ACS Chemical Biology最新文献_第4页

Structural Elucidation and Covalent Modulation of the Autorepressed Orphan Nuclear Receptor NR2F6 自抑制孤儿核受体NR2F6的结构解析和共价调控。

IF 3.8 2区生物学

ACS Chemical Biology Pub Date : 2025-09-10 DOI: 10.1021/acschembio.5c00475

Guido J. M. Oerlemans, Maxime C. M. van den Oetelaar, Siebe P. van den Elzen and Luc Brunsveld*,

{"title":"Structural Elucidation and Covalent Modulation of the Autorepressed Orphan Nuclear Receptor NR2F6","authors":"Guido J. M. Oerlemans, Maxime C. M. van den Oetelaar, Siebe P. van den Elzen and Luc Brunsveld*, ","doi":"10.1021/acschembio.5c00475","DOIUrl":"10.1021/acschembio.5c00475","url":null,"abstract":"The orphan nuclear receptor NR2F6 (Nuclear Receptor subfamily 2 group F member 6) is an emerging therapeutic target for cancer immunotherapy. Upregulation of NR2F6 expression in tumor cells has been linked to proliferation and metastasis, while in immune cells NR2F6 inhibits antitumor T-cell responses. Small molecule modulation of NR2F6 activity might therefore be a novel strategy in cancer treatment, benefiting from this dual role of NR2F6. However, there are no molecular strategies available for targeting NR2F6, hampered among others by lack of structural insights and appropriate biochemical assays. To overcome these challenges, several noncanonical nuclear receptor coregulator peptide motifs were identified to be constitutively recruited to the NR2F6 ligand binding domain (LBD). Co-crystallization of the NR2F6 LBD with a peptide from the coregulator Nuclear Receptor Binding SET Domain Protein 1 (NSD1) enabled, for the first time, the structural elucidation of the unliganded (apo) form of NR2F6. This revealed an autorepressed, homodimeric LBD conformation in which helix 12 folds over the canonical coregulator binding site, generating an alternative contact surface for NSD1 binding. Screening of a focused library of covalent NR probes identified compounds that preferentially target a cysteine residue near the NSD1 binding site, inhibiting NR2F6 coregulator recruitment. Combined, these results provide structural insights into the ligand-independent transcriptional activity of NR2F6 and may serve as a starting point for the development of novel NR2F6 modulators.","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"20 9","pages":"2308–2317"},"PeriodicalIF":3.8,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acschembio.5c00475","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145032391","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Bacillus spp. Antibacterial Activity Induced by Triphenyl Tetrazolium Chloride against Ralstonia solanacearum: Oxidative Stress Response and Metabolome Changes 三苯基四氮唑氯诱导芽孢杆菌对茄枯菌的抑菌活性：氧化应激反应和代谢组变化。

IF 3.8 2区生物学

ACS Chemical Biology Pub Date : 2025-09-04 DOI: 10.1021/acschembio.5c00171

Carolina González-Marín, Camilo García-Botero, Estefanía Metaute-Molina, Andrés Mauricio Caraballo-Rodríguez, Pieter C. Dorrestein and Valeska Villegas-Escobar*,

{"title":"Bacillus spp. Antibacterial Activity Induced by Triphenyl Tetrazolium Chloride against Ralstonia solanacearum: Oxidative Stress Response and Metabolome Changes","authors":"Carolina González-Marín, Camilo García-Botero, Estefanía Metaute-Molina, Andrés Mauricio Caraballo-Rodríguez, Pieter C. Dorrestein and Valeska Villegas-Escobar*, ","doi":"10.1021/acschembio.5c00171","DOIUrl":"10.1021/acschembio.5c00171","url":null,"abstract":"High salt concentrations affect the electron transport chain of bacterial cells, leading to an oxidative stress response that encompasses the formation of reactive oxygen species (ROS). The salt 2,3,5-triphenyltetrazolium chloride (TTC) triggers antibacterial activity against the phytopathogen Ralstonia solanacearum in Bacillus species; however, the underlying mechanisms remain unknown. Here, we tested the hypothesis that TTC-inducible activity is related to the formation of ROS and its metabolites. We found that l-ascorbic acid, superoxide dismutase, and catalase counteracted TTC-inducible activity in various Bacillus species. Furthermore, R. solanacearum exhibited a higher susceptibility to H2O2 than Bacillus spp. Genomic analysis showed differences in stress-related genes, with Bacillus strains containing the ROS scavengers bacillithiol and bacillibactin, while glutathione inR. solanacearum. Multivariate analysis indicated that the Bacillus species and TTC influence Bacillus metabolome, resulting in higher levels of quinazoline alkaloids, with potential antibacterial activity against R. solanacearum. Results suggest that TTC induces the production of O2•– and H2O2 and metabolites that arrest R. solanacearum growth.","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"20 9","pages":"2081–2094"},"PeriodicalIF":3.8,"publicationDate":"2025-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144990970","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

Photoinduced Nitric Oxide Exchange in the Diazeniumdiolate Siderophore, Pandorachelin 光诱导一氧化氮交换的双氮二酸铁载体。

IF 3.8 2区生物学

ACS Chemical Biology Pub Date : 2025-09-02 DOI: 10.1021/acschembio.5c00484

Melanie Susman, Christina Makris and Alison Butler*,

{"title":"Photoinduced Nitric Oxide Exchange in the Diazeniumdiolate Siderophore, Pandorachelin","authors":"Melanie Susman, Christina Makris and Alison Butler*, ","doi":"10.1021/acschembio.5c00484","DOIUrl":"10.1021/acschembio.5c00484","url":null,"abstract":"C-diazeniumdiolate siderophores are a small class of photoactive bacterial Fe(III) chelators. Driven by genome mining, we discovered a new C-type diazeniumdiolate siderophore, pandorachelin, produced by the rhizospheric bacterium, Pandoraea norimbergensis DSM 11628. The biosynthetic gene cluster encoding the production of pandorachelin is conserved across several Pandoraea species. Pandoraea spp. are environmentally widespread and are increasingly prevalent clinical pathogens, spurring new interest in their metabolites. UV irradiation photolytically cleaves the N–N bonds within the diazeniumdiolate-containing graminine constituents of pandorachelin. With EPR spin trapping, we directly detect nitric oxide released from the two C-diazeniumdiolate ligands of pandorachelin upon UV irradiation. Additionally, we show that nitric oxide can react with the intermediates during the photoreaction to reconstruct the diazeniumdiolate groups via exchange of the distal nitric oxide (NO) and thereby recover Fe(III)-binding capacity. The photochemistry of this class of siderophores points to a broader biological role, both in their propensity to release the biological signaling molecule, nitric oxide, and in their ability to undergo photoinduced NO exchange.","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"20 9","pages":"2318–2327"},"PeriodicalIF":3.8,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144935660","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 “Identification and Characterization of the Biosynthesis of the Hybrid NRPS-NIS Siderophore Nocardichelin” 修正“nrpps - nis铁载体Nocardichelin的生物合成鉴定与表征”。

IF 3.8 2区生物学

ACS Chemical Biology Pub Date : 2025-09-02 DOI: 10.1021/acschembio.5c00636

Mercedes B. Fisk, Jocelyn Barrera Ramirez, Collin E. Merrick, Timothy A. Wencewicz and Andrew M. Gulick*,

引用次数: 0

Temporal and Spatial Characterization of CUL3KLHL20-Driven Targeted Degradation of BET Family BRD Proteins by the Macrocycle-Based Degrader BTR2004 cul3klhl20驱动的大循环降解剂BTR2004靶向降解BET家族BRD蛋白的时空特征

IF 3.8 2区生物学

ACS Chemical Biology Pub Date : 2025-09-02 DOI: 10.1021/acschembio.5c00343

Phoebe H. Fechtmeyer, Cameron Martinez and Johannes T.-H. Yeh*,

{"title":"Temporal and Spatial Characterization of CUL3KLHL20-Driven Targeted Degradation of BET Family BRD Proteins by the Macrocycle-Based Degrader BTR2004","authors":"Phoebe H. Fechtmeyer, Cameron Martinez and Johannes T.-H. Yeh*, ","doi":"10.1021/acschembio.5c00343","DOIUrl":"10.1021/acschembio.5c00343","url":null,"abstract":"Targeted protein degradation (TPD) is a promising modality that leverages the endogenous cellular protein degradation machinery to degrade selected proteins. Recently, we validated CUL3KLHL20 E3 ligase as a new actionable E3 ligase for TPD application by developing a synthetic macrocycle ligand to engage KLHL20. Linking the KLHL20 ligand to JQ1, we created the PROTAC molecule BTR2004, which exhibited potent degradation of BET family proteins BRD 2, 3, and 4. As CUL3KLHL20 is new to the TPD field, here we report the first temporal and spatial characterization of CUL3KLHL20-driven TPD with BTR2004. Our study revealed the target protein degradation kinetics, BTR2004 intracellular activity half-life, and the onset of BTR2004 cell permeabilization. Employing proximity ligation and confocal microscopy techniques, we also illustrate the subcellular location of the ternary complex assembly upon BTR2004 treatment. These characterizations provide further insight into the processes that govern TPD and features that could be incorporated into the design of future macrocyclic PROTAC molecules.","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"20 9","pages":"2056–2062"},"PeriodicalIF":3.8,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144935593","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

ATP Regeneration by Polyphosphate Kinase Powers Efficient Oligosaccharide Synthesis Catalyzed by Glycoside Phosphorylases 多磷酸激酶的ATP再生促进了糖苷磷酸化酶催化的高效低聚糖合成。

IF 3.8 2区生物学

ACS Chemical Biology Pub Date : 2025-09-02 DOI: 10.1021/acschembio.5c00567

Xiaocong Wu, Shuang Xing, Di Ma, Haodong Wu, Guofeng Gu* and Xianwei Liu*,

引用次数: 0

Time-Resolved Analysis of Protein–Protein Ensembles Using a Destabilizing Domain to Map Dynamic Interactions of SARS-CoV-2 nsp15 利用不稳定结构域对SARS-CoV-2 nsp15的动态相互作用进行蛋白质-蛋白质组合的时间分辨分析。

IF 3.8 2区生物学

ACS Chemical Biology Pub Date : 2025-09-01 DOI: 10.1021/acschembio.5c00377

Crissey Cameron, R. Mason Clark, Adam M. Metts, Runze M. Jiang, Toya D. Scaggs, Kwangho Kim, Gary A. Sulikowski and Lars Plate*,

{"title":"Time-Resolved Analysis of Protein–Protein Ensembles Using a Destabilizing Domain to Map Dynamic Interactions of SARS-CoV-2 nsp15","authors":"Crissey Cameron, R. Mason Clark, Adam M. Metts, Runze M. Jiang, Toya D. Scaggs, Kwangho Kim, Gary A. Sulikowski and Lars Plate*, ","doi":"10.1021/acschembio.5c00377","DOIUrl":"10.1021/acschembio.5c00377","url":null,"abstract":"Dynamic protein–protein interactions are key drivers of many cellular processes. Determining the relative sequence and precise timing of these interactions is crucial for elucidating the functional dynamics of biological processes. Here, we developed a time-resolved analysis of protein–protein ensembles using a destabilizing domain (TRAPPED) to study protein–protein interactions in a temporal manner. We have taken advantage of a dihydrofolate reductase-destabilizing domain (DHFR(DD)) that can be fused to a protein of interest and is constitutively degraded by the proteosome. Addition of the ligand trimethoprim (TMP) can stabilize DHFR(DD), preventing proteasomal degradation of the fusion protein and thereby inducing accumulation in cells. We synthesized and optimized TRimethoprim Analog Probes that maintain stabilization activity and contain a terminal alkyne for Click functionalization and a thiol reactive group to covalently tag DHFR(DD). Click reaction with a biotin tag and subsequent streptavidin enrichment enable time-resolved mass spectrometric identification of interacting partners. We evaluated the timing of protein interactions of SARS-CoV-2 and SARS-CoV nonstructural protein 15 (nsp15) over a 2 h period. We found interactors GEMIN5 and YBX3, known regulators of SARS-CoV-2 infection that bind viral RNA, as well as CACYBP and FHL1 that implicate nsp15 in the disruption of host ERK1/2 signaling. We further revealed that these interactions remain relatively steady from 0 to 2 h post translation of nsp15. TRAPPED methodology can be applied to determine the sequence and timing of protein–protein interactions of temporally regulated biological processes such as viral infection or signal transduction.","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"20 9","pages":"2229–2242"},"PeriodicalIF":3.8,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acschembio.5c00377","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144935591","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Structural Basis of Substrate Recognition and Nucleotide Specificity in the Class III-b LanKC Enzyme SalKC 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 : 2025-08-29 DOI: 10.1021/acschembio.5c00378

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

{"title":"Structural Basis of Substrate Recognition and Nucleotide Specificity in the Class III-b LanKC Enzyme SalKC","authors":"Yifan Li, Kai Shao, Yicong Li, Bee Koon Gan and Min Luo*, ","doi":"10.1021/acschembio.5c00378","DOIUrl":"10.1021/acschembio.5c00378","url":null,"abstract":"Lanthipeptides are ribosomally synthesized and post-translationally modified peptides (RiPPs) with potent antimicrobial functions. Their biosynthesis is carried out by dedicated biosynthetic enzymes, including the recently described Class III-b LanKC enzymes, which represent a newly defined subclass of trifunctional synthetases. Here, we report the high-resolution cryo-EM structure and biochemical characterization of SalKC from Streptococcus salivarius, which catalyzes the maturation of the antimicrobial peptide salivaricin. SalKC adopts a conserved dimeric architecture stabilized by a His36 hotspot, mirroring that of the previously characterized PneKC. Cryo-EM structure resolved to sub-3.0 Å revealed the side chains of the bound leader peptide in atomic detail, allowing clear visualization of a conserved recognition motif and offering new structural insight into peptide engagement. Biochemical assays showed that SalKC prefers ATP over GTP, contrasting with the GTP-preferring PneKC. Structural comparison identified a single amino acid switch: Lys303 in SalKC versus His300 in PneKC, as the key determinant of this specificity. Mutation of Lys303 to histidine reverses nucleotide preference, confirming its functional role. Together, these findings revealed conserved principles and specialized adaptations within Class III-b LanKC enzymes and provided a molecular framework for understanding their substrate and cofactor selectivity.","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"20 9","pages":"2255–2265"},"PeriodicalIF":3.8,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144935585","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

Streamlined Fragment-Based Discovery Platform for Targeting Structured RNAs 针对结构化rna的流线型片段发现平台。

IF 3.8 2区生物学

ACS Chemical Biology Pub Date : 2025-08-29 DOI: 10.1021/acschembio.5c00372

Yilin Jia, Amirhossein Taghavi, Patrick R. A. Zanon and Matthew D. Disney*,

{"title":"Streamlined Fragment-Based Discovery Platform for Targeting Structured RNAs","authors":"Yilin Jia, Amirhossein Taghavi, Patrick R. A. Zanon and Matthew D. Disney*, ","doi":"10.1021/acschembio.5c00372","DOIUrl":"10.1021/acschembio.5c00372","url":null,"abstract":"Fragment-based drug discovery typically relies on specialized spectrometric methods to identify low-affinity compounds that bind to biomolecules. Here, we report a proof-of-concept study on the development of a streamlined fragment-based screening platform for small molecules targeting RNA. This method employs low molecular weight fragments appended with a diazirine reactive moiety and an alkyne tag. Upon photolysis and click chemistry with an azide-containing fluorophore, these compounds can be visualized for binding to the r(CUG) repeat expansion [r(CUG)exp] implicated in myotonic dystrophy type 1 (DM1). Fragments were found to bind the 1 × 1 nucleotide U/U internal loops formed when r(CUG)exp folds, guiding the design of homodimeric compounds capable of interacting with adjacent internal loops in a single molecule. One dimeric compound exhibited enhanced affinity and was converted into a proximity-induced covalent binder for prolonged target occupancy. This work establishes a versatile platform for targeting structured RNAs with potential applications across a variety of disease-relevant RNA targets.","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"20 9","pages":"2243–2254"},"PeriodicalIF":3.8,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acschembio.5c00372","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144935627","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Chemoselective Installation of Electrophilic Warheads onto C-Terminal Peptide Hydrazides for Covalent Protease Inhibitor Synthesis 共价蛋白酶抑制剂合成中c端肽酰肼上亲电战斗部的化学选择性安装。

IF 3.8 2区生物学

ACS Chemical Biology Pub Date : 2025-08-27 DOI: 10.1021/acschembio.5c00281

Shaun O’Hare, Kateryna A. Tolmachova and Jeffrey W. Bode*,

{"title":"Chemoselective Installation of Electrophilic Warheads onto C-Terminal Peptide Hydrazides for Covalent Protease Inhibitor Synthesis","authors":"Shaun O’Hare, Kateryna A. Tolmachova and Jeffrey W. Bode*, ","doi":"10.1021/acschembio.5c00281","DOIUrl":"10.1021/acschembio.5c00281","url":null,"abstract":"Covalent binders to protein targets offer a powerful approach to the generation of tool compounds and an increasingly common strategy for therapeutic development. The installation of electrophiles onto peptide binders, however, is often precluded by standard conditions for peptide synthesis, which involve strong nucleophiles, bases, and acids. The introduction of C-terminal electrophiles is further complicated by the C → N directionality of standard solid-phase peptide synthesis. Here, we employ chemoselective, site-specific functionalization of C-terminal peptide acyl hydrazides to install strong electrophiles on unprotected peptides. Using automated, high-throughput liquid handling and solid-phase extraction techniques, we have established a combinatorial workflow for the synthesis of peptide-derived covalent protease inhibitors. This methodology enables the synthesis and initial screening of inhibitor libraries in a 96-well plate format without the need for chromatographic purification prior to enzyme inhibition studies, leading to the identification of covalent Cathepsin S inhibitors active in the nanomolar range. When tested in cells, the covalent probes revealed strong off-target interactions with the protein disulfide isomerase PDIA1. These findings both underscore the role of chemoselective chemistries for covalent probe synthesis and highlight the utility of the platform for both the rapid identification of potent inhibitors and the detection of potential off-target interactions.","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"20 9","pages":"2134–2141"},"PeriodicalIF":3.8,"publicationDate":"2025-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144935784","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