ACS Chemical Biology最新文献

{"title":"Split-Small GTPase Reassembly as a Method to Control Cellular Signaling with User-Defined Inputs","authors":"Yuchen He,&nbsp;Benjamin M. Faulkner,&nbsp;Rachel S. Weatherford,&nbsp;Emily Hyun and Cliff I. Stains*,&nbsp;","doi":"10.1021/acschembio.5c00083","DOIUrl":"10.1021/acschembio.5c00083","url":null,"abstract":"<p >Small GTPases are critical signaling enzymes that control diverse cellular functions, such as cell migration and proliferation. However, dissecting the roles of these enzymes in cellular signaling is hindered by the lack of a plug-and-play methodology for the direct, temporal control of small GTPase activity by using user-defined inputs. Herein, we present a method that pairs split-small GTPases with user-defined chemical inducer of dimerization (CID) systems in a plug-and-play manner to directly control small GTPase signaling in living cells. The modularity of split-small GTPase systems allows for the selection of CIDs with minimal off-target effects on the pathway being studied. Our results highlight the ability to obtain consistent pathway activation with varying CID systems for direct control of MAPK signaling, filopodia formation, and cell retraction. Thus, split-small GTPase systems provide a customizable platform for the development of temporally gated systems for directly controlling cellular signaling with user-defined inputs.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"20 9","pages":"2049–2055"},"PeriodicalIF":3.8,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12442047/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144935669","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}

{"title":"Design of Hyperglycosylated Zika Virus E Proteins that Focus Antibody Recognition on the Complex E Dimer Epitope","authors":"Margarette C. Mariano,&nbsp;Matthew Gregory Hvasta,&nbsp;Kimberly A. Dowd,&nbsp;Wei-Chiao Huang,&nbsp;Helen S. Jung,&nbsp;Lamount R. Evanson,&nbsp;George I. Georgiev,&nbsp;Julia C. Frei,&nbsp;Jonathan F. Lovell,&nbsp;Theodore C. Pierson,&nbsp;Brian Kuhlman and Jonathan R. Lai*,&nbsp;","doi":"10.1021/acschembio.5c00253","DOIUrl":"10.1021/acschembio.5c00253","url":null,"abstract":"<p >Zika virus (ZIKV) and dengue virus serotypes 1–4 (DENV1–4) are flaviviruses spread by <i>Aedes</i> mosquitoes. ZIKV infection can cause Guillain–Barré syndrome and microcephaly, while severe dengue can lead to hemorrhagic fever and death. DENV infection of ZIKV-immune individuals is linked to severe clinical outcomes due to antibody-dependent enhancement (ADE) of infection. Thus, the development of broadly protective vaccines is an important objective. We focus on the E dimer epitope (EDE) of ZIKV, which is targeted by broadly neutralizing antibodies that protect against ZIKV and DENV1–4. We engineered ZIKV E dimer variants containing non-native asparagine-linked glycosylation sites to block antibody responses to regions outside the EDE using a structure-based iterative design approach. One candidate, SC30m53, bound EDE mAbs but not other mAbs and induced a potently neutralizing response against ZIKV and moderately cross-neutralizing responses against DENV1–3 in mice. These findings suggest that hyperglycosylation provides a promising approach to focusing the immune response on key epitopes.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"20 9","pages":"2105–2119"},"PeriodicalIF":3.8,"publicationDate":"2025-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144935899","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":"Conformational Frustration at the Protein–Glycan Interface of a Nonmitogenic Anti-HIV Lectin Results in Altered Quaternary Structure","authors":"Vaishali Narayanan,&nbsp;Avadhesha Surolia and Ashok Sekhar*,&nbsp;","doi":"10.1021/acschembio.5c00347","DOIUrl":"10.1021/acschembio.5c00347","url":null,"abstract":"<p >Lectins are carbohydrate-binding proteins that have enormous therapeutic value because of their potent antiviral activity. However, the design of lectins for targeted intervention is marred by our poor understanding of protein-glycan recognition. Here, we focus on the mannose-specific lectin horcolin, which is nonmitogenic and shows dose-dependent inhibition of HIV infection. Saturation transfer and relaxation dispersion NMR experiments reveal that the lectin-glycan interface is conformationally frustrated, resulting in the formation of a minor state with a millisecond time-scale lifetime. There is a rearrangement of the quaternary structure of horcolin in this minor state that manifests as a noncanonical tetramer. The glycan-binding site is sequestered at the tetrameric interface, suggesting that the tetramer could serve as an autoinhibitory conformation. However, glycan recognition itself occurs via the major dimeric conformation through a “ground-state conformational selection” mechanism. We also demonstrate that the tetramer is destabilized by mannose and that conformational frustration is alleviated in the lectin-glycan complex. Our work illustrates how the architecture of biomolecular assemblies is molded in response to conflicting evolutionary signals such as folding and recognition. The work also provides insights into protein-glycan recognition that could have potential implications for deploying lectins as antiviral agents.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"20 9","pages":"2204–2218"},"PeriodicalIF":3.8,"publicationDate":"2025-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144935911","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":"Dovitinib Ameliorates Inflammation-Related Diseases by Inhibiting Necroptosis and Ferroptosis","authors":"Yingying Lin,&nbsp;Jianting Feng,&nbsp;Mingyuan Zhao,&nbsp;Libo Zhang,&nbsp;Yan Li,&nbsp;Xuan Chen,&nbsp;Chuibing Lin,&nbsp;Junxiong Lin,&nbsp;Qiaofa Lin,&nbsp;Jingyi Li,&nbsp;Lanqin Wu* and Lisheng Li*,&nbsp;","doi":"10.1021/acschembio.5c00327","DOIUrl":"10.1021/acschembio.5c00327","url":null,"abstract":"<p >Abnormal and dysregulated cell death plays important roles in organ injury. Necroptosis and ferroptosis are two distinct types of regulated cell death that can trigger inflammation and are involved in organ injury. The inhibition of necroptosis and ferroptosis is proposed to be beneficial for treating multiple pathological conditions. To find out necroptosis and ferroptosis inhibitors, we used a small-molecule compound library for screening and identified a clinically advanced compound, Dovitinib (Dov), as a potent dual inhibitor of necroptosis and ferroptosis. Dov inhibited tumor necrosis factor (TNF)-induced necroptosis by regulating receptor-interacting protein kinase 1 (RIPK1) and alleviated TNF-mediated systemic inflammatory response syndrome. Additionally, Dov inhibited ferroptosis by regulating the NRF2/HMOX1 axis and lipid peroxidation and protected against concanavalin A-induced acute liver injury. Thus, our work revealed that Dov is a dual inhibitor of necroptosis and ferroptosis and provides a potential therapeutic drug or combination approach for treating necroptosis- and ferroptosis-related diseases.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"20 9","pages":"2191–2203"},"PeriodicalIF":3.8,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144935949","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":"A Multi-Split-and-Mix Platform for a Variety of Targeted Protein Degradation","authors":"Yuechen Wang,&nbsp;Qinhong Luo,&nbsp;Yun Xing,&nbsp;Rui Wang,&nbsp;Fenfang Yang,&nbsp;Weifan Cao,&nbsp;Zigang Li* and Feng Yin*,&nbsp;","doi":"10.1021/acschembio.5c00444","DOIUrl":"10.1021/acschembio.5c00444","url":null,"abstract":"<p >PROTAC, as a highly valued bifunctional molecule, provides a new approach for the drug development of traditional undruggable targets, which holds significant potential in cancer therapy and other disease treatments. However, due to the complicated design process and hard synthesis task, the development of traditional PROTAC drugs is both complex and costly, especially for the design of multitargeting PROTACs. Herein, considering the flexibility and efficacy of the split-and-mix strategy, we proposed a novel Multi-SM-PROTAC platform capable of stable performance with over three ligands simultaneously. In this study, the self-assembly advantage of the split-and-mix strategy was utilized to easily achieve: (1) the simultaneous degradation of dual targets, (2) multi-E3 ligase-mediated degradation of a single target, and (3) multi-E3 ligase-mediated degradation of dual targets. By successfully degrading multiple proteins, it was proven that the Multi-SM-PROTAC platform could achieve multimodule selection and programming for specific therapeutic goals, demonstrating its broad application prospects in drug discovery.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"20 9","pages":"2287–2297"},"PeriodicalIF":3.8,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144935786","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":"Amphipathic Proline-Rich Cell Penetrating Peptides for Targeting Mitochondria","authors":"Adeline Schmitt,&nbsp; and ,&nbsp;Helma Wennemers*,&nbsp;","doi":"10.1021/acschembio.5c00479","DOIUrl":"10.1021/acschembio.5c00479","url":null,"abstract":"<p >Cell-penetrating peptides (CPPs) offer a platform for targeted intracellular delivery. Here, we developed amphipathic oligoprolines for targeting mitochondria. The rigid peptides feature cationic guanidinium and hydrophobic cyclohexyl groups aligned along the edges of the polyproline II (PPII) helical backbone. Systematic variations of the hydrophobicity through C-terminal and backbone modifications provided CPPs with enhanced cellular uptake and mitochondrial selectivity. Comparative studies with conformationally more flexible analogs revealed the benefit of aligned cationic and hydrophobic residues on a rigid backbone for mitochondria targeting. Notably, the amphipathic peptides undergo time-dependent intracellular redistribution, leading to selective and prolonged mitochondrial residency. Our findings established design principles for optimizing CPPs to target mitochondria.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"20 9","pages":"2298–2307"},"PeriodicalIF":3.8,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acschembio.5c00479","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144870132","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}

{"title":"Phage Selection of Cyclic Peptides Inhibiting Aminoglycoside Phosphotransferases to Control Resistant Bacteria","authors":"Qiannan Guo,&nbsp;Hui Zeng and Xu-Dong Kong*,&nbsp;","doi":"10.1021/acschembio.5c00366","DOIUrl":"10.1021/acschembio.5c00366","url":null,"abstract":"<p >The clinical threat of aminoglycoside phosphotransferases (APHs) stems from their efficient inactivation of aminoglycosides, driving multidrug resistance through broad-spectrum antibiotic modification. While peptide-based inhibitors represent a promising therapeutic modality, current candidates lack sufficient potency against APHs. To address this limitation, we employed phage display technology to screen large cyclic peptide libraries (structural diversity &gt;10¹¹) against APH(3′)-Ia, a clinically relevant enzyme derived from <i>Escherichia coli</i>. Our selection identified cyclic peptide families exhibiting nanomolar binding affinities characterized by two conserved motifs: CXW(P/L)LC and CP(W/F)YC. Intriguingly, divalent cations (Mg²⁺ and Ca²⁺) enhanced peptide–APH interactions, suggesting a metal-dependent binding mechanism. Competitive fluorescence polarization assays revealed that these cyclic peptides primarily occupy the ATP-binding pocket of APH(3′)-Ia, with representative candidate A-L3 demonstrating significant enzymatic inhibition. This study establishes a foundation for developing APH-targeted antibiotic adjuvants through (1) identification of novel cyclic peptide scaffolds with inhibitory potential, (2) elucidation of divalent metal ion effects on inhibitor binding, and (3) mechanistic insights into ATP-binding site competition. These findings provide critical structural and functional information to guide the rational design of next-generation antibiotic resistance breakers.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"20 9","pages":"2219–2228"},"PeriodicalIF":3.8,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144870155","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":"An Integral Activity-Based Protein Profiling Method for Higher Throughput Determination of Protein Target Sensitivity to Small Molecules","authors":"Chathuri J. Kombala,&nbsp;Agne Sveistyte,&nbsp;Tong Zhang,&nbsp;Leo J. Gorham,&nbsp;Gerard X. Lomas,&nbsp;John T. Melchior,&nbsp;Priscila M. Lalli,&nbsp;Vanessa L. Paurus,&nbsp;Stephen J. Callister,&nbsp;Aaron T. Wright* and Vivian S. Lin*,&nbsp;","doi":"10.1021/acschembio.5c00412","DOIUrl":"10.1021/acschembio.5c00412","url":null,"abstract":"<p >Activity-based protein profiling (ABPP) is a chemoproteomic technique that uses small molecule probes to label active enzymes selectively and covalently in complex proteomes. Competitive ABPP, which involves treatment of the active proteome with an analyte of interest, is especially powerful for profiling how small molecules impact specific protein activities. Advances in higher throughput workflows have made it possible to generate extensive competitive ABPP data across diverse biological samples, making this approach highly appealing for characterizing shared and unique proteins affected by perturbations such as drug or chemical exposures. To use the competitive ABPP approach effectively to understand potential adverse effects of chemicals of concern (CoC), a wide range of concentrations may be needed, particularly for chemicals that lack potency or toxicity data. In this work, we present an integral competitive ABPP method that enables target sensitivity determination for different organophosphate (OP) pesticides as model toxicants. Using previously developed OP-ABPs, we optimized conditions for tandem mass tag (TMT) multiplexing of ABPP samples and compared conventional competitive ABPP involving samples at discrete paraoxon concentrations to pooled samples across that same concentration range. We then expanded our approach to compare protein target sensitivities toward two additional OP pesticides, chlorpyrifos oxon and malaoxon. The results showed that differences in integral intensities for the pooled competition sample can be used to evaluate the relative sensitivity of specific proteins without increasing the overall number of samples. For 8 CoC concentrations of interest, this strategy reduced the number of TMT plexes and the corresponding number of LC–MS/MS analyses 3-fold. We envision the integral ABPP (IABPP) method will provide a means to screen diverse chemicals more rapidly to identify both high and low sensitivity protein targets.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"20 9","pages":"2277–2286"},"PeriodicalIF":3.8,"publicationDate":"2025-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144853918","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":"Characterizing the Biochemical Role of an Unusual Fatty Acyl-AMP Ligase from a Hybrid PKS-NRPS Pathway in Nematodes","authors":"Matthew T. Gordon,&nbsp;Melisa S. Gonzalez,&nbsp; Priya,&nbsp;Rongrong Yu,&nbsp;Elijah Abraham,&nbsp;Xiang Li,&nbsp;Dilip V. Prajapati and Rebecca A. Butcher*,&nbsp;","doi":"10.1021/acschembio.5c00237","DOIUrl":"10.1021/acschembio.5c00237","url":null,"abstract":"<p >PKAL-1 is a fatty acyl-AMP ligase that plays an essential role in the biosynthesis of the nemamides, hybrid polyketide-nonribosomal peptides from nematodes that promote recovery from starvation-induced larval arrest. This enzyme traffics biosynthetic intermediates between two enzymatic assembly lines: the hybrid polyketide synthase-nonribosomal peptide synthetase PKS-1 and the nonribosomal peptide synthetase NRPS-1. Specifically, a <i>pkal-1</i> mutant worm strain does not produce the nemamides but accumulates a β-amino-containing polyketide, named nematide A, which is made by PKS-1 and is potentially loaded by PKAL-1 onto NRPS-1. Here, however, we show that PKAL-1 does not accept β-amino-containing substrates. Furthermore, phylogenetic and structural analyses of PKAL-1 indicate that it is likely missing key residues in its active site for binding to a β-amino group. By analyzing a panel of alternative substrates in biochemical assays, we show that PKAL-1 prefers α,β-unsaturated substrates. Our work potentially suggests an alternative model for nemamide biosynthesis whereby PKAL-1 loads an α,β-unsaturated substrate onto NRPS-1 and the β-amino group is installed later in the biosynthetic pathway. Furthermore, our data could indicate that nematide A is separate from the biosynthetic intermediates that are passed between PKS-1 and NRPS-1 in the construction of the nemamides and may have its own signaling function. Thus, PKAL-1 may help to regulate what is made by the PKS-1-NRPS-1 assembly line, either nematide A or the nemamides.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"20 9","pages":"2095–2104"},"PeriodicalIF":3.8,"publicationDate":"2025-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144853919","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 “A Novel Use of Gentamicin in the ROS-Mediated Sensitization of NCI-H460 Lung Cancer Cells to Various Anticancer Agents”","authors":"Michael F. Cuccarese,&nbsp;Amit Singh,&nbsp;Mansoor Amiji and George A. O’Doherty*,&nbsp;","doi":"10.1021/acschembio.5c00602","DOIUrl":"10.1021/acschembio.5c00602","url":null,"abstract":"","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"20 9","pages":"2350–2351"},"PeriodicalIF":3.8,"publicationDate":"2025-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144853920","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}