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A Scavenger Hunt for a DyP-Peroxidase from a Metagenome: Curated Peroxidase Database-Assisted Primer Design and Protein Structure Elucidation. 从宏基因组中寻找dyp -过氧化物酶:策划过氧化物酶数据库辅助引物设计和蛋白质结构解析。
IF 3.5 2区 生物学
ACS Chemical Biology Pub Date : 2025-07-18 Epub Date: 2025-07-02 DOI: 10.1021/acschembio.5c00323
Shaimaa Tarek, Yasmin ElMaghloob, Hong Smith, Thomas J Smith, Marwa T ElRakaiby, Mohamed H Habib
{"title":"A Scavenger Hunt for a DyP-Peroxidase from a Metagenome: Curated Peroxidase Database-Assisted Primer Design and Protein Structure Elucidation.","authors":"Shaimaa Tarek, Yasmin ElMaghloob, Hong Smith, Thomas J Smith, Marwa T ElRakaiby, Mohamed H Habib","doi":"10.1021/acschembio.5c00323","DOIUrl":"10.1021/acschembio.5c00323","url":null,"abstract":"<p><p>Dye-decolorizing peroxidase (DyP)-type peroxidases are heme-containing enzymes that play a role in lignin synthesis and degradation and dye decolorization. Despite numerous studies about this class of enzymes, the enzyme remains under-explored. We used 1000 DyP sequences retrieved from the NCBI database to forge a phylogenetic tree. Nodes in the tree, where sequences displayed a degree of conservation, were used to design degenerate primers to locate DyP-peroxidase sequences from the DNA extract of a tannery wastewater sample. After PCR amplification and visualization using agarose electrophoresis, a band at the expected size of a DyP peroxidase (500-700 bp) was seen. TA cloning followed by blue-white colony selection validated our finding after amplicon sequencing of the PCR product to confirm the presence of an <i>Acinetobacter</i> species DyP-peroxidase. Our metagenomic DyP displayed 99% similarity to the DyP-peroxidase sequence found in the <i>Acinetobacter baumannii</i> ATCC 19606 strain. As a result, and due to the minute differences between our found DyP and the ATCC 19606 strain DyP, we expressed the latter cloned in a pET28b(+) vector and purified it from culture medium using <i>Escherichia coli</i> SoluBl21 as a host strain. A crude oxidation assay using 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) deemed the enzyme active as shown by the formation of a green color. The crystal structure of the enzyme was solved at 2.6 Å resolution (PDB ID 9OBR) using X-ray crystallography and presented as a hexamer in solution.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":"1783-1791"},"PeriodicalIF":3.5,"publicationDate":"2025-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144551414","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
IF 3.5 2区 生物学
ACS Chemical Biology Pub Date : 2025-07-18
Hu Zhu, Harrison C. Daly, Tae Gyun Yang, Josh Born, Gisela Andrea Camacho-Hernandez, Mingyang Yuan, Mari Inglese, Vinoth Kumar Chenniappan, Kris Zimmerman, Robin Hurst, Xin Hu, Amy Hauck Newman, Sergi Ferré, Rachel Friedman Ohana, Matthew D. Hall and Samarjit Patnaik*, 
{"title":"","authors":"Hu Zhu,&nbsp;Harrison C. Daly,&nbsp;Tae Gyun Yang,&nbsp;Josh Born,&nbsp;Gisela Andrea Camacho-Hernandez,&nbsp;Mingyang Yuan,&nbsp;Mari Inglese,&nbsp;Vinoth Kumar Chenniappan,&nbsp;Kris Zimmerman,&nbsp;Robin Hurst,&nbsp;Xin Hu,&nbsp;Amy Hauck Newman,&nbsp;Sergi Ferré,&nbsp;Rachel Friedman Ohana,&nbsp;Matthew D. Hall and Samarjit Patnaik*,&nbsp;","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"20 7","pages":"XXX-XXX XXX-XXX"},"PeriodicalIF":3.5,"publicationDate":"2025-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acschembio.5c00166","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144646172","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
IF 3.5 2区 生物学
ACS Chemical Biology Pub Date : 2025-07-18
Shijie Shen, Changbiao Chi, Keqiang Fan, Qian Zhang, Yang Xu, Jinmin Gao, Huitao Hu, Lijun Wang, Donghui Yang, Ming Ma* and Guohui Pan*, 
{"title":"","authors":"Shijie Shen,&nbsp;Changbiao Chi,&nbsp;Keqiang Fan,&nbsp;Qian Zhang,&nbsp;Yang Xu,&nbsp;Jinmin Gao,&nbsp;Huitao Hu,&nbsp;Lijun Wang,&nbsp;Donghui Yang,&nbsp;Ming Ma* and Guohui Pan*,&nbsp;","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"20 7","pages":"XXX-XXX XXX-XXX"},"PeriodicalIF":3.5,"publicationDate":"2025-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acschembio.5c00040","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144646183","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
IF 3.5 2区 生物学
ACS Chemical Biology Pub Date : 2025-07-18
Zachary D. Baker, Andrew R. Thompson, David D. Thomas and Nicholas M. Levinson*, 
{"title":"","authors":"Zachary D. Baker,&nbsp;Andrew R. Thompson,&nbsp;David D. Thomas and Nicholas M. Levinson*,&nbsp;","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"20 7","pages":"XXX-XXX XXX-XXX"},"PeriodicalIF":3.5,"publicationDate":"2025-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acschembio.5c00224","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144646194","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
IF 3.5 2区 生物学
ACS Chemical Biology Pub Date : 2025-07-18
Jeremy W. Harris, Flávio Antônio de Oliveira Simões, Erin N. Ryerson and William M. Marsiglia*, 
{"title":"","authors":"Jeremy W. Harris,&nbsp;Flávio Antônio de Oliveira Simões,&nbsp;Erin N. Ryerson and William M. Marsiglia*,&nbsp;","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"20 7","pages":"XXX-XXX XXX-XXX"},"PeriodicalIF":3.5,"publicationDate":"2025-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acschembio.5c00213","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144646185","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
IF 3.5 2区 生物学
ACS Chemical Biology Pub Date : 2025-07-18
Zelin Li, Yi Zhang, Jun Liang, Fengyu Jia, Jiacai Song, Demeng Sun, Chaowei Shi*, Changlin Tian* and Pan Shi*, 
{"title":"","authors":"Zelin Li,&nbsp;Yi Zhang,&nbsp;Jun Liang,&nbsp;Fengyu Jia,&nbsp;Jiacai Song,&nbsp;Demeng Sun,&nbsp;Chaowei Shi*,&nbsp;Changlin Tian* and Pan Shi*,&nbsp;","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"20 7","pages":"XXX-XXX XXX-XXX"},"PeriodicalIF":3.5,"publicationDate":"2025-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acschembio.5c00257","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144646186","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
Investigation of Glutarimide N-Alkylated Derivatives of Lenalidomide. 来那度胺戊二胺n -烷基化衍生物的研究。
IF 3.5 2区 生物学
ACS Chemical Biology Pub Date : 2025-07-18 Epub Date: 2025-06-16 DOI: 10.1021/acschembio.5c00272
Farah Kabir, Toshiaki Sonobe, Qian Zhu, Nandini Vallavoju, Yuka Amako, Christina M Woo
{"title":"Investigation of Glutarimide <i>N</i>-Alkylated Derivatives of Lenalidomide.","authors":"Farah Kabir, Toshiaki Sonobe, Qian Zhu, Nandini Vallavoju, Yuka Amako, Christina M Woo","doi":"10.1021/acschembio.5c00272","DOIUrl":"10.1021/acschembio.5c00272","url":null,"abstract":"<p><p>Lenalidomide is a thalidomide derivative that engages the E3 ligase substrate receptor cereblon (CRBN) to promote targeted protein degradation. Lenalidomide possesses a glutarimide moiety, which is responsible for CRBN engagement, and an isoindoline moiety, which promotes neosubstrate recruitment. Modification of the glutarimide is a generalizable prodrug strategy to inhibit CRBN binding for the selective activation of CRBN-dependent activity, yet these compounds may possess CRBN-independent effects. We prepared six <i>N</i>-alkylated glutarimide derivatives and found CRBN-independent effects on TNFα inhibition and selective effects in the cell viability profiles. Evaluation of selected compounds by global proteomics in KG1a cells reveals that the downregulation of Rab28 is CRBN-independent and mediated by autophagy. Finally, we developed a representative prodrug to demonstrate the enzymatic release of lenalidomide. Collectively, although some CRBN-independent properties are observed, modification of glutarimide is a generally viable strategy to prevent CRBN engagement in a prodrug strategy.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":"1756-1763"},"PeriodicalIF":3.5,"publicationDate":"2025-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144309239","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
Feature-Based Molecular Networking Guided Characterization of Clonocoprogen Siderophores with Anti-Pseudomonas aeruginosa Activity in Nematodes through Immune Up-Regulating Effects. 基于特征的分子网络引导下,通过免疫上调作用表征线虫抗铜绿假单胞菌活性的克隆原铁载体。
IF 3.5 2区 生物学
ACS Chemical Biology Pub Date : 2025-07-18 Epub Date: 2025-06-22 DOI: 10.1021/acschembio.5c00178
Guoliang Zhu, Weize Yuan, Kun Wang, Huimin Wu, Kangjie Lv, Xinye Wang, Alex Tuffour, Biao Ren, Jingyu Zhang, Chenglin Jiang, Yi Jiang, Tom Hsiang, Peter Shen Yu, Frederick M Ausubel, Lixin Zhang, Huanqin Dai, Xueting Liu
{"title":"Feature-Based Molecular Networking Guided Characterization of Clonocoprogen Siderophores with Anti-<i>Pseudomonas aeruginosa</i> Activity in Nematodes through Immune Up-Regulating Effects.","authors":"Guoliang Zhu, Weize Yuan, Kun Wang, Huimin Wu, Kangjie Lv, Xinye Wang, Alex Tuffour, Biao Ren, Jingyu Zhang, Chenglin Jiang, Yi Jiang, Tom Hsiang, Peter Shen Yu, Frederick M Ausubel, Lixin Zhang, Huanqin Dai, Xueting Liu","doi":"10.1021/acschembio.5c00178","DOIUrl":"10.1021/acschembio.5c00178","url":null,"abstract":"<p><p>Antibiotic resistance poses a severe threat to human health, necessitating research into antibiotics with unique mechanisms to combat drug resistance. Natural siderophores and their synthetic derivatives have become a promising resource for the development of anti-infectious agents. In this study, we introduce a new anti-infective agent with a mode of action that enhances host immunity without exerting direct antibacterial activity. We identified immune-activating clonocoprogen siderophores from the fungus <i>Clonostachys rosea</i> isolate CR15020 using an integrated approach, including genome mining, feature-based molecular networking (FBMN) and a nematode screening model. Although these siderophores displayed no inherent antibacterial properties, they significantly improved survival of <i>Caenorhabditis elegans</i> exposed to <i>Pseudomonas aeruginosa</i>, with EC<sub>50</sub> values ranging from 1.85 to 10.86 μM. This protection was achieved through up-regulation of the nematode's p38-MAPK and DAF/IGF immune pathways, as well as reducing the excretion of pyoverdine by <i>P. aeruginosa</i>. By leveraging immune modulation rather than direct bacterial inhibition, this approach offers a promising alternative to conventional antibiotics, addressing the urgent challenge of antibiotic resistance.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":"1450-1456"},"PeriodicalIF":3.5,"publicationDate":"2025-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144367624","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
Distal Covalent Targeting Suppresses Signaling of Oncogenic K-Ras(G13C) in Cancer Cells. 远端共价靶向抑制癌细胞中致癌K-Ras(G13C)的信号传导。
IF 3.5 2区 生物学
ACS Chemical Biology Pub Date : 2025-07-18 Epub Date: 2025-07-09 DOI: 10.1021/acschembio.5c00249
Qinheng Zheng, Tianfang Shen, Julius Pampel, Kevan M Shokat
{"title":"Distal Covalent Targeting Suppresses Signaling of Oncogenic K-Ras(G13C) in Cancer Cells.","authors":"Qinheng Zheng, Tianfang Shen, Julius Pampel, Kevan M Shokat","doi":"10.1021/acschembio.5c00249","DOIUrl":"10.1021/acschembio.5c00249","url":null,"abstract":"<p><p>Oncogenic mutations of Ras are among the most common genetic alterations in human cancer, with an estimated disease burden of >3 million new patients per year worldwide. Despite widespread appreciation of the importance of Ras in cancer, direct binding ligands, which block downstream signaling, were not reported until 2013 due to the lack of obvious drug binding pockets in the protein. The clinically approved K-Ras inhibitors are mutant-selective as they rely on covalent recognition of the highly nucleophilic somatic cysteine residue of K-Ras(G12C). Recent preclinical reports of noncovalent K-Ras binding inhibitors have emerged, which lack mutant specificity and exhibit varying degrees of biochemical preference for mutant K-Ras over the wild-type. An adjacent glycine-13 mutation, p. G13C, particularly abundant in lung, colorectal, and pancreatic cancer, has not been targeted with an approved therapeutic molecule. Here, we report a series of targeted electrophiles designed to covalently modify Cys13 in K-Ras(G13C), overcoming the structural challenge posed by its shifted position relative to Cys12 in K-Ras(G12C). These inhibitors effectively alkylate K-Ras(G13C) in both GDP- and GTP-bound states, block effector interactions, and suppress the growth of K-Ras(G13C)-mutation cancer cell lines. Our findings expand the landscape of covalent K-Ras inhibitors beyond G12 mutations, providing a new therapeutic strategy for K-Ras(G13C)-driven cancers.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":"1696-1706"},"PeriodicalIF":3.5,"publicationDate":"2025-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144590021","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
Targeted O-GlcNAcylation of CK2α Triggers Its Ubiquitin-Proteasome Degradation and Alters Downstream Phosphorylation. CK2α靶向o - glcn酰化触发其泛素蛋白酶体降解并改变下游磷酸化。
IF 3.5 2区 生物学
ACS Chemical Biology Pub Date : 2025-07-18 Epub Date: 2025-06-16 DOI: 10.1021/acschembio.5c00223
Tongyang Xu, Bowen Ma, Yuanpei Li, Zhihao Guo, Miaomiao Zhang, Billy Wai-Lung Ng
{"title":"Targeted O-GlcNAcylation of CK2α Triggers Its Ubiquitin-Proteasome Degradation and Alters Downstream Phosphorylation.","authors":"Tongyang Xu, Bowen Ma, Yuanpei Li, Zhihao Guo, Miaomiao Zhang, Billy Wai-Lung Ng","doi":"10.1021/acschembio.5c00223","DOIUrl":"10.1021/acschembio.5c00223","url":null,"abstract":"<p><p>O-Linked β-<i>N</i>-acetylglucosamine-modification (O-GlcNAcylation) is an important post-translational modification (PTM), yet dissecting its protein-specific functions has remained challenging. Here, we applied our previously reported chemical biology tool, the O-GlcNAcylation Targeting Chimera (OGTAC), to specifically induce O-GlcNAcylation of the casein kinase II subunit α (CK2α) at Ser347 in living cells. We found that this targeted O-GlcNAcylation destabilized CK2α through ubiquitin-proteasome degradation and enhanced its interaction with cereblon (CRBN). Overexpression and knockdown experiments also indicated CK2α as a substrate of the Cullin-RING E3 ubiquitin ligase 4-CRBN (CRL4<sup>CRBN</sup>) E3 ligase complex. Furthermore, the OGTAC-induced O-GlcNAcylation of CK2α reprogrammed phosphorylation of Akt and PFKP. These findings reveal that a single O-GlcNAc modification can serve as a molecular switch, controlling the protein stability and downstream phosphorylation of CK2α. More broadly, our results highlight the profound utility of the OGTAC-mediated O-GlcNAcylation to interrogate its cellular functions with specificity, overcoming limitations inherent to prior global perturbation methods.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":"1646-1659"},"PeriodicalIF":3.5,"publicationDate":"2025-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12281484/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144300535","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
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