ACS Chemical Biology最新文献

Improved Nucleoside (2'-Deoxy)Ribosyltransferases Maximize Enzyme Promiscuity while Maintaining Catalytic Efficiency. 改进的核苷（2'-脱氧）核糖基转移酶在保持催化效率的同时最大限度地提高酶的混杂性。

IF 3.8 2区生物学

ACS Chemical Biology Pub Date : 2025-10-17 DOI: 10.1021/acschembio.5c00120

Peijun Tang, Greice M Zickuhr, Alison L Dickson, Christopher J Harding, Suneeta Devi, Tomas Lebl, David J Harrison, Rafael G da Silva, Clarissa M Czekster

{"title":"Improved Nucleoside (2'-Deoxy)Ribosyltransferases Maximize Enzyme Promiscuity while Maintaining Catalytic Efficiency.","authors":"Peijun Tang, Greice M Zickuhr, Alison L Dickson, Christopher J Harding, Suneeta Devi, Tomas Lebl, David J Harrison, Rafael G da Silva, Clarissa M Czekster","doi":"10.1021/acschembio.5c00120","DOIUrl":"https://doi.org/10.1021/acschembio.5c00120","url":null,"abstract":"Nucleoside analogues have been extensively used to treat viral and bacterial infections and cancer for more than 60 years. However, their chemical synthesis is complex and often requires multiple steps and a dedicated synthetic route for every new nucleoside to be produced. Wild type nucleoside 2'-deoxyribosyltransferase enzymes are promising for biocatalysis. Guided by the structure of the enzyme from the thermophilic organism Chroococcidiopsis thermalis PCC 7203 (CtNDT) bound to the ribonucleoside analogue Immucillin-H, we designed mutants of CtNDT and the psychrotolerant Bacillus psychrosaccharolyticus (BpNDT) to improve catalytic efficiency with 3'-deoxynucleosides and ribonucleosides, while maintaining nucleobase promiscuity to generate over 100 distinct nucleoside products. Enhanced catalytic efficiency toward ribonucleosides and 3'-deoxyribonucleosides occurred via gains in turnover rate, rather than improved substrate binding. We determined the crystal structures of two engineered variants as well as kinetic parameters with different substrates, unveiling molecular details underlying their expanded substrate scope. Our rational approach generated robust enzymes and a roadmap for reaction conditions applicable to a wide variety of substrates.","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145311972","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

Leveraging Vulnerabilities in Copper Trafficking for Synergistic Antifungal Activity. 利用铜贩运的漏洞协同抗真菌活性。

IF 3.8 2区生物学

ACS Chemical Biology Pub Date : 2025-10-16 DOI: 10.1021/acschembio.5c00525

Catherine A Denning-Jannace, Katherine J James, Carlos R Monteagudo, Grace R Sturrock, Amy T R Robison, Francesca A Vaccaro, Sophia A Kuhn, Michael C Fitzgerald, Katherine J Franz

{"title":"Leveraging Vulnerabilities in Copper Trafficking for Synergistic Antifungal Activity.","authors":"Catherine A Denning-Jannace, Katherine J James, Carlos R Monteagudo, Grace R Sturrock, Amy T R Robison, Francesca A Vaccaro, Sophia A Kuhn, Michael C Fitzgerald, Katherine J Franz","doi":"10.1021/acschembio.5c00525","DOIUrl":"https://doi.org/10.1021/acschembio.5c00525","url":null,"abstract":"Candida albicans is an opportunistic fungal pathogen that causes millions of infections per year, for which more efficacious treatments are needed. Observations that azole antifungals incite C. albicans to adjust a variety of metal-dependent processes led us to hypothesize that vulnerabilities in metallohomeostasis incurred by drug stress could be leveraged by compounds that interrupt metal trafficking. Here, we show that tetrathiomolybdate (TTM), a copper (Cu) chelator that interferes with Cu trafficking and use, inhibits growth of C. albicans on its own and synergizes with select azoles to enhance antifungal activity. Proteomic and biochemical experiments revealed that TTM causes differential expression and stabilization of proteins involved in fermentation and oxidative stress responses in C. albicans. The synergy between TTM and azoles was found to arise from increased expression and stability of the nitric oxide dioxygenase Yhb1, a response driven by the decreased stability and activity incurred by TTM of CuZn superoxide dismutase 1. Addition of imidazole-based antifungals highjacks this stress response by inhibiting Yhb1. This study highlights the centrality of Cu homeostasis as a regulatory hub connecting energy production, oxidative stress management, and overall cellular fitness in ways that can be pharmacologically manipulated to enhance efficacy of existing antifungal agents.","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145306368","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

Fragment-Based Discovery of a Small-Molecule RhoGDI2 Ligand, HR3119, that Inhibits Cancer Cell Migration. 基于片段的小分子RhoGDI2配体HR3119抑制癌细胞迁移的发现

IF 3.8 2区生物学

ACS Chemical Biology Pub Date : 2025-10-16 DOI: 10.1021/acschembio.5c00361

Mingqing Liu, Shizhang Wan, Shuangxi Guo, Jiuyang Liu, Wenqian Li, Lei Wang, Fudong Li, Jiahai Zhang, Xing Liu, Dan Liu, Xuebiao Yao, Jia Gao, Ke Ruan, Wei He

{"title":"Fragment-Based Discovery of a Small-Molecule RhoGDI2 Ligand, HR3119, that Inhibits Cancer Cell Migration.","authors":"Mingqing Liu, Shizhang Wan, Shuangxi Guo, Jiuyang Liu, Wenqian Li, Lei Wang, Fudong Li, Jiahai Zhang, Xing Liu, Dan Liu, Xuebiao Yao, Jia Gao, Ke Ruan, Wei He","doi":"10.1021/acschembio.5c00361","DOIUrl":"https://doi.org/10.1021/acschembio.5c00361","url":null,"abstract":"Guanine nucleotide dissociation inhibitors (GDIs) proteins, including RhoGDI2, regulate the functions of Ras superfamily proteins that are known to be important cancer drug targets. Given the challenges in directly targeting Ras superfamily proteins with small molecules, targeting GDIs represents a unique opportunity but has seen limited success. In this work, we discovered HR3119 as the first ligand of RhoGDI2 with low-micromolar affinity (Kd = 8 μM) starting from a millimolar binding affinity fragment hit (Kd = 714 μM). HR3119 and its derivatives were rationally designed based on a series of ligand-bound RhoGDI2 crystal structures. HR3119 occupies the protein-protein interaction interface between RhoGDI2 and its endogenous ligand Rac1 to disrupt RhoGDI2-Rac1 binding. Interestingly, the complex structure suggests that (6R)-HR3119 preferentially bound to RhoGDI2 when crystallized with a racemic mixture. The purified (6R)-HR3119 demonstrated a nearly 100-fold binding affinity advantage compared to (6S)-HR3119. Finally, (6R)-HR3119 engaged with RhoGDI2 in cells and suppressed the migration of aggressive breast cancer cells. Our work provides insights into the discovery of small-molecule compounds targeting RhoGDI2 in terms of methodology, chemistry starting points, compound design, and phenotype studies, underscoring exciting new perspectives in early drug discovery.","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145297899","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 Probe Approach Reveals Endo-α-mannosidase Triages Misfolded Glycoproteins in the Calnexin/Calreticulin Cycle. 化学探针方法揭示Endo-α-甘露糖苷酶在钙连联蛋白/钙网蛋白循环中分类错误折叠的糖蛋白。

IF 3.8 2区生物学

ACS Chemical Biology Pub Date : 2025-10-16 DOI: 10.1021/acschembio.5c00532

Akito Taira, Makoto Hirano, Taiki Kuribara, Chie Watanabe, Satoshi Hiraki, Mitsuaki Hirose, Zalihe Hakki, Spencer J Williams, Yukishige Ito, Kiichiro Totani

{"title":"Chemical Probe Approach Reveals Endo-α-mannosidase Triages Misfolded Glycoproteins in the Calnexin/Calreticulin Cycle.","authors":"Akito Taira, Makoto Hirano, Taiki Kuribara, Chie Watanabe, Satoshi Hiraki, Mitsuaki Hirose, Zalihe Hakki, Spencer J Williams, Yukishige Ito, Kiichiro Totani","doi":"10.1021/acschembio.5c00532","DOIUrl":"https://doi.org/10.1021/acschembio.5c00532","url":null,"abstract":"Protein N-glycosylation contributes to folding and quality control of secretory proteins involved in protein misfolding diseases. A central quality control machinery of nascent glycoproteins in the endoplasmic reticulum (ER) is the calnexin/calreticulin (CNX/CRT) cycle. This cycle assists and checks protein folding by monitoring glycan structure, however how terminally misfolded glycoproteins are discharged from the cycle has remained unclear. Here, we leveraged chemical probes to identify a previously uncharacterized ER endo-α-mannosidase complex (ER-EM) that provides this missing release step. ER-EM selectively cleaves the terminal Glc-Man disaccharide from glucosylated high-mannose glycans only when the glycan is attached to a hydrophobic aglycone─an intrinsic marker of misfolded proteins─thereby converting Glc1Man9GlcNAc2 to Man8AGlcNAc2 glycans that cannot bind CNX/CRT. This activity is allosterically stimulated by hydrophobic ligands and shares the same aglycone preference as the folding sensor UDP-glucose: glycoprotein glucosyltransferase 1 (UGGT1), creating a two-tier surveillance system in which UGGT1 reglucosylates incompletely folded proteins, whereas ER-EM ejects those that fail to mature. Proteomic and native-gel analyses revealed that ER-EM is an ∼ 800 kDa assembly composed of at least carboxylesterase 1D (Ces1d), ERp57 and UGGT1; the lack of activity of recombinant Ces1d alone underscores that the catalytic function arises only through the concerted action of this multisubunit complex. ER-EM therefore acts as a folding-status-dependent triage factor that liberates terminally misfolded glycoproteins from the CNX/CRT cycle and targets them for degradation, adding a critical new branch to the ER quality-control network.","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145306394","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

Reversible Antagonism of Dopamine D1 Receptor Using a Photoswitchable Remotely Tethered Ligand. 利用可光切换的远程拴链配体对多巴胺D1受体的可逆拮抗作用。

IF 3.8 2区生物学

ACS Chemical Biology Pub Date : 2025-10-16 DOI: 10.1021/acschembio.5c00441

Belinda E Hetzler, Prashant Donthamsetti, Robert M Wolesensky, Cherise Stanley, Ehud Y Isacoff, Dirk Trauner

引用次数: 0

Addition to "Structural Basis of Substrate Recognition and Nucleotide Specificity in the Class III-b LanKC Enzyme SalKC". 补充“III-b类LanKC酶SalKC底物识别和核苷酸特异性的结构基础”。

IF 3.8 2区生物学

ACS Chemical Biology Pub Date : 2025-10-16 DOI: 10.1021/acschembio.5c00755

Yifan Li, Kai Shao, Yicong Li, Bee Koon Gan, Min Luo

引用次数: 0

Dissecting the Mechanisms Underlying Substrate Recognition and Functional Regulation of O-GlcNAc Cycling Enzymes. 剖析O-GlcNAc循环酶的底物识别和功能调控机制。

IF 3.8 2区生物学

ACS Chemical Biology Pub Date : 2025-10-15 DOI: 10.1021/acschembio.5c00633

Ziyong Z Hong, Jacques Lowe, Jiaoyang Jiang

{"title":"Dissecting the Mechanisms Underlying Substrate Recognition and Functional Regulation of O-GlcNAc Cycling Enzymes.","authors":"Ziyong Z Hong, Jacques Lowe, Jiaoyang Jiang","doi":"10.1021/acschembio.5c00633","DOIUrl":"https://doi.org/10.1021/acschembio.5c00633","url":null,"abstract":"Protein O-linked β-N-acetylglucosamine (O-GlcNAc) modification, known as O-GlcNAcylation, is an essential post-translational modification (PTM) that plays critical roles in regulating various cellular processes, ranging from transcription and signal transduction to protein degradation. O-GlcNAcylation levels are dynamically regulated by a single pair of human enzymes: O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA). Dysregulation of O-GlcNAcylation has been implicated in many diseases, including cancer, diabetes, neurodegeneration, and cardiovascular disorders. In the past decade, remarkable progress has been achieved regarding the structures of OGT and OGA proteins, as well as a series of innovative chemical and engineered tools that inhibit or induce the activities of these enzymes. While initial studies mainly focused on the catalytic domains of these enzymes, recent research has begun to uncover the structural and functional roles of non-catalytic regions. Notably, domains such as OGT's tetratricopeptide repeat (TPR) and intervening domain (Int-D), as well as OGA's stalk domain and pseudo histone acetyltransferase (pHAT) domain, have emerged as critical contributors to enzyme functions. This Account discusses recent progress in studying these essential enzymes, especially highlighting their unique structural features and intrinsic flexibility as potential mechanisms underlying their substrate recognition and functional regulation. New perspectives and research directions are also discussed. Such information is expected to facilitate the rational design of novel modulators of OGT and OGA to enable more specific functional control and potential treatment of disease.","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145297911","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

Chemoproteomic Profiling Reveals that Triiodothyronine Covalently Labels Cellular Proteins. 化学蛋白质组学分析揭示三碘甲状腺原氨酸共价标记细胞蛋白。

IF 3.8 2区生物学

ACS Chemical Biology Pub Date : 2025-10-14 DOI: 10.1021/acschembio.5c00539

Qian Zeng, Xiaoqiao Yan, Junyi Li, Yifei Wang, Ruichen Li, Guowan Zheng, Minghua Ge, Jingyan Ge

{"title":"Chemoproteomic Profiling Reveals that Triiodothyronine Covalently Labels Cellular Proteins.","authors":"Qian Zeng, Xiaoqiao Yan, Junyi Li, Yifei Wang, Ruichen Li, Guowan Zheng, Minghua Ge, Jingyan Ge","doi":"10.1021/acschembio.5c00539","DOIUrl":"https://doi.org/10.1021/acschembio.5c00539","url":null,"abstract":"Thyroid hormone triiodothyronine (T3) is a critical regulator of mammalian development and metabolism, traditionally recognized for its actions. In this study, we initially designed and synthesized a novel T3-based photoaffinity probe in order to identify T3-interacting proteins in live cells. Remarkably, our results demonstrate that T3 can covalently bind to cellular proteins independently of photoirradiation. To validate this covalent labeling, a fluorescein-modified T3 probe (FIT3) was utilized, and a CO/IP combined SILAC approach was applied to profile covalently labeled proteins. Focusing on one putative target, succinate dehydrogenase subunit A (SDHA), site-mapping analysis identified cysteine residues as likely covalent modification sites mediated by a nucleophilic reaction through iodine leaving from T3. Further, two activity-based probes bearing alkyne click handles at distinct positions on the T3 scaffold were further used to expand the profiling of covalent T3 targets. This approach uncovered over 1000 candidate proteins, including ATP1A1, HSP90AB1, and PRDX1, with selected targets validated by Western blotting. These findings reveal a previously unrecognized mode of thyroid hormone action involving covalent protein modification, challenging the classical paradigm of thyroid hormone signaling and offering new insights into hormone biology and potential therapeutic targets.","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145285025","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

Correction to "Understanding the Glycosylation Pathways Involved in the Biosynthesis of the Sulfated Glycan Ligands for Siglecs". 对“理解Siglecs硫酸化聚糖配体生物合成中涉及的糖基化途径”的更正。

IF 3.8 2区生物学

ACS Chemical Biology Pub Date : 2025-10-13 DOI: 10.1021/acschembio.5c00772

Jaesoo Jung, Edward N Schmidt, Hua-Chien Chang, Zeinab Jame-Chenarboo, Jhon R Enterina, Kelli A McCord, Taylor E Gray, Lauren Kageler, Chris D St Laurent, Chao Wang, Ryan A Flynn, Peng Wu, Kay-Hooi Khoo, Matthew S Macauley

引用次数: 0

Development of Second-Generation Acyl Silane Photoaffinity Probes for Cellular Chemoproteomic Profiling. 用于细胞化学蛋白质组学分析的第二代酰基硅烷光亲和探针的研制。

IF 3.8 2区生物学

ACS Chemical Biology Pub Date : 2025-10-12 DOI: 10.1021/acschembio.5c00396

Annika C S Page, Lauren M Orr, Margot L Meyers, Bridget P Belcher, Theodore G Coffey, Spencer O Scholz, Sabine Cismoski, Daniel K Nomura, F Dean Toste

{"title":"Development of Second-Generation Acyl Silane Photoaffinity Probes for Cellular Chemoproteomic Profiling.","authors":"Annika C S Page, Lauren M Orr, Margot L Meyers, Bridget P Belcher, Theodore G Coffey, Spencer O Scholz, Sabine Cismoski, Daniel K Nomura, F Dean Toste","doi":"10.1021/acschembio.5c00396","DOIUrl":"10.1021/acschembio.5c00396","url":null,"abstract":"Deconvolution of the protein targets of hit compounds from phenotypic screens, often conducted in live cells, is critical for understanding mechanism of action and identifying potentially hazardous off-target interactions. While photoaffinity labeling and chemoproteomics are long-established approaches for discovering small-molecule-protein interactions in live cells, there are a relatively small number of photoaffinity labeling strategies that can be applied for chemoproteomic target identification studies. Recently, we reported a novel chemical framework for photoaffinity labeling based on the photo-Brook rearrangement of acyl silanes and demonstrated its ability, when appended to protein-targeting ligands, to label recombinant proteins. Here, we report the application of these probes to live cell photoaffinity workflows, demonstrate their complementarity to current state-of-the-art minimalist diazirine-based photoaffinity probes, and introduce a modular synthetic route to access acyl silane scaffolds with improved labeling properties.","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145273100","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