ACS Chemical Biology最新文献

筛选
英文 中文
SHAPE-Based Chemical Probes for Studying preQ1-RNA Interactions in Living Bacteria. 基于形状的化学探针研究活菌中preQ1-RNA相互作用
IF 3.8 2区 生物学
ACS Chemical Biology Pub Date : 2025-10-10 DOI: 10.1021/acschembio.5c00548
José A Reyes Franceschi, Emilio L Cárdenas, Brandon J C Klein, Chase A Weidmann, Amanda L Garner
{"title":"SHAPE-Based Chemical Probes for Studying preQ<sub>1</sub>-RNA Interactions in Living Bacteria.","authors":"José A Reyes Franceschi, Emilio L Cárdenas, Brandon J C Klein, Chase A Weidmann, Amanda L Garner","doi":"10.1021/acschembio.5c00548","DOIUrl":"10.1021/acschembio.5c00548","url":null,"abstract":"<p><p>Interrogating RNA-small molecule interactions inside cells is critical for advancing RNA-targeted drug discovery. In particular, chemical probing technologies that both identify small molecule-bound RNAs and define their binding sites in the complex cellular environment will be key to establishing the on-target activity necessary for successful hit-to-lead campaigns. Using the small molecule metabolite preQ<sub>1</sub> and its cognate riboswitch RNA as a model, herein we describe a chemical probing strategy for filling this technological gap. Building on well-established RNA acylation chemistry employed by <i>in vivo</i> click-selective 2'-hydroxyl acylation analyzed by primer extension (icSHAPE) probes, we developed an icSHAPE-based preQ<sub>1</sub> probe that retains biological activity in a preQ<sub>1</sub> riboswitch reporter assay and successfully enriches the preQ<sub>1</sub> riboswitch from living bacterial cells. Further, we map the preQ<sub>1</sub> binding site on probe-modified riboswitch RNA by mutational profiling (MaP). As the need for rapid profiling of on- and off-target small molecule interactions continues to grow, this chemical probing strategy offers a method to interrogate cellular RNA-small molecule interactions and supports the future development of RNA-targeted therapeutics.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145273169","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
Virus Propagation Linked to Exceedingly Rare Gene-Expression Errors: A Single-Molecule Microscopy Demonstration. 与极其罕见的基因表达错误相关的病毒传播:单分子显微镜演示。
IF 3.8 2区 生物学
ACS Chemical Biology Pub Date : 2025-10-10 DOI: 10.1021/acschembio.5c00638
Raquel Luzón-Hidalgo, Gianluca D'Agostino, Valeria A Risso, Asuncion Delgado, Beatriz Ibarra-Molero, Luis A Campos, Jose Requejo-Isidro, Jose M Sanchez-Ruiz
{"title":"Virus Propagation Linked to Exceedingly Rare Gene-Expression Errors: A Single-Molecule Microscopy Demonstration.","authors":"Raquel Luzón-Hidalgo, Gianluca D'Agostino, Valeria A Risso, Asuncion Delgado, Beatriz Ibarra-Molero, Luis A Campos, Jose Requejo-Isidro, Jose M Sanchez-Ruiz","doi":"10.1021/acschembio.5c00638","DOIUrl":"https://doi.org/10.1021/acschembio.5c00638","url":null,"abstract":"<p><p>Many viruses use programmed frameshifting and stop-codon misreading to synthesize functional proteins at high levels. The underlying mechanisms involve complex RNA sequence/structure motifs and likely reflect optimization driven by natural selection of inefficient, nonprogrammed processes. Then, it follows from basic evolutionary theory that low levels of proteins generated through gene expression errors could provide viruses with some survival advantage. Here, we devise an experimental demonstration of this possibility. Phage T7 recruits the host thioredoxin as an essential processivity factor for the viral DNA polymerase. We inserted early stop codons in the thioredoxin gene and appended to its end the sequence encoding for a photoconvertible fluorescent protein. Virus replication was not abolished. Single-molecule localization microscopy showed that the phage replicates even when there are only about 10 thioredoxin molecules per host cell on average, a number orders of magnitude below typical cellular protein levels. We show that this seemingly shocking result can be understood in molecular and evolutionary terms as a consequence of the polymerase-thioredoxin complex displaying high kinetic stability and a long residence time, as these are required to ensure high polymerase processivity. More generally, our demonstration that virus replication may be enabled by proteins at exceedingly low copy number suggests that viruses have access to the wide diversity of protein variants harboring phenotypic mutations as a result of gene expression errors. This mechanism could play a role, for instance, in cross-species transmission by enabling virus survival in the new host before adaptations appear at the genetic level.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145273143","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
Biosynthesis of Antifungal Fusacandins Reveals Distinctive Fungal C- and Iterative O-type Glycosyltransferases 抗真菌Fusacandins的生物合成揭示了独特的真菌C型和迭代o型糖基转移酶。
IF 3.8 2区 生物学
ACS Chemical Biology Pub Date : 2025-10-06 DOI: 10.1021/acschembio.5c00589
Xin Wang, , , Cheng-Jun Cao, , and , Yi Zou*, 
{"title":"Biosynthesis of Antifungal Fusacandins Reveals Distinctive Fungal C- and Iterative O-type Glycosyltransferases","authors":"Xin Wang,&nbsp;, ,&nbsp;Cheng-Jun Cao,&nbsp;, and ,&nbsp;Yi Zou*,&nbsp;","doi":"10.1021/acschembio.5c00589","DOIUrl":"10.1021/acschembio.5c00589","url":null,"abstract":"<p >Fusacandin A (<b>1</b>) is a glycolipid natural product that targets β-1,3-glucan synthase and exhibits significant antifungal activity. Its most impressive structural feature is a <i>C</i>-arylglycosyl hydroxybenzyl moiety with a varying degree of <i>O</i>-glycosylation. In this study, the biosynthetic gene cluster (<i>sac</i>) of fusacandin A was identified from <i>Fusarium sacchari</i>, and subsequent investigations of the assembly line revealed two key glycosyltransferases (GTs): a <i>C</i>-GT SacA, which catalyzes regioselective <i>C</i>-glucosylation at the C-6 of 3,5-dihydroxybenzyl alcohol (<b>7</b>) to form aryl-glucoside (<b>8</b>); and an <i>O</i>-GT SacH, which catalyzes a rare iterative <i>O</i>-galactosylation step on <b>9</b> to generate fusacandin B (<b>2</b>). Further <i>in vitro</i> biochemical assays and molecular docking experiments revealed the broad substrate tolerance and the key catalytic residues for both GTs. Two unusual esterification steps catalyzed by a <i>C</i>-terminal carnitine <i>O</i>-acyltransferase (cAT) domain of highly reducing polyketide synthase (hrPKS) SacB and a transmembrane acyltransferase (mAT) SacG were also identified, respectively. In addition, the relationship of structural moiety to the antifungal activity of fusacandins was investigated. Our work not only uncovers the assembly logic of these complex and synthetically challenging molecules but also provides valuable glycosyltransferase biocatalysts for the future biomimetic or chemo-enzymatic synthesis of more potent fusacandin derivatives.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"20 10","pages":"2494–2502"},"PeriodicalIF":3.8,"publicationDate":"2025-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145230976","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
Taxodione Inhibits Glioblastoma Proliferation and Potentiates the Cytotoxicity of Paclitaxel 紫杉二酮抑制胶质母细胞瘤增殖并增强紫杉醇的细胞毒性。
IF 3.8 2区 生物学
ACS Chemical Biology Pub Date : 2025-10-06 DOI: 10.1021/acschembio.5c00452
Kyle J. Parella, , , Megan M. Solans, , , Cynthia Vied, , , Svetlana N. Kononenko, , , Hanna Colegrove, , , Diego A. R. Zorio, , , Vitalii S. Basistyi, , and , James H. Frederich*, 
{"title":"Taxodione Inhibits Glioblastoma Proliferation and Potentiates the Cytotoxicity of Paclitaxel","authors":"Kyle J. Parella,&nbsp;, ,&nbsp;Megan M. Solans,&nbsp;, ,&nbsp;Cynthia Vied,&nbsp;, ,&nbsp;Svetlana N. Kononenko,&nbsp;, ,&nbsp;Hanna Colegrove,&nbsp;, ,&nbsp;Diego A. R. Zorio,&nbsp;, ,&nbsp;Vitalii S. Basistyi,&nbsp;, and ,&nbsp;James H. Frederich*,&nbsp;","doi":"10.1021/acschembio.5c00452","DOIUrl":"10.1021/acschembio.5c00452","url":null,"abstract":"<p >Glioblastoma rapidly acquires resistance to conventional genotoxic therapy. This behavior is closely associated with the enhancement of stem-cell-like character during disease progression. Farnesyl diphosphate synthase (FDPS) plays an important role in maintaining such stem-cell-like features. This finding has stimulated interest in FDPS as a neuro-oncology drug target; however, the lack of CNS-permeable inhibitors has hampered further development. In this study we explored the utility of taxodione, a diterpenoid described as an FDPS inhibitor and predicted to penetrate the blood-brain-barrier. The effects of taxodione were compared to its congener 7-(2′-oxohexyl)-taxodione and a known FDPS inhibitor in U87MG glioblastoma cells. Taxodione was the only treatment that significantly reduced the size of tumor spheroids in a temporal and dose-dependent manner. This activity was associated with FDPS inhibition and the transcriptional downregulation of other mevalonate pathway genes. Consistent with this putative mechanism of action, taxodione sensitized glioblastoma cells to subnanomolar concentrations of paclitaxel.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"20 10","pages":"2368–2374"},"PeriodicalIF":3.8,"publicationDate":"2025-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145237456","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
Mechanism and Utility of the ATP-Grasp Enzyme BesA for the Synthesis of Non-natural Alkyne-Containing Dipeptides Applicable for Click Chemistry atp -抓取酶BesA合成非天然含炔二肽的机理及应用
IF 3.8 2区 生物学
ACS Chemical Biology Pub Date : 2025-10-05 DOI: 10.1021/acschembio.5c00676
Hono Otsuka,  and , Takashi Fujishiro*, 
{"title":"Mechanism and Utility of the ATP-Grasp Enzyme BesA for the Synthesis of Non-natural Alkyne-Containing Dipeptides Applicable for Click Chemistry","authors":"Hono Otsuka,&nbsp; and ,&nbsp;Takashi Fujishiro*,&nbsp;","doi":"10.1021/acschembio.5c00676","DOIUrl":"10.1021/acschembio.5c00676","url":null,"abstract":"<p >Terminal alkyne-containing biomolecules are key compounds utilized in bioorthogonal chemistry via azide–alkyne cycloaddition click chemistry. Various synthetic strategies for the introduction of the terminal alkyne to biomolecules have been developed; however, an enzymatic terminal alkyne-modifying system is not well-explored because the biosynthetic systems for terminal alkynes are rare. Recently, BesA, a member of the ATP-grasp enzyme family, has been reported to exclusively utilize terminal alkyne-containing <span>l</span>-propargylglycine and <span>l</span>-glutamic acid as substrates in the synthesis of γ-<span>l</span>-glutamyl-<span>l</span>-propargylglycine. Because of its use of the terminal alkyne for click chemistry, a BesA-based catalytic system is regarded as a potentially attractive biocatalyst for the enrichment of terminal alkyne-containing biomolecules. Toward developing BesA-based biocatalysts, it is important to understand the structure-based mechanism of action of BesA, especially recognition of the terminal alkyne. Here, we elucidate the structural basis of BesA for synthesis of γ-<span>l</span>-glutamyl-<span>l</span>-propargylglycine. The X-ray crystal analysis of BesA unveiled a narrow substrate-binding cleft, beside Y33, R50, R365, and R404 as conserved residues among BesA enzymes from <i>Streptomyces</i>, as the active site for binding of two amino acids, <span>l</span>-propargylglycine and <span>l</span>-glutamic acid. In particular, the region beside Y33 is likely to accommodate the terminal alkyne of <span>l</span>-propargylglycine via CH−π interaction based on the dipeptide-docking simulation of BesA and the results of the activity assay of the BesA Y33A variant. Furthermore, we demonstrate a BesA-catalyzed conjugation system for the synthesis of non-natural alkyne-containing dipeptides. The BesA R50A variant showed a little activity for ligation between <span>l</span>-propargylglycine and 1-methyl-<span>l</span>-glutamate, affording 1-methyl-<span>l</span>-glutamyl-<span>l</span>-propargylglycine. Moreover, the BesA wild-type showed activity for ligation of <span>l</span>-homopropargylglycine and <span>l</span>-glutamic acid, yielding γ-<span>l</span>-glutamyl-<span>l</span>-homopropargylglycine. Structural comparison of BesA with proteins that possibly bind the alkynes shows the significance of Tyr in recognition of the alkynes. These findings highlight the usefulness of BesA-based biocatalytic systems in expanding the chemical space of alkyne-containing peptides applicable for click chemistry as well as understanding alkyne recognition by proteins.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"20 10","pages":"2521–2532"},"PeriodicalIF":3.8,"publicationDate":"2025-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145231014","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
A Cell-Potent Bisubstrate Inhibitor to Probe NatD Acetyltransferase Activity 一种检测NatD乙酰转移酶活性的细胞有效双底物抑制剂。
IF 3.8 2区 生物学
ACS Chemical Biology Pub Date : 2025-10-04 DOI: 10.1021/acschembio.5c00666
Yi-Hsun Ho, , , Emma K. Seipp, , , Thitiwat Larndate, , and , Rong Huang*, 
{"title":"A Cell-Potent Bisubstrate Inhibitor to Probe NatD Acetyltransferase Activity","authors":"Yi-Hsun Ho,&nbsp;, ,&nbsp;Emma K. Seipp,&nbsp;, ,&nbsp;Thitiwat Larndate,&nbsp;, and ,&nbsp;Rong Huang*,&nbsp;","doi":"10.1021/acschembio.5c00666","DOIUrl":"10.1021/acschembio.5c00666","url":null,"abstract":"<p >N-terminal acetyltransferase D (NatD) is a highly selective enzyme that acetylates the α-N-terminal amine of histones H4 and H2A, which share the SGRGK motif. Elevated NatD expression has been observed in lung, colorectal, breast, and bone cancer tissues, and is correlated with poor patient survival in these cancer types. In non-small cell lung cancer, NatD depletion reduces progression by repressing the epithelial-to-mesenchymal transition (EMT). Hence, NatD is a potential epigenetic target for lung cancer. To unravel the functions of NatD, a cell-potent and selective NatD inhibitor is needed to investigate the acetyltransferase activity of NatD in cancer progression. We previously reported potent and selective NatD bisubstrate inhibitors, designed by covalently linking coenzyme A to peptide substrates via an acetyl and propionyl linker. However, these inhibitors are not cell-active, limiting their application for cellular studies. Here, we designed cell-permeable bisubstrate analogs by attaching cell-penetrating peptides (CPP) to the bisubstrate inhibitor. The inhibitor displayed a <i>K</i><sub>i</sub> value of 23 nM and effectively reduced cellular Nα-acetylation on histone H4, leading to reduced migration in lung cancer cells by modulating the expression of <i>E</i>-cadherin, <i>N</i>-cadherin, and vimentin. Our findings demonstrate that the CPP-conjugated NatD inhibitor serves as a valuable chemical probe for elucidating the biological roles of NatD in lung cancer, laying the groundwork for future therapeutic strategies targeting NatD.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"20 10","pages":"2512–2520"},"PeriodicalIF":3.8,"publicationDate":"2025-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145228347","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
Iodo-Labeling of Peptides for Quantitative MALDI MS Analysis─Screening for Bacteria-Binding Peptides from a Glycine-Zipper Library 用于MALDI质谱定量分析的多肽碘标记─甘氨酸拉链文库中细菌结合肽的筛选。
IF 3.8 2区 生物学
ACS Chemical Biology Pub Date : 2025-10-02 DOI: 10.1021/acschembio.5c00423
Liao Hu, , , C. Logan Mackay, , , David J. Clarke*, , and , Annamaria Lilienkampf*, 
{"title":"Iodo-Labeling of Peptides for Quantitative MALDI MS Analysis─Screening for Bacteria-Binding Peptides from a Glycine-Zipper Library","authors":"Liao Hu,&nbsp;, ,&nbsp;C. Logan Mackay,&nbsp;, ,&nbsp;David J. Clarke*,&nbsp;, and ,&nbsp;Annamaria Lilienkampf*,&nbsp;","doi":"10.1021/acschembio.5c00423","DOIUrl":"10.1021/acschembio.5c00423","url":null,"abstract":"<p >Matrix-assisted laser desorption ionization mass spectrometry (MALDI MS) is widely valued for its speed and sensitivity in biomolecular analysis, yet the inherently nonquantitative nature hampers its use in many applications including high-throughput screening. Here, we introduce an iodo-based labeling strategy that enables accurate quantification of peptides and peptide libraries using high-resolution MALDI FT-ICR MS. The peptides are coupled at the N-terminus with benzoic acid (BA) or 4-iodobenzoic acid (IBA) to generate the analyte and its internal standard, respectively, differing only by a single iodine substitution. This new labeling strategy was first validated using a simple four-peptide mixture, and subsequently applied to quantitatively evaluate glycine-zipper peptide libraries containing up to 125 members for the discovery of bacterial-binding peptides. Screening of these libraries against Gram-negative <i>Escherichia coli</i> and Gram-positive <i>Bacillus subtilis</i> revealed peptides with strong and selective interactions with the bacteria. This universally applicable, cost-effective, and straightforward approach for peptide quantification significantly enhances the reliability and accuracy of high-throughput peptide screening via MALDI FT-ICR MS.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"20 10","pages":"2404–2412"},"PeriodicalIF":3.8,"publicationDate":"2025-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145211123","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
Thiophene Esters Are Not Selective for H2S and Undergo Thiol and Esterase Cleavage 噻吩酯对硫化氢没有选择性,并经过硫醇和酯酶的切割。
IF 3.8 2区 生物学
ACS Chemical Biology Pub Date : 2025-10-01 DOI: 10.1021/acschembio.5c00527
Haley M. Smith, , , Aleanna J. Lengkong, , , Christopher A. Steven, , , Ally N. Stonas, , and , Michael D. Pluth*, 
{"title":"Thiophene Esters Are Not Selective for H2S and Undergo Thiol and Esterase Cleavage","authors":"Haley M. Smith,&nbsp;, ,&nbsp;Aleanna J. Lengkong,&nbsp;, ,&nbsp;Christopher A. Steven,&nbsp;, ,&nbsp;Ally N. Stonas,&nbsp;, and ,&nbsp;Michael D. Pluth*,&nbsp;","doi":"10.1021/acschembio.5c00527","DOIUrl":"10.1021/acschembio.5c00527","url":null,"abstract":"<p >Hydrogen sulfide (H<sub>2</sub>S) fluorescent probes are important tools for imaging and understanding H<sub>2</sub>S in biology. One significant requirement for such probes is that they are highly selective for H<sub>2</sub>S over competing analytes, which are often present at much higher levels than endogenous H<sub>2</sub>S. Different approaches have been used to generate selective H<sub>2</sub>S probes, and recently, highly selective probes using 2-thiophene esters have been reported. We report here that in contrast to prior reports, thiophene ester probes are not selective for H<sub>2</sub>S but rather report on both biothiols and esterase activity. We do demonstrate, however, that the rate of reactivity toward H<sub>2</sub>S can be enhanced by incorporating an <i>ortho</i> aldehyde, leading to an 85-fold rate enhancement. We anticipate that this work will further clarify effective approaches for selective H<sub>2</sub>S detection and also advance strategies for improving the selectivity of electrophilic probes for H<sub>2</sub>S and other related nucleophiles.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"20 10","pages":"2375–2380"},"PeriodicalIF":3.8,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145197459","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 Nitrogen Pyramidalization via N-H/N Interactions that Stabilize the δ/α Conformations in Turns, Loops, and 310- and α-Helices. 酰胺氮金字塔化通过N- h /N相互作用稳定在匝、环、310-和α-螺旋中的δ/α构象。
IF 3.8 2区 生物学
ACS Chemical Biology Pub Date : 2025-10-01 DOI: 10.1021/acschembio.5c00451
Noah J Daniecki, Glenn P A Yap, Neal J Zondlo
{"title":"Amide Nitrogen Pyramidalization via N-H/N Interactions that Stabilize the δ/α Conformations in Turns, Loops, and 3<sub>10</sub>- and α-Helices.","authors":"Noah J Daniecki, Glenn P A Yap, Neal J Zondlo","doi":"10.1021/acschembio.5c00451","DOIUrl":"https://doi.org/10.1021/acschembio.5c00451","url":null,"abstract":"<p><p>N-H/N interactions, between an amide N-H on one residue (<i>i</i> + 1) and the amide N lone pair on the prior (<i>i</i>) residue, have been observed in key structures in proteins, including turns, loops, and α-helices. However, there remains an incomplete understanding about the inherent nature of N-H/N interactions and how they can impact protein structure and dynamics. The crystal structure of a molecule (Boc-hyp(4-I-Ph)-NHCy) with an N-H<sub><i>i</i>+1</sub>/N<i><sub>i</sub></i> interaction was obtained. This structure had a close H<sub><i>i</i>+1</sub>···N<i><sub>i</sub></i> distance of 2.30 Å, well below the 2.75 Å sum of the van der Waals radii of H and N. This structure exhibited substantial (12°; 0.17 Å) pyramidalization (partial sp<sup>3</sup> character) of the proline N<i><sub>i</sub></i> nitrogen. This pyramidalization reduces the planarity and electron delocalization inherent to an amide bond, as a result of the nitrogen N<i><sub>i</sub></i> lone pair engaging directly with the hydrogen on the subsequent amide. DFT calculations on Ac-Pro-NHMe indicate that nitrogen pyramidalization and partial loss of amide planarity are inherent features of an N-H/N interaction. In addition, calculations demonstrate that the δ conformation, which has an N-H/N interaction, exhibits a substantially lower barrier to proline <i>cis</i>-<i>trans</i> isomerism than the PPII conformation, which lacks an N-H/N interaction, and that a closer N-H/N interaction and greater N pyramidalization are observed in the transition state than in the ground states. Analysis of small-molecule crystal structures indicates that close H···N distances and substantial N<i><sub>i</sub></i> pyramidalization are inherent to N-H/N interactions. N-H/N interactions are ubiquitous in the PDB at all 20 canonical amino acids when they are in the δ/α<sub>R</sub> or δ'/α<sub>L</sub> conformations, consistent with N-H/N interactions being central local structural elements in proteins, as well as in early folding transitions in proteins (single residue δ/α<sub>R</sub> → type I β-turn → 3<sub>10</sub>-helix → α-helix).</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145204941","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
A Caspase-1-cathepsin AND-Gate Probe for Selective Imaging of Inflammasome Activation caspase -1-组织蛋白酶和门探针用于炎性小体激活的选择性成像。
IF 3.8 2区 生物学
ACS Chemical Biology Pub Date : 2025-09-30 DOI: 10.1021/acschembio.5c00408
Shiyu Chen, , , Una Goncin, , , Jiyun Zhu, , , Shih-Po Su, , , Traci Ann Czyzyk, , , Corin O. Miller, , , Raana Kashfi Sadabad*, , and , Matthew Bogyo*, 
{"title":"A Caspase-1-cathepsin AND-Gate Probe for Selective Imaging of Inflammasome Activation","authors":"Shiyu Chen,&nbsp;, ,&nbsp;Una Goncin,&nbsp;, ,&nbsp;Jiyun Zhu,&nbsp;, ,&nbsp;Shih-Po Su,&nbsp;, ,&nbsp;Traci Ann Czyzyk,&nbsp;, ,&nbsp;Corin O. Miller,&nbsp;, ,&nbsp;Raana Kashfi Sadabad*,&nbsp;, and ,&nbsp;Matthew Bogyo*,&nbsp;","doi":"10.1021/acschembio.5c00408","DOIUrl":"10.1021/acschembio.5c00408","url":null,"abstract":"<p >Caspase-1 is a key mediator of the inflammasome pathway, which is associated with several inflammatory disorders including obesity, diabetes mellitus, cardiovascular diseases, cancers, and chronic respiratory diseases. Although substrate-based probes can be used to visualize the activity of caspase-1, none are selective enough for use as imaging agents. Here, we report the design and synthesis of an AND-gate substrate probe (<b>Cas1-Cat-Cy7</b>) that requires processing by both caspase-1 and cathepsins to produce a signal. Because both enzymes are found together and active in tissue locations where cells are undergoing caspase-1-mediated pyroptosis, the resulting probe can be used to image sites of caspase-1-mediated inflammation. We demonstrate that the probe produces selective signals in <i>ex vivo</i> biochemical and cellular assays and in a mouse model of acute inflammation.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"20 10","pages":"2363–2367"},"PeriodicalIF":3.8,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145190449","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
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
相关产品
×
本文献相关产品
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:604180095
Book学术官方微信