ACS Chemical Biology最新文献

Chemoproteomics Discovery of a Central Nervous System-Penetrant Covalent Inhibitor of PIKfyve. 一种中枢神经系统渗透共价PIKfyve抑制剂的化学蛋白质组学发现。

IF 3.6 2区生物学

ACS Chemical Biology Pub Date : 2026-11-06 DOI: 10.1021/acschembio.6c00795

Antony J Burton, Louis S Chupak, Alison J Davis, Ahmed S A Mady, Mirco Meniconi, Barry Teobald, Bryan W Dorsey, Lauren R Byrne, Ryan Mulhern, Berent Lundeen, Elizabeth W Sorensen, Bharti Patel, Sean Brennan, Dhiraj Kormocha, Ruben Tommasi, Graham L Simpson, Jeffrey W Keillor, Laura D'Agostino, Elayne Penebre, Pearl S Huang

{"title":"Chemoproteomics Discovery of a Central Nervous System-Penetrant Covalent Inhibitor of PIKfyve.","authors":"Antony J Burton, Louis S Chupak, Alison J Davis, Ahmed S A Mady, Mirco Meniconi, Barry Teobald, Bryan W Dorsey, Lauren R Byrne, Ryan Mulhern, Berent Lundeen, Elizabeth W Sorensen, Bharti Patel, Sean Brennan, Dhiraj Kormocha, Ruben Tommasi, Graham L Simpson, Jeffrey W Keillor, Laura D'Agostino, Elayne Penebre, Pearl S Huang","doi":"10.1021/acschembio.6c00795","DOIUrl":"https://doi.org/10.1021/acschembio.6c00795","url":null,"abstract":"PIKfyve is a lipid kinase involved in regulating protein clearance mechanisms and is a promising target for the treatment of neurodegenerative diseases. We present the discovery and optimization of a central nervous system (CNS)-penetrant covalent PIKfyve inhibitor, DUN'058, which achieves sustained target occupancy in vivo. Covalent screening hits, identified from chemoproteomics experiments performed in live cells, were rapidly optimized to deliver a brain-penetrant covalent inhibitor of PIKfyve. This covalency centred approach employed a suite of mass spectrometry, biochemical and in vivo assays to optimize compound potency, selectivity, and CNS permeability. The target nucleophile, cysteine 1970, is on a flexible loop that appears distal from the kinase active site, highlighting the power of chemoproteomics screening to identify novel nucleophilic amino acids for covalent modification. DUN'058 achieves efficient covalency at the target cysteine, as well as highly selective covalent and reversible selectivity profiles. Covalent PIKfyve inhibition results in modulation of downstream pathway activity, including activation of the transcription factor TFEB, upregulation of protein clearance pathways, and increased GPNMB transcription and secretion of exosome markers. When dosed in vivo, DUN'058 achieves sustained target occupancy in the brains of mice long after systemic compound clearance. The development of DUN'058 is a demonstration of chemoproteomics-based discovery for a high value CNS target, providing an orally bioavailable and covalent PIKfyve inhibitor.","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.6,"publicationDate":"2026-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149356940","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

Genome Mining-Driven Discovery of the Sactipeptide Smithiosin in Probiotic, Thermophilic Strain Bacillus smithii. 基因组挖掘驱动的益生菌嗜热菌株史密斯芽孢杆菌sacti肽Smithiosin的发现。

IF 3.6 2区生物学

ACS Chemical Biology Pub Date : 2026-11-05 DOI: 10.1021/acschembio.6c00179

Sara Vasciaveo, Yechen Zhou, Yaoyu Ding, Charlotte K Hind, Á Tamás Gräff, Amy H Camp, J Mark Sutton, Sarah M Barry, Rachael Dickman

{"title":"Genome Mining-Driven Discovery of the Sactipeptide Smithiosin in Probiotic, Thermophilic Strain Bacillus smithii.","authors":"Sara Vasciaveo, Yechen Zhou, Yaoyu Ding, Charlotte K Hind, Á Tamás Gräff, Amy H Camp, J Mark Sutton, Sarah M Barry, Rachael Dickman","doi":"10.1021/acschembio.6c00179","DOIUrl":"https://doi.org/10.1021/acschembio.6c00179","url":null,"abstract":"Sactipeptides are a class of ribosomally synthesised and post-translationally modified peptides (RiPPs), which have a cyclic topology formed by unique thioether crosslinks called sactionines. Sactionines are introduced by radical S-adenosylmethionine (rSAM) enzymes between cysteine residues and the α-carbon of other amino acids. Genome sequencing has revealed many putative sactipeptide biosynthetic gene clusters; however, few sactipeptides have been isolated and characterised. Here, we use genome mining to identify a novel sactipeptide from Bacillus smithii. The novel sactipeptide, named smithiosin, was extracted from the industrially important thermophile B. smithii and characterised as a novel homologue of the previously characterised sactipeptide subtilosin A from B. subtilis. Furthermore, the smithiosin precursor peptide gene was heterologously expressed in the subtilosin A producer Bacillus subtilis 168 without knockout of the native precursor peptide, successfully leading to the production of both subtilosin A and smithiosin. This demonstrates for the first time that a non-native precursor peptide is able to outcompete the subtilosin A precursor for all of the native biosynthetic enzymes in B. subtilis, including the radical SAM enzyme AlbA. It also opens a potential new opportunity for screening non-native precursor peptides with the subtilosin A biosynthetic enzymes via heterologous expression in B. subtilis.","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.6,"publicationDate":"2026-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149331691","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

Domain Swapping Reveals Direction-Dependent Compatibility of Fungal Polyketide Synthase-Nonribosomal Peptide Synthetase Off-Loading Domains. 结构域交换揭示真菌聚酮合成酶-非核糖体肽合成酶卸载结构域的方向依赖性相容性。

IF 3.6 2区生物学

ACS Chemical Biology Pub Date : 2026-11-05 DOI: 10.1021/acschembio.6c00598

Shusuke Sato, Takahiro Ugai, Momoka Yamane, Xueting Liu, Hideaki Oikawa, Atsushi Minami

{"title":"Domain Swapping Reveals Direction-Dependent Compatibility of Fungal Polyketide Synthase-Nonribosomal Peptide Synthetase Off-Loading Domains.","authors":"Shusuke Sato, Takahiro Ugai, Momoka Yamane, Xueting Liu, Hideaki Oikawa, Atsushi Minami","doi":"10.1021/acschembio.6c00598","DOIUrl":"https://doi.org/10.1021/acschembio.6c00598","url":null,"abstract":"Two fungal natural products, hirsutellone and didymellamide, are proposed to be biosynthesized from closely related β-ketoamide intermediates despite producing structurally distinct cyclic products. This unusual biosynthetic relationship raises the question of whether the corresponding polyketide synthase-nonribosomal peptide synthetase (PKS-NRPS) off-loading domains are functionally interchangeable. Here, we identified and characterized HirA, a PKS-NRPS involved in hirsutellone biosynthesis, and used it together with AsolS, a PKS-NRPS involved in didymellamide biosynthesis, as a model system to investigate the compatibility of fungal PKS-NRPS off-loading domains. Heterologous expression in Aspergillus oryzae established that HirA produces a β-ketoamide intermediate possessing a nonaketide polyketide chain closely related to that generated by AsolS. Reciprocal domain swapping revealed asymmetric compatibility: artificial fusion of the HirA-derived reductase domain to the AsolS assembly line supported productive processing of the AsolS-derived intermediate, whereas reciprocal fusion of the Dieckmann cyclase domain yielded the C18-derived product at a low level but did not produce the expected tetramic acid derivative. These results demonstrate that off-loading activity can be retained following domain swapping between distinct fungal PKS-NRPS systems, but the extent of productive processing is strongly direction-dependent. Taken together, our findings identify direction-dependent compatibility and fusion-site dependence as important constraints for engineering fungal PKS-NRPS off-loading domains.","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.6,"publicationDate":"2026-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149339889","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

Glycocalyx Remodeling Shapes Cancer Cell Mechanics. 糖萼重塑塑造癌细胞力学。

IF 3.6 2区生物学

ACS Chemical Biology Pub Date : 2026-11-04 DOI: 10.1021/acschembio.6c00749

Karim Almahayni, Hussein H Hammoud, Casia Wardzala, Rachel E Detwiler, Despina Soteriou, Jana Bachir Salvador, Ke Wang, Carla Brunner, Nazlican Yurekli, Matthew Paszek, Stephanie Möllmert, Jessica Kramer Stratton, Jochen Guck, Leonhard Möckl

{"title":"Glycocalyx Remodeling Shapes Cancer Cell Mechanics.","authors":"Karim Almahayni, Hussein H Hammoud, Casia Wardzala, Rachel E Detwiler, Despina Soteriou, Jana Bachir Salvador, Ke Wang, Carla Brunner, Nazlican Yurekli, Matthew Paszek, Stephanie Möllmert, Jessica Kramer Stratton, Jochen Guck, Leonhard Möckl","doi":"10.1021/acschembio.6c00749","DOIUrl":"https://doi.org/10.1021/acschembio.6c00749","url":null,"abstract":"The glycocalyx - a complex meshwork of sugars, proteins, and lipids - coats all human cells and plays a crucial role in cell signaling and immune system regulation. While an understanding of its biochemical functions is emerging, its influence on cell mechanics remains comparably underexplored. Recent evidence suggests that the glycocalyx regulates membrane morphology and cell adhesion, yet its mechanical role has been difficult to study, primarily due to the absence of high-throughput analysis strategies that account for cell-to-cell variability. Here, we overcome this challenge by integrating real-time deformability cytometry (RT-DC) with genetic and chemical glycocalyx engineering to tune the glycocalyx state and assess how cell mechanics are affected. Using this approach, we uncovered mechanical adaptations that contribute to promoting cell migration and metastasis. These findings establish glycocalyx remodeling as a regulator of cancer-cell mechanics and a potential target for therapeutic intervention.","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.6,"publicationDate":"2026-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149316090","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

Lysine-Targeted Covalent Inhibition of eIF4E with an Anionic Electrophile Warhead. 阴离子亲电弹头对赖氨酸靶向eIF4E共价抑制作用的研究。

IF 3.6 2区生物学

ACS Chemical Biology Pub Date : 2026-11-03 DOI: 10.1021/acschembio.6c00714

Paramita Pal, Erika M James, Caitlyn E Given, Hong Yue, Rebecca J Metivier, Jianwei Che, Eric S Fischer, Lyn H Jones

{"title":"Lysine-Targeted Covalent Inhibition of eIF4E with an Anionic Electrophile Warhead.","authors":"Paramita Pal, Erika M James, Caitlyn E Given, Hong Yue, Rebecca J Metivier, Jianwei Che, Eric S Fischer, Lyn H Jones","doi":"10.1021/acschembio.6c00714","DOIUrl":"https://doi.org/10.1021/acschembio.6c00714","url":null,"abstract":"Covalent strategies offer a powerful route to expand the druggable proteome, yet selective lysine targeting remains difficult due to the high pKa and protonation of the amine side chain. The translation initiation factor eIF4E, an mRNA cap-binding protein that controls nuclear export and translation of oncogenic transcripts, has long been considered an undruggable RNA-binding protein. We apply an anionic electrophile strategy that converts a carboxylic acid within a reversible eIF4E ligand into a vinyl acylsulfonamide warhead, preserving salt-bridge and hydrogen bonding interactions in the cap-binding pocket and facilitating Lys162 deprotonation to enable site-specific engagement. This single-step transformation yields JL-03, a potent covalent eIF4E inhibitor with excellent stability toward biological nucleophiles, consistent with context-dependent activation of the warhead in the binding site. In cells, JL-03 achieves robust target engagement and suppresses translation of the oncogenic driver cyclin D. JL-03 reduces the viability of HOXA9-high acute myeloid leukemia cells with greater potency than reversible eIF4E inhibitors and synergizes with the menin inhibitor revumenib, demonstrating that coordinated transcriptional and translational blockade exhausts leukemic dependencies. These findings establish eIF4E as a tractable covalent target and highlight anionic electrophile installation as a generalizable strategy for lysine-directed covalent inhibitor design.","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.6,"publicationDate":"2026-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149316091","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 Small Molecule Inhibitor of the Staphylococcus aureusagr Quorum Sensing System with Low-Nanomolar Potency. 具有低纳摩尔效力的金黄色葡萄球菌群体感应系统的小分子抑制剂。

IF 3.6 2区生物学

ACS Chemical Biology Pub Date : 2026-11-03 DOI: 10.1021/acschembio.6c00735

A P Clay, Thomas J Polaske, Helen E Blackwell

引用次数: 0

Mapping the Sequence Preference of the Generalist Class II Lanthipeptide Synthetase ProcM by mRNA Display. 利用mRNA显示技术绘制多面手II类硫肽合成酶ProcM的序列偏好。

IF 3.6 2区生物学

ACS Chemical Biology Pub Date : 2026-10-30 DOI: 10.1021/acschembio.6c00753

Yao Ouyang, Hassan Nadeem, Yuki Goto, Diwakar Shukla, Wilfred A van der Donk

{"title":"Mapping the Sequence Preference of the Generalist Class II Lanthipeptide Synthetase ProcM by mRNA Display.","authors":"Yao Ouyang, Hassan Nadeem, Yuki Goto, Diwakar Shukla, Wilfred A van der Donk","doi":"10.1021/acschembio.6c00753","DOIUrl":"https://doi.org/10.1021/acschembio.6c00753","url":null,"abstract":"The biosynthetic machineries of ribosomally synthesized and post-translationally modified peptides (RiPPs) are often substrate tolerant. A remarkable example is the class II lanthipeptide synthetase ProcM, which naturally functions as a generalist enzyme that has not evolved to use a specific substrate during its evolutionary history. Although ProcM has been studied extensively, the sequence features associated with productive modification remain underexplored. In this study, we use the ultrahigh-throughput mRNA display technique to map the sequence compatibility of ProcM across a focused library. This approach expands the landscape of ProcM reactivity beyond native substrates and individually characterized variants. Machine learning (ML) analysis revealed that the dataset contains sequence patterns associated with ProcM reactivity, with models achieving a balanced accuracy of 0.73. This moderate predictive performance contrasts with the near-perfect accuracy reported for specialized enzymes. This finding suggests that predicting substrate compatibility for generalist enzymes is more challenging due to uneven representation of reactive and nonreactive sequences and limitations of the available data. Our results provide a high-throughput view of ProcM reactivity and highlight differences with previous high-throughput studies on substrate selectivity of RiPP modification enzymes. Future studies will need to assess whether these differences are common when comparing generalist with specialist enzymes.","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.6,"publicationDate":"2026-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149293170","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 1,2-Dioxetane-Based Chemiluminescent Probe for In Vivo Copper Imaging. 基于1,2-二氧乙烷的体内铜成像化学发光探针。

IF 3.6 2区生物学

ACS Chemical Biology Pub Date : 2026-10-29 DOI: 10.1021/acschembio.6c00617

Rokia Osman, Caleb M Griffin, Yitong Kang, Ralph P Mason, Alexander R Lippert

{"title":"A 1,2-Dioxetane-Based Chemiluminescent Probe for In Vivo Copper Imaging.","authors":"Rokia Osman, Caleb M Griffin, Yitong Kang, Ralph P Mason, Alexander R Lippert","doi":"10.1021/acschembio.6c00617","DOIUrl":"https://doi.org/10.1021/acschembio.6c00617","url":null,"abstract":"Copper is involved in healthy physiology and aberrant pathology with prominent roles in Wilson's and Menkes diseases. Tracking its reactivity in living systems is crucial to understanding its biological function and could be helpful in identifying targeted therapies. We developed a turn-on chemiluminescent copper probe CpCL, which was designed by linking a picolinic acid moiety to the phenolic substituent of a spiroadamantane 1,2-dioxetane. Reaction of CpCL with copper results in formation of a copper complex intermediate that releases the phenolate upon hydrolysis, followed by initiation of a chemiluminescence reaction for light emission. The probe displayed excellent selectivity for Cu2+ compared to other competitive metal ions, with a sensitive limit of detection of 360 nM. The mechanism was studied using initial rate kinetics to provide an estimated pseudo-first-order rate constant of 5.18 ± 0.38 × 10-5 s-1 for the hydrolysis of the copper-bound probe. The probe was then validated in living mice using the copper chelator ATN-224 as a negative control, demonstrating that it can be used to monitor copper ions in vivo.","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.6,"publicationDate":"2026-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149293082","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 BromoTag-Based Toolkit for Rapid Modulation of Chemically Induced Proximity. 基于bromotag的化学诱导接近快速调制工具箱。

IF 3.6 2区生物学

ACS Chemical Biology Pub Date : 2026-10-29 DOI: 10.1021/acschembio.6c00616

Gianna M Colombo, DaWon Kim, Muhammad Murtaza Hassan, Steven M Corsello

{"title":"A BromoTag-Based Toolkit for Rapid Modulation of Chemically Induced Proximity.","authors":"Gianna M Colombo, DaWon Kim, Muhammad Murtaza Hassan, Steven M Corsello","doi":"10.1021/acschembio.6c00616","DOIUrl":"https://doi.org/10.1021/acschembio.6c00616","url":null,"abstract":"Mammalian cells control a wide range of essential processes via protein-protein interactions (PPIs), including signal transduction, gene expression, cell cycle regulation, and metabolism. Pathologic alterations in PPIs have been linked to many human diseases. Thus, the ability to rapidly and selectively induce PPIs in cultured cells is crucial for many fields of biological research. One proven approach is the use of synthetic bivalent chemical ligands to selectively recruit protein domains with engineered mutations (i.e., \"bump-and-hole\"). Developing new PPI chemical inducers with unique protein domains enables multiplexing and potentially expands the breadth of recruitable proteins. Herein, we describe the design and characterization of a BromoTag- and dTAG-based toolkit to induce protein homo- and heterodimerization. Using a NanoBiT split-luciferase assay, we characterized a library of BromoTag-based homo- (BromoTag/BromoTag) and heterobivalent (BromoTag/dTAG) compounds for their ability to induce neo-PPIs. Compounds were evaluated for activity across multiple cellular applications, including caspase-9 and c-Kit tyrosine kinase activation, with comparable activity to other dimerizer systems. This BromoTag-based protein dimerization toolkit provides a useful alternative to current controlled dimerization systems that will enable robust prototyping of chemically induced proximity.","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.6,"publicationDate":"2026-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149293160","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

Directed Evolution of the Cbx1 Chromodomain Generates a High-Affinity Trimethyllysine-Binding Variant. Cbx1染色体结构域的定向进化产生高亲和力三甲基赖氨酸结合变体。

IF 3.6 2区生物学

ACS Chemical Biology Pub Date : 2026-10-29 DOI: 10.1021/acschembio.6c00573

Shuhao Li, Dingyi Wang, Binyi Yang, Guosong Dong, Huadong Liu, Bing Wang, Lei Li

{"title":"Directed Evolution of the Cbx1 Chromodomain Generates a High-Affinity Trimethyllysine-Binding Variant.","authors":"Shuhao Li, Dingyi Wang, Binyi Yang, Guosong Dong, Huadong Liu, Bing Wang, Lei Li","doi":"10.1021/acschembio.6c00573","DOIUrl":"https://doi.org/10.1021/acschembio.6c00573","url":null,"abstract":"Directed evolution is a powerful and versatile strategy for engineering proteins with enhanced affinity and tailored molecular recognition properties. Here, we applied phage display-guided directed evolution to enhance the binding of the wild-type Cbx1 chromodomain (Cbx1-CD) to an H3K9me3-containing peptide. Screening a soft-randomized library targeting residues surrounding the aromatic cage yielded C29, which bound the H3K9me3 peptide with a KD of 57 nM and exhibited an approximately 14-fold lower dissociation rate constant than Cbx1-CD. Across an H3K9me3-derived alanine-scanning series and a peptide panel, C29 showed stronger binding signals than Cbx1-CD for multiple peptides containing trimethyllysine (Kme3), suggesting lower flanking-sequence dependence for C29 than for Cbx1-CD. An AlphaFold3 model of the C29-H3K9me3 complex suggested local changes in the hydrophobic and electrostatic environment surrounding the Kme3-binding pocket, providing a mechanistic hypothesis for C29's enhanced affinity and reduced flanking-sequence dependence. When two Kme3-containing peptides were spiked into a 100-fold molar excess of unmodified background peptides, C29-conjugated beads effectively enriched both Kme3 peptides relative to the unmodified background. These findings define C29 as a high-affinity Kme3-binding Cbx1 chromodomain variant and support its further evaluation as an affinity reagent for Kme3-containing peptide enrichment.","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.6,"publicationDate":"2026-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149284189","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