ACS Chemical Biology最新文献

{"title":"Design of Fluorescent Membrane Scaffold Proteins for Nanodiscs","authors":"Estevan Cleveland,&nbsp;Aiden R. Wolf,&nbsp;Shawn Chen,&nbsp;Farhana Afrin Mohona,&nbsp;Isaac Kailat,&nbsp;Brian H. Tran,&nbsp;Suresh Babu Lavanya,&nbsp;Nicholas Primanis-Erickson,&nbsp;Yi-Chih Lin,&nbsp;Michael T. Marty","doi":"10.1021/acschembio.6c00340","DOIUrl":"https://doi.org/10.1021/acschembio.6c00340","url":null,"abstract":"<p>Nanodiscs are nanoscale lipid bilayer membrane mimetics surrounded by two membrane scaffold proteins (MSPs). They are widely used as soluble cassettes for membrane proteins and lipids in diverse applications in structural, functional, and biophysical studies. The original MSP was derived directly from human apolipoprotein A-1, and novel constructs have been adapted from this original design, including fluorescent nanodiscs of varying designs. However, chemical derivatization with fluorophores can be expensive, and prior designs of split fluorescent proteins fused to MSP were limited in the color palette available. Here, we developed MSPs with a wide range of different fluorescent C-terminal protein tags, including a versatile HaloTag fusion. These fluorescent MSPs were purified following typical MSP purification procedures with similar yield. Then, we demonstrate that fluorescent MSPs form nanodiscs with similar structure and stoichiometry to conventional MSP nanodiscs. They are also suitable for assembly of nanodiscs with embedded integral membrane protein. Finally, we apply these constructs to monitor peripheral membrane protein binding to lipids via fluorescence resonance energy transfer. These fluorescent MSP constructs enable a range of different applications and provide a versatile template for future design of nanodiscs with unique functions.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"21 9","pages":"2179–2187"},"PeriodicalIF":3.6,"publicationDate":"2026-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148985188","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}

{"title":"PhenoDEL: A Novel Screening Strategy Based on Intracellular Protein Degradation Activity","authors":"Yuichi Onda,&nbsp;Yurika Ochi,&nbsp;Toshihiro Araki,&nbsp;Miho Kageoka-Takahashi,&nbsp;Shuzo Takeda,&nbsp;Kazunori Yamada,&nbsp;Takehiko Ueda,&nbsp;Ken Ohno,&nbsp;Minoru Tanaka,&nbsp;Daiki Sakai,&nbsp;Miki Hasegawa,&nbsp;Yoshihito Tanaka","doi":"10.1021/acschembio.6c00234","DOIUrl":"https://doi.org/10.1021/acschembio.6c00234","url":null,"abstract":"<p>Targeted proteindegradation (TPD), including proteolysis targetingchimeras (PROTACs) and molecular glue degraders (MGDs), is a promisingtherapeutic approach. However, systematic discovery of such smallmolecules remains a major challenge. Here, we present PhenoDEL, anovel phenotypic DNA-encoded library (DEL) screening platform thatintegrates one-bead one-compound DEL (OBOC-DEL) with the Beacon optofluidicsystem for single-cell analysis. By coculturing individual OBOC-DELbeads and engineered reporter cells in nanoliter-scale chambers, PhenoDELenables time-resolved, single-cell phenotypic evaluation and directlinkage between compound identity and intracellular response. As aproof-of-concept, we demonstrate discrimination of active and inactiveon-bead compounds using an FKBP12^F36V-EGFP degradationreporter in PC-3 cells, followed by DNA barcode decoding.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"21 9","pages":"2157–2168"},"PeriodicalIF":3.6,"publicationDate":"2026-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148985215","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}

{"title":"Lipidation as a Driver of Spatial Organization and Function in Proteins and Nucleic Acids","authors":"Han Zhang,&nbsp;Enver Cagri Izgu","doi":"10.1021/acschembio.6c00528","DOIUrl":"https://doi.org/10.1021/acschembio.6c00528","url":null,"abstract":"<p>Beyond serving as passive structural barriers, cellular membranes actively drive the spatial organization and compartmentalized function of macromolecules. Here, we review the interplay between lipid chemistry and lipidation-dependent spatial organization across both proteins and nucleic acids. This paradigm reflects a deep chemical continuity rooted in prebiotic evolution, where vesicles self-assembled from simple amphiphiles facilitate the membrane association of primitive polymers. In extant biology, highly regulated enzymatic lipidation serves as a critical determinant for membrane association, intracellular trafficking, and organization of the proteome. Synthetic lipid modification of nucleic acids transforms them into amphiphilic biomaterials with emergent properties spanning functional supramolecular assembly and systemic biodistribution, ultimately enabling advanced therapeutic modulation of gene expression.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"21 9","pages":"2070–2081"},"PeriodicalIF":3.6,"publicationDate":"2026-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148980747","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}

{"title":"Democratizing LYTACs—A Modular Click Chemistry Platform for the Rapid Assembly of Lysosome-Targeting Chimeras","authors":"Peter A. Szijj,&nbsp;Sherry Li,&nbsp;Madeline K. Gilbert,&nbsp;Chloë Wood Rollock,&nbsp;Mariko Morimoto,&nbsp;Carolyn R. Bertozzi","doi":"10.1021/acschembio.6c00315","DOIUrl":"10.1021/acschembio.6c00315","url":null,"abstract":"<p>Lysosome-targeting chimeras (LYTACs) are emerging therapeutics that mediate extracellular targeted protein degradation. Through simultaneous engagement of a target protein of interest and a lysosomal trafficking receptor, these bifunctional molecules can facilitate the degradation of both secreted and cell-surface proteins. The original LYTACs were designed to engage the cation-independent mannose-6-phosphate receptor (CI-M6PR) via complex glycopolymer or glycopolypeptide ligands conjugated to target-specific antibodies. However, the complexity of these ligands has limited the broader adoption of LYTACs as research tools. Here, we describe a simple, rapid, and modular click chemistry platform for the generation of CI-M6PR-binding LYTACs. The approach utilizes only commercially available reagents and standard laboratory equipment and allows for the conversion of virtually any antibody into a LYTAC. This method for “democratizing” LYTAC generation should facilitate the widespread adoption of these tools for biological discovery.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"21 9","pages":"2119–2127"},"PeriodicalIF":3.6,"publicationDate":"2026-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148860257","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}

{"title":"Linker Histone H1 Phosphorylation Promotes DNA Damage Repair during Replication Stress","authors":"Brittney D. Bobowski,&nbsp;Sarah C. Faulkner,&nbsp;Hugo B. Pinto,&nbsp;Ceyda Durmaz,&nbsp;Yuxiang Li,&nbsp;Matthew R. Teater,&nbsp;Gabriella N.L. Chua,&nbsp;Emily C. Beckwitt,&nbsp;Nicole S. Walker,&nbsp;Tracy Biaco,&nbsp;Casey Chan,&nbsp;Michael E. O’Donnell,&nbsp;Shixin Liu,&nbsp;Ari M. Melnick,&nbsp;Arthur I. Skoultchi,&nbsp;Yael David","doi":"10.1021/acschembio.6c00475","DOIUrl":"10.1021/acschembio.6c00475","url":null,"abstract":"<p>DNA replication fidelity depends on the integrity of the replication fork to prevent DNA damage and preserve genome stability. Disruptions to this process can trigger replication stress, leading to the accumulation of single-strand DNA (ssDNA) and double-strand breaks (DSBs), which drive mutagenesis and ultimately contribute to disease. While the roles of core histones and their post-translational modifications in this context have been more well-studied, far less is known about how linker histones regulate the replication stress response. Here, we demonstrate that the S-phase–phosphorylated form of the linker histone H1 (pH1) plays a key role in DNA damage repair at collapsed replication forks, both <em>in vitro</em> and in cells. Using phosphomimic and phosphonull H1 mutants, we show that phosphorylation enhances H1 assembly with ssDNA. Utilizing intein chemistry for the site-specific incorporation of a photocrosslinker to the C-terminus of H1, we map the direct interactors of H1. We identify phosphorylated H1 at replication forks, where it engages replication machinery and DNA damage response factors, including Histone PARylation Factor 1 (HPF1). We further demonstrate that ssDNA induces pH1-HPF1 interactions that promote liquid-like assemblies, correlating with reduced DNA damage and histone PARylation. Consistent with this role, reduction of total H1 increases cellular sensitivity to DNA damage, a phenotype that is partially rescued by reintroduction of H1.4. Together, these findings establish pH1 as a new regulator of DNA damage repair at collapsed replication forks through the controlled sequestration of repair factors.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"21 9","pages":"2322–2335"},"PeriodicalIF":3.6,"publicationDate":"2026-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148885690","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}

{"title":"Substrate-Derived Peptides for Selective Covalent Inhibition of Protein Tyrosine Kinases","authors":"Minhee Lee,&nbsp;Andrew C. Johns,&nbsp;Zijing Wang,&nbsp;Devon A. Semoy,&nbsp;Neel H. Shah","doi":"10.1021/acschembio.6c00468","DOIUrl":"10.1021/acschembio.6c00468","url":null,"abstract":"<p>Protein tyrosine kinases are important regulators of cell signaling, and aberrant kinase activity contributes to many human diseases, including cancers. All protein tyrosine kinases share a highly conserved ATP-binding pocket but diverge in their substrate-binding sites in order to mediate distinct signaling events. Many potent and efficacious ATP-competitive tyrosine kinase inhibitors have been developed; however, it remains challenging to achieve on-target selectivity across different kinases and target-specific disease mutants, given the high degree of conservation in the ATP-binding pocket. By contrast, the variable substrate-binding site offers an opportunity for selective inhibition, provided molecules can be targeted to this site. Here, we present a modular strategy to design selective, peptide-based covalent inhibitors of tyrosine kinases with a distinct binding mode from existing ATP-competitive inhibitors. Using Src kinase as a model system, we demonstrate that Src-selective reactivity can be achieved by first designing an optimized substrate peptide and then strategically positioning an electrophile on the peptide to target a nonconserved cysteine on the kinase. We show that substrate-derived covalent peptides can inhibit kinase activity, bind simultaneously with an ATP-competitive inhibitor, and even inhibit the activity of kinases bearing a common drug resistance mutation. We further explore the application of this approach to develop an inhibitor of the cancer-relevant fibroblast growth factor receptor 1 kinase that shows selectivity for an oncogenic mutant over the wild-type enzyme. Our modular strategy to generate selective covalent peptides targeting protein tyrosine kinases provides a promising framework for future chemical probe and drug development efforts.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"21 9","pages":"2306–2321"},"PeriodicalIF":3.6,"publicationDate":"2026-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148860248","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}

{"title":"Correction to “Mass Spectrometry-Based Screening Reveals Inhibitors of Cholesterol 25-Hydroxylase”","authors":"Atikur Rahman,&nbsp;Elijah H. Hayes,&nbsp;Yoshio Yamauchi,&nbsp;Hodaka Saito,&nbsp;Zita Hubler,&nbsp;Drew J. Adams","doi":"10.1021/acschembio.6c00639","DOIUrl":"10.1021/acschembio.6c00639","url":null,"abstract":"","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"21 9","pages":"2514–2514"},"PeriodicalIF":3.6,"publicationDate":"2026-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148890405","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}

{"title":"Modulation Sterol Regulatory Element-Binding Protein Signaling: Mechanisms, Probes, and Roles in Disease","authors":"Karthik Ramachandran,&nbsp;Luis Agustin E. Pilapil,&nbsp;G. Ekin Atilla-Gokcumen","doi":"10.1021/acschembio.6c00590","DOIUrl":"10.1021/acschembio.6c00590","url":null,"abstract":"<p>Maintenance of lipid homeostasis requires cells to coordinate lipid synthesis precisely. Sterol regulatory element-binding proteins (SREBPs) represent one of the central mechanisms by which cells sense lipid availability and adjust the biosynthesis of fatty acids, cholesterol, and phospholipids in response to metabolic and other changes. Dysregulation of SREBP signaling has been implicated in a broad spectrum of diseases, where altered lipid metabolism reshapes membrane organization, cellular signaling, and stress adaptation. In this review, we summarize the molecular mechanisms governing SREBP activation and systems-level regulation. Particular emphasis is placed on the approaches that have enabled interrogation of SREBP signaling. We discuss imaging-based assays, perturbation strategies, pharmacological inhibitors, lipidomics, and other approaches that collectively allow SREBP activity to be interrogated across spatial, biochemical, and metabolic scales. Finally, we highlight how integration of systems-level approaches can refine our understanding of membrane homeostasis and reveal new opportunities for therapeutic intervention in diseases driven by altered SREBP metabolism.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"21 9","pages":"2082–2092"},"PeriodicalIF":3.6,"publicationDate":"2026-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148878574","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}

{"title":"From Inhibitor to Reporter: Nirmatrelvir-Derived Fluorogenic Substrates for the SARS-CoV-2 Main Protease","authors":"Rabea Voget,&nbsp;Victoria Steiger,&nbsp;Katharina Sylvester,&nbsp;Chun-Chiao Yang,&nbsp;Louisa von Kohout,&nbsp;Dominik Thimm,&nbsp;Julian Breidenbach,&nbsp;Norbert Sträter,&nbsp;Christa E. Müller,&nbsp;Michael Gütschow","doi":"10.1021/acschembio.6c00577","DOIUrl":"10.1021/acschembio.6c00577","url":null,"abstract":"<p>The SARS-CoV-2 main protease (M^pro) is a key antiviral drug target due to its essential role in the pathogen’s replication cycle. The development of potent next-generation M^pro inhibitors is of great importance to ensure the availability of safe and effective COVID-19 therapeutics. Associated research necessitates robust and highly sensitive biochemical assays for the early kinetic characterization of M^pro inhibitor candidates. These assays often reach their limits when characterizing highly potent inhibitors, with a common bottleneck being the insufficient catalytic efficiency and competitive capacity of employed M^pro substrates. To optimize assays for highly active M^pro inhibitors by providing M^pro substrates with improved kinetic features, we created a library of fluorogenic substrates (<strong>2</strong>–<strong>8</strong>). These reporters were structurally derived from the well-established M^pro substrate Boc-Abu-Tle-Leu-Gln-AMC (<strong>1</strong>) and the clinically approved covalent-reversible M^pro inhibitor nirmatrelvir. Kinetic evaluation of <strong>1</strong>–<strong>8</strong> identified hit compound <strong>6</strong> with about ten-fold improved catalytic efficiency (<em>k</em>_cat/<em>K</em>_m = 21,400 M^–1 s^–1) compared to parent substrate <strong>1</strong> (<em>k</em>_cat/<em>K</em>_m = 2410 M^–1 s^–1). Substrate <strong>6</strong> was successfully applied for the kinetic characterization of three highly potent M^pro inhibitors. Comparative X-ray crystallographic analyses revealed high similarity in the molecular interactions of the C145A mutant M^pro with nirmatrelvir and with a peptide whose sequence was derived from a natural M^pro substrate. The tetrapeptidic AMC derivative <strong>6</strong> will serve as a valuable biochemical tool contributing to the optimization of SARS-CoV-2 M^pro-directed drug research.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"21 9","pages":"2451–2465"},"PeriodicalIF":3.6,"publicationDate":"2026-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148896218","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}

{"title":"Redox-Dependent Lipophilicity of Phenazine Metabolites Is Modulated by Intramolecular Hydrogen Bonds and Controls Their Biological Distribution","authors":"Korbinian O. Thalhammer,&nbsp;Matthew Scurria,&nbsp;Jinyang Li,&nbsp;Inês B. Trindade,&nbsp;Osvaldo Gutierrez,&nbsp;Stuart J. Conway,&nbsp;Dianne K. Newman","doi":"10.1021/acschembio.6c00422","DOIUrl":"10.1021/acschembio.6c00422","url":null,"abstract":"<p>Phenazines are redox-active microbial metabolites produced and secreted in diverse ecological contexts from soils to chronic infections. Phenazines can function variously as antibiotics, extracellular electron shuttles, and nutrient scavengers. Key to understanding the impact of these functions is a robust expectation of phenazine retention or diffusion in a given context. But predicting phenazine fate and transport is difficult because of the chemical complexity of their local microenvironments. To address this challenge, we measured the octanol-water distribution coefficient (LogD) as a proxy for the lipophilicity of three naturally occurring phenazines produced by the opportunistic pathogen <em>Pseudomonas aeruginosa</em>: phenazine-1-carboxylic acid, phenazine-1-carboxamide, and pyocyanin. We investigated the behavior of both oxidized and reduced forms of these phenazines across broad ionic strength and pH conditions. While the ionic context exerts only small effects, the pH and redox state contribute strongly and independently to changes in phenazine lipophilicity. The pH trends are expected, but the observed redox dependence is generally missed by existing lipophilicity calculation methods. Additional experiments and density functional theory modeling of phenazines in their reduced and oxidized forms reveal that intramolecular hydrogen bonding contributes significantly to the increased lipophilicity of reduced phenazines that possess H-bond-accepting substituents in the 1-position, a phenomenon likely generalizable to other redox-active natural products with comparable intramolecular hydrogen-bonding frameworks. These results explain phenazine behavior in a biological context: redox state alone significantly alters retention of pyocyanin in planktonic <em>P. aeruginosa</em> cells, with the reduced species being predominantly retained by membranes.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"21 9","pages":"2253–2262"},"PeriodicalIF":3.6,"publicationDate":"2026-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148807879","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}