ACS Chemical Biology最新文献

{"title":"Effect of pH-Responsive Ligands on mRNA Knockdown in EGFR-Targeting Ligand-Conjugated siRNAs.","authors":"Toshimasa Harumoto, Ryohei Kawai, Keiichi Motosawa, Junko Iwano, Yasuo Koda, Yuuki Hirata, Keiji Uehara","doi":"10.1021/acschembio.4c00507","DOIUrl":"10.1021/acschembio.4c00507","url":null,"abstract":"<p><p>Ligand-conjugated small interfering RNAs (siRNAs) have emerged as a powerful approach to developing nucleic acid-based medicines. To achieve efficient mRNA knockdown, it is important to select targeting receptors with high expression and ligands that exhibit rapid internalization. However, the key characteristics of ligand-receptor sets involved in the postinternalization process remain largely unclear. In this study, we investigated the effect of ligand-receptor binding dissociation under low pH conditions, known as a postendocytic environment. Specifically, we chemically synthesized several modified epidermal growth factor (EGF) ligands that showed a variety of binding activities to the EGF receptor (EGFR) at low pH. Among these modified ligands, the siRNA conjugate with chemically synthesized EGF H10Y/H16Y, which is a less pH-responsive variant, exhibited reduced internalization and mRNA knockdown activity at high concentrations in EGFR-expressing cells. Additionally, we explored the use of antibody-related molecules (anti-EGFR IgG and Fab) as targeting moieties for siRNA conjugates. The anti-EGFR Fab-siRNA, which showed dissociation of EGF under low pH conditions, demonstrated stronger internalization and mRNA knockdown activity compared to the anti-EGFR IgG-siRNA, which strongly binds EGF at low pH. These data emphasize the importance of intracellular ligand-receptor dissociation and provide insights for future advancements in the field.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":"297-308"},"PeriodicalIF":3.5,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143077848","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":"Silyl-Lipid Functionalized <i>N</i>-Acyl Homoserine Lactones as Modulators of Bacterial Cell-Cell Communication.","authors":"Linnea S Dolph, Emma E Santa, Irene M Stoutland, Kelsey M Mesa, Cole C Dickson, Helen E Blackwell, Annaliese K Franz","doi":"10.1021/acschembio.4c00720","DOIUrl":"10.1021/acschembio.4c00720","url":null,"abstract":"<p><p>We report silyl-lipid derivatives of <i>N</i>-acyl l-homoserine lactones (AHLs) that have nanomolar activities in LuxR-type quorum sensing receptors in Gram-negative bacterial pathogens. A collection of silyl-lipid AHLs were designed and synthesized to represent three general structural classes based on native AHL signals and synthetic LuxR-type receptor modulators. The synthetic routes feature straightforward hydrosilylation and aryl silylation reactions to access silyl-lipid groups that are not readily accessible in analogous all-carbon chemistry. Of the 17 compounds evaluated, eight silyl-lipid AHLs were identified with either nanomolar agonistic or submicromolar antagonistic activities in the LasR receptor from the common pathogen <i>Pseudomonas aeruginosa</i> using <i>E. coli</i> reporter gene assays. Several silyl-lipid AHL agonists retained high activities in LasR in a native <i>P. aeruginosa</i> reporter system and also were active in another related LuxR-type receptor, EsaR from <i>Pantoea stewartii</i>. Light scattering and computational experiments indicate that the silyl-lipid group can alter the aggregation capabilities and lipophilicities of AHLs relative to native all-carbon tails, engendering larger aggregate formation in water and higher lipophilicities on average. These properties, along with their strong activity profiles in LuxR-type receptors, suggest silyl-lipid AHLs could provide value as chemical probes to study the mechanisms of quorum sensing in Gram-negative bacteria and the roles of signal lipophilicity in this chemical communication process.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":"412-420"},"PeriodicalIF":3.5,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11851432/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143404891","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":"Insights into Free Drug Release from Efficacious <i>N</i>-Acyl <i>O</i>-Aminophenol Duocarmycin Prodrugs.","authors":"Nilanjana Chakraborty, Jelena Momirov, Aleksandar Radakovic, Shreyosree Chatterjee, Aaron M Kirchhoff, Anna-Lena Kolb, Thomas J West, Brittany B Sanchez, Salvador Martinez-Bartolome, Anthony Saviola, Daniel McClatchy, John R Yates, Jason S Chen, Luke L Lairson, Brunie H Felding, Dale L Boger","doi":"10.1021/acschembio.4c00754","DOIUrl":"10.1021/acschembio.4c00754","url":null,"abstract":"<p><p>Acyclic and cyclic <i>N</i>-acyl <i>O</i>-aminophenol prodrugs of duocarmycin analogues were reported as members of a unique class of reductively cleaved prodrugs that map seamlessly onto the duocarmycin family of natural products. Although these prodrugs were explored with the expectations that they may be cleaved selectively within hypoxic tumor environments that have intrinsically higher concentrations of reducing nucleophiles, the remarkable stability of some such prodrugs suggests another mechanism of free drug release is operative. The prototype of such chemically unreactive <i>N</i>-acyl <i>O</i>-aminophenol prodrugs is <b>1</b>, which proved remarkably efficacious <i>in vivo</i> in vertebrate tumor models; was found to lack the toxicity that is characteristic of traditional chemotherapeutic drugs as well as the free drugs in the class (e.g., myelosuppression); and displayed a preferential site (intracellular), a slow and sustained rate, and a potentially unique mechanism of free drug release. Herein, we detail studies that provide insights into this stereoselective mechanism of free drug release. Combined, the results of the studies are consistent with an exclusive protein-mediated (enantio)selective activation and free drug release from prodrug <b>1</b> by N-O bond cleavage preferentially in cancer cell lines versus cultured normal human cell lines effected by a cytosolic cysteine-based enzyme and suggest that the activating protein is one that is selectively expressed, upregulated, or preferentially activated in cancer cell lines, potentially constituting a new oncology targeted precision therapy.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":"442-454"},"PeriodicalIF":3.5,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11908632/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143381163","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":"Bisecting N-Acetylglucosamine of the N-Glycan of Immunoglobulin G Does Not Affect Binding to Fc Gamma Receptors","authors":"Gerlof P. Bosman,&nbsp;Inèz D. Stoof,&nbsp;Hans P. Bastiaansen,&nbsp;Linda Quarles van Ufford,&nbsp;Justyna M. Dobruchowska,&nbsp;Jan-Willem H. Langenbach,&nbsp;Bhargavi M. Boruah,&nbsp;Kelley W. Moremen,&nbsp;Arthur E. H. Bentlage,&nbsp;Suzanne N. Lissenberg-Thunnissen,&nbsp;Gestur Vidarsson and Geert-Jan Boons*,&nbsp;","doi":"10.1021/acschembio.4c0080710.1021/acschembio.4c00807","DOIUrl":"https://doi.org/10.1021/acschembio.4c00807https://doi.org/10.1021/acschembio.4c00807","url":null,"abstract":"<p >Monoclonal antibodies (mAb) produced in 1,4-mannosyl-glycoprotein 4-<i>N</i>-acetylglucosaminyltransferase (MGAT3) overexpressing cell lines have superior <i>in vitro</i> and <i>in vivo</i> activities. The <i>N</i>-glycan of the Fc-region of these mAbs have increased levels of bisecting <i>N</i>-acetylglucosamine (GlcNAc) and reduced core-fucosylation. Although a reduction in core-fucosylation will improve FcγRIIIa binding and antibody-dependent cellular cytotoxicity (ADCC) activity, the influence of bisecting GlcNAc on these activities has been difficult to probe. Here, we describe the preparation of a unique series of homogeneous glycoforms of trastuzumab (Herceptin) with and without core-fucose and with and without bisecting GlcNAc and examine binding to a comprehensive panel of Fcγ receptors. The glycoforms of trastuzumab were prepared by treatment with wild-type Endo-S2 to cleave the chitobiose core of the <i>N</i>-glycan to leave GlcNAc-Fuc that was exposed to an α-fucosidase to provide trastuzumab-GlcNAc. Glycan oxazolines with and without bisecting GlcNAc were prepared by enzymatic remodeling of a sialoglycopeptide isolated from egg yolk powder, which were employed in transglycosylations with trastuzumab-GlcNAc and trastuzumab-GlcNAc-Fuc catalyzed by Endo-S2 D184M resulting in well-defined glycoforms. As expected, core-fucosylation had a major effect on FcγRIIIa binding, which was not influenced by the presence of bisecting GlcNAc. It was found that an A2-glycan (GlcNAc₂Man₃GlcNAc₂) modified by bisecting GlcNAc cannot be core-fucosylated by FUT8. Thus, bisecting GlcNAc has only an indirect influence on FcγRIIIa binding and subsequent ADCC activity by inhibiting core-fucosylation. The results described here provide an understanding of the properties of therapeutic monoclonal antibodies.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"20 3","pages":"680–689 680–689"},"PeriodicalIF":3.5,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acschembio.4c00807","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143666945","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":"Imaging and Tracking RNA in Live Mammalian Cells via Fluorogenic Photoaffinity Labeling","authors":"Alexandria L. Quillin,&nbsp;Diane B. Karloff,&nbsp;Tewoderos M. Ayele,&nbsp;Tatiana F. Flores,&nbsp;Gerry Chen,&nbsp;Zachary T. McEachin,&nbsp;Arielle N. Valdez-Sinon and Jennifer M. Heemstra*,&nbsp;","doi":"10.1021/acschembio.4c0084810.1021/acschembio.4c00848","DOIUrl":"https://doi.org/10.1021/acschembio.4c00848https://doi.org/10.1021/acschembio.4c00848","url":null,"abstract":"<p >Cellular RNA labeling using light-up aptamers that bind to and activate fluorogenic molecules has gained interest in recent years as an alternative to protein-based RNA labeling approaches. Aptamer-based systems are genetically encodable and cover the entire visible spectrum. However, the inherently temporary nature of the noncovalent aptamer–fluorogen interaction limits the utility of these systems in that imaging does not withstand dye washout, and dye dissociation can compromise RNA tracking. We propose that these limitations can be averted through covalent RNA labeling. Here, we describe a photoaffinity approach in which the aptamer ligand is functionalized with a photoactivatable diazirine reactive group such that irradiation with UV light results in covalent attachment to the RNA of interest. In addition to the robustness of the covalent linkage, this approach benefits from the ability to achieve spatiotemporal control over RNA labeling. To demonstrate this approach, we incorporated a photoaffinity linker into malachite green and fused a single copy of the malachite green aptamer to a Cajal body-associated small nuclear RNA of interest as well as a cytoplasmic mRNA. We observed improved sensitivity for live cell imaging of the target RNA upon UV irradiation and demonstrated visualization of RNA dynamics over a time scale of minutes. The covalent attachment uniquely enables these time-resolved experiments, whereas in noncovalent approaches, the dye molecule can be transferred between different RNA molecules, compromising tracking. We envision future applications of this method for a wide range of investigations into the cellular localization, dynamics, and protein-binding properties of cellular RNAs.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"20 3","pages":"707–720 707–720"},"PeriodicalIF":3.5,"publicationDate":"2025-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143666911","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":"Visualizing Intracellular Localization of Natural-Product-Based Chemical Probes Using Click-Correlative Light and Electron Microscopy","authors":"Eva Schaller,&nbsp;Julian Hofmann,&nbsp;Pamela Maher,&nbsp;Christian Stigloher and Michael Decker*,&nbsp;","doi":"10.1021/acschembio.4c0084910.1021/acschembio.4c00849","DOIUrl":"https://doi.org/10.1021/acschembio.4c00849https://doi.org/10.1021/acschembio.4c00849","url":null,"abstract":"<p >Flavonoids such as sterubin and fisetin─and derivatives thereof─show strong neuroprotective effects <i>in vitro</i> as well as <i>in vivo</i>, combined with negligible toxicity and can therefore be considered novel treatment options for neurodegenerative diseases such as Alzheimer’s disease. However, their subcellular locations responsible for neuroprotection and exact modes of action still remain unclear. Here, we present chemical probes based on both flavonoids sterubin and fisetin that were utilized in fluorescence microscopy and click-correlative light and electron microscopy to detect and visualize the localization of specific intracellular targets. We successfully adapted the workflow of correlative light and electron microscopy to a click-chemistry-based approach in a murine hippocampal cell line (HT22) on ultrathin resin sections making visualization of a small molecule for the first time possible in this setup. Utilizing this newly adapted technique, we could demonstrate that sterubin and fisetin show specific enrichment in the endoplasmic reticulum.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"20 3","pages":"721–730 721–730"},"PeriodicalIF":3.5,"publicationDate":"2025-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143666910","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":"Silyl-Lipid Functionalized N-Acyl Homoserine Lactones as Modulators of Bacterial Cell–Cell Communication","authors":"Linnea S. Dolph,&nbsp;Emma E. Santa,&nbsp;Irene M. Stoutland,&nbsp;Kelsey M. Mesa,&nbsp;Cole C. Dickson,&nbsp;Helen E. Blackwell* and Annaliese K. Franz*,&nbsp;","doi":"10.1021/acschembio.4c0072010.1021/acschembio.4c00720","DOIUrl":"https://doi.org/10.1021/acschembio.4c00720https://doi.org/10.1021/acschembio.4c00720","url":null,"abstract":"<p >We report silyl-lipid derivatives of <i>N</i>-acyl <span>l</span>-homoserine lactones (AHLs) that have nanomolar activities in LuxR-type quorum sensing receptors in Gram-negative bacterial pathogens. A collection of silyl-lipid AHLs were designed and synthesized to represent three general structural classes based on native AHL signals and synthetic LuxR-type receptor modulators. The synthetic routes feature straightforward hydrosilylation and aryl silylation reactions to access silyl-lipid groups that are not readily accessible in analogous all-carbon chemistry. Of the 17 compounds evaluated, eight silyl-lipid AHLs were identified with either nanomolar agonistic or submicromolar antagonistic activities in the LasR receptor from the common pathogen <i>Pseudomonas aeruginosa</i> using <i>E. coli</i> reporter gene assays. Several silyl-lipid AHL agonists retained high activities in LasR in a native <i>P. aeruginosa</i> reporter system and also were active in another related LuxR-type receptor, EsaR from <i>Pantoea stewartii</i>. Light scattering and computational experiments indicate that the silyl-lipid group can alter the aggregation capabilities and lipophilicities of AHLs relative to native all-carbon tails, engendering larger aggregate formation in water and higher lipophilicities on average. These properties, along with their strong activity profiles in LuxR-type receptors, suggest silyl-lipid AHLs could provide value as chemical probes to study the mechanisms of quorum sensing in Gram-negative bacteria and the roles of signal lipophilicity in this chemical communication process.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"20 2","pages":"412–420 412–420"},"PeriodicalIF":3.5,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acschembio.4c00720","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143452405","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":"Transcriptomics-Driven Discovery of New Meroterpenoid Rhynchospenes Involved in the Virulence of the Barley Pathogen Rhynchosporium commune","authors":"Reynaldi Darma,&nbsp;Zhuo Shang*,&nbsp;Joe Bracegirdle,&nbsp;Stephen Moggach,&nbsp;Megan C. McDonald,&nbsp;Andrew M. Piggott,&nbsp;Peter S. Solomon* and Yit-Heng Chooi*,&nbsp;","doi":"10.1021/acschembio.4c0073110.1021/acschembio.4c00731","DOIUrl":"https://doi.org/10.1021/acschembio.4c00731https://doi.org/10.1021/acschembio.4c00731","url":null,"abstract":"<p ><i>Rhynchosporium commune</i>, the causal agent of barley scald disease, poses a major threat to global barley production. Despite its significant impact, the molecular mechanisms underlying <i>R. commune</i>’s infection process remain largely unexplored. To address this, we analyzed the differential gene expression data of <i>R. commune</i> WAI453 cultivated under both <i>in planta</i> and <i>in vitro</i> conditions, aiming to identify secondary metabolite biosynthetic gene clusters that are potentially involved in the pathogenicity of <i>R. commune</i>. Our analysis revealed increased expression of a polyketide-terpene gene cluster (the <i>rhy</i> cluster), containing a specific myeloblastosis (MYB)-type transcription factor gene <i>rhyM</i>, during <i>in planta</i> growth. Overexpression of <i>rhyM</i> in an axenic culture activated the expression of the <i>rhy</i> cluster, resulting in the production of a series of new meroterpenoid metabolites, which we named rhynchospenes A–E. Their structures were elucidated through a combination of spectroscopic methods and single crystal X-ray diffraction analysis. Infiltration of rhynchospenes into barley leaves resulted in strong necrosis, with rhynchospene B demonstrating the highest phytotoxicity and causing necrosis at a minimum concentration of 50 ppm. Silencing <i>rhyM</i> in <i>R. commune</i> WAI453 confirmed the role of rhynchospenes as virulence factors in barley disease. The resulting mutant showed significantly reduced expression of the <i>rhy</i> cluster <i>in planta</i> compared to the wild-type strain and decreased virulence in seedling pathogenicity assays on barley. The characterization of the <i>rhy</i> cluster and rhynchospenes provided insights into the role of secondary metabolites in <i>R. commune</i> virulence and barley scald disease development. The study also highlights the potential use of MYB-type transcription factor overexpression in uncovering cryptic SMs involved in pathogenicity and host adaptations.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"20 2","pages":"421–431 421–431"},"PeriodicalIF":3.5,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143452719","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":"Regulatory and Catalytic Domains of Poly(ADP-ribose) Polymerases Cross-Complement for DNA-Break-Dependent Allosteric Stimulation of Catalytic Activity","authors":"Makwana Milee,&nbsp;Shanavas P Greeshma,&nbsp;Waghela Deeksha and Eerappa Rajakumara*,&nbsp;","doi":"10.1021/acschembio.4c0058210.1021/acschembio.4c00582","DOIUrl":"https://doi.org/10.1021/acschembio.4c00582https://doi.org/10.1021/acschembio.4c00582","url":null,"abstract":"<p >Allosteric regulation is achieved by regulatory domains that sense stimuli and induce conformational changes in the functional domain that performs the catalytic activity of the enzyme. Poly-ADP-ribose polymerases (PARPs) are modular enzymes present across all domains of life including Archaea, Bacteria, and Eukarya. A typical domain architecture of PARPs consists of a conserved C-terminal catalytic domain (CAT) associated with multiple distinct N-terminal sensory and/or regulatory domains which together serve as regulatory region (REG). In this study, we investigated whether REG of different orthologs and paralogs of PARPs from mammals (hPARP1 and hPARP2), plants (atPARP2), and bacteria (haPARP) can assemble with CAT of each other to generate functional chimeric assemblies. We have employed qualitative and quantitative enzyme activity assays along with binding studies to examine these in vitro chimeric assemblies. The <i>cis</i>-complemented REG and CAT of hPARP2 exhibited micromolar binding affinity, suggesting that these domains can interact independent of allosteric ligands. Also, our results show that REG and CAT of PARP proteins can assemble in a functionally active conformation in the presence of DNA implying that REG and CAT are not required to be present on a single polypeptide for catalytic activity stimulation. Interestingly, only CAT of atPARP2 displayed functional complementation with REG of the other studied PARPs. Conversely, REG of hPARP1 and atPARP2 failed to <i>cross</i>-complement CAT of other PARPs while REG of hPARP2 showed robust <i>cross</i>-complementation. Our novel studies on chimeric PARP assemblies can be developed as a powerful synthetic biology tool to interrogate and control their activities in living cells. In addition, by co-engineering non-complementing REG and CAT domains of different PARPs, new functional chimeric PARPs can be developed for selective allosteric ligand-dependent regulation of PARP systems. Furthermore, our study can facilitate the understanding of the coevolution of REG and CAT domains in PARP enzymes.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"20 3","pages":"607–619 607–619"},"PeriodicalIF":3.5,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143666887","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":"Workflow for E3 Ligase Ligand Validation for PROTAC Development","authors":"Nebojša Miletić,&nbsp;Janik Weckesser,&nbsp;Thorsten Mosler,&nbsp;Rajeshwari Rathore,&nbsp;Marina E. Hoffmann,&nbsp;Paul Gehrtz,&nbsp;Sarah Schlesiger,&nbsp;Ingo V. Hartung,&nbsp;Nicola Berner,&nbsp;Stephanie Wilhelm,&nbsp;Juliane Müller,&nbsp;Bikash Adhikari,&nbsp;Václav Němec,&nbsp;Saran Aswathaman Sivashanmugam,&nbsp;Lewis Elson,&nbsp;Hanna Holzmann,&nbsp;Martin P. Schwalm,&nbsp;Lasse Hoffmann,&nbsp;Kamal Rayees Abdul Azeez,&nbsp;Susanne Müller,&nbsp;Bernhard Kuster,&nbsp;Elmar Wolf,&nbsp;Ivan Đikić and Stefan Knapp*,&nbsp;","doi":"10.1021/acschembio.4c0081210.1021/acschembio.4c00812","DOIUrl":"https://doi.org/10.1021/acschembio.4c00812https://doi.org/10.1021/acschembio.4c00812","url":null,"abstract":"<p >Proteolysis targeting chimeras (PROTACs) have gained considerable attention as a new modality in drug discovery. The development of PROTACs has been mainly focused on using CRBN (Cereblon) and VHL (Von Hippel-Lindau ligase) E3 ligase ligands. However, the considerable size of the human E3 ligase family, newly developed E3 ligase ligands, and the favorable druggability of some E3 ligase families hold the promise that novel degraders with unique pharmacological properties will be designed in the future using this large E3 ligase space. Here, we developed a workflow aiming to improve and streamline the evaluation of E3 ligase ligand efficiency for PROTAC development and the assessment of the corresponding “degradable” target space using broad-spectrum kinase inhibitors and the well-established VHL ligand VH032 as a validation system. Our study revealed VH032 linker attachment points that are highly efficient for kinase degradation as well as some of the pitfalls when using protein degradation as a readout. For instance, cytotoxicity was identified as a major mechanism leading to PROTAC- and VHL-independent kinase degradation. The combination of E3 ligase ligand negative controls, competition by kinase parent compounds, and neddylation and proteasome inhibitors was essential to distinguish between VHL-dependent and -independent kinase degradation events. We share here the findings and limitations of our study and hope that this study will provide guidance for future evaluations of new E3 ligase ligand systems for degrader development.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"20 2","pages":"507–521 507–521"},"PeriodicalIF":3.5,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acschembio.4c00812","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143452570","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}