ACS Chemical Biology最新文献_第5页

Strategic Acyl Carrier Protein Engineering Enables Functional Type II Polyketide Synthase Reconstitution In Vitro. 战略性酰基载体蛋白工程实现功能性II型聚酮合成酶的体外重组。

IF 3.5 2区生物学

ACS Chemical Biology Pub Date : 2025-01-17 Epub Date: 2025-01-02 DOI: 10.1021/acschembio.4c00678

Kevin Li, Yae In Cho, Mai Anh Tran, Christoph Wiedemann, Shuaibing Zhang, Rebecca S Koweek, Ngọc Khánh Hoàng, Grayson S Hamrick, Margaret A Bowen, Bashkim Kokona, Pierre Stallforth, Joris Beld, Ute A Hellmich, Louise K Charkoudian

{"title":"Strategic Acyl Carrier Protein Engineering Enables Functional Type II Polyketide Synthase Reconstitution In Vitro.","authors":"Kevin Li, Yae In Cho, Mai Anh Tran, Christoph Wiedemann, Shuaibing Zhang, Rebecca S Koweek, Ngọc Khánh Hoàng, Grayson S Hamrick, Margaret A Bowen, Bashkim Kokona, Pierre Stallforth, Joris Beld, Ute A Hellmich, Louise K Charkoudian","doi":"10.1021/acschembio.4c00678","DOIUrl":"10.1021/acschembio.4c00678","url":null,"abstract":"Microbial polyketides represent a structurally diverse class of secondary metabolites with medicinally relevant properties. Aromatic polyketides are produced by type II polyketide synthase (PKS) systems, each minimally composed of a ketosynthase-chain length factor (KS-CLF) and a phosphopantetheinylated acyl carrier protein (holo-ACP). Although type II PKSs are found throughout the bacterial kingdom, and despite their importance to strategic bioengineering, type II PKSs have not been well-studied in vitro. In cases where the KS-CLF can be accessed via E. coli heterologous expression, often the cognate ACPs are not activatable by the broad specificity Bacillus subtilis surfactin-producing phosphopantetheinyl transferase (PPTase) Sfp and, conversely, in systems where the ACP can be activated by Sfp, the corresponding KS-CLF is typically not readily obtained. Here, we report the high-yield heterologous expression of both cyanobacterial Gloeocapsa sp. PCC 7428 minimal type II PKS (gloPKS) components in E. coli, which allowed us to study this minimal type II PKS in vitro. Initially, neither the cognate PPTase nor Sfp converted gloACP to its active holo state. However, by examining sequence differences between Sfp-compatible and -incompatible ACPs, we identified two conserved residues in gloACP that, when mutated, enabled high-yield phosphopantetheinylation of gloACP by Sfp. Using analogous mutations, other previously Sfp-incompatible type II PKS ACPs from different bacterial phyla were also rendered activatable by Sfp. This demonstrates the generalizability of our approach and breaks down a longstanding barrier to type II PKS studies and the exploration of complex biosynthetic pathways.","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":"197-207"},"PeriodicalIF":3.5,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11744666/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142918804","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

A Small-Molecule Inhibitor of Gut Bacterial Urease Protects the Host from Liver Injury. 肠道细菌脲酶小分子抑制剂保护宿主免受肝损伤。

IF 3.5 2区生物学

ACS Chemical Biology Pub Date : 2025-01-17 Epub Date: 2025-01-08 DOI: 10.1021/acschembio.3c00556

Khyle C Richards-Corke, Yindi Jiang, Vladimir Yeliseyev, Yancong Zhang, Eric A Franzosa, Zhipeng A Wang, Maheeshi Yapa Abeywardana, Phillip A Cole, Curtis Huttenhower, Lynn Bry, Emily P Balskus

{"title":"A Small-Molecule Inhibitor of Gut Bacterial Urease Protects the Host from Liver Injury.","authors":"Khyle C Richards-Corke, Yindi Jiang, Vladimir Yeliseyev, Yancong Zhang, Eric A Franzosa, Zhipeng A Wang, Maheeshi Yapa Abeywardana, Phillip A Cole, Curtis Huttenhower, Lynn Bry, Emily P Balskus","doi":"10.1021/acschembio.3c00556","DOIUrl":"10.1021/acschembio.3c00556","url":null,"abstract":"Hyperammonemia is characterized by the accumulation of ammonia within the bloodstream upon liver injury. Left untreated, hyperammonemia contributes to conditions such as hepatic encephalopathy that have high rates of patient morbidity and mortality. Previous studies have identified gut bacterial urease, an enzyme that converts urea into ammonia, as a major contributor to systemic ammonia levels. Here, we demonstrate use of benurestat, a clinical candidate used against ureolytic organisms in encrusted uropathy, to inhibit urease activity in gut bacteria. Benurestat inhibits ammonia production by urease-encoding gut bacteria and is effective against individual microbes and complex gut microbiota. When administered to conventional mice with liver injury induced by thioacetamide exposure, benurestat reduced gut and serum ammonia levels and rescued 100% of mice from lethal acute liver injury. Overall, this study provides an important proof-of-concept for modulating host ammonia levels and microbiota-driven risks for hyperammonemia with gut microbiota-targeted small-molecule inhibitors.","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":"48-55"},"PeriodicalIF":3.5,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11744669/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142941418","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

Mapping the FGF2 Interactome Identifies a Functional Proteoglycan Coreceptor. 定位FGF2相互作用组鉴定功能性蛋白聚糖辅助受体。

IF 3.5 2区生物学

ACS Chemical Biology Pub Date : 2025-01-17 Epub Date: 2024-12-20 DOI: 10.1021/acschembio.4c00475

Meg Critcher, Jia Meng Pang, Mia L Huang

引用次数: 0

High-Throughput Computer Screen Aids Discovery of Methotrexate as miR-20b Inhibitor to Suppress Nonsmall Cell Lung Cancer Progression. 高通量计算机筛选有助于发现甲氨蝶呤作为miR-20b抑制剂抑制非小细胞肺癌进展。

IF 3.5 2区生物学

ACS Chemical Biology Pub Date : 2025-01-17 Epub Date: 2024-12-30 DOI: 10.1021/acschembio.4c00706

Xiaorui Shi, Chong Hu, Liangli Fan, Bin Guo, Jingyu Zhang, Chu Tang, Fu Wang

{"title":"High-Throughput Computer Screen Aids Discovery of Methotrexate as miR-20b Inhibitor to Suppress Nonsmall Cell Lung Cancer Progression.","authors":"Xiaorui Shi, Chong Hu, Liangli Fan, Bin Guo, Jingyu Zhang, Chu Tang, Fu Wang","doi":"10.1021/acschembio.4c00706","DOIUrl":"10.1021/acschembio.4c00706","url":null,"abstract":"MicroRNAs (miRNAs) play a significant role in tumor progression, and regulating miRNA expression with small molecules may offer a new approach to cancer therapy. Among them, miRNA-20b has been found to be dysregulated in several cancers, including nonsmall cell lung cancer (NSCLC). Herein, an in silico high-throughput computer screen was conducted to identify small molecules that downregulate miR-20b using the three-dimensional structure of the Dicer binding site on pre-miR-20b. Among 1058 small molecule compounds, Methotrexate (MTX), was discovered to be a potential miR-20b-specific inhibitor, which has been found to suppress miR-20b by specifically blocking Dicer processing in p53 wild-type A549 NSCLC cells but not in H1299 cells with p53 depletion. MTX effectively inhibited the proliferation, survival, migration, and invasion of A549 cells in a dose-dependent manner. Furthermore, the treatment of MTX up-regulated the expression of miR-20b target genes PTEN, STAT3, and HIF1α. Notably, MTX also significantly inhibited tumor growth in a mouse xenograft tumor model of NSCLC, with no observed tissue toxicity. Our findings indicate that MTX may have a novel role as an established drug in p53 wild-type NSCLC tumor therapy by down-regulating miR-20b expression. These findings are expected to provide preclinical evidence for miR-20b-targeting NSCLC therapeutic strategies.","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":"208-218"},"PeriodicalIF":3.5,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142906176","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

Painting Cell-Cell Interactions by Horseradish Peroxidase and Endogenously Generated Hydrogen Peroxide. 辣根过氧化物酶和内源性过氧化氢的细胞间相互作用。

IF 3.5 2区生物学

ACS Chemical Biology Pub Date : 2025-01-17 Epub Date: 2024-12-18 DOI: 10.1021/acschembio.4c00419

Youngjoon Cho, Inyoung Jeong, Kwang-Eun Kim, Hyun-Woo Rhee

{"title":"Painting Cell-Cell Interactions by Horseradish Peroxidase and Endogenously Generated Hydrogen Peroxide.","authors":"Youngjoon Cho, Inyoung Jeong, Kwang-Eun Kim, Hyun-Woo Rhee","doi":"10.1021/acschembio.4c00419","DOIUrl":"10.1021/acschembio.4c00419","url":null,"abstract":"Cell-cell interactions are fundamental in biology for maintaining physiological conditions with direct contact being the most straightforward mode of interaction. Recent advancements have led to the development of various chemical tools for detecting or identifying these interactions. However, the use of exogenous cues, such as toxic reagents, bulky probes, and light irradiation, can disrupt normal cell physiology. For example, the toxicity of hydrogen peroxide (H2O2) limits the applications of peroxidases in the proximity labeling field. In this study, we aimed to address this limitation by demonstrating that membrane-localized horseradish peroxidase (HRP-TM) efficiently utilizes endogenously generated extracellular H2O2. By harnessing endogenous H2O2, we observed that HRP-TM-expressing cells can effectively label contacting cells without the need for exogenous H2O2 treatment. Furthermore, we confirmed that HRP-TM labels proximal cells in an interaction-dependent manner. These findings offer a novel approach for studying cell-cell interactions under more physiological conditions without the confounding effects of exogenous stimuli. Our study contributes to elucidating cell-cell interaction networks in various model organisms, providing valuable insights into the dynamic interplay between cells in their native network.","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":"86-93"},"PeriodicalIF":3.5,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142845265","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 Impact of Sugar Conformation on the Single-Stranded DNA Selectivity of APOBEC3A and APOBEC3B Enzymes. 糖构象对 APOBEC3A 和 APOBEC3B 酶单链 DNA 选择性的影响

IF 3.5 2区生物学

ACS Chemical Biology Pub Date : 2025-01-17 Epub Date: 2024-12-16 DOI: 10.1021/acschembio.4c00540

Mackenzie K Wyllie, Clare K Morris, Nicholas H Moeller, Henry A M Schares, Ramkumar Moorthy, Christopher A Belica, Michael J Grillo, Özlem Demir, Alex M Ayoub, Michael A Carpenter, Hideki Aihara, Reuben S Harris, Rommie E Amaro, Daniel A Harki

{"title":"The Impact of Sugar Conformation on the Single-Stranded DNA Selectivity of APOBEC3A and APOBEC3B Enzymes.","authors":"Mackenzie K Wyllie, Clare K Morris, Nicholas H Moeller, Henry A M Schares, Ramkumar Moorthy, Christopher A Belica, Michael J Grillo, Özlem Demir, Alex M Ayoub, Michael A Carpenter, Hideki Aihara, Reuben S Harris, Rommie E Amaro, Daniel A Harki","doi":"10.1021/acschembio.4c00540","DOIUrl":"10.1021/acschembio.4c00540","url":null,"abstract":"The APOBEC3 family of polynucleotide cytidine deaminases has diverse roles as viral restriction factors and oncogenic mutators. These enzymes convert cytidine to uridine in single-stranded (ss)DNA, inducing genomic mutations that promote drug resistance and tumor heterogeneity. Of the seven human APOBEC3 members, APOBEC3A (A3A) and APOBEC3B (A3B) are most implicated in driving pro-tumorigenic mutations. How these enzymes engage and selectively deaminate ssDNA over RNA is not well understood. We previously conducted molecular dynamics (MD) simulations that support the role of sugar conformation as a key molecular determinant in nucleic acid recognition by A3B. We hypothesize that A3A and A3B selectively deaminate substrates in the 2'-endo (DNA) conformation and show reduced activity for 3'-endo (RNA) conformation substrates. Consequently, we have characterized A3A- and A3B-binding and deaminase activity with chimeric oligonucleotides containing cytidine analogues that promote either the 2'-endo or 3'-endo conformation. Using fluorescence polarization and gel-based deamination assays, we determined that sugar conformation preferentially impacts the ability of these enzymes to deaminate substrates and less so binding to substrates. Using MD simulations, we identify specific active site interactions that promote selectivity based on the 2'-endo conformation. These findings help inform the biological functions of A3A and A3B in providing antiviral innate immunity and pathogenic functions in cancer.","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":"117-127"},"PeriodicalIF":3.5,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142826638","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

Bioluminescent Probes for the Detection of Superoxide and Nitric Oxide. 用于超氧化物和一氧化氮检测的生物发光探针。

IF 3.5 2区生物学

ACS Chemical Biology Pub Date : 2025-01-17 Epub Date: 2024-12-16 DOI: 10.1021/acschembio.4c00551

Matthew A Larsen, Mike Valley, Natasha Karassina, Hui Wang, Wenhui Zhou, Jolanta Vidugiriene

引用次数: 0

12/15-Lipoxygenase-Derived Electrophilic Lipid Modifications in Phagocytic Macrophages. 12/15-脂氧化酶衍生的巨噬细胞亲电性脂质修饰。

IF 3.5 2区生物学

ACS Chemical Biology Pub Date : 2025-01-16 DOI: 10.1021/acschembio.4c00624

Kaiyuan Deng, Yosuke Isobe, Kazuya Tsumagari, Taiga Kato, Hiroyuki Arai, Koshi Imami, Makoto Arita

{"title":"12/15-Lipoxygenase-Derived Electrophilic Lipid Modifications in Phagocytic Macrophages.","authors":"Kaiyuan Deng, Yosuke Isobe, Kazuya Tsumagari, Taiga Kato, Hiroyuki Arai, Koshi Imami, Makoto Arita","doi":"10.1021/acschembio.4c00624","DOIUrl":"https://doi.org/10.1021/acschembio.4c00624","url":null,"abstract":"Macrophages remove apoptotic cells via phagocytosis, also known as efferocytosis, during inflammation to maintain tissue homeostasis. This process is accompanied by various metabolic changes in macrophages including the production of lipid metabolites by fatty acid oxygenases. Among these, highly reactive metabolites, called lipid-derived electrophiles (LDEs), modify cysteines and other nucleophilic amino acids in intracellular proteins. However, the landscape and functions of the modifications by these electrophilic metabolites have been poorly characterized. In this study, we used activity-based protein profiling to quantitatively profile the cysteine reactivity landscape and identify the potential targets of endogenous LDE modification during efferocytosis in mouse peritoneal macrophages. Using this methodology, we identified multiple cysteine sites that are highly likely to be modified by LDEs generated by 12/15-lipoxygenase (12/15-LOX), an efferocytosis-related fatty acid oxygenase that is highly expressed in peritoneal macrophages. Among these, actin-depolymerizing protein Cofilin-1 was found to be a target of 12/15-LOX-derived LDEs. In vitro Cofilin-1 activity was attenuated by 12/15-LOX-derived LDEs, and intracellular actin stabilization and efferocytosis were substantially enhanced by the LDE treatment of mouse peritoneal macrophages. These results highlighted the role of intracellular LDE modification during efferocytosis in macrophages.","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142995957","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

Amide Internucleoside Linkages Suppress the MicroRNA-like Off-Target Activity of Short Interfering RNA. 酰胺核苷间键抑制短干扰RNA的microrna样脱靶活性。

IF 3.5 2区生物学

ACS Chemical Biology Pub Date : 2025-01-15 DOI: 10.1021/acschembio.4c00824

Chandan Pal, Michael Richter, Jayamini Harasgama, Eriks Rozners

{"title":"Amide Internucleoside Linkages Suppress the MicroRNA-like Off-Target Activity of Short Interfering RNA.","authors":"Chandan Pal, Michael Richter, Jayamini Harasgama, Eriks Rozners","doi":"10.1021/acschembio.4c00824","DOIUrl":"https://doi.org/10.1021/acschembio.4c00824","url":null,"abstract":"RNA interference (RNAi) has rapidly matured as a novel therapeutic approach. In this field, chemical modifications have been critical to the clinical success of short interfering RNAs (siRNAs). Notwithstanding the significant advances, achieving robust durability and gene silencing in extrahepatic tissues, as well as reducing off-target effects of siRNA, are areas where chemical modifications can still improve siRNA performance. The present study developed the challenging synthesis of amide-linked guanosine dimers (GAM1G and GAM1A) and completed an \"amide walk\" one by one, systematically replacing every internucleoside phosphate with an amide linkage in a guide strand targeting the PIK3CB gene. Dual-luciferase and RT-qPCR assays in HeLa cells showed that, in a model system of unmodified siRNAs, the amide linkage at position 3 (between nucleosides 3 and 4) suppressed the cleavage of off-target YY1 and FADD mRNAs similarly to the industry gold standard modification glycol nucleic acid (GNA). These results suggest that amide linkages in the seed region have strong potential to improve the specificity of siRNAs by suppressing the microRNA-like off-target activity.","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142981985","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

Mapping snoRNA Targets Transcriptome-Wide with snoKARR-seq. 利用snoKARR-seq在转录组范围内定位snoRNA目标。

IF 3.5 2区生物学

ACS Chemical Biology Pub Date : 2025-01-14 DOI: 10.1021/acschembio.4c00813

Bei Liu

引用次数: 0