Jieyu Wang, Jialong Peng, Ming Cai, Yangbing Li, Fang He, Hong-Hui Wang, Zhou Nie
{"title":"Engineering H<sub>2</sub>S-Activatable Aptameric Binders for Tailored Cell Manipulation.","authors":"Jieyu Wang, Jialong Peng, Ming Cai, Yangbing Li, Fang He, Hong-Hui Wang, Zhou Nie","doi":"10.1021/acschembio.5c00201","DOIUrl":"https://doi.org/10.1021/acschembio.5c00201","url":null,"abstract":"<p><p>Cell surface receptors play a crucial role in mediating cellular communication and precisely regulating cellular functions. Dysregulation of these receptors is closely associated with various diseases. To enable precise and dynamic receptor control, we developed a gas-responsive aptameric binder based on a chemically masked configuration, enabling stimulus-triggered reactivation. Specifically, the receptor-targeting activity of the aptamer is sterically blocked via azide modifications at critical residues, with selective restoration of function upon exposure to hydrogen sulfide (H<sub>2</sub>S), enabling precise receptor modulation. Using this strategy, we successfully achieved H<sub>2</sub>S-triggered receptor dimerization, leading to controlled activation of downstream signaling pathways and regulation of cellular behaviors such as migration and proliferation. Furthermore, we extended this approach to facilitate highly selective receptor degradation. By harnessing gasotransmitter cues for molecular switching, this system expands the toolkit for receptor engineering and holds great potential for targeted therapeutic interventions in regenerative medicine and oncology.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144582598","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}
Nisansala Vithanage, Rifat Hasan Apurba, Hamza Enesi Ozomarisi, Carson J Bair, Eve L Sugg, Victor K Outlaw
{"title":"SARS-CoV-2 Omicron Variant Spike Glycoprotein Mutation Q954H Enhances Fusion Core Stability.","authors":"Nisansala Vithanage, Rifat Hasan Apurba, Hamza Enesi Ozomarisi, Carson J Bair, Eve L Sugg, Victor K Outlaw","doi":"10.1021/acschembio.5c00208","DOIUrl":"https://doi.org/10.1021/acschembio.5c00208","url":null,"abstract":"<p><p>The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant-of-concern has rapidly spread across the globe to become the dominant form of COVID-19 infection. The Omicron Spike (S) glycoprotein, which mediates viral entry into cells, possesses up to 34 mutations that contribute to the variant's increased transmissibility and decreased susceptibility to antibody-mediated immunity from vaccines or prior infections. One of those mutations, Q954H, occurs within the N-terminal heptad repeat (HR1) domain. During viral entry, the HR1 domain coassembles with the C-terminal heptad repeat (HR2) domain to form a stable six-helix bundle or \"fusion core\" structure, which brings the viral envelope and host membrane into proximity and thermodynamically drives membrane fusion. Here, we demonstrate that the Q954H mutation enhances the interaction between the HR1 and HR2 domains, thereby stabilizing the fusion core assembly relative to prior variants. We also report the first X-ray crystal structure of the Omicron S fusion core, which reveals that the Q954H side chain forms a N···H-O hydrogen bond with the side chain hydroxyl of S1175 within the HR2 domain, as well as an unexpected C-H···O hydrogen bonding interaction with the backbone carbonyl of N1173. Co-assembly with a synthetic depsipeptide, in which the amide of N1173 is replaced with an ester, results in a decreased assembly stability, providing evidence to support the importance of the observed hydrogen bond network. These insights will be valuable for analyzing the factors that drive viral evolution and for the development of inhibitors of SARS-CoV-2 entry.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144574336","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}
Hu Zhu, Harrison C Daly, Tae Gyun Yang, Josh Born, Gisela Andrea Camacho-Hernandez, Mingyang Yuan, Mari Inglese, Vinoth Kumar Chenniappan, Kris Zimmerman, Robin Hurst, Xin Hu, Amy Hauck Newman, Sergi Ferré, Rachel Friedman Ohana, Matthew D Hall, Samarjit Patnaik
{"title":"Development of a HiBiT Peptide-Based NanoBRET Ligand Binding Assay for Galanin Receptor 1 in Live Cells.","authors":"Hu Zhu, Harrison C Daly, Tae Gyun Yang, Josh Born, Gisela Andrea Camacho-Hernandez, Mingyang Yuan, Mari Inglese, Vinoth Kumar Chenniappan, Kris Zimmerman, Robin Hurst, Xin Hu, Amy Hauck Newman, Sergi Ferré, Rachel Friedman Ohana, Matthew D Hall, Samarjit Patnaik","doi":"10.1021/acschembio.5c00166","DOIUrl":"https://doi.org/10.1021/acschembio.5c00166","url":null,"abstract":"<p><p>Galanin is a neuroendocrine peptide that regulates a wide range of physiological functions, including feeding and energy homeostasis, mood and anxiety, and modulation of pain. The function of the galanin peptide is mediated through its three galanin receptors, namely, GALR1, GALR2, and GALR3, which belong to the G protein-coupled receptor family. To measure the interaction of ligands with galanin receptor 1 (GALR1) in living cells, we developed a novel HiBiT peptide-based NanoBRET ligand binding assay. We generated six bioluminescence resonance energy transfer (BRET) tracers composed of modified and truncated galanin peptide derivatives tagged with a 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) acceptor fluorophore. The fluorophore-tagged peptide tracers were evaluated in cells expressing GALR1 tagged with HiBiT, an 11-amino acid subunit of NanoLuc, which, upon high affinity complementation with the cell-impermeable subunit LgBiT, reconstituted a functional NanoLuc luciferase. Addition of the furimazine substrate induced BRET to the BODIPY fluorophore acceptor component of the galanin-derived peptide tracers and produced a fluorescence signal output. Using this BRET assay, we characterized the binding affinity and binding kinetics of tracers with GALR1 in both equilibrium and real time. To validate our assay, we evaluated the binding affinity and function of a panel of unmodified galanin-derived peptide ligands through the competitive displacement of bound fluorescent galanin tracers. Our data showed that the binding affinity of these galanin peptide ligands correlated well with their rank order in β-arrestin recruitment and internalization functional assays. This study demonstrates that the HiBiT peptide-based NanoBRET ligand binding assay is a valuable system for studying the ligand engagement of GALR1 in living cells, offering an alternative to neuropeptide radioligand binding assays.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144564147","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}
Shaimaa Tarek, Yasmin ElMaghloob, Hong Smith, Thomas J Smith, Marwa T ElRakaiby, Mohamed H Habib
{"title":"A Scavenger Hunt for a DyP-Peroxidase from a Metagenome: Curated Peroxidase Database-Assisted Primer Design and Protein Structure Elucidation.","authors":"Shaimaa Tarek, Yasmin ElMaghloob, Hong Smith, Thomas J Smith, Marwa T ElRakaiby, Mohamed H Habib","doi":"10.1021/acschembio.5c00323","DOIUrl":"https://doi.org/10.1021/acschembio.5c00323","url":null,"abstract":"<p><p>Dye-decolorizing peroxidase (DyP)-type peroxidases are heme-containing enzymes that play a role in lignin synthesis and degradation and dye decolorization. Despite numerous studies about this class of enzymes, the enzyme remains under-explored. We used 1000 DyP sequences retrieved from the NCBI database to forge a phylogenetic tree. Nodes in the tree, where sequences displayed a degree of conservation, were used to design degenerate primers to locate DyP-peroxidase sequences from the DNA extract of a tannery wastewater sample. After PCR amplification and visualization using agarose electrophoresis, a band at the expected size of a DyP peroxidase (500-700 bp) was seen. TA cloning followed by blue-white colony selection validated our finding after amplicon sequencing of the PCR product to confirm the presence of an <i>Acinetobacter</i> species DyP-peroxidase. Our metagenomic DyP displayed 99% similarity to the DyP-peroxidase sequence found in the <i>Acinetobacter baumannii</i> ATCC 19606 strain. As a result, and due to the minute differences between our found DyP and the ATCC 19606 strain DyP, we expressed the latter cloned in a pET28b(+) vector and purified it from culture medium using <i>Escherichia coli</i> SoluBl21 as a host strain. A crude oxidation assay using 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) deemed the enzyme active as shown by the formation of a green color. The crystal structure of the enzyme was solved at 2.6 Å resolution (PDB ID 9OBR) using X-ray crystallography and presented as a hexamer in solution.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144551414","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}
Stephen B Ruiz, Daniel E Tylawsky, Janki Shah, Michelle Saoi, Brandon Cuevas, Shanay Desai, Boglarka Racz, Ana Marie Perea, Arianna R Izawa-Ishiguro, Justin Cross, Daniel A Heller
{"title":"Phospholipase PAFAH2 Mediates Ferroptosis Surveillance and Lipid Remodeling to Promote Resistance in KEAP1 Mutant Cancers.","authors":"Stephen B Ruiz, Daniel E Tylawsky, Janki Shah, Michelle Saoi, Brandon Cuevas, Shanay Desai, Boglarka Racz, Ana Marie Perea, Arianna R Izawa-Ishiguro, Justin Cross, Daniel A Heller","doi":"10.1021/acschembio.5c00273","DOIUrl":"https://doi.org/10.1021/acschembio.5c00273","url":null,"abstract":"<p><p>Although ferroptosis resistance is prevalent among many cancer cell types, precisely how ferroptosis surveillance mechanisms are induced remains elusive due to the heterogeneity of the cellular mutational status and metabolic states. Here, we find that phospholipase PAFAH2 regulates ferroptosis through its unique ability to specifically detoxify membrane-bound oxidized phospholipids in KEAP1 mutant and NRF2-active cancer cells. We show that the genetic or chemical perturbation of PAFAH2 is sufficient to sensitize KEAP1 mutant lung adenocarcinoma cells to ferroptosis. Lipidomic analyses reveal that PAFAH2 inhibition shifts the cellular lipidome to a distinctly ferroptosis state characterized by the enrichment of key phospholipids previously identified to be important in ferroptosis, like ether-linked phosphatidylethanolamines. Finally, we comparatively assessed the antitumor efficacy of PAFAH2 inhibitor monotherapy versus cotreatment with a nanoparticle-stabilized GPX4 inhibitor formulation. Our findings support that the broad applicability of PAFAH2 inhibition can be used in ferroptosis induction and abrogation of ferroptosis resistance across cancer types.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144537385","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}
Maria J Ortiz-Ruiz, Olajumoke Popoola, Konstantinos Mitsopoulos, Robert Te-Poele, Rahul S Samant, Gary Box, Will Court, Alexis De Haven Brandon, Sharon Gowan, Aurelie Mallinger, Toby Roe, Kate Swabey, Melanie Valenti, Bissan Al-Lazikani, Julian Blagg, Christina Esdar, Kai Schiemann, Dirk Wienke, Suzanne A Eccles, Paul Workman, Paul A Clarke
{"title":"Mediator Kinase Inhibitor Selectivity and Activity in Colorectal Cancer.","authors":"Maria J Ortiz-Ruiz, Olajumoke Popoola, Konstantinos Mitsopoulos, Robert Te-Poele, Rahul S Samant, Gary Box, Will Court, Alexis De Haven Brandon, Sharon Gowan, Aurelie Mallinger, Toby Roe, Kate Swabey, Melanie Valenti, Bissan Al-Lazikani, Julian Blagg, Christina Esdar, Kai Schiemann, Dirk Wienke, Suzanne A Eccles, Paul Workman, Paul A Clarke","doi":"10.1021/acschembio.5c00338","DOIUrl":"https://doi.org/10.1021/acschembio.5c00338","url":null,"abstract":"<p><p>The Mediator complex is a regulator of gene expression, influencing chromatin structure and RNA polymerase II-mediated transcription. Its activity is controlled by a protein kinase module, which includes cyclin-dependent kinases 8 and 19, that phosphorylates RNA polymerase II and transcription factors to regulate gene expression. Using orthogonal approaches combining chemical and genetic tools, we demonstrated the selectivity of our small-molecule inhibitors derived from 3,4,5-trisubstituted pyridine and 3-methyl-1<i>H</i>-pyrazolo[3,4-<i>b</i>]pyridine chemical series in human colorectal cell culture and tumor xenograft models. The lack of activity of our inhibitors in CDK8/19 double knockout models, with respect to molecular, proliferative, and antitumor end points, revealed their specificity and dependence on these kinases. Using our chemical probes and knockout models, we explored Mediator kinase function in human colorectal cancer cells. Phospho-proteome profiling revealed substrates enriched with transcription and chromatin regulators, while promoter reporter experiments identified transcription factor binding sites, including TCF/LEF and AP1, regulated by Mediator kinases. Additionally, altered phosphorylation of several Mediator subunits suggests a mechanism for the rapid regulation of the Mediator complex. Overall, our results demonstrate that CDK8 and CDK19 play pivotal roles in regulating gene expression associated with oncogene activation and signaling pathways. Further studies are warranted to elucidate their broader cellular roles and regulatory mechanisms. The selective inhibitors validated in this study will provide valuable tools for such mechanistic investigations into Mediator kinase functions and their potential therapeutic exploitation.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144551415","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":"Quantitative Proteomics Reveals the Role of Lysine Lactylation in Lenalidomide-Resistance in Multiple Myeloma Cells.","authors":"Xinlong Guo, Xuelian Ren, Cong Yan, He Huang","doi":"10.1021/acschembio.5c00270","DOIUrl":"https://doi.org/10.1021/acschembio.5c00270","url":null,"abstract":"<p><p>Multiple myeloma (MM) is a hematologic malignancy characterized by abnormal plasma cell proliferation, with lenalidomide emerging as a primary treatment. However, prolonged use often leads to drug resistance, underscoring the need to understand the resistance mechanisms. Protein post-translational modifications (PTMs) play crucial roles in disease development, including chemoresistance. Here, we investigate the involvement of new types of PTMs, focusing on lysine lactylation (Kla), in lenalidomide-resistance. Glycolysis-driven elevation of Kla levels was observed in lenalidomide-resistant MM cells, and the subsequent inhibition of glycolytic activity significantly reversed the lenalidomide-resistance phenotype. Through quantitative proteome, lactylome, and acetylome analyses, we identified 7493 proteins, 1241 Kla sites, and 9313 lysine acetylation (Kac) sites, thereby revealing differential protein expression and PTM profiles in lenalidomide-resistant cells. Proteomic analysis revealed that a series of chemoresistance-related proteins were upregulated, and a number of Cullin-RING Ligase 4-Cereblon (CRL4<sup>CRBN</sup>) regulatory factors were downregulated. Lactylome analysis revealed that numerous chemoresistance-related proteins exhibited increased Kla levels in lenalidomide-resistant MM cells, suggesting that Kla played an important role in the development of lenalidomide-resistance in LenR MM cells. Notably, histone H4K8la was associated with upregulation of chemoresistance-related genes cyclin-dependent kinase 6 (CDK6) and enoyl-CoA hydratase (ECHS1). Our findings shed light on the epigenetic mechanisms underlying lenalidomide-resistance in MM, offering insights for overcoming chemoresistance.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144537386","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}
Magdalena Niemczura, Aleksi Nuutila, Rongbin Wang, Katariina Rauhanen, S Eric Nybo, Mikko Metsä-Ketelä
{"title":"Three-Enzyme Cascade Catalyzes Conversion of Auramycinone to Resomycin in Chartreusin Biosynthesis.","authors":"Magdalena Niemczura, Aleksi Nuutila, Rongbin Wang, Katariina Rauhanen, S Eric Nybo, Mikko Metsä-Ketelä","doi":"10.1021/acschembio.5c00205","DOIUrl":"https://doi.org/10.1021/acschembio.5c00205","url":null,"abstract":"<p><p>Chartreusin is a potent antiproliferative agent that contains a unique aromatic pentacyclic bislactone carbon scaffold. The biosynthesis of type II polyketide aglycone has been extensively investigated and shown to proceed through a tetracyclic anthracycline intermediate. The last remaining unknown steps are the conversion of auramycinone to resomycin C. Here we have discovered three enzymes that play crucial roles in two mechanistically distinct dehydration reactions. We show that ChaX is an NAD(P)H-dependent auramycinone quinone reductase that allows the cyclase-like ChaU to catalyze the formation of 9,10-dehydroauramycinone via a carbanion intermediate. In contrast, the cyclase-like ChaJ, homologous to ChaU, is responsible for subsequent 7,8-dehydration via a canonical carbocation intermediate, yielding resomycin C. The results were confirmed via assembly of the biosynthetic pathway for production of resomycin C in <i>Streptomyces coelicolor</i> M1152Δ<i>matAB</i>. The work expands the catalytic repertoire of the SnoaL protein family, which has previously been associated with anthracycline fourth-ring cyclization and two-component 1-hydroxylation.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144537387","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}
Panayotis C Theodoropoulos, Holly H Guo, Wentian Wang, Eric Crossley, Giomar Rivera Cancel, Min Fang, Thu Nguyen, Hamid Baniasadi, Noelle S Williams, Joseph M Ready, Jef K De Brabander, Deepak Nijhawan
{"title":"Correction to \"Thiophenyl Derivatives of Nicotinamide Are Metabolized by the NAD Salvage Pathway into Unnatural NAD Derivatives That Inhibit IMPDH and Are Toxic to Peripheral Nerve Cancers\".","authors":"Panayotis C Theodoropoulos, Holly H Guo, Wentian Wang, Eric Crossley, Giomar Rivera Cancel, Min Fang, Thu Nguyen, Hamid Baniasadi, Noelle S Williams, Joseph M Ready, Jef K De Brabander, Deepak Nijhawan","doi":"10.1021/acschembio.5c00436","DOIUrl":"10.1021/acschembio.5c00436","url":null,"abstract":"","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144525304","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}
Lisa M Boatner, Jerome Eberhardt, Flowreen Shikwana, Matthew Holcomb, Peiyuan Lee, Kendall N Houk, Stefano Forli, Keriann M Backus
{"title":"CIAA: Integrated Proteomics and Structural Modeling for Understanding Cysteine Reactivity with Iodoacetamide Alkyne.","authors":"Lisa M Boatner, Jerome Eberhardt, Flowreen Shikwana, Matthew Holcomb, Peiyuan Lee, Kendall N Houk, Stefano Forli, Keriann M Backus","doi":"10.1021/acschembio.5c00225","DOIUrl":"https://doi.org/10.1021/acschembio.5c00225","url":null,"abstract":"<p><p>Cysteine residues play key roles in protein structure and function and can serve as targets for chemical probes and even drugs. Chemoproteomic studies have revealed that heightened cysteine reactivity toward electrophilic probes, such as iodoacetamide alkyne (IAA), is indicative of likely residue functionality. However, while the cysteine coverage of chemoproteomic studies has increased substantially, these methods still provide only a partial assessment of proteome-wide cysteine reactivity, with cysteines from low-abundance proteins and tough-to-detect peptides still largely refractory to chemoproteomic analysis. Here, we integrate cysteine chemoproteomic reactivity data sets with structure-guided computational analysis to delineate key structural features of proteins that favor elevated cysteine reactivity toward IAA. We first generated and aggregated multiple descriptors of cysteine microenvironment, including amino acid content, solvent accessibility, residue proximity, secondary structure, and predicted p<i>K</i><sub>a</sub>. We find that no single feature is sufficient to accurately predict the reactivity. Therefore, we developed the CIAA (Cysteine reactivity toward IodoAcetamide Alkyne) method, which utilizes a Random Forest model to assess cysteine reactivity by incorporating descriptors that characterize the three-dimensional (3D) structural properties of thiol microenvironments. We trained the CIAA model on existing and newly generated cysteine chemoproteomic reactivity data paired with high-resolution crystal structures from the Protein Data Bank (PDB), with cross-validation against an external data set. CIAA analysis reveals key features driving cysteine reactivity, such as backbone hydrogen bond donor atoms, and reveals still underserved needs in the area of computational predictions of cysteine reactivity, including challenges surrounding protein structure selection data set curation. Thus, our work provides a strong foundation for deploying artificial intelligence (AI) on cysteine chemoproteomic data sets.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144525303","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}