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Visualizing Intracellular Localization of Natural-Product-Based Chemical Probes Using Click-Correlative Light and Electron Microscopy.
IF 3.5 2区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-02-15 DOI: 10.1021/acschembio.4c00849
Eva Schaller, Julian Hofmann, Pamela Maher, Christian Stigloher, Michael Decker

Flavonoids such as sterubin and fisetin─and derivatives thereof─show strong neuroprotective effects in vitro as well as in vivo, 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.

{"title":"Visualizing Intracellular Localization of Natural-Product-Based Chemical Probes Using Click-Correlative Light and Electron Microscopy.","authors":"Eva Schaller, Julian Hofmann, Pamela Maher, Christian Stigloher, Michael Decker","doi":"10.1021/acschembio.4c00849","DOIUrl":"https://doi.org/10.1021/acschembio.4c00849","url":null,"abstract":"<p><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":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143424617","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}
引用次数: 0
Imaging and Tracking RNA in Live Mammalian Cells via Fluorogenic Photoaffinity Labeling.
IF 3.5 2区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-02-15 DOI: 10.1021/acschembio.4c00848
Alexandria L Quillin, Diane B Karloff, Tewoderos M Ayele, Tatiana F Flores, Gerry Chen, Zachary T McEachin, Arielle N Valdez-Sinon, Jennifer M Heemstra

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.

{"title":"Imaging and Tracking RNA in Live Mammalian Cells via Fluorogenic Photoaffinity Labeling.","authors":"Alexandria L Quillin, Diane B Karloff, Tewoderos M Ayele, Tatiana F Flores, Gerry Chen, Zachary T McEachin, Arielle N Valdez-Sinon, Jennifer M Heemstra","doi":"10.1021/acschembio.4c00848","DOIUrl":"https://doi.org/10.1021/acschembio.4c00848","url":null,"abstract":"<p><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":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143424616","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}
引用次数: 0
Silyl-Lipid Functionalized N-Acyl Homoserine Lactones as Modulators of Bacterial Cell-Cell Communication.
IF 3.5 2区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-02-13 DOI: 10.1021/acschembio.4c00720
Linnea S Dolph, Emma E Santa, Irene M Stoutland, Kelsey M Mesa, Cole C Dickson, Helen E Blackwell, Annaliese K Franz

We report silyl-lipid derivatives of N-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 Pseudomonas aeruginosa using E. coli reporter gene assays. Several silyl-lipid AHL agonists retained high activities in LasR in a native P. aeruginosa reporter system and also were active in another related LuxR-type receptor, EsaR from Pantoea stewartii. 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.

{"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":"https://doi.org/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":""},"PeriodicalIF":3.5,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Regulatory and Catalytic Domains of Poly(ADP-ribose) Polymerases Cross-Complement for DNA-Break-Dependent Allosteric Stimulation of Catalytic Activity.
IF 3.5 2区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-02-12 DOI: 10.1021/acschembio.4c00582
Makwana Milee, Shanavas P Greeshma, Waghela Deeksha, Eerappa Rajakumara

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 cis-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 cross-complement CAT of other PARPs while REG of hPARP2 showed robust cross-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.

{"title":"Regulatory and Catalytic Domains of Poly(ADP-ribose) Polymerases Cross-Complement for DNA-Break-Dependent Allosteric Stimulation of Catalytic Activity.","authors":"Makwana Milee, Shanavas P Greeshma, Waghela Deeksha, Eerappa Rajakumara","doi":"10.1021/acschembio.4c00582","DOIUrl":"10.1021/acschembio.4c00582","url":null,"abstract":"<p><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":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143397478","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}
引用次数: 0
Transcriptomics-Driven Discovery of New Meroterpenoid Rhynchospenes Involved in the Virulence of the Barley Pathogen Rhynchosporium commune.
IF 3.5 2区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-02-12 DOI: 10.1021/acschembio.4c00731
Reynaldi Darma, Zhuo Shang, Joe Bracegirdle, Stephen Moggach, Megan C McDonald, Andrew M Piggott, Peter S Solomon, Yit-Heng Chooi

Rhynchosporium commune, the causal agent of barley scald disease, poses a major threat to global barley production. Despite its significant impact, the molecular mechanisms underlying R. commune's infection process remain largely unexplored. To address this, we analyzed the differential gene expression data of R. commune WAI453 cultivated under both in planta and in vitro conditions, aiming to identify secondary metabolite biosynthetic gene clusters that are potentially involved in the pathogenicity of R. commune. Our analysis revealed increased expression of a polyketide-terpene gene cluster (the rhy cluster), containing a specific myeloblastosis (MYB)-type transcription factor gene rhyM, during in planta growth. Overexpression of rhyM in an axenic culture activated the expression of the rhy 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 rhyM in R. commune WAI453 confirmed the role of rhynchospenes as virulence factors in barley disease. The resulting mutant showed significantly reduced expression of the rhy cluster in planta compared to the wild-type strain and decreased virulence in seedling pathogenicity assays on barley. The characterization of the rhy cluster and rhynchospenes provided insights into the role of secondary metabolites in R. commune 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.

{"title":"Transcriptomics-Driven Discovery of New Meroterpenoid Rhynchospenes Involved in the Virulence of the Barley Pathogen <i>Rhynchosporium commune</i>.","authors":"Reynaldi Darma, Zhuo Shang, Joe Bracegirdle, Stephen Moggach, Megan C McDonald, Andrew M Piggott, Peter S Solomon, Yit-Heng Chooi","doi":"10.1021/acschembio.4c00731","DOIUrl":"https://doi.org/10.1021/acschembio.4c00731","url":null,"abstract":"<p><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":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143397479","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}
引用次数: 0
Workflow for E3 Ligase Ligand Validation for PROTAC Development.
IF 3.5 2区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-02-11 DOI: 10.1021/acschembio.4c00812
Nebojša Miletić, Janik Weckesser, Thorsten Mosler, Rajeshwari Rathore, Marina E Hoffmann, Paul Gehrtz, Sarah Schlesiger, Ingo V Hartung, Nicola Berner, Stephanie Wilhelm, Juliane Müller, Bikash Adhikari, Václav Němec, Saran Aswathaman Sivashanmugam, Lewis Elson, Hanna Holzmann, Martin P Schwalm, Lasse Hoffmann, Kamal Rayees Abdul Azeez, Susanne Müller, Bernhard Kuster, Elmar Wolf, Ivan Đikić, Stefan Knapp

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.

{"title":"Workflow for E3 Ligase Ligand Validation for PROTAC Development.","authors":"Nebojša Miletić, Janik Weckesser, Thorsten Mosler, Rajeshwari Rathore, Marina E Hoffmann, Paul Gehrtz, Sarah Schlesiger, Ingo V Hartung, Nicola Berner, Stephanie Wilhelm, Juliane Müller, Bikash Adhikari, Václav Němec, Saran Aswathaman Sivashanmugam, Lewis Elson, Hanna Holzmann, Martin P Schwalm, Lasse Hoffmann, Kamal Rayees Abdul Azeez, Susanne Müller, Bernhard Kuster, Elmar Wolf, Ivan Đikić, Stefan Knapp","doi":"10.1021/acschembio.4c00812","DOIUrl":"https://doi.org/10.1021/acschembio.4c00812","url":null,"abstract":"<p><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":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143389493","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}
引用次数: 0
Insights into Free Drug Release from Efficacious N-Acyl O-Aminophenol Duocarmycin Prodrugs.
IF 3.5 2区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-02-09 DOI: 10.1021/acschembio.4c00754
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

Acyclic and cyclic N-acyl O-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 N-acyl O-aminophenol prodrugs is 1, which proved remarkably efficacious in vivo 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 1 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.

{"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":"https://doi.org/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":""},"PeriodicalIF":3.5,"publicationDate":"2025-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Alternative Approach to Sequence-Specific Recognition of DNA: Cooperative Stacking of Dication Dimers─Sensitivity to Compound Curvature, Aromatic Structure, and DNA Sequence.
IF 3.5 2区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-02-07 DOI: 10.1021/acschembio.4c00800
Ananya Paul, J Ross Terrell, Abdelbasset A Farahat, Edwin N Ogbonna, Arvind Kumar, David W Boykin, Stephen Neidle, W David Wilson

With the growing number and diversity of known genome sequences, there is an increasing opportunity to regulate gene expression through synthetic, cell-permeable small molecules. Enhancing the DNA sequence recognition abilities of minor groove compounds has the potential to broaden their therapeutic applications with significant implications for areas such as modulating transcription factor activity. While various classes of minor groove binding agents can selectively identify pure AT and mixed AT and GC base pair(s) containing sequences, there remains a lack of compounds capable of distinguishing between different AT sequences. In this work, we report on the design compounds that exhibit selective binding to -TTAA- or -TATA- containing DNA minor groove sequences compared with other AT ones. Several studies have shown that the -AATT- and -TTAA- sequences have distinct physical and interaction properties, especially in terms of their different requirements for recognition in the minor groove. Achieving strong, selective minor groove binding at -TTAA- sequences has been challenging, but DB1003, a benzimidazole-furan-furan diamidine, has demonstrated cooperative dimeric binding activity at -TTAA-. It has significantly less binding preference for AATT. To better understand and modify the selectivity, we synthesized a set of rationally designed analogs of DB1003 by altering the position of the five-membered heterocyclic structure. Binding affinities and stoichiometries obtained from biosensor-surface plasmon resonance experiments show that DB1992, a benzimidazolefuran-thiophene diamidine, binds strongly to -TTAA- as a positive cooperative dimer with high cooperativity. The high-resolution crystal structure of the TTAA-DNA-DB1992 complex reveals that DB1992 binds as an antiparallel π-stacked dimer with numerous diverse contacts to the DNA minor groove. This distinctive binding arrangement and the properties of diamidines at the -TTAA- minor groove demonstrate that benzimidazole-furan-thiophene is a unique DNA binding pharmacophore. Competition mass spectroscopy and circular dichroism studies confirmed the binding stoichiometry and selectivity preference of the compounds for the -TTAA- sequence.

{"title":"Alternative Approach to Sequence-Specific Recognition of DNA: Cooperative Stacking of Dication Dimers─Sensitivity to Compound Curvature, Aromatic Structure, and DNA Sequence.","authors":"Ananya Paul, J Ross Terrell, Abdelbasset A Farahat, Edwin N Ogbonna, Arvind Kumar, David W Boykin, Stephen Neidle, W David Wilson","doi":"10.1021/acschembio.4c00800","DOIUrl":"https://doi.org/10.1021/acschembio.4c00800","url":null,"abstract":"<p><p>With the growing number and diversity of known genome sequences, there is an increasing opportunity to regulate gene expression through synthetic, cell-permeable small molecules. Enhancing the DNA sequence recognition abilities of minor groove compounds has the potential to broaden their therapeutic applications with significant implications for areas such as modulating transcription factor activity. While various classes of minor groove binding agents can selectively identify pure AT and mixed AT and GC base pair(s) containing sequences, there remains a lack of compounds capable of distinguishing between different AT sequences. In this work, we report on the design compounds that exhibit selective binding to -TTAA- or -TATA- containing DNA minor groove sequences compared with other AT ones. Several studies have shown that the -AATT- and -TTAA- sequences have distinct physical and interaction properties, especially in terms of their different requirements for recognition in the minor groove. Achieving strong, selective minor groove binding at -TTAA- sequences has been challenging, but DB1003, a benzimidazole-furan-furan diamidine, has demonstrated cooperative dimeric binding activity at -TTAA-. It has significantly less binding preference for AATT. To better understand and modify the selectivity, we synthesized a set of rationally designed analogs of DB1003 by altering the position of the five-membered heterocyclic structure. Binding affinities and stoichiometries obtained from biosensor-surface plasmon resonance experiments show that DB1992, a benzimidazolefuran-thiophene diamidine, binds strongly to -TTAA- as a positive cooperative dimer with high cooperativity. The high-resolution crystal structure of the TTAA-DNA-DB1992 complex reveals that DB1992 binds as an antiparallel π-stacked dimer with numerous diverse contacts to the DNA minor groove. This distinctive binding arrangement and the properties of diamidines at the -TTAA- minor groove demonstrate that benzimidazole-furan-thiophene is a unique DNA binding pharmacophore. Competition mass spectroscopy and circular dichroism studies confirmed the binding stoichiometry and selectivity preference of the compounds for the -TTAA- sequence.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143370104","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}
引用次数: 0
siRNA-Mimetic Ratiometric pH (sMiRpH) Probes for Improving Cell Delivery and mRNA Knockdown.
IF 3.5 2区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-02-05 DOI: 10.1021/acschembio.4c00545
Madison R Herling, Lizeth Lopez Vazquez, Ivan J Dmochowski

Second-generation siRNA-mimetic ratiometric pH probes (sMiRpH-2) were developed by hybridizing a 3'-FAM-labeled 2'-OMe RNA strand with a 3'-Cy5-labeled 25mer RNA strand. These duplexes demonstrated the silencing of cytoplasmic mRNA targets in HeLa cells as measured by RT-qPCR and supported by western blot analysis. Fluorescence intensity and lifetime measurements revealed that a single guanosine (G) positioned adjacent to FAM achieves substantial static quenching at pH 5, with additional collisional quenching rendering the dye almost nonemissive. A FAM-G π-π stacking interaction was evidenced by a red-shifted absorbance spectrum for FAM. Decreased quenching at near-neutral pH enhances the FAM dynamic range in the physiologic pH window and improves the differentiation in cells between endocytic entrapment and cytoplasmic release. Flow cytometric analysis of intracellular pH and uptake using sMiRpH-2 was corroborated by live cell confocal microscopy and found to be predictive of knockdown efficacy. A sMiRpH-2 probe successfully predicted the relative efficacy of two transfection agents in more challenging SK-OV-3 cells, which highlights its use for the rapid assessment of nonviral siRNA delivery vectors.

{"title":"siRNA-Mimetic Ratiometric pH (sMiRpH) Probes for Improving Cell Delivery and mRNA Knockdown.","authors":"Madison R Herling, Lizeth Lopez Vazquez, Ivan J Dmochowski","doi":"10.1021/acschembio.4c00545","DOIUrl":"https://doi.org/10.1021/acschembio.4c00545","url":null,"abstract":"<p><p>Second-generation siRNA-mimetic ratiometric pH probes (sMiRpH-2) were developed by hybridizing a 3'-FAM-labeled 2'-OMe RNA strand with a 3'-Cy5-labeled 25mer RNA strand. These duplexes demonstrated the silencing of cytoplasmic mRNA targets in HeLa cells as measured by RT-qPCR and supported by western blot analysis. Fluorescence intensity and lifetime measurements revealed that a single guanosine (G) positioned adjacent to FAM achieves substantial static quenching at pH 5, with additional collisional quenching rendering the dye almost nonemissive. A FAM-G π-π stacking interaction was evidenced by a red-shifted absorbance spectrum for FAM. Decreased quenching at near-neutral pH enhances the FAM dynamic range in the physiologic pH window and improves the differentiation in cells between endocytic entrapment and cytoplasmic release. Flow cytometric analysis of intracellular pH and uptake using sMiRpH-2 was corroborated by live cell confocal microscopy and found to be predictive of knockdown efficacy. A sMiRpH-2 probe successfully predicted the relative efficacy of two transfection agents in more challenging SK-OV-3 cells, which highlights its use for the rapid assessment of nonviral siRNA delivery vectors.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143254073","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}
引用次数: 0
Scaffolding Activities of Pseudodeacetylase HDAC7.
IF 3.5 2区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-02-05 DOI: 10.1021/acschembio.4c00753
Ishadi K M Kodikara, Mary Kay H Pflum

Histone deacetylase (HDAC) enzymes remove acetyl groups from acetyllysine-containing proteins, including nucleosomal histones to control gene expression. Beyond fundamental cell biology, HDAC activity is linked to various cancers, with many HDAC inhibitors developed as anticancer therapeutics. Among the 11 metal-dependent HDAC proteins, the four class IIa isoforms (HDAC4, 5, 7, and 9) are "pseudodeacetylases" without measurable enzymatic activity due to mutation of a catalytic tyrosine. Deacetylase-related activities of class IIa HDAC proteins are attributed to scaffolding functions, where recruitment of an active HDAC isoform leads to bound substrate deacetylation. Scaffolding of class IIa proteins beyond simple recruitment of an active HDAC is only starting to emerge. This review explores the various scaffolding roles of HDAC7, including recently reported acetylation-mediated reversible scaffolding, which is a form of acetyllysine-binding reader function. Studying the functional roles of HDAC7 will provide molecular insight into normal and pathological conditions, which could facilitate drug design.

{"title":"Scaffolding Activities of Pseudodeacetylase HDAC7.","authors":"Ishadi K M Kodikara, Mary Kay H Pflum","doi":"10.1021/acschembio.4c00753","DOIUrl":"https://doi.org/10.1021/acschembio.4c00753","url":null,"abstract":"<p><p>Histone deacetylase (HDAC) enzymes remove acetyl groups from acetyllysine-containing proteins, including nucleosomal histones to control gene expression. Beyond fundamental cell biology, HDAC activity is linked to various cancers, with many HDAC inhibitors developed as anticancer therapeutics. Among the 11 metal-dependent HDAC proteins, the four class IIa isoforms (HDAC4, 5, 7, and 9) are \"pseudodeacetylases\" without measurable enzymatic activity due to mutation of a catalytic tyrosine. Deacetylase-related activities of class IIa HDAC proteins are attributed to scaffolding functions, where recruitment of an active HDAC isoform leads to bound substrate deacetylation. Scaffolding of class IIa proteins beyond simple recruitment of an active HDAC is only starting to emerge. This review explores the various scaffolding roles of HDAC7, including recently reported acetylation-mediated reversible scaffolding, which is a form of acetyllysine-binding reader function. Studying the functional roles of HDAC7 will provide molecular insight into normal and pathological conditions, which could facilitate drug design.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143254150","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}
引用次数: 0
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