ChemBioChemPub Date : 2025-07-24DOI: 10.1002/cbic.202500401
Julie Maibøll Buhl, Sujata Mahapatra, Magnus Kjærgaard, Frans A A Mulder
{"title":"Quantification of Small Molecule Partitioning in a Biomolecular Condensate with 2D Nuclear Magnetic Resonance Spectroscopy.","authors":"Julie Maibøll Buhl, Sujata Mahapatra, Magnus Kjærgaard, Frans A A Mulder","doi":"10.1002/cbic.202500401","DOIUrl":"https://doi.org/10.1002/cbic.202500401","url":null,"abstract":"<p><p>Several intrinsically disordered proteins have been shown to undergo phase separation into a dense and dilute phase and this process is intimately linked with the regulation of cellular processes. It is therefore highly relevant to know how metabolites partition between these phases. It is shown here that the partitioning of components in a complex mixture can be robustly obtained from a single set of 2D nuclear magnetic resonance (NMR) spectra recorded on the dilute and dense phases separately using \"time-zero extrapolated\" heteronuclear single quantum coherence (HSQC<sub>0</sub>) spectroscopy. The spectral separation power of 2D NMR spectroscopy circumvents the need for physical isolation or workup of the mixture components in the two samples. Using quantitative 1D <sup>1</sup>H NMR, it is validated that the HSQC<sub>0</sub> approach effectively removes all the undermining effects that plague quantification in common 2D NMR experiments, including differential attenuation due to relaxation in the two phases, pulse imperfections, partial decoupling, off-resonance effects, and incomplete coherence transfer in case of scalar coupling variation. These results should be of widespread interest as partitioning into biomolecular condensates is crucial for the calibration of computational physicochemical models of phase separation and key to the further understanding of cellular biochemistry involving membrane-less organelles.</p>","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":" ","pages":"e2500401"},"PeriodicalIF":2.6,"publicationDate":"2025-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144697185","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ChemBioChemPub Date : 2025-07-24DOI: 10.1002/cbic.202500438
Marcos Accioly, Kawana Rosa, Andressa G Soliani, Suzete M Cerutti, Cristiano Raminelli
{"title":"Stereoselective Synthesis of Cannabidiol and its Unnatural Enantiomer to Evaluate Anxiolytic-Like Properties and Memory Interactions.","authors":"Marcos Accioly, Kawana Rosa, Andressa G Soliani, Suzete M Cerutti, Cristiano Raminelli","doi":"10.1002/cbic.202500438","DOIUrl":"https://doi.org/10.1002/cbic.202500438","url":null,"abstract":"<p><p>(-)-Cannabidiol (CBD) is a nonpsychotropic phytocannabinoid found in Cannabis strains with well-established pharmacological applications. Conversely, (+)-cannabidiol (ent-CBD), the non-natural enantiomer of CBD, has been involved in a limited number of pharmacological studies. Therefore, CBD and ent-CBD are synthesized using (R)-(-)- and (S)-(+)-carvone as starting materials, respectively, via a highly diastereoselective 10-camphorsulfonic acid (CSA) catalyzed Friedel-Crafts reaction as the key step. Pharmacological studies are conducted using the plus-maze discriminative avoidance task (PM-DAT) to evaluate the interaction between memory and anxiety-like behavior as well as spontaneous motor activity in both young adult and aged male mice. The results show that ent-CBD at a dose of 20 mg kg<sup>-1</sup> has an anxiolytic-like effect in aged male mice. In addition, ent-CBD did not impair discriminative avoidance memory formation at all doses evaluated.</p>","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":" ","pages":"e2500438"},"PeriodicalIF":2.6,"publicationDate":"2025-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144697186","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ChemBioChemPub Date : 2025-07-24DOI: 10.1002/cbic.202500330
Rui Kamada, Shuya Sakaguchi, Madoka Kanno, Takaaki Ozawa, Natsumi Nakagawa, James G Omichinski, Kazuyasu Sakaguchi
{"title":"Dominant-Negative Effects of p53 R337 Variants in Li-Fraumeni Syndrome: Impact on Tetramer Formation and Transcriptional Activity.","authors":"Rui Kamada, Shuya Sakaguchi, Madoka Kanno, Takaaki Ozawa, Natsumi Nakagawa, James G Omichinski, Kazuyasu Sakaguchi","doi":"10.1002/cbic.202500330","DOIUrl":"https://doi.org/10.1002/cbic.202500330","url":null,"abstract":"<p><p>Li-Fraumeni syndrome (LFS) is an inherited cancer predisposition disorder caused by heterozygous TP53 mutations. Among these, missense mutations at Arg337-such as R337C and R337H-are common in LFS patients. Although many studies have characterized individual p53 variants in LFS, the impact of tetramerization domain (TD) mutations on wild-type (WT) p53 function remains unclear. Herein, a novel FRET-based assay system that enables the simultaneous detection of heterotetramer formation and p53-dependent transcriptional activity in live cells is developed. These results show that the heteromultimerization of the R337C variant with WT p53 is only slightly reduced compared to WT homotetramers, yet its transcriptional activity is diminished by over 50%. In contrast, the R337H variant forms heterotetramers at near-normal levels but exhibits markedly compromised transcriptional activity. These findings reveal a previously unrecognized dominant-negative-like effect, suggesting reduced p53 function is due not only to decreased tetramer formation but also to diminished heterotetramer stability. Moreover, the LFS-associated p53TD variants show a greater loss of activity against the low-affinity, apoptosis-inducing bax response element than against the high-affinity, cell cycle arrest-related CDKN1A response element. Collectively, this study demonstrates that p53TD mutations can exert dominant-negative effects, advancing the understanding of p53 heteromultimer function in LFS pathogenesis. These mechanistic insights into p53 heterotetramer stability may not only inform genetic screening strategies for LFS but also support future therapeutic approaches aimed at restoring p53 function by stabilizing mutant tetramers.</p>","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":" ","pages":"e2500330"},"PeriodicalIF":2.6,"publicationDate":"2025-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144697184","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ChemBioChemPub Date : 2025-07-24DOI: 10.1002/cbic.202500454
Angela Berg, Martin Gräber, Thorsten Berg
{"title":"Activity Analysis of the P2X Receptor Antagonist PPADS against Signal Transducer and Activator of Transcription Proteins.","authors":"Angela Berg, Martin Gräber, Thorsten Berg","doi":"10.1002/cbic.202500454","DOIUrl":"https://doi.org/10.1002/cbic.202500454","url":null,"abstract":"<p><p>The small molecule PPADS is a P2X receptor antagonist. Analysis of a library of known bioactive compounds in competitive fluorescence polarization-based assays indicates that PPADS and its isomer iso-PPADS also possess activity against members of the signal transducer and activator of transcription (STAT) family of transcription factors, in particular STAT4, STAT5a, and STAT5b. These results are also supported by HTRF assays. PPADS protects STAT4 and STAT5a/STAT5b from thermal degradation in cell lysates to a higher extent than STAT3. Combined data from this article and a previous article suggest that aromatic disulfonate antagonists of P2X receptors might serve as promising starting points for the development of inhibitors of STAT proteins.</p>","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":" ","pages":"e2500454"},"PeriodicalIF":2.6,"publicationDate":"2025-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144697183","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ChemBioChemPub Date : 2025-07-21DOI: 10.1002/cbic.202500474
Dattatraya Uttam Ukale, Tuomas Lönnberg
{"title":"Hybridization Probes Featuring a Pyrenylpyridine C-Nucleoside or Its Palladacycle as a Fluorescent Sensor Moiety.","authors":"Dattatraya Uttam Ukale, Tuomas Lönnberg","doi":"10.1002/cbic.202500474","DOIUrl":"https://doi.org/10.1002/cbic.202500474","url":null,"abstract":"<p><p>A C-nucleoside analog having pyren-1-ylpyridine as the base moiety has been synthesized and incorporated in the middle of a short oligodeoxynucleotide. A portion of this oligonucleotide is cyclopalladated at the modified residue, and the potential of both the metal-free and the palladacyclic oligonucleotide as hybridization probes for single-nucleotide polymorphism genotyping is assessed by melting studies on relevant duplexes using various techniques. Conventional ultraviolet (UV) melting profiles at 260 nm reveal considerable destabilization of the palladacyclic duplexes relative to their metal-free counterparts. Circular dichroism melting temperatures are higher than their UV counterparts, especially with the palladacyclic duplexes. Cyclopalladation markedly reduces the fluorescence emission of the pyrenylpyridine moiety, but both the metal-free and the palladacyclic oligonucleotide exhibit a qualitatively similar pattern of increased fluorescence on hybridization with a complementary sequence, consistent with the pyrene ring being \"pushed out\" of the base stack. Emission at low temperature is dependent on the nucleobase paired with the pyrenylpyridine base surrogate with both of the modified oligonucleotides. This discrimination is stronger with the palladacyclic oligonucleotide, possibly owing to Pd(II)-mediated base pairing.</p>","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":" ","pages":"e2500474"},"PeriodicalIF":2.6,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144673420","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ChemBioChemPub Date : 2025-07-21DOI: 10.1002/cbic.202500351
Simone Adorinni, Silvia Marchesan
{"title":"Gold Nanoparticles Guided by Self-Assembling Peptides: From Sequence to Superstructure.","authors":"Simone Adorinni, Silvia Marchesan","doi":"10.1002/cbic.202500351","DOIUrl":"https://doi.org/10.1002/cbic.202500351","url":null,"abstract":"<p><p>Peptide-based supramolecular assemblies have emerged as useful scaffolds to control the synthesis and spatial organization of gold nanoparticles (AuNPs) into nanocomposite superstructures. This concept article summarizes recent progress in the design of peptide-directed AuNP assemblies, focusing on how subtle variations in peptide sequence, conjugation strategy, and synthesis conditions influence NP morphology, chiral arrangement, and the resulting optical properties. It highlights key strategies for rationally tailoring structural parameters, such as particle size, shape, and interparticle spacing, which determine the collective optical and plasmonic behaviors of the assemblies. The fundamental design rules discussed here provide critical insights for constructing programmable AuNP-based nanomaterials, potentially useful in diverse fields including sensing, optical devices, and catalysis. Finally, it outlines current challenges and propose directions to further exploit the unique versatility of peptide-nanoparticle hybrid systems in nanotechnology.</p>","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":" ","pages":"e2500351"},"PeriodicalIF":2.6,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144673419","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Front Cover: Exploiting SpyTag/SpyCatcher Technology to Design New Artificial Catalytic Copper Proteins (ChemBioChem 14/2025)","authors":"Silvia Gentili, Francesca Miglioli, Valentina Borghesani, Gloria Spagnoli, Denise Bellotti, Davide Cavazzini, Remo Guerrini, Maurizio Remelli, Giovanni Maestri, Simone Ottonello, Angelo Bolchi, Matteo Tegoni","doi":"10.1002/cbic.202581401","DOIUrl":"https://doi.org/10.1002/cbic.202581401","url":null,"abstract":"<p>Designing artificial metal sites in proteins is challenging due to the need to place the metal site in precise positions and to tailor the coordination environment of the metal. In article 10.1002/cbic.202500208, Matteo Tegoni and co-workers use a modular approach using the SpyTag/SpyCatcher technology to provide the Spy construct with a Cu<sup>2+</sup>/ATCUN site. The reconstituted copper protein showed enhanced ROS catalytic activity. This strategy enables versatile metalloprotein design by shifting complexity from a protein to a peptide.\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":"26 14","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/cbic.202581401","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144666242","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ChemBioChemPub Date : 2025-07-14DOI: 10.1002/cbic.202500194
Tong Ye Wang, Amit Bijlani, Emily Hoi Pui Chao, Philip E Johnson, Sergey N Krylov
{"title":"A Browser-Based Tool for Assessing Accuracy of Isothermal Titration Calorimetry-Derived Parameters: K<sub>d</sub>, ΔH°, and n.","authors":"Tong Ye Wang, Amit Bijlani, Emily Hoi Pui Chao, Philip E Johnson, Sergey N Krylov","doi":"10.1002/cbic.202500194","DOIUrl":"https://doi.org/10.1002/cbic.202500194","url":null,"abstract":"<p><p>Accurate determination of equilibrium dissociation constants (K<sub>d</sub>) is essential for decision-making in drug discovery and diagnostics development. Isothermal titration calorimetry (ITC), which requires no reactant labeling or immobilization, is commonly used to validate K<sub>d</sub> values from high-throughput screens. Yet, like other methods, ITC results can be skewed by systematic errors in reactant concentrations, a fact that is often overlooked, potentially leading to misinformed decisions. To address this, accuracy confidence intervals (ACI)-ITC is developed, a browser-based tool that calculates ACI for ITC-derived parameters, offering probabilistic ranges for the true values of K<sub>d</sub>, enthalpy change (ΔH°), and binding stoichiometry (n). Unlike traditional confidence intervals that consider only random errors, ACI-ITC explicitly accounts for systematic errors, providing a more accurate framework to assess experimental reliability. Alongside a user-friendly interface, it offers detailed guidance for determining uncertainties in concentrations and heat, which are critical inputs for assessing measurement accuracy. The tool's browser-based accessibility (https://aci.sci.yorku.ca) eliminates the need for specialized installation, enabling cross-platform compatibility and streamlining accuracy assessments. By highlighting the importance of systematic errors and providing a structured approach for their evaluation, ACI-ITC supports more robust conclusions, fosters better-informed decisions based on ITC measurements, and enhances the reliability of research findings.</p>","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":" ","pages":"e2500194"},"PeriodicalIF":2.6,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144625094","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ChemBioChemPub Date : 2025-07-14DOI: 10.1002/cbic.202500352
Victoria S Halls, Larry L David, Keith D Zientek, Kirsten J Lampi
{"title":"Isomerized and Racemized Aspartyl and Deamidated Asparagine Residues Identified in ɣS-Crystallin.","authors":"Victoria S Halls, Larry L David, Keith D Zientek, Kirsten J Lampi","doi":"10.1002/cbic.202500352","DOIUrl":"https://doi.org/10.1002/cbic.202500352","url":null,"abstract":"<p><p>ɣS-crystallin is a major protein of the human lens and is highly modified with age and cataract due to a lack of lens protein turnover. Previous studies identify some sites of isomerization and racemization of deamidated asparaginyl and aspartyl residues in ɣS but have been limited due to the complexity of isoforms and difficulty in characterizing deamidation posttranslational modifications. A total of 32 stable isotope-labeled peptides are created for ɣS residues 7-18, 72-78, and 131-145, containing L-Asp, D-Asp, L-isoAsp, and D-isoAsp at D12, N14, N76, D77, and N143 to act as internal chromatography standards spiked into tryptic digests of nuclear insoluble protein of a cataractous human lens. High-resolution mass spectrometry is used to accurately assign deamidation status using the 19 mDa mass defect between isotopic peaks of deamidated and nondeamidated peptides. While peptides containing D-forms of Asp and isoAsp were assigned, the predominant isoforms contained L-isoAsp. High-resolution mass spectrometry using wide single ion monitoring data-independent acquisition also greatly improved the reliable identification of peptide deamidation states. These results will aid creation of ɣS using native chemical ligation to examine the role of isoAsp in crystallin aggregation and cataract.</p>","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":" ","pages":"e2500352"},"PeriodicalIF":2.6,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144625095","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Front Cover: Hybrid Molecules of Small Molecular and Peptidic HIV Fusion Inhibitors (ChemBioChem 13/2025)","authors":"Kohei Tsuji, Takuya Kobayakawa, Peter Bolah, Soshi Nishimura, Tsutomu Murakami, Hirokazu Tamamura","doi":"10.1002/cbic.202581301","DOIUrl":"https://doi.org/10.1002/cbic.202581301","url":null,"abstract":"<p>HIV-1 fusion inhibitors are useful and intelligent chemotherapeutics because the membrane fusion step of HIV-1 replication is the last chance to block the virus extracellularly. Hybrids of peptidomimetic small compounds and peptides are designed as heterodimeric molecules of HIV-1 fusion inhibitors. The hybrid molecules can compensate the drawbacks of homodimeric molecules of small compounds or peptides and therefore effectively block HIV-1 fusion. More details can be found in article 10.1002/cbic.202500230 by Tsutomu Murakami, Hirokazu Tamamura, and co-workers.\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":"26 13","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/cbic.202581301","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144598258","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}