Communications Chemistry最新文献_第2页

A quantitative analysis of ligand binding at the protein-lipid bilayer interface.

IF 5.9 2区化学

Communications Chemistry Pub Date : 2025-03-22 DOI: 10.1038/s42004-025-01472-8

Allison Pearl Barkdull, Matthew Holcomb, Stefano Forli

{"title":"A quantitative analysis of ligand binding at the protein-lipid bilayer interface.","authors":"Allison Pearl Barkdull, Matthew Holcomb, Stefano Forli","doi":"10.1038/s42004-025-01472-8","DOIUrl":"10.1038/s42004-025-01472-8","url":null,"abstract":"The majority of drugs target membrane proteins, and many of these proteins contain ligand binding sites embedded within the lipid bilayer. However, targeting these therapeutically relevant sites is hindered by limited characterization of both the sites and the molecules that bind to them. Here, we introduce the Lipid-Interacting LigAnd Complexes Database (LILAC-DB), a curated dataset of 413 structures of ligands bound at the protein-bilayer interface. Analysis of these structures reveals that ligands binding to lipid-exposed sites exhibit distinct chemical properties, such as higher calculated partition coefficient (clogP), molecular weight, and a greater number of halogen atoms, compared to ligands that bind to soluble proteins. Additionally, we demonstrate that the atomic properties of these ligands vary significantly depending on their depth within and exposure to the lipid bilayer. We also find that ligand binding sites exposed to the bilayer have distinct amino acid compositions compared to other protein regions, which may aid in the identification of lipid-exposed binding sites. This analysis provides valuable guidelines for researchers pursuing structure-based drug discovery targeting underexploited ligand binding sites at the protein-lipid bilayer interface.","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"89"},"PeriodicalIF":5.9,"publicationDate":"2025-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11929912/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143691224","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

Interface-edited solid-state NMR to study cell interfaces.

IF 5.9 2区化学

Communications Chemistry Pub Date : 2025-03-22 DOI: 10.1038/s42004-025-01473-7

Thomas Kress, Melinda J Duer

{"title":"Interface-edited solid-state NMR to study cell interfaces.","authors":"Thomas Kress, Melinda J Duer","doi":"10.1038/s42004-025-01473-7","DOIUrl":"10.1038/s42004-025-01473-7","url":null,"abstract":"Cell membrane interfaces, including the glycocalyx, play a crucial role in regulating signaling and molecular interactions, yet their molecular composition remains challenging to study in intact cells. Existing techniques often require extensive sample preparation or lack specificity for probing interfacial components directly. Here, we introduce a solid-state nuclear magnetic resonance (ssNMR) tool to fingerprint the molecular structure of the cell glycocalyx in intact cells within their native environment, offering insights relevant to drug delivery, tissue engineering, and biomedical research. Building on Goldman-Shen cross-polarization (CP) experiments, which exploit proton spin diffusion to generate 13C spectra near cell membranes, our enhanced approach provides spectral information from the membrane interface and its surroundings, probing a region up to 10 nm. Using interface-edited CP (1D) and PDSD (2D) spectra, we demonstrate spectral fingerprints of the mammalian cell glycocalyx. This method opens new avenues for studying cell interfaces in a dehydrated yet native-like state, preserving membrane composition and advancing structural biology.","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"86"},"PeriodicalIF":5.9,"publicationDate":"2025-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11929740/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143691228","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

Structural insight into the cGAS active site explains differences between therapeutically relevant species.

IF 5.9 2区化学

Communications Chemistry Pub Date : 2025-03-22 DOI: 10.1038/s42004-025-01481-7

Alexander M Skeldon, Li Wang, Nicolas Sgarioto, Ramsay E Beveridge, Silas Chan, Stephane Dorich, Valerie Dumais, Nadine Fradet, Samuel Gaudreault, Philippe LeGros, Daniel McKay, Ria Seliniotakis, Daniel V Sietsema, Lingling Zhang, Marc-Olivier Boily, Jason D Burch, Alex Caron, Lee D Fader, Lodoe Lama, Wei Xie, Dinshaw J Patel, Thomas Tuschl, Michael A Crackower, Kelly A Pike

{"title":"Structural insight into the cGAS active site explains differences between therapeutically relevant species.","authors":"Alexander M Skeldon, Li Wang, Nicolas Sgarioto, Ramsay E Beveridge, Silas Chan, Stephane Dorich, Valerie Dumais, Nadine Fradet, Samuel Gaudreault, Philippe LeGros, Daniel McKay, Ria Seliniotakis, Daniel V Sietsema, Lingling Zhang, Marc-Olivier Boily, Jason D Burch, Alex Caron, Lee D Fader, Lodoe Lama, Wei Xie, Dinshaw J Patel, Thomas Tuschl, Michael A Crackower, Kelly A Pike","doi":"10.1038/s42004-025-01481-7","DOIUrl":"10.1038/s42004-025-01481-7","url":null,"abstract":"Cyclic GMP-AMP synthase (cGAS) is an intracellular sensor of double-stranded DNA that triggers a pro-inflammatory response upon binding. The interest in cGAS as a drug discovery target has increased substantially over the past decade due to growing evidence linking its activation to numerous peripheral and neurological diseases. Here, we report the binding mode of previously described cGAS inhibitors while also uncovering the structural basis for the interspecies potency shifts within this chemotype. A single threonine to isoleucine substitution between human and mouse cGAS drives compound activity, as demonstrated by biochemical, cellular, and in vivo studies. Finally, we utilize a structurally enabled design approach to engineer a novel chemical inhibitor with excellent potency for both human and mouse enzymes by targeting key interactions within the enzyme active site. Overall, this work provides the framework for rational optimization of cGAS inhibitors and potential preclinical translational strategies.","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"88"},"PeriodicalIF":5.9,"publicationDate":"2025-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11929900/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143691145","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

Recent progress in triplet energy transfer systems toward organic afterglow materials.

IF 5.9 2区化学

Communications Chemistry Pub Date : 2025-03-21 DOI: 10.1038/s42004-025-01465-7

Kaiwen Wu, Dan Liu, Lixun Zhu, Tianhao Wu, Yanning Xu, Chenghan He, Yu Xiong, Zheng Zhao, Ben Zhong Tang

引用次数: 0

Dynamics of vibrationally coupled intersystem crossing in state-of-the-art organic optoelectronic materials.

IF 5.9 2区化学

Communications Chemistry Pub Date : 2025-03-18 DOI: 10.1038/s42004-025-01485-3

J P A Souza, L Benatto, G Candiotto, L Wouk, M Koehler

{"title":"Dynamics of vibrationally coupled intersystem crossing in state-of-the-art organic optoelectronic materials.","authors":"J P A Souza, L Benatto, G Candiotto, L Wouk, M Koehler","doi":"10.1038/s42004-025-01485-3","DOIUrl":"10.1038/s42004-025-01485-3","url":null,"abstract":"This work investigates intersystem crossing (ISC) induced by spin-orbit coupling (SOC) in state-of-the-art non-fullerene acceptors (NFAs). A quantum chemistry study analyzed SOC in 10 NFAs using the optimized geometry of the ground state (OGGS), revealing the importance of excited-state character (local or charge transfer) in determining SOC. However, ISC rates calculated with Marcus formalism were significantly lower than experimental values, showing that the three-state model (S1, T1, and T2) is insufficient. A simplified method to calculate coupled probabilities was proposed, leveraging a quantum walk on a one-dimensional graph. This approach aligned ISC rates with experimental data and explained Y6's higher triplet state efficiency compared to ITIC-like NFAs. Further, the dihedral angle (ϕ) in IT-4Cl and Y6 was analyzed. Y6's unique excited-state potential energy curve (PEC) showed a minimum at ϕ ≈ 90o. Using PECs, ISC rates were refined, showing coupling via ϕ vibrations. Finally, the Wentzel-Kramers-Brillouin (WKB) approximation explained Y6's photoluminescence at low temperatures, highlighting non-adiabatic phenomena crucial for understanding the photophysics of organic semiconductors. Triplet states act as channels that enhance recombination, reducing the optoelectronic efficiency of semiconductor devices. Therefore, understanding and controlling these states can contribute to improving the efficiency of organic solar cells (OSCs) and organic light-emitting diodes (OLEDs).","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"84"},"PeriodicalIF":5.9,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11920221/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143656032","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

Multicomponent dynamics in amorphous ice studied using X-ray photon correlation spectroscopy at elevated pressure and cryogenic temperatures.

IF 5.9 2区化学

Communications Chemistry Pub Date : 2025-03-16 DOI: 10.1038/s42004-025-01480-8

Aigerim Karina, Hailong Li, Tobias Eklund, Marjorie Ladd-Parada, Bernhard Massani, Mariia Filianina, Neha Kondedan, Andreas Rydh, Klara Holl, Ryan Trevorah, Simo Huotari, Robert P C Bauer, Claudia Goy, Nele N Striker, Francesco Dallari, Fabian Westermeier, Michael Sprung, Felix Lehmkühler, Katrin Amann-Winkel

{"title":"Multicomponent dynamics in amorphous ice studied using X-ray photon correlation spectroscopy at elevated pressure and cryogenic temperatures.","authors":"Aigerim Karina, Hailong Li, Tobias Eklund, Marjorie Ladd-Parada, Bernhard Massani, Mariia Filianina, Neha Kondedan, Andreas Rydh, Klara Holl, Ryan Trevorah, Simo Huotari, Robert P C Bauer, Claudia Goy, Nele N Striker, Francesco Dallari, Fabian Westermeier, Michael Sprung, Felix Lehmkühler, Katrin Amann-Winkel","doi":"10.1038/s42004-025-01480-8","DOIUrl":"10.1038/s42004-025-01480-8","url":null,"abstract":"Knowing the pressure dependence of glass forming liquids is important in various contexts. Here, we study the case of supercooled water, which has at least two different amorphous states with different densities. The pressure dependencies of the two glass transitions are predicted to show opposite behaviour, crossing in the P-T plane at elevated pressure. The experimental identification of the glass transition at elevated pressure and cryo-conditions is technically difficult. Moreover, in the case of amorphous ices, the glass transition is interrupted by crystallization, which makes it even more challenging. We show the feasibility of performing X-ray photon correlation spectroscopy experiments at elevated pressure using a diamond anvil cell at cryogenic temperatures. We observe two dynamic components when approaching the glass transition temperature. For high-density amorphous ice at a pressure of around (0.08 ± 0.02) GPa we determine the glass transition to be at higher temperatures compared to ambient conditions.","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"82"},"PeriodicalIF":5.9,"publicationDate":"2025-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11911450/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143647576","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

Ultraviolet irradiation penetration depth on TiO₂.

IF 5.9 2区化学

Communications Chemistry Pub Date : 2025-03-16 DOI: 10.1038/s42004-025-01487-1

Bugrahan Guner, Mohammad Safikhani-Mahmoudi, Fengmiao Li, Ke Zou, Omur E Dagdeviren

引用次数: 0

Multiphase detection of crucial biological amines using a 2,4,6-tristyrylpyrylium dye.

IF 5.9 2区化学

Communications Chemistry Pub Date : 2025-03-15 DOI: 10.1038/s42004-025-01459-5

Shivani Tripathi, Banchhanidhi Prusti, Manab Chakravarty

{"title":"Multiphase detection of crucial biological amines using a 2,4,6-tristyrylpyrylium dye.","authors":"Shivani Tripathi, Banchhanidhi Prusti, Manab Chakravarty","doi":"10.1038/s42004-025-01459-5","DOIUrl":"10.1038/s42004-025-01459-5","url":null,"abstract":"The strong electrophilicity of arylpyrylium salts was recognized for the colorimetric detection of vital amine analytes, limited to ammonia or methylamines and putrescine as biogenic amine. This report presents conformationally twisted, electrophilic triphenylamine-linked 2,4,6-tristyrylpyrylium salt PyTPA as a single dye to sense various aliphatic/aromatic biogenic amines, nicotine, and guanidine rapidly in nanomolar concentrations. This unexplored styrylpyrylium design offers specific electronic conjugations, steric/geometric constraints with hydrophobicity, and decent thermal/photostability, facilitating precise diverse amines detection in unique fashions. The deep-violet solution/solid dye responded remarkably at 298 K with quick decoloration against putrescine, cadaverine, spermidine, spermine, histamines, serotonin, and 2-phenylethylamine. Further, this dye could detect nicotine at 313 K and guanidine at 298 K distinctively with diminished absorption and unexpected red-shifted emission enhancement. Variation in mechanistic path is recognized in detecting amines holding mono/di-NH2 groups and short/ long alkane chains, elucidated by mass, 1H-NMR, FT-IR, SEM, PXRD, and XPS studies. The notable detection of these biogenic amines in different phases is employed for onsite applications to detect fresh chicken and tuna. Nicotine in natural tobacco leaves was identified. Such pyrylium salt provides promising advancements in this class of molecules in detecting diverse biologically significant amines.","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"81"},"PeriodicalIF":5.9,"publicationDate":"2025-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11910641/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143633735","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

Orthogonally conjugated phthalocyanine-porphyrin oligomer for NIR photothermal-photodynamic antibacterial treatment.

IF 5.9 2区化学

Communications Chemistry Pub Date : 2025-03-14 DOI: 10.1038/s42004-025-01470-w

Guixue Lian, Wanru Zhao, Gaoqiang Ma, Sen Zhang, Ailin Wu, Lin Wang, Dongjiao Zhang, Wei Liu, Jianzhuang Jiang

{"title":"Orthogonally conjugated phthalocyanine-porphyrin oligomer for NIR photothermal-photodynamic antibacterial treatment.","authors":"Guixue Lian, Wanru Zhao, Gaoqiang Ma, Sen Zhang, Ailin Wu, Lin Wang, Dongjiao Zhang, Wei Liu, Jianzhuang Jiang","doi":"10.1038/s42004-025-01470-w","DOIUrl":"10.1038/s42004-025-01470-w","url":null,"abstract":"With the increase of antibiotic resistance worldwide, there is an urgent demand to develop new fungicides and approaches to address the threat to human health posed by the ineffectiveness of traditional antibiotics. In this work, an orthogonal conjugated uniform oligomer bactericide of SiPc-ddCPP was constructed between silicon phthalocyanine and porphyrin, which can effectively treat infection through photodynamic-photothermal combined therapy without considering drug resistance. Compared with organic photothermal agents induced by unstable H-aggregation with blue-shifted absorption and fluorescence/ROS quenching, this orthogonal-structured uniform SiPc-ddCPP nanoparticle shows remarkably stability and NIR photothermal effect (η = 31.15%) along with fluorescence and ROS generation. Antibacterial studies have shown that both Gram-positive and Gram-negative bacteria could be efficiently annihilated in a few minutes through synergistic PDT-PTT along with satisfactory bacterial targeting. These results suggest SiPc-ddCPP is a multifunctional NIR bactericide, which afford a new approach of synergistic PDT-PTT sterilization to conquer the crisis of antibiotic resistance.","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"80"},"PeriodicalIF":5.9,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11909192/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143633746","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

Opportunities and challenges in modelling ligand adsorption on semiconductor nanocrystals.

IF 5.9 2区化学

Communications Chemistry Pub Date : 2025-03-13 DOI: 10.1038/s42004-025-01471-9

Xin Qi

引用次数: 0