9,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144502449","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The multifaceted repertoire of cellular reactive metabolites 细胞反应性代谢物的多面曲目
IF 6.9 2区 生物学
Current Opinion in Chemical Biology Pub Date : 2025-06-27 DOI: 10.1016/j.cbpa.2025.102607
Yimon Aye, Christine Winterbourn
{"title":"The multifaceted repertoire of cellular reactive metabolites","authors":"Yimon Aye,&nbsp;Christine Winterbourn","doi":"10.1016/j.cbpa.2025.102607","DOIUrl":"10.1016/j.cbpa.2025.102607","url":null,"abstract":"","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":"87 ","pages":"Article 102607"},"PeriodicalIF":6.9,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144490209","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Chemical synthesis and biological functions of carbohydrates 碳水化合物的化学合成及生物功能
IF 6.9 2区 生物学
Current Opinion in Chemical Biology Pub Date : 2025-06-27 DOI: 10.1016/j.cbpa.2025.102617
You Yang, Biao Yu
{"title":"Chemical synthesis and biological functions of carbohydrates","authors":"You Yang,&nbsp;Biao Yu","doi":"10.1016/j.cbpa.2025.102617","DOIUrl":"10.1016/j.cbpa.2025.102617","url":null,"abstract":"","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":"87 ","pages":"Article 102617"},"PeriodicalIF":6.9,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144490210","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Recent advances in chemical proteomics for protein profiling and targeted degradation 化学蛋白质组学在蛋白质分析和靶向降解方面的最新进展
IF 6.9 2区 生物学
Current Opinion in Chemical Biology Pub Date : 2025-06-26 DOI: 10.1016/j.cbpa.2025.102605
Peng-Kai Liu , Zicong Wang , Lingjun Li
{"title":"Recent advances in chemical proteomics for protein profiling and targeted degradation","authors":"Peng-Kai Liu ,&nbsp;Zicong Wang ,&nbsp;Lingjun Li","doi":"10.1016/j.cbpa.2025.102605","DOIUrl":"10.1016/j.cbpa.2025.102605","url":null,"abstract":"<div><div>Chemical proteomics has emerged as a powerful approach to decipher protein function, interactions, and targeted degradation pathways in complex biological systems. Recent advances in chemical labeling strategies, including activity-based protein profiling (ABPP), proximity labeling (PL), and proteolysis-targeting chimeras (PROTACs), have facilitated a deeper understanding of protein function and interaction networks. First, ABPP employs covalent probes to selectively label active enzymes, uncovering functional proteomics and drug–target interactions. Innovations such as PhosID-ABPP and streamlined cysteine ABPP have improved site-specific quantification and throughput, enabling proteome-wide analysis of enzyme activity and small-molecule interactions. Second, PL enables the characterization of transient protein–protein interactions using enzymatic or chemically triggered approaches. Advances including TurboID and TransitID enhanced the spatiotemporal resolution of PL. Third, PROTACs expand the scope of targeted protein degradation by leveraging the ubiquitin–proteasome system. Collectively, we highlight recent advancements in integrating mass spectrometry (MS) with these methodologies in the field of chemical proteomics.</div></div>","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":"87 ","pages":"Article 102605"},"PeriodicalIF":6.9,"publicationDate":"2025-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144481106","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Recent advances in metallophore research uncover functions in quorum sensing, antimicrobial activity, and lanthanide acquisition 最近的研究进展揭示了金属团在群体感应、抗菌活性和镧系元素获取方面的功能
IF 6.9 2区 生物学
Current Opinion in Chemical Biology Pub Date : 2025-06-19 DOI: 10.1016/j.cbpa.2025.102604
Ghazal Kamyabi, Erica L. Debley, Elizabeth M. Nolan
{"title":"Recent advances in metallophore research uncover functions in quorum sensing, antimicrobial activity, and lanthanide acquisition","authors":"Ghazal Kamyabi,&nbsp;Erica L. Debley,&nbsp;Elizabeth M. Nolan","doi":"10.1016/j.cbpa.2025.102604","DOIUrl":"10.1016/j.cbpa.2025.102604","url":null,"abstract":"<div><div>Metallophores are metal-chelating secondary metabolites that bacteria, fungi, and other organisms produce to acquire essential metal nutrients from their environment. This review highlights some recent discoveries in the field: the role of yersiniabactin in quorum sensing, the capacity of aspergillomarasmine A to inhibit bacterial Ni uptake, and the identification of methylolanthanin, a novel metallophore that enables bacterial lanthanide acquisition.</div></div>","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":"87 ","pages":"Article 102604"},"PeriodicalIF":6.9,"publicationDate":"2025-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144322528","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Ion transport across biological membranes 离子在生物膜上的传输
IF 6.9 2区 生物学
Current Opinion in Chemical Biology Pub Date : 2025-06-18 DOI: 10.1016/j.cbpa.2025.102606
Robin S. Bon, Matthew J. Langton
{"title":"Ion transport across biological membranes","authors":"Robin S. Bon,&nbsp;Matthew J. Langton","doi":"10.1016/j.cbpa.2025.102606","DOIUrl":"10.1016/j.cbpa.2025.102606","url":null,"abstract":"","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":"87 ","pages":"Article 102606"},"PeriodicalIF":6.9,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144307246","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Chemical tools to study and modulate glycan-mediated host-bacteria interactions 研究和调节聚糖介导的宿主-细菌相互作用的化学工具
IF 6.9 2区 生物学
Current Opinion in Chemical Biology Pub Date : 2025-06-04 DOI: 10.1016/j.cbpa.2025.102603
Divya Bhargava , Aniqa Chowdhury , Danielle H. Dube
{"title":"Chemical tools to study and modulate glycan-mediated host-bacteria interactions","authors":"Divya Bhargava ,&nbsp;Aniqa Chowdhury ,&nbsp;Danielle H. Dube","doi":"10.1016/j.cbpa.2025.102603","DOIUrl":"10.1016/j.cbpa.2025.102603","url":null,"abstract":"<div><div>Glycans cover the surfaces of all cells, where they are poised to mediate a two-way discourse between bacteria and host cells. In some instances, glycan-mediated interactions foster a symbiotic state, and in others, they tip the balance toward disease. Chemical biology approaches have begun to reveal the roles of glycans in host-bacteria interactions and provide novel pathways to modulate these interactions. Here, we highlight recent advances in the development and application of chemical biology tools to delineate the roles of glycans in bacterial adhesion, bacterial evasion of the host immune system, host recognition of bacterial cells, and endogenous mechanisms to maintain symbiosis. Further, we present glycan-based strategies to disrupt host-pathogen interactions and to promote the growth of beneficial bacteria.</div></div>","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":"87 ","pages":"Article 102603"},"PeriodicalIF":6.9,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144212337","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Probing ligand-induced local stability shifts: A sensitive approach to identify target proteins and binding sites at the proteomic scale 探测配体诱导的局部稳定性转移：一种在蛋白质组学尺度上识别靶蛋白和结合位点的敏感方法
IF 6.9 2区 生物学
Current Opinion in Chemical Biology Pub Date : 2025-05-31 DOI: 10.1016/j.cbpa.2025.102602
Keyun Wang , Yanan Li , Yanni Ma , Mingliang Ye
{"title":"Probing ligand-induced local stability shifts: A sensitive approach to identify target proteins and binding sites at the proteomic scale","authors":"Keyun Wang ,&nbsp;Yanan Li ,&nbsp;Yanni Ma ,&nbsp;Mingliang Ye","doi":"10.1016/j.cbpa.2025.102602","DOIUrl":"10.1016/j.cbpa.2025.102602","url":null,"abstract":"<div><div>Deciphering ligand-induced structural alterations represents a critical frontier in functional proteomics, offering transformative potential for both target identification and mechanistic understanding of ligand actions. Therefore, it is of great interest to develop robust proteomic approaches to uncover the binding relationship between ligands and the targeting proteins. The ligand modification-free approaches have the advantages of bypassing chemical modification and thus are broadly applicable to diverse ligands. Herein, in this review, we will introduce some recent methodology advancements for modification-free approaches in the identification of interactions between ligands and proteins. Especially, we will focus on a newly developed method, peptide-centric local stability assay (PELSA), which was designed to probe the ligand-induced local stability shifts and was demonstrated to have high sensitivity in revealing the binding regions at proteome level. The continued refinement and wider implementation of such technologies are expected to revolutionize fundamental research related with ligand–protein interactions.</div></div>","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":"87 ","pages":"Article 102602"},"PeriodicalIF":6.9,"publicationDate":"2025-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144184648","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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