Frontiers in Chemistry最新文献

{"title":"NanoAbLLaMA: construction of nanobody libraries with protein large language models.","authors":"Xin Wang, Haotian Chen, Bo Chen, Lixin Liang, Fengcheng Mei, Bingding Huang","doi":"10.3389/fchem.2025.1545136","DOIUrl":"10.3389/fchem.2025.1545136","url":null,"abstract":"<p><strong>Introduction: </strong>Traditional methods for constructing synthetic nanobody libraries are labor-intensive and time-consuming. This study introduces a novel approach leveraging protein large language models (LLMs) to generate germline-specific nanobody sequences, enabling efficient library construction through statistical analysis.</p><p><strong>Methods: </strong>We developed NanoAbLLaMA, a protein LLM based on LLaMA2, fine-tuned using low-rank adaptation (LoRA) on 120,000 curated nanobody sequences. The model generates sequences conditioned on germlines (IGHV3-301 and IGHV3S5301). Training involved dataset preparation from SAbDab and experimental data, alignment with IMGT germline references, and structural validation using ImmuneBuilder and Foldseek.</p><p><strong>Results: </strong>NanoAbLLaMA achieved near-perfect germline generation accuracy (100% for IGHV3-301, 95.5% for IGHV3S5301). Structural evaluations demonstrated superior predicted Local Distance Difference Test (pLDDT) scores (90.32 ± 10.13) compared to IgLM (87.36 ± 11.17), with comparable TM-scores. Generated sequences exhibited fewer high-risk post-translational modification sites than IgLM. Statistical analysis of CDR regions confirmed diversity, particularly in CDR3, enabling the creation of synthetic libraries with high humanization (>99.9%) and low risk.</p><p><strong>Discussion: </strong>This work establishes a paradigm shift in nanobody library construction by integrating LLMs, significantly reducing time and resource demands. While NanoAbLLaMA excels in germline-specific generation, limitations include restricted germline coverage and framework flexibility. Future efforts should expand germline diversity and incorporate druggability metrics for clinical relevance. The model's code, data, and resources are publicly available to facilitate broader adoption.</p>","PeriodicalId":12421,"journal":{"name":"Frontiers in Chemistry","volume":"13 ","pages":"1545136"},"PeriodicalIF":3.8,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11893428/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143604419","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Novel idebenone derivatives attenuated oxidative stress injury and myocardial damage.","authors":"Yuwei Peng, Yishan Guo, Xinyi Yang, Yulan Liu, Xun Xu, Junhong Chen, Xueyi Liu, Zhenrou Xie, Zhiqiang Yu, Dudu Wu, Zhi Chen","doi":"10.3389/fchem.2025.1544616","DOIUrl":"10.3389/fchem.2025.1544616","url":null,"abstract":"<p><p>Oxidative stress-induced cardiomyocyte apoptosis was the primary causative factor of cardiovascular disease (CVD). However, the existing therapy drugs for oxidative stress were much less investigated, which underlined the necessity for new drug discovery and development. Herein, we aimed to synthesize several novel idebenone (IDE) derivatives and investigate the protective effect and mechanism of these derivatives against H₂O₂-induced oxidative stress injury in H9C2 cells by determining cell proliferation rate, detecting the reactive oxygen species (ROS) level, and the expression of related proteins. Additionally, the study also investigated the protective effect of IDE-1 pretreatment on Balb/c mice after hypoxia-reoxygenation. <i>In vivo</i> experiments, the damage to cardiomyocytes was assessed using hematoxylin-eosin (HE) staining and terminal deoxynucleotidyl transferase-mediated dUTP-biotin nick end labeling (TUNEL) staining. The results showed that IDE-1 possessed the highest antioxidant damage activity among all IDE derivatives, which could notably decrease the levels of intracellular ROS. Furthermore, the antioxidant mechanism was confirmed to be potentially linked to the expression levels of the oxidation-related pathway heme oxygenase-1 (HO-1) and the apoptosis-related pathway Bcl-2/Bax and caspase-3. Our results demonstrated that IDE derivatives could be a new research direction for the treatment of cardiovascular diseases associated with oxidative stress.</p>","PeriodicalId":12421,"journal":{"name":"Frontiers in Chemistry","volume":"13 ","pages":"1544616"},"PeriodicalIF":3.8,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11891201/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143596370","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Electrospun MXene/polyimide nanofiber composite separator for enhancing thermal stability and ion transport of lithium-ion batteries.","authors":"Yitian Wu, Wenhui Wei, Tianxue Feng, Wenwen Li, Xiaoyu Wang, Tao Wu, Xingshuang Zhang","doi":"10.3389/fchem.2025.1555323","DOIUrl":"10.3389/fchem.2025.1555323","url":null,"abstract":"<p><p>Safety of lithium-ion batteries (LIBs) has garnered significant attention. As an essential component of batteries, the separator plays a crucial role in separating the positive and negative electrodes, preventing short circuits, and allowing ion transport. Therefore, it is necessary to develop a high-performance separator that is both thermally stable and capable of rapid Li⁺ transport. Polyimide (PI) is a material with high thermal stability, but low electrolyte wettability and high interfacial resistance of PI restrict its application in high-performance LIBs batteries. MXene possesses excellent mechanical properties and good electrolyte affinity. PI/MXene nanofiber composite separator. Combines the high thermal stability of PI with the superior electrolyte wettability of MXene. It exhibits a high tensile strength of 19.6 MPa, low bulk resistance (2.5 Ω), and low interfacial resistance (174 Ω), as well as a low electrolyte contact angle of 29°, while retaining the high-temperature resistance and flame retardancy of PI. Batteries assembled with this composite separator demonstrated a specific capacity of 111.0 mAh g^-1 and a capacity retention rate of 66% at 2C. In long-term cycling tests of LiFePO₄ half-cells at 1C, after 200 charge-discharge cycles, the PI/MXene battery showed a discharge specific capacity of 126.7 mAh g^-1 and a capacity retention rate of 91%. Additionally, the battery operated normally at 120°C. The composite separator, by integrating the high thermal stability of PI with the excellent electrolyte wettability and conductivity of MXene, demonstrates significant advantages in enhancing battery safety and cycling performance. Through this composite structure can provide a more reliable and safe solution for high-performance LIBs.</p>","PeriodicalId":12421,"journal":{"name":"Frontiers in Chemistry","volume":"13 ","pages":"1555323"},"PeriodicalIF":3.8,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11885268/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143585084","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Corrigendum: Antioxidant, Anti-Alzheimer's, anticancer, and cytotoxic properties of peanut oil: <i>in vitro</i>, <i>in silico</i>, and GC-MS analysis.","authors":"Hanène Djeghim, Djamila Benouchenne, El Hassen Mokrani, Huda Alsaeedi, David Cornu, Mikhael Bechelany, Ahmed Barhoum","doi":"10.3389/fchem.2025.1563210","DOIUrl":"10.3389/fchem.2025.1563210","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.3389/fchem.2024.1487084.].</p>","PeriodicalId":12421,"journal":{"name":"Frontiers in Chemistry","volume":"13 ","pages":"1563210"},"PeriodicalIF":3.8,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11885912/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143585081","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Editorial: Frontiers in Chemistry: 10 years anniversary.","authors":"Steven L Suib","doi":"10.3389/fchem.2025.1572259","DOIUrl":"https://doi.org/10.3389/fchem.2025.1572259","url":null,"abstract":"","PeriodicalId":12421,"journal":{"name":"Frontiers in Chemistry","volume":"13 ","pages":"1572259"},"PeriodicalIF":3.8,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11883550/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143572667","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring imaged capillary isoelectric focusing parameters for enhanced charge variants quality control.","authors":"Virginia Ghizzani, Alessandro Ascione, Federico Gonnella, Gabriella Massolini, Francesca Luciani","doi":"10.3389/fchem.2025.1536222","DOIUrl":"10.3389/fchem.2025.1536222","url":null,"abstract":"<p><p>Biopharmaceuticals are increasingly utilised in the treatment of oncological, inflammatory, and autoimmune diseases, largely due to their exceptional specificity in targeting antigens. However, their structural complexity, heterogeneity, and sensitivity pose crucial challenges in their production, purification, and delivery. Charge heterogeneity analysis, a Critical Quality Attribute of these biomolecules used in their Quality Control, is often performed using separative analytical techniques such as imaged capillary Isoelectric Focusing (icIEF). Recognized as a gold standard by the industry, icIEF leverages a pH gradient to provide high-resolution profiling of charge variants in biotherapeutics. In this review, critical experimental parameters for icIEF method development in the context of biotherapeutic drug development and QC will be discussed. Key aspects, including sample preparation, capillary properties, carrier ampholytes, stabilizers, and detection are examined, and supported by recent literature. Advances in icIEF technology and its expanding applications underline its robustness, reproducibility, and compliance with regulatory standards, affirming its pivotal role in ensuring the identity and consistency of biological products.</p>","PeriodicalId":12421,"journal":{"name":"Frontiers in Chemistry","volume":"13 ","pages":"1536222"},"PeriodicalIF":3.8,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11904914/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143624143","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Heterogeneous Fenton-like CuO-CoO_x/SBA-15 catalyst for organic pollutant degradation: synthesis, performance, and mechanism.","authors":"Jinwei Li, Yifei Wei, Qiang Liu, Huanhuan Guan, Chengchun Jiang, Xiaohui Sun","doi":"10.3389/fchem.2025.1552002","DOIUrl":"10.3389/fchem.2025.1552002","url":null,"abstract":"<p><p>In this study, CuO-CoO_x/SBA-15 catalysts were successfully synthesized via ultrasonic impregnation, and their performance in degrading nitrobenzene within a Fenton-like system was investigated. The catalyst materials were characterized using X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), inductively coupled plasma mass spectrometry (ICP-MS), scanning electron microscopy (SEM), transmission electron microscope(TEM) and energy-dispersive X-ray spectroscopy (EDS). The CuO-CoO_x/SBA-15 catalysts featured well-distributed CuO-CoO_x nanoparticles within the mesoporous SBA-15 support. Compared to CuO/SBA-15 and Co₃O₄/SBA-15 catalysts with similar microstructures, the CuO-CoO_x/SBA-15 catalysts exhibited Cu-Co dual active centers and a higher abundance of redox-active sites. During catalytic degradation, H₂O₂ was continuously activated on the catalyst surface through efficient Cu⁺/Cu²⁺ and Co²⁺/Co³⁺ redox cycles. The experimental conditions (initial pH, catalyst dosage, and H₂O₂ dosage) were optimized, resulting in 99% nitrobenzene removal over a wide pH range (3.0-9.0). The primary mechanisms for the oxidation and subsequent removal of nitrobenzene in the CuO-CoO_x/SBA-15-H₂O₂ system were identified as reactions with hydroxyl radicals (·OH).</p>","PeriodicalId":12421,"journal":{"name":"Frontiers in Chemistry","volume":"13 ","pages":"1552002"},"PeriodicalIF":3.8,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11880010/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143566647","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Construction of pH-responsive hydrogel coatings on titanium surfaces for antibacterial and osteogenic properties.","authors":"Shan Peng, Yueru Liu, Wei Zhao, Xinpeng Liu, Ronghua Yu, Yonglin Yu","doi":"10.3389/fchem.2025.1546637","DOIUrl":"10.3389/fchem.2025.1546637","url":null,"abstract":"<p><p>Infection is one of the leading causes of failure in titanium-based implant materials during clinical surgeries, often resulting in delayed or non-union of bone healing. Furthermore, the overuse of antibiotics can lead to bacterial resistance. Therefore, developing a novel titanium-based implant material with both antimicrobial and osteogenic properties is of great significance. In this study, chitosan (CS), polydopamine (PDA), and antimicrobial peptides (AMPs) HHC36 were applied to modify the surface of titanium, resulting in the successful preparation of the composite material Ti-PDA-CS/PDA@HHC36 (abbreviated as T-P-C/P@H). CS promotes osteogenesis and cell adhesion, providing an ideal microenvironment for bone repair. PDA enhances the material's biocompatibility and corrosion resistance, offering cell adhesion sites, while both components exhibit pH-responsive characteristics. The HHC36 effectively prevents infection, protecting the bone repair material from bacterial damage. Overall, the synergistic effects of these components in T-P-C/P@H not only confer excellent antimicrobial and osteogenic properties but also improve biocompatibility, offering a new strategy for applying titanium-based implants in clinical settings.</p>","PeriodicalId":12421,"journal":{"name":"Frontiers in Chemistry","volume":"13 ","pages":"1546637"},"PeriodicalIF":3.8,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11883361/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143572665","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Therapeutic potential of <i>Laurus nobilis</i> extract by experimental and computational approaches: phenolic content and bioactivities for antioxidant, antidiabetic, and anticholinergic properties.","authors":"Sevgi Altın, Mesut Işık, Cemalettin Alp, Emrah Dikici, Ekrem Köksal, Kevser Kübra Kırboğa, Mithun Rudrapal, Gourav Rakshit, Şükrü Beydemir, Johra Khan","doi":"10.3389/fchem.2025.1541250","DOIUrl":"10.3389/fchem.2025.1541250","url":null,"abstract":"<p><strong>Introduction: </strong><i>Laurus nobilis</i> (LN), has traditional medicinal uses, and this study investigates its therapeutic potential by focusing on its phenolic content and bioactivities such as antioxidant, antidiabetic, and anticholinergic properties. Phenolic compounds play key roles in reducing oxidative stress and modulating enzymatic activities, relevant to metabolic and neurodegenerative disorders.</p><p><strong>Methods: </strong>LN leaf extracts were prepared via ethanol maceration, followed by filtration and concentration. Phenolic content was analyzed using LC-MS/MS. Antioxidant activity was assessed through ferric thiocyanate, DPPH, ABTS, and FRAP assays. Enzyme inhibition assays targeted AChE, BChE, and α-GLY, with IC50 values from dose-response curves. <i>In silico</i> analyses were conducted using molecular docking techniques to predict the binding mechanisms of identified phenolic compounds with the active sites of target enzymes, evaluating binding affinities and interaction profiles.</p><p><strong>Results: </strong>Vanillic acid and catechin hydrate were the most abundant phenolics. LN extract showed strong lipid peroxidation inhibition (50.53%) compared to Trolox (28.33%) and α-tocopherol (37.79%). Moderate radical scavenging and metal reduction potentials were observed. IC50 values were 2.57 µg/L for AChE, 3.78 µg/L for BChE, and 4.65 µg/L for α-GLY, indicating notable bioactivity. <i>In silico</i> studies confirmed strong binding affinities of phenolics to target enzymes.</p><p><strong>Discussion: </strong>LN extracts demonstrated promising antioxidant, antidiabetic, and anticholinergic activities, attributed to high phenolic content. Enzyme inhibition results suggest potential in managing metabolic and neurodegenerative disorders. <i>In silico</i> findings support these bioactivities, highlighting LN's therapeutic potential.</p>","PeriodicalId":12421,"journal":{"name":"Frontiers in Chemistry","volume":"13 ","pages":"1541250"},"PeriodicalIF":3.8,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11880275/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143566652","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The usefulness of infrared spectroscopy and X-ray powder diffraction in the analysis of falsified, illegal, and medicinal products.","authors":"Anna Mocarska, Karolina Piorunska, Jan K Maurin, Agata Blazewicz","doi":"10.3389/fchem.2025.1536209","DOIUrl":"10.3389/fchem.2025.1536209","url":null,"abstract":"<p><p>One way to combat the black pharmaceutical market is to exchange experience and knowledge among the laboratories involved in this fight. A beneficial approach is compiling application examples that demonstrate the development and growing potential of the two analytical techniques that are undoubtedly useful in investigating pharmacologically active ingredients found in products dangerous to consumers health and life. Attenuated total reflectance Fourier transform infrared spectroscopy and X-ray powder diffraction are nondestructive techniques substantial for examining evidence seized by the police, demanding minimal preparation of the sample. Importantly, they are among the few that do not negatively impact the environment because they do not require the production or disposal of chemical reagents or solvents, aligning with the principles of green chemistry. Both techniques provide consistent, reproducible results, essential for legal and scientific validity.</p>","PeriodicalId":12421,"journal":{"name":"Frontiers in Chemistry","volume":"13 ","pages":"1536209"},"PeriodicalIF":3.8,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11879982/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143566649","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}