Pub Date : 2025-02-07DOI: 10.1016/j.chembiol.2025.01.006
Jason Z. Zhang, Nathan Greenwood, Jason Hernandez, Josh T. Cuperus, Buwei Huang, Bryan D. Ryder, Christine Queitsch, Jason E. Gestwicki, David Baker
Protein quality control (PQC) is carried out in part by the chaperone Hsp70 in concert with adapters of the J-domain protein (JDP) family. The JDPs, also called Hsp40s, are thought to recruit Hsp70 into complexes with specific client proteins. However, the molecular principles regulating this process are not well understood. We describe the de novo design of Hsp70 binding proteins that either inhibit or stimulate Hsp70 ATPase activity. An ATPase stimulating design promoted the refolding of denatured luciferase in vitro, similar to native JDPs. Targeting of this design to intracellular condensates resulted in their nearly complete dissolution and revealed roles as cell growth promoting signaling hubs. The designs inform our understanding of chaperone structure-function relationships and provide a general and modular way to target PQC systems to regulate condensates and other cellular targets.
{"title":"De novo designed Hsp70 activator dissolves intracellular condensates","authors":"Jason Z. Zhang, Nathan Greenwood, Jason Hernandez, Josh T. Cuperus, Buwei Huang, Bryan D. Ryder, Christine Queitsch, Jason E. Gestwicki, David Baker","doi":"10.1016/j.chembiol.2025.01.006","DOIUrl":"https://doi.org/10.1016/j.chembiol.2025.01.006","url":null,"abstract":"Protein quality control (PQC) is carried out in part by the chaperone Hsp70 in concert with adapters of the J-domain protein (JDP) family. The JDPs, also called Hsp40s, are thought to recruit Hsp70 into complexes with specific client proteins. However, the molecular principles regulating this process are not well understood. We describe the <em>de novo</em> design of Hsp70 binding proteins that either inhibit or stimulate Hsp70 ATPase activity. An ATPase stimulating design promoted the refolding of denatured luciferase <em>in vitro</em>, similar to native JDPs. Targeting of this design to intracellular condensates resulted in their nearly complete dissolution and revealed roles as cell growth promoting signaling hubs. The designs inform our understanding of chaperone structure-function relationships and provide a general and modular way to target PQC systems to regulate condensates and other cellular targets.","PeriodicalId":265,"journal":{"name":"Cell Chemical Biology","volume":"141 1","pages":""},"PeriodicalIF":8.6,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143258446","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-28DOI: 10.1016/j.chembiol.2025.01.003
Maysam Mansouri, Martin Fussenegger
Human body cells and our daily electronic devices both communicate information within their distinct worlds by regulating the flow of electrons across specified membranes. While electronic devices depend on the flow of electrons generated by conductive materials to communicate within a digital network, biological systems use ion gradients, created in analog biochemical reactions, to trigger biological data transmission throughout multicellular systems. Electrogenetics is an emerging concept in synthetic biology in which electrons generated by digital electronic devices program customized electron-responsive biological units within living cells. In this paper, we outline endeavors to design direct electrogenetic interfaces to control cell behaviors in therapeutically engineered mammalian cells. We also discuss prospects for the world of electrogenetics, focusing on how to engineer the next generation of therapeutic cells controlled by electronic devices and the internet of the body.
{"title":"Engineering electrogenetic interfaces for mammalian cell control","authors":"Maysam Mansouri, Martin Fussenegger","doi":"10.1016/j.chembiol.2025.01.003","DOIUrl":"https://doi.org/10.1016/j.chembiol.2025.01.003","url":null,"abstract":"Human body cells and our daily electronic devices both communicate information within their distinct worlds by regulating the flow of electrons across specified membranes. While electronic devices depend on the flow of electrons generated by conductive materials to communicate within a digital network, biological systems use ion gradients, created in analog biochemical reactions, to trigger biological data transmission throughout multicellular systems. Electrogenetics is an emerging concept in synthetic biology in which electrons generated by digital electronic devices program customized electron-responsive biological units within living cells. In this paper, we outline endeavors to design direct electrogenetic interfaces to control cell behaviors in therapeutically engineered mammalian cells. We also discuss prospects for the world of electrogenetics, focusing on how to engineer the next generation of therapeutic cells controlled by electronic devices and the internet of the body.","PeriodicalId":265,"journal":{"name":"Cell Chemical Biology","volume":"19 1","pages":""},"PeriodicalIF":8.6,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143050284","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-16DOI: 10.1016/j.chembiol.2024.10.010
Kevin A. Scott , Hiroyuki Kojima , Nathalie Ropek , Charles D. Warren , Tiffany L. Zhang , Simon J. Hogg , Henry Sanford , Caroline Webster , Xiaoyu Zhang , Jahan Rahman , Bruno Melillo , Benjamin F. Cravatt , Jiankun Lyu , Omar Abdel-Wahab , Ekaterina V. Vinogradova
Despite significant interest in therapeutic targeting of splicing, few chemical probes are available for the proteins involved in splicing. Here, we show that elaborated stereoisomeric acrylamide EV96 and its analogues lead to a selective T cell state-dependent loss of interleukin 2-inducible T cell kinase (ITK) by targeting one of the core splicing factors SF3B1. Mechanistic investigations suggest that the state-dependency stems from a combination of differential protein turnover rates and extensive ITK mRNA alternative splicing. We further introduce the most comprehensive list to date of proteins involved in splicing and leverage cysteine- and protein-directed activity-based protein profiling with electrophilic scout fragments to demonstrate covalent ligandability for many classes of splicing factors and splicing regulators in T cells. Taken together, our findings show how chemical perturbation of splicing can lead to immune state-dependent changes in protein expression and provide evidence for the broad potential to target splicing factors with covalent chemistry.
尽管人们对剪接的靶向治疗非常感兴趣，但很少有化学探针可用于参与剪接的蛋白质。在这里，我们展示了精心制作的立体异构体丙烯酰胺 EV96 及其类似物通过靶向核心剪接因子之一 SF3B1，导致白细胞介素 2 诱导型 T 细胞激酶（ITK）的选择性 T 细胞状态依赖性缺失。 机制研究表明，状态依赖性源于不同的蛋白质周转率和广泛的 ITK mRNA 交替剪接。我们进一步介绍了迄今为止最全面的参与剪接的蛋白质列表，并利用半胱氨酸和蛋白质定向活性的蛋白质剖析以及亲电侦察片段证明了 T 细胞中许多种类的剪接因子和剪接调节因子的共价配体性。总之，我们的研究结果表明了剪接的化学扰动如何导致蛋白质表达的免疫状态依赖性变化，并为利用共价化学作用靶向剪接因子的广泛潜力提供了证据。
{"title":"Covalent targeting of splicing in T cells","authors":"Kevin A. Scott , Hiroyuki Kojima , Nathalie Ropek , Charles D. Warren , Tiffany L. Zhang , Simon J. Hogg , Henry Sanford , Caroline Webster , Xiaoyu Zhang , Jahan Rahman , Bruno Melillo , Benjamin F. Cravatt , Jiankun Lyu , Omar Abdel-Wahab , Ekaterina V. Vinogradova","doi":"10.1016/j.chembiol.2024.10.010","DOIUrl":"10.1016/j.chembiol.2024.10.010","url":null,"abstract":"<div><div>Despite significant interest in therapeutic targeting of splicing, few chemical probes are available for the proteins involved in splicing. Here, we show that elaborated stereoisomeric acrylamide EV96 and its analogues lead to a selective T cell state-dependent loss of interleukin 2-inducible T cell kinase (ITK) by targeting one of the core splicing factors SF3B1. Mechanistic investigations suggest that the state-dependency stems from a combination of differential protein turnover rates and extensive ITK mRNA alternative splicing. We further introduce the most comprehensive list to date of proteins involved in splicing and leverage cysteine- and protein-directed activity-based protein profiling with electrophilic scout fragments to demonstrate covalent ligandability for many classes of splicing factors and splicing regulators in T cells. Taken together, our findings show how chemical perturbation of splicing can lead to immune state-dependent changes in protein expression and provide evidence for the broad potential to target splicing factors with covalent chemistry.</div></div>","PeriodicalId":265,"journal":{"name":"Cell Chemical Biology","volume":"32 1","pages":"Pages 201-218.e17"},"PeriodicalIF":6.6,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142696958","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-16DOI: 10.1016/j.chembiol.2024.12.012
Judith Behnsen, Kerwyn Casey Huang, Matthew T. Sorbara, Meng C. Wang, Jun Yu, Melody Y. Zeng
The field of microbiome research has experienced remarkable growth, leading to unprecedented discoveries of the molecular mechanisms that dictate host-microbiota interactions and their crucial roles in human health. In this “chemical biology of the microbiome” focus issue from Cell Chemical Biology, this Voices piece asks researchers from a range of backgrounds to share their insights on the most exciting recent developments in the microbiome field.
{"title":"New opportunities in mechanistic and functional microbiome studies","authors":"Judith Behnsen, Kerwyn Casey Huang, Matthew T. Sorbara, Meng C. Wang, Jun Yu, Melody Y. Zeng","doi":"10.1016/j.chembiol.2024.12.012","DOIUrl":"10.1016/j.chembiol.2024.12.012","url":null,"abstract":"<div><div>The field of microbiome research has experienced remarkable growth, leading to unprecedented discoveries of the molecular mechanisms that dictate host-microbiota interactions and their crucial roles in human health. In this “chemical biology of the microbiome” focus issue from <em>Cell Chemical Biology</em>, this Voices piece asks researchers from a range of backgrounds to share their insights on the most exciting recent developments in the microbiome field.</div></div>","PeriodicalId":265,"journal":{"name":"Cell Chemical Biology","volume":"32 1","pages":"Pages 5-8"},"PeriodicalIF":6.6,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142986892","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-16DOI: 10.1016/j.chembiol.2024.12.009
Katerina Jones, Camila Bernardo de Brito, Mariana Xavier Byndloss
In an interview with Samantha Nelson, a scientific editor of Cell Chemical Biology, the authors of the review entitled “Metabolic tug-o-war: Microbial metabolism shapes colonization resistance against enteric pathogens” share their perspectives on the field and their lives as scientists.
在接受《细胞化学生物学》（Cell Chemical Biology）科学编辑萨曼莎-尼尔森（Samantha Nelson）的采访时，题为《新陈代谢拉锯战：微生物新陈代谢塑造了对肠道病原体的定植抗性》的综述作者分享了他们对这一领域的看法以及作为科学家的生活：微生物新陈代谢决定了对肠道病原体的定植抵抗力 "的评论文章的作者分享了他们对这一领域的看法以及他们作为科学家的生活。
{"title":"Meet the authors: Katerina Jones, Camila Bernardo de Brito, and Mariana Xavier Byndloss","authors":"Katerina Jones, Camila Bernardo de Brito, Mariana Xavier Byndloss","doi":"10.1016/j.chembiol.2024.12.009","DOIUrl":"10.1016/j.chembiol.2024.12.009","url":null,"abstract":"<div><div>In an interview with Samantha Nelson, a scientific editor of <em>Cell Chemical Biology</em>, the authors of the review entitled “<span><span>Metabolic tug-o-war: Microbial metabolism shapes colonization resistance against enteric pathogens</span><svg><path></path></svg></span>” share their perspectives on the field and their lives as scientists.</div></div>","PeriodicalId":265,"journal":{"name":"Cell Chemical Biology","volume":"32 1","pages":"Pages 3-4"},"PeriodicalIF":6.6,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142986931","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-16DOI: 10.1016/j.chembiol.2024.12.004
Christopher Whidbey
Microbiomes exist in ecological niches ranging from the ocean and soil to inside of larger organisms like plants and animals. Within these niches, microbes play key roles in biochemical processes that impact larger phenomena, such as biogeochemical cycling or health. By understanding of how these processes occur at the molecular level, it may be possible to develop new interventions to address global problems. The complexity of these systems poses challenges to more traditional techniques. Chemical biology can help overcome these challenges by providing tools that are broadly applicable and can obtain molecular-level information about complex systems. This primer is intended to serve as a brief introduction to chemical biology and microbiome science, to highlight some of the ways that these two disciplines complement each other, and to encourage dialog and collaboration between these fields.
{"title":"The right tool for the job: Chemical biology and microbiome science","authors":"Christopher Whidbey","doi":"10.1016/j.chembiol.2024.12.004","DOIUrl":"10.1016/j.chembiol.2024.12.004","url":null,"abstract":"<div><div>Microbiomes exist in ecological niches ranging from the ocean and soil to inside of larger organisms like plants and animals. Within these niches, microbes play key roles in biochemical processes that impact larger phenomena, such as biogeochemical cycling or health. By understanding of how these processes occur at the molecular level, it may be possible to develop new interventions to address global problems. The complexity of these systems poses challenges to more traditional techniques. Chemical biology can help overcome these challenges by providing tools that are broadly applicable and can obtain molecular-level information about complex systems. This primer is intended to serve as a brief introduction to chemical biology and microbiome science, to highlight some of the ways that these two disciplines complement each other, and to encourage dialog and collaboration between these fields.</div></div>","PeriodicalId":265,"journal":{"name":"Cell Chemical Biology","volume":"32 1","pages":"Pages 83-97"},"PeriodicalIF":6.6,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142929676","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-16DOI: 10.1016/j.chembiol.2024.07.011
Natavan Dudkina , Hyun Bong Park , Deguang Song , Abhishek Jain , Sajid A. Khan , Richard A. Flavell , Caroline H. Johnson , Noah W. Palm , Jason M. Crawford
Altered human aldo-keto reductase family 1 member C3 (AKR1C3) expression has been associated with poor prognosis in diverse cancers, ferroptosis resistance, and metabolic diseases. Despite its clinical significance, the endogenous biochemical roles of AKR1C3 remain incompletely defined. Using untargeted metabolomics, we identified a major transformation mediated by AKR1C3, in which a spermine oxidation product “sperminal” is reduced to “sperminol.” Sperminal causes DNA damage and activates the DNA double-strand break response, whereas sperminol induces autophagy in vitro. AKR1C3 also pulls down acyl-pyrones and pyrone-211 inhibits AKR1C3 activity. Through G protein-coupled receptor ligand screening, we determined that pyrone-211 is also a potent agonist of the semi-orphan receptor GPR84. Strikingly, mammalian fatty acid synthase produces acyl-pyrones in vitro, and this production is modulated by NADPH. Taken together, our studies support a regulatory role of AKR1C3 in an expanded polyamine pathway and a model linking fatty acid synthesis and NADPH levels to GPR84 signaling.
{"title":"Human AKR1C3 binds agonists of GPR84 and participates in an expanded polyamine pathway","authors":"Natavan Dudkina , Hyun Bong Park , Deguang Song , Abhishek Jain , Sajid A. Khan , Richard A. Flavell , Caroline H. Johnson , Noah W. Palm , Jason M. Crawford","doi":"10.1016/j.chembiol.2024.07.011","DOIUrl":"10.1016/j.chembiol.2024.07.011","url":null,"abstract":"<div><div>Altered human aldo-keto reductase family 1 member C3 (AKR1C3) expression has been associated with poor prognosis in diverse cancers, ferroptosis resistance, and metabolic diseases. Despite its clinical significance, the endogenous biochemical roles of AKR1C3 remain incompletely defined. Using untargeted metabolomics, we identified a major transformation mediated by AKR1C3, in which a spermine oxidation product “sperminal” is reduced to “sperminol.” Sperminal causes DNA damage and activates the DNA double-strand break response, whereas sperminol induces autophagy <em>in vitro</em>. AKR1C3 also pulls down acyl-pyrones and pyrone-211 inhibits AKR1C3 activity. Through G protein-coupled receptor ligand screening, we determined that pyrone-211 is also a potent agonist of the semi-orphan receptor GPR84. Strikingly, mammalian fatty acid synthase produces acyl-pyrones <em>in vitro</em>, and this production is modulated by NADPH. Taken together, our studies support a regulatory role of AKR1C3 in an expanded polyamine pathway and a model linking fatty acid synthesis and NADPH levels to GPR84 signaling.</div></div>","PeriodicalId":265,"journal":{"name":"Cell Chemical Biology","volume":"32 1","pages":"Pages 126-144.e18"},"PeriodicalIF":6.6,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142007975","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-16DOI: 10.1016/j.chembiol.2024.07.012
Eric M. Brown , Phuong N.U. Nguyen , Ramnik J. Xavier
The strong association of the human leukocyte antigen B∗27 alleles (HLA-B∗27) with spondyloarthritis and related rheumatic conditions has long fascinated researchers, yet the precise mechanisms underlying its pathogenicity remain elusive. Here, we review how interplay between the microbiome, the immune system, and the enigmatic HLA-B∗27 could trigger spondyloarthritis, with a focus on whether HLA-B∗27 presents an arthritogenic peptide. We propose mechanisms by which the unique biochemical characteristics of the HLA-B∗27 protein structure, particularly its peptide binding groove, could dictate its propensity to induce pathological T cell responses. We further provide new insights into how TRBV9+ CD8+ T cells are implicated in the disease process, as well as how the immunometabolism of T cells modulates tissue-specific inflammatory responses in spondyloarthritis. Finally, we present testable models and suggest approaches to this problem in future studies given recent advances in computational biology, chemical biology, structural biology, and small-molecule therapeutics.
人类白细胞抗原B∗27等位基因（HLA-B∗27）与脊柱关节炎及相关风湿病的密切关系一直令研究人员着迷，但其致病的确切机制却仍然难以捉摸。在这里，我们回顾了微生物组、免疫系统和神秘的 HLA-B∗27 之间的相互作用是如何诱发脊柱关节炎的，重点是 HLA-B∗27 是否会产生致关节炎肽。我们提出了 HLA-B∗27 蛋白结构的独特生化特性（尤其是其肽结合槽）可能决定其诱导病理 T 细胞反应倾向的机制。我们进一步提供了关于 TRBV9+ CD8+ T 细胞如何参与疾病过程以及 T 细胞的免疫代谢如何调节脊柱关节炎组织特异性炎症反应的新见解。最后，鉴于计算生物学、化学生物学、结构生物学和小分子疗法的最新进展，我们提出了可检验的模型，并建议在未来研究中解决这一问题的方法。
{"title":"Emerging biochemical, microbial and immunological evidence in the search for why HLA-B∗27 confers risk for spondyloarthritis","authors":"Eric M. Brown , Phuong N.U. Nguyen , Ramnik J. Xavier","doi":"10.1016/j.chembiol.2024.07.012","DOIUrl":"10.1016/j.chembiol.2024.07.012","url":null,"abstract":"<div><div>The strong association of the human leukocyte antigen B<sup>∗</sup>27 alleles (<em>HLA-B<sup>∗</sup>27</em>) with spondyloarthritis and related rheumatic conditions has long fascinated researchers, yet the precise mechanisms underlying its pathogenicity remain elusive. Here, we review how interplay between the microbiome, the immune system, and the enigmatic HLA-B<sup>∗</sup>27 could trigger spondyloarthritis, with a focus on whether HLA-B<sup>∗</sup>27 presents an arthritogenic peptide. We propose mechanisms by which the unique biochemical characteristics of the HLA-B<sup>∗</sup>27 protein structure, particularly its peptide binding groove, could dictate its propensity to induce pathological T cell responses. We further provide new insights into how TRBV9<sup>+</sup> CD8<sup>+</sup> T cells are implicated in the disease process, as well as how the immunometabolism of T cells modulates tissue-specific inflammatory responses in spondyloarthritis. Finally, we present testable models and suggest approaches to this problem in future studies given recent advances in computational biology, chemical biology, structural biology, and small-molecule therapeutics.</div></div>","PeriodicalId":265,"journal":{"name":"Cell Chemical Biology","volume":"32 1","pages":"Pages 12-24"},"PeriodicalIF":6.6,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142015826","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-16DOI: 10.1016/j.chembiol.2024.10.007
Marco Jochem , Anna Schrempf , Lina-Marie Wagner , Dmitri Segal , Jose Cisneros , Amanda Ng , Georg E. Winter , Jeroen Krijgsveld
Targeted protein degradation (TPD) has emerged as a powerful strategy to selectively eliminate cellular proteins using small-molecule degraders, offering therapeutic promise for targeting proteins that are otherwise undruggable. However, a remaining challenge is to unambiguously identify primary TPD targets that are distinct from secondary downstream effects in the proteome. Here we introduce an approach for selective analysis of protein degradation by mass spectrometry (DegMS) at proteomic scale, which derives its specificity from the exclusion of confounding effects of altered transcription and translation induced by target depletion. We show that the approach efficiently operates at the timescale of TPD (hours) and we demonstrate its utility by analyzing the cyclin K degraders dCeMM2 and dCeMM4, which induce widespread transcriptional downregulation, and the GSPT1 degrader CC-885, an inhibitor of protein translation. Additionally, we apply DegMS to characterize a previously uncharacterized degrader, and identify the zinc-finger protein FIZ1 as a degraded target.
{"title":"Degradome analysis to identify direct protein substrates of small-molecule degraders","authors":"Marco Jochem , Anna Schrempf , Lina-Marie Wagner , Dmitri Segal , Jose Cisneros , Amanda Ng , Georg E. Winter , Jeroen Krijgsveld","doi":"10.1016/j.chembiol.2024.10.007","DOIUrl":"10.1016/j.chembiol.2024.10.007","url":null,"abstract":"<div><div>Targeted protein degradation (TPD) has emerged as a powerful strategy to selectively eliminate cellular proteins using small-molecule degraders, offering therapeutic promise for targeting proteins that are otherwise undruggable. However, a remaining challenge is to unambiguously identify primary TPD targets that are distinct from secondary downstream effects in the proteome. Here we introduce an approach for selective analysis of protein degradation by mass spectrometry (DegMS) at proteomic scale, which derives its specificity from the exclusion of confounding effects of altered transcription and translation induced by target depletion. We show that the approach efficiently operates at the timescale of TPD (hours) and we demonstrate its utility by analyzing the cyclin K degraders dCeMM2 and dCeMM4, which induce widespread transcriptional downregulation, and the GSPT1 degrader CC-885, an inhibitor of protein translation. Additionally, we apply DegMS to characterize a previously uncharacterized degrader, and identify the zinc-finger protein FIZ1 as a degraded target.</div></div>","PeriodicalId":265,"journal":{"name":"Cell Chemical Biology","volume":"32 1","pages":"Pages 192-200.e6"},"PeriodicalIF":6.6,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142599577","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-16DOI: 10.1016/j.chembiol.2024.10.013
Olivia N. Rebeck , Miranda J. Wallace , Jerome Prusa , Jie Ning , Esse M. Evbuomwan , Sunaina Rengarajan , LeMoyne Habimana-Griffin , Suryang Kwak , David Zahrah , Jason Tung , James Liao , Bejan Mahmud , Skye R.S. Fishbein , Erick S. Ramirez Tovar , Rehan Mehta , Bin Wang , Mark G. Gorelik , Beth A. Helmink , Gautam Dantas
Engineered probiotics are an emerging platform for in situ delivery of therapeutics to the gut. Herein, we developed an orally administered, yeast-based therapeutic delivery system to deliver next-generation immune checkpoint inhibitor (ICI) proteins directly to gastrointestinal tumors. We engineered Saccharomyces cerevisiae var. boulardii (Sb), a probiotic yeast with high genetic tractability and innate anticancer activity, to secrete “miniature” antibody variants that target programmed death ligand 1 (Sb_haPD-1). When tested in an ICI-refractory colorectal cancer (CRC) mouse model, Sb_haPD-1 significantly reduced intestinal tumor burden and resulted in significant shifts to the immune cell profile and microbiome composition. This oral therapeutic platform is modular and highly customizable, opening new avenues of targeted drug delivery that can be applied to treat a myriad of gastrointestinal malignancies.
{"title":"A yeast-based oral therapeutic delivers immune checkpoint inhibitors to reduce intestinal tumor burden","authors":"Olivia N. Rebeck , Miranda J. Wallace , Jerome Prusa , Jie Ning , Esse M. Evbuomwan , Sunaina Rengarajan , LeMoyne Habimana-Griffin , Suryang Kwak , David Zahrah , Jason Tung , James Liao , Bejan Mahmud , Skye R.S. Fishbein , Erick S. Ramirez Tovar , Rehan Mehta , Bin Wang , Mark G. Gorelik , Beth A. Helmink , Gautam Dantas","doi":"10.1016/j.chembiol.2024.10.013","DOIUrl":"10.1016/j.chembiol.2024.10.013","url":null,"abstract":"<div><div>Engineered probiotics are an emerging platform for <em>in situ</em> delivery of therapeutics to the gut. Herein, we developed an orally administered, yeast-based therapeutic delivery system to deliver next-generation immune checkpoint inhibitor (ICI) proteins directly to gastrointestinal tumors. We engineered <em>Saccharomyces cerevisiae</em> var. <em>boulardii</em> (<em>Sb</em>), a probiotic yeast with high genetic tractability and innate anticancer activity, to secrete “miniature” antibody variants that target programmed death ligand 1 (<em>Sb</em>_haPD-1). When tested in an ICI-refractory colorectal cancer (CRC) mouse model, <em>Sb</em>_haPD-1 significantly reduced intestinal tumor burden and resulted in significant shifts to the immune cell profile and microbiome composition. This oral therapeutic platform is modular and highly customizable, opening new avenues of targeted drug delivery that can be applied to treat a myriad of gastrointestinal malignancies.</div></div>","PeriodicalId":265,"journal":{"name":"Cell Chemical Biology","volume":"32 1","pages":"Pages 98-110.e7"},"PeriodicalIF":6.6,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142673596","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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