Communications Chemistry最新文献_第3页

Deciphering the complexities of crystalline state(s) with molecular simulations. 用分子模拟破译晶体状态的复杂性。

IF 6.2 2区化学

Communications Chemistry Pub Date : 2025-09-26 DOI: 10.1038/s42004-025-01667-z

Caroline Desgranges, Jerome Delhommelle

引用次数: 0

Trends in actinide electronic structure revealed from asymmetric, isostructural transuranic metallocenes. 非对称等结构超铀茂金属中锕系元素电子结构的变化趋势。

IF 6.2 2区化学

Communications Chemistry Pub Date : 2025-09-26 DOI: 10.1038/s42004-025-01646-4

Cambell S Conour, Mikaela Mary F Pyrch, Nicholas J Katzer, Asmita Sen, Megan R Keener, Joshua J Woods, Jochen Autschbach, Polly L Arnold

{"title":"Trends in actinide electronic structure revealed from asymmetric, isostructural transuranic metallocenes.","authors":"Cambell S Conour, Mikaela Mary F Pyrch, Nicholas J Katzer, Asmita Sen, Megan R Keener, Joshua J Woods, Jochen Autschbach, Polly L Arnold","doi":"10.1038/s42004-025-01646-4","DOIUrl":"10.1038/s42004-025-01646-4","url":null,"abstract":"The study of actinide electronic structure and bonding within rigorously controlled environments is fundamental to advancing nuclear applications. Here, we report a new set of isostructural actinide organometallics; An(COTbig)2, (An = Th, U, Np, and Pu), where COTbig is the bulky 1,4-bis(triphenylsilyl)-substituted cyclooctatetraenyl dianion (1,4-(Ph3Si)2C8H6)2-. The actinide(IV) metallocene sandwiches have a clam-shell structure, offering a new molecular symmetry to explore f-orbital contributions in bonding. Combined experimental and computational studies reveal that An(COTbig)2 complexes strongly differ from the previously published coplanar An(COT)2 sandwiches due to the bent geometry and electron-withdrawing nature of the substituents. While COTbig displays comparatively weaker electron donation, the low-energy f-f transitions in An(COTbig)2 have increased molar absorptivity consistent with the removal of the parity selection rule and better energetic matching between ligand and actinide 5f orbitals as the series is traversed. For Pu(COTbig)2, covalent mixing of donor 5f metal orbitals and the ligand-π orbitals is especially strong.","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"280"},"PeriodicalIF":6.2,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12475471/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145173934","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

High-throughput proteome integral solubility alteration assay for low cell input using One-Tip. 使用One-Tip进行低细胞输入的高通量蛋白质组积分溶解度改变测定。

IF 6.2 2区化学

Communications Chemistry Pub Date : 2025-09-26 DOI: 10.1038/s42004-025-01670-4

Maico Lechner, Pierre Sabatier, Jesper V Olsen

{"title":"High-throughput proteome integral solubility alteration assay for low cell input using One-Tip.","authors":"Maico Lechner, Pierre Sabatier, Jesper V Olsen","doi":"10.1038/s42004-025-01670-4","DOIUrl":"10.1038/s42004-025-01670-4","url":null,"abstract":"Mass spectrometry-based versions of the cellular thermal shift assay (CETSA), like proteome integral solubility alteration (PISA), enable simultaneous monitoring of thousands of proteins for drug-target engagement. These methods are constrained in throughput and scalability, while the sample requirement limits the applicability to widely available material. Here, we combine PISA with the One-Tip method to simplify and streamline sample preparation. Using the mass spectrometry-compatible n-Dodecyl-β-D-Maltoside (DDM) non-ionic detergent for cell lysis in PISA sample preparation enables direct transfer to One-Tip with decreasing cell requirements down to 200 cells per µL. One-Tip provides similar depth and higher reproducibility, with lower material and solvent usage and a faster proteolytic digestion compared to a conventional sample cleaning and digestion protocol, making it a cost-effective, fast, and user-friendly option. To demonstrate its scalability, we applied One-Tip-PISA in a 96-well plate format, profiling a kinase inhibitor panel, allowing cell treatment to injection within 12 h, enhancing workflow efficiency and accessibility for a wide range of laboratories.","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"282"},"PeriodicalIF":6.2,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12474936/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145173889","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A comparative study of machine learning models on molecular fingerprints for odor decoding. 分子指纹气味解码机器学习模型的比较研究。

IF 6.2 2区化学

Communications Chemistry Pub Date : 2025-09-25 DOI: 10.1038/s42004-025-01651-7

Jinyoung Suh, Yeonju Hong, Chunho Park

{"title":"A comparative study of machine learning models on molecular fingerprints for odor decoding.","authors":"Jinyoung Suh, Yeonju Hong, Chunho Park","doi":"10.1038/s42004-025-01651-7","DOIUrl":"10.1038/s42004-025-01651-7","url":null,"abstract":"Understanding how molecular structure relates to odor perception is a longstanding problem, with important implications for fragrance development and sensory science. In this study, we present an advanced comparative analysis of machine learning approaches for predicting fragrance odors, examining both individual descriptor-based models and integrated frameworks. Using a curated dataset of 8681 compounds from ten expert sources, we benchmark functional group fingerprints, classical molecular descriptors, and Morgan structural fingerprints across Random Forest, eXtreme Gradient Boosting, and Light Gradient Boosting Machine. The Morgan-fingerprint-based XGBoost model achieves the highest discrimination (AUROC 0.828, AUPRC 0.237), outperforming descriptor-based models. Our findings highlight the superior representational capacity of molecular fingerprints to capture olfactory cues, not only achieving high predictive performance but also revealing a continuous, interpretable scent space that aligns with perceptual and chemical relationships. This paves the way for data-driven research into olfactory mechanisms, alongside the next generation of in silico odor prediction.","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"278"},"PeriodicalIF":6.2,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12462479/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145148040","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Current landscape of plasma proteomics from technical innovations to biological insights and biomarker discovery. 血浆蛋白质组学的现状，从技术创新到生物学见解和生物标志物的发现。

IF 6.2 2区化学

Communications Chemistry Pub Date : 2025-09-25 DOI: 10.1038/s42004-025-01665-1

Douglas Y Kirsher, Shreya Chand, Aron Phong, Bich Nguyen, Balazs G Szoke, Sara Ahadi

{"title":"Current landscape of plasma proteomics from technical innovations to biological insights and biomarker discovery.","authors":"Douglas Y Kirsher, Shreya Chand, Aron Phong, Bich Nguyen, Balazs G Szoke, Sara Ahadi","doi":"10.1038/s42004-025-01665-1","DOIUrl":"10.1038/s42004-025-01665-1","url":null,"abstract":"Plasma is a rich source of biomolecules, including proteins, that reflect both health and disease. Due to their key roles in biological processes, proteins hold significant potential as biomarkers, fueling the rise of plasma proteome profiling in recent years. However, comprehensive comparisons of the performance of different plasma proteomics platforms are limited. Our study addresses this gap by conducting a direct comparison of eight platforms, representing both affinity-based and diverse mass spectrometry approaches, and covering over 13,000 proteins. By applying these platforms to the same cohort, we systematically assess their performance, identifying key differences and complementary strengths. Our findings offer valuable insights for researchers, highlighting trade-offs in coverage and their implications for biomarker discovery and clinical applications. This study serves as an essential resource, offering both technical evaluation and biological insights to support the development of novel diagnostics and therapeutics through plasma proteomics.","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"279"},"PeriodicalIF":6.2,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12462477/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145148060","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Ligand-induced conformations and dynamic allosteric motions of IDO1 affecting the recruitment of a protein signaling partner. 配体诱导的构象和IDO1的动态变构运动影响蛋白质信号伙伴的募集。

IF 6.2 2区化学

Communications Chemistry Pub Date : 2025-09-24 DOI: 10.1038/s42004-025-01648-2

Alice Coletti, Elisa Bianconi, Sofia Rossini, Alessandra Altomare, Andrea Butticè, Daniele Mazzoletti, Giada Mondanelli, Andrea Carotti, Giancarlo Aldini, Riccardo Miggiano, Ciriana Orabona, Joshua Salafsky, Antonio Macchiarulo

{"title":"Ligand-induced conformations and dynamic allosteric motions of IDO1 affecting the recruitment of a protein signaling partner.","authors":"Alice Coletti, Elisa Bianconi, Sofia Rossini, Alessandra Altomare, Andrea Butticè, Daniele Mazzoletti, Giada Mondanelli, Andrea Carotti, Giancarlo Aldini, Riccardo Miggiano, Ciriana Orabona, Joshua Salafsky, Antonio Macchiarulo","doi":"10.1038/s42004-025-01648-2","DOIUrl":"10.1038/s42004-025-01648-2","url":null,"abstract":"Indoleamine 2,3-dioxygenase 1 (IDO1) is a moonlight protein endowed with catalytic and signaling functions. It plays a pivotal role in the immune breaking mechanism leading to immunosuppression in cancer microenvironment. Intense research efforts have been devoted to designing catalytic inhibitors for developing immunotherapies, yet neglecting the enzyme's signaling function. A few IDO1 inhibitors have reached the clinical stage, including navoximod, epacadostat and linrodostat. Using second harmonic generation analysis (SHG) and molecular dynamics simulations, here we show that these clinical inhibitors can induce distinct allosteric motions in the enzyme that affect the stability of the transient signaling complex between IDO1 and Src tyrosine kinase. Next generation sequencing demonstrates that, despite sharing a similar ability to inhibit the enzyme's catalytic function, all three catalytic inhibitors modulate the IDO1's signaling function in different ways, regulating distinct transcriptomes in SKOV3 cells.","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"277"},"PeriodicalIF":6.2,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12460605/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145136621","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Probing three-dimensional cyclooctatetraene for nucleobase modification in aptamer selection. 探索三维环四烯在适体选择中的核碱基修饰。

IF 6.2 2区化学

Communications Chemistry Pub Date : 2025-09-15 DOI: 10.1038/s42004-025-01629-5

Greta Charlotte Dahm, Usman Akhtar, Alix Bouvier-Müller, Laura Lim, Fabienne Levi-Acobas, Pierre Nicolas Bizat, Germain Niogret, Julian A Tanner, Frédéric Ducongé, Marcel Hollenstein

{"title":"Probing three-dimensional cyclooctatetraene for nucleobase modification in aptamer selection.","authors":"Greta Charlotte Dahm, Usman Akhtar, Alix Bouvier-Müller, Laura Lim, Fabienne Levi-Acobas, Pierre Nicolas Bizat, Germain Niogret, Julian A Tanner, Frédéric Ducongé, Marcel Hollenstein","doi":"10.1038/s42004-025-01629-5","DOIUrl":"10.1038/s42004-025-01629-5","url":null,"abstract":"Decoration of aptamers with chemical modifications at the level of nucleobases grants access to alternative binding modes, which often result in improved binding properties. Most functional groups involved in such endeavours mimic the side chains of amino acids or are based on sp2-dominated moieties. While this approach has met undeniable success, trends in modern drug discovery seem to favor sp3-rich compounds over aromatic derivatives. Here, we report the use of a nucleotide modified with the three-dimensional, highly flexible cyclooctatetraene carboxylate (COTc). This nucleotide was engaged in an SELEX experiment against the biomarker PvLDH. Tightly binding aptamers were identified, which displayed dissociation constants in the low nM range, representing a significant improvement compared to previously identified cubamers. These modified aptamers clearly underscore the usefulness of COTc as a bioisostere replacement of aromatic moieties not only in small compounds but also in functional nucleic acids.","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"276"},"PeriodicalIF":6.2,"publicationDate":"2025-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12436594/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145069213","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Systematic variation of the acceptor electrophilicity in donor-acceptor-donor emitters exhibiting efficient room temperature phosphorescence suited for digital luminescence. 供体-受体-供体发射体中受体亲电性的系统变化，表现出适合数字发光的高效室温磷光。

IF 6.2 2区化学

Communications Chemistry Pub Date : 2025-09-10 DOI: 10.1038/s42004-025-01620-0

Uliana Tsiko, Jannis Fidelius, Sebastian Kaiser, Heidi Thomas, Yana Bui Thi, Jan J Weigand, Juozas V Grazulevicius, Karl Sebastian Schellhammer, Sebastian Reineke

{"title":"Systematic variation of the acceptor electrophilicity in donor-acceptor-donor emitters exhibiting efficient room temperature phosphorescence suited for digital luminescence.","authors":"Uliana Tsiko, Jannis Fidelius, Sebastian Kaiser, Heidi Thomas, Yana Bui Thi, Jan J Weigand, Juozas V Grazulevicius, Karl Sebastian Schellhammer, Sebastian Reineke","doi":"10.1038/s42004-025-01620-0","DOIUrl":"10.1038/s42004-025-01620-0","url":null,"abstract":"Purely organic materials showing efficient and persistent emission via room temperature phosphorescence (RTP) allow the design of minimalistic yet powerful technological solutions for sensing, bioimaging, information storage, and safety applications using the photonic design principle of digital luminescence. Although several promising materials exist, a deep understanding of the underlying structure-property relationship and, thus, development of rational design strategies are widely missing. Some of the best purely organic emitters follow the donor-acceptor-donor design motif. In this study, the influence of the acceptor unit on the photophysical properties is systematically analyzed by synthesizing and characterizing variations of the RTP emitter 4,4'-dithianthrene-1-yl-benzophenone (BP-2TA). The most promising candidates are also tested in programmable luminescent tags as a potential application field for information storage. While no significant influence by the electrophilicity index of the acceptor moiety on the RTP emission is observed, the results support the design of molecules with pronounced hybridization as obtained for the newly synthesized emitter demonstrating superior RTP efficiency combined with improved stability.","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"274"},"PeriodicalIF":6.2,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12423317/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145032978","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Triplet-harvesting materials. Triplet-harvesting材料。

IF 6.2 2区化学

Communications Chemistry Pub Date : 2025-09-10 DOI: 10.1038/s42004-025-01639-3

Huifang Shi, Youngmin You, Yanli Zhao

引用次数: 0

Probing the anion binding promiscuity of the soluble nitrate sensor NreA from Staphylococcus carnosus. 肉葡萄球菌可溶性硝酸盐传感器NreA阴离子结合混杂性的探讨。

IF 6.2 2区化学

Communications Chemistry Pub Date : 2025-09-10 DOI: 10.1038/s42004-025-01660-6

Ke Ji, Elizabeth K Pack, Caden Maydew, Kevin A Alberto, Sameera Abeyrathna, Rhiza Lyne E Villones, Humera Gull, Gabriele Meloni, Steven O Nielsen, Sheel C Dodani

{"title":"Probing the anion binding promiscuity of the soluble nitrate sensor NreA from Staphylococcus carnosus.","authors":"Ke Ji, Elizabeth K Pack, Caden Maydew, Kevin A Alberto, Sameera Abeyrathna, Rhiza Lyne E Villones, Humera Gull, Gabriele Meloni, Steven O Nielsen, Sheel C Dodani","doi":"10.1038/s42004-025-01660-6","DOIUrl":"10.1038/s42004-025-01660-6","url":null,"abstract":"Promiscuity, or selectivity on a spectrum, is an encoded feature in biomolecular anion recognition. To unravel the molecular drivers of promiscuous anion recognition, we have employed a comprehensive approach - spanning experiment and theory - with the Staphylococcus carnosus nitrate regulatory element A (ScNreA) as a model. Thermodynamic analysis reveals that ScNreA complexation with native nitrate and nitrite or non-native iodide is an exothermic process. Further deconvolution of the association and dissociation kinetics for each anion reveals that the release event can be limiting, in turn, giving rise to the observed selectivity: nitrate > iodide > nitrite. These conclusions are supplemented with molecular dynamics simulations that capture an entry and exit pathway coupled to subtle global protein motions unique to each anion. Taken together, our data point to how structural plasticity of the binding pocket controls the relative promiscuity of ScNreA to guarantee physiological nitrate sensing.","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"275"},"PeriodicalIF":6.2,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12423327/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145032937","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0