Frontiers in Chemistry最新文献

{"title":"Kinetics of the mechanochemical transformations in the \"glycine - oxalic acid dihydrate\" system revisited: The role of water.","authors":"Evgeniy Losev, Polina Kalinina, Artem Golomolzin, Viktoria Kolesnikova, Elena Boldyreva","doi":"10.3389/fchem.2025.1540129","DOIUrl":"https://doi.org/10.3389/fchem.2025.1540129","url":null,"abstract":"<p><p><b>Introduction:</b> Kinetics of the mechanochemical transformations in the \"glycine-oxalic acid dihydrate\" system were revisited, in order to compare the results obtained for ball milling of the same reactants in different ball-milling devices.<b>Methods:</b> The results obtained in a commercial vibrational mill NARVA Vibrator DDR-GM9458 (ex situ study, this work) were compared with the previously published studies: ex situ in a home-made restricted-impact device and in situ in a Retsch MM400 vibrational mill.<b>Results:</b> We studied the effect of various factors on the mechanochemical transformations in this system under different conditions, such as the air humidity, the effect of the frequency of mechanical pulses on the existence of the induction period, the effect of the starting glycine polymorph on the duration of the induction period in case of a high-frequency vibrational ball milling, or the formation of G2O and GO as two competing products, the former dominating at the early stage of treatment as a \"kinetic\", faster crystallizing phase, and the latter formed as the only final thermodynamically stable product after a prolonged treatment.<b>Discussion:</b> The abovementioned results were interpreted consistently considering the possibility that water released from oxalic acid crystal hydrate may have a significant effect on the mechanochemical transformations, even though it does not enter crystal structures of bis-glycinium oxalate (G2O) and glycinium semioxalate (GO) products.</p>","PeriodicalId":12421,"journal":{"name":"Frontiers in Chemistry","volume":"13 ","pages":"1540129"},"PeriodicalIF":3.8,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11975923/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143810905","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":"Chemoinformatics analysis of <i>Mangifera indica</i> leaves extracted phytochemicals as potential EGFR kinase modulators.","authors":"Md Abdullah Al Mashud, Ajoy Kumer, Ismat Jahan, Md Mehedi Hasan Somrat, Md Enamul Kabir Talukder, Md Mashiar Rahman, A F M Shahab Uddin, Md Harun-Or-Rashid, Md Mizanur Rahman, Mohammad Harun-Ur-Rashid, Gamal A Shazly, Youssouf Ali Younous","doi":"10.3389/fchem.2025.1524384","DOIUrl":"10.3389/fchem.2025.1524384","url":null,"abstract":"<p><p>Breast cancer, being among the most frequent and fatal cancers in women, is an enormous issue globally. The critical requirement for novel treatment methods is underscored by its high mortality rate and relentless advancement. Even though breast cancer is one of the world's most common causes of death, the therapeutic avenue is still limited. The aim of this work is to investigate the potential inhibitory effects of specific compounds present in leaf extract from <i>Mangifera indica</i> on the growth of drug-resistant breast cancer protease PDB ID 3w32. The chemical compounds present in <i>Mangifera indica</i> leaves were used to analyze using molecular modeling techniques, such as molecular docking, molecular dynamics (MD) simulations, quantum mechanics (QM) calculations, and the Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) method, in order to examine three key chemical constituents: quercetin (08), catechin (09), and elagic acid (10). The ligands undergo extensive testing to figure out how effective they are against the 3w32-overexpressing breast cancer protein. Quantum calculations retaining HOMO-LUMO analysis might identify important characteristics of molecules, such as chemical potential, electronegativity, hardness, softness, and orbital energy gaps. According to the molecular docking inquiry, ligands 08, 09, and 10 are strong candidates with strong binding affinity for the breast cancer protein that overexpresses 3w32. The protein binding site stability of the chosen natural ligands was verified by MD simulation. These three ligands not only surpass the efficacy of the FDA-approved treatment, but also fulfill the requirements for a possible new inhibitor of breast cancer.</p>","PeriodicalId":12421,"journal":{"name":"Frontiers in Chemistry","volume":"13 ","pages":"1524384"},"PeriodicalIF":3.8,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11973374/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143803057","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 the antimicrobial potential of lactobacilli against early-stage and mature biofilms of <i>Staphylococcus aureus</i> and <i>Pseudomonas aeruginosa</i>.","authors":"Niharika Singh, Rohini Devidas Gulhane, Anamika Singh, Maitri Goel, Pudke Payal Udelal, Vikas Sangwan, Manvesh Kumar Sihag, Gunjan Goel, Harsh Panwar, Anil Kumar Puniya","doi":"10.3389/fchem.2025.1425666","DOIUrl":"10.3389/fchem.2025.1425666","url":null,"abstract":"<p><p>Bacterial biofilms are dynamic, complex, and very adaptive, and they can cause health problems in both humans and animals while also posing a serious threat to various industries. This study explores the potential of cell-free preparations of lactobacilli isolated from breast milk (HM; n = 11) and infant fecal (IF; n = 15) samples to impact the growth of <i>Staphylococcus aureus</i> and <i>Pseudomonas aeruginosa</i> biofilms. The anti-biofilm activity of three distinct cell-free preparations, namely, untreated cell-free supernatant (CFS), pH-neutralized CFS (N-CFS), and heat-treated CFS (H-CFS), was examined against both early-stage and mature biofilms. The post-incubation strategy examined the impact on mature biofilms, while the co-incubation treatment assessed the impact of CFS on adhesion and initial colonization. Compared to post-incubation treatment (HM3, 67.12%), the CFSs exhibited greater inhibitory activity during co-incubation (IF9, 85.19%). Based on the findings, untreated CFS exhibited the most promising biofilm inactivation, although its activity was not completely lost upon pH neutralization and heat treatment. Treatment with H-CFSs and N-CFSs moderately reduced the population of <i>S. aureus</i> and <i>P. aeruginosa</i> bacterial cells within the biofilm by 40%-60%. Microscopic observations showed that after CFS treatment, the integrity of the biofilm conformation was disrupted. According to principal component analysis (PCA) (significance level at <i>p</i> < 0.05), the most promising anti-biofilm activity against both test pathogens was found in the CFS of <i>Lacticaseibacillus paracasei</i> HM1.</p>","PeriodicalId":12421,"journal":{"name":"Frontiers in Chemistry","volume":"13 ","pages":"1425666"},"PeriodicalIF":3.8,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11969340/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143794894","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":"Enhanced spectral signatures with Ag nanoarrays in hyperspectral microscopy for CNN-based microplastics classfication.","authors":"Xinwei Dong, Xu Zhao, Jianing Xu, Qianqian Chen, Hanwen Luo, Fuxin Zheng, Tao Zhang, Yansheng Liu","doi":"10.3389/fchem.2025.1562743","DOIUrl":"10.3389/fchem.2025.1562743","url":null,"abstract":"<p><p>Microplastics are a pervasive pollutant in aquatic ecosystems, raising critical environmental and public health concerns and driving the need for advanced detection technologies. Microscopic hyperspectral imaging (micro-HSI), known for its ability to simultaneously capture spatial and spectral information, has shown promise in microplastic analysis. However, its widespread application is hindered by limitations such as low signal-to-noise ratios (SNR) and reduced sensitivity to smaller microplastic particles. To address these challenges, this study investigates the use of Ag nanoarrays as reflective substrates for micro-HSI. The localized surface plasmon resonance (LSPR) effect of Ag nanoarrays enhances spectral resolution by suppressing background reflections and isolating microplastic reflection bands from interference. This improvement results in significantly increased SNR and more distinct spectral features. When analyzed using a 3D-2D convolutional neural network (3D-2D CNN), the integration of Ag nanoarrays improved classification accuracy from 90.17% to 98.98%. These enhancements were further validated through Support Vector Machine (SVM) analyses, demonstrating the robustness and reliability of the proposed approach. This study demonstrates the potential of combining Ag nanoarrays with 3D-2D CNN models to enhance micro-HSI performance, offering a novel and effective solution for precise microplastics detection and advancing chemical analysis, environmental monitoring, and related fields.</p>","PeriodicalId":12421,"journal":{"name":"Frontiers in Chemistry","volume":"13 ","pages":"1562743"},"PeriodicalIF":3.8,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11968667/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143794891","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":"Achieving efficient red room-temperature phosphorescence in two-dimensional hybrid halide perovskites by manganese doping.","authors":"Hui Zhu, Suqin Wang, Ming Sheng, Shao Bo, Yu He, Zhuang Liu, Min Li, Guangtao Zhou","doi":"10.3389/fchem.2025.1533513","DOIUrl":"10.3389/fchem.2025.1533513","url":null,"abstract":"<p><p>Red room-temperature phosphorescence (RTP), characterized by its long emission wavelength and lifetime, has broad applications in various fields, including bioimaging, light-emitting diodes (LEDs), information encryption, and photodetectors. Two-dimensional (2D) hybrid halide perovskites are a novel class of organic-inorganic hybrid composite materials. Their diverse binary combinations offer a versatile platform for designing energy transfer pathway and introducing emerging optical phenomena, making them promising candidates for developing the next-generation of RTP materials. However, currently reported red RTP halide perovskites are scarce and often suffer from low quantum efficiency and short lifetime. Herein, we developed a series of 2D hybrid halide perovskites with efficient red RTP through doping manganese ions and found that the modified materials exhibit a significantly enhanced photoluminescence quantum yield of 66.38%, which is eight times higher than that of the original perovskite host. Moreover, the phosphorescence lifetime can be extended up to 12 ms. In-depth mechanistic investigations reveal that the exceptional luminescent performance originates from efficient energy transfer be-tween the host matrix and manganese ions. Furthermore, red-emitting LEDs have been successfully fabricated with these RTP materials as emitting layers, highlighting the promising applications of 2D hybrid halide perovskites in lighting applications.</p>","PeriodicalId":12421,"journal":{"name":"Frontiers in Chemistry","volume":"13 ","pages":"1533513"},"PeriodicalIF":3.8,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11968679/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143794888","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":"Investigating the use of low and high-density polyethylene blends with waste material from three-layer factory tube for the third layer of shock tubes.","authors":"Ali Khalili Gashtroudkhani, Mohammad Dahmardeh Ghaleno, Saeed Soltan Abadi, Maryam Pouyani","doi":"10.3389/fchem.2025.1545984","DOIUrl":"10.3389/fchem.2025.1545984","url":null,"abstract":"<p><p>Polymeric shock tubes are now widely used in explosives systems for drilling and mining operations. Most shock tubes on the market consist of three layers of polymer, the first layer being Surlyn 8940 copolymer, the second layer Nucrel 31001 and the outer layer Borostar ME 6053 medium density polyethylene. Surlyn and Nucrel are usually sourced from DuPont, polyethylene from Charlotte Boralis. the main goal in this research is reducing the price of final shock tube and reuse the waste tube of plant (rejected shock tube) with improving the properties of product. For reaching to this goal, using polyethylene blend with available raw materials in the country and mixing them with rework from the shock tube production plant. For this purpose, different proportions of low- and high-Density polyethylene are blend using a twin-screw extruder and finally mixed with some of the factory's polymer rework. In the first phase, the low-density polyethylene LDPE 020, the high-density polyethylene HDPE HI 0500 and the filler calcium carbonate were blend in a twin-screw extruder and compounded with different percentages of 20/75/5, 30/65/5, 40/55/5 and 47/47/6 percent respectively. In the second phase, the resulting blend was mixed physically with 5, 10 and 15 percent three-layer tube rework (which was crushed with a crusher or pelletizer). The results showed that the 47/47/6 percent mixture had the best composition in terms of the production process, the properties of blend in terms of tensile strength (17/3 MPa), elongation percentage (458%) was suitable. In order to reduce the waste and cost of the product, the best processing results, product properties and costs are obtained when the above composition is mixed with crushed shock tube rework in a ratio of 90/10 (blend/rework). Tensile strength at break was 20/01 MPa and elongation at break was 478%. After evaluating the raw materials and accepting the results, the polymer blends were used on an industrial scale to produce shock tubes. The performance of the resulting shock tubes was then compared using various tests, including mechanical tests, oil penetration resistance, thermal shrinkage (in 60°C: upper 7% and in 80°C: upper 9%), burst strength, thermal aging (before aging:170 N, after aging: N₅, N₆, N₇, N₈: upper 170 N), and explosion velocity (upper 1890 m/s). The results showed that by using the polymer blend with rework, the mechanical properties of the shock tubes produced met the standard (tensile strength of more than 170 N/m² and elongation percentage of more than 220). The results of the oil penetration resistance (45-50 h), burst strength and aging tests also showed that all shock tubes manufactured with the new third layer had acceptable properties and were on the same level as shock tubes made of Boralis polyethylene.</p>","PeriodicalId":12421,"journal":{"name":"Frontiers in Chemistry","volume":"13 ","pages":"1545984"},"PeriodicalIF":3.8,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11961897/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143771923","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":"Illegal and falsified medicines self-administrated in not approved post-cycle therapy after the cessation of anabolic-androgenic steroids - qualitative analysis.","authors":"Agata Blazewicz, Magdalena Poplawska, Beata Daniszewska, Karolina Piorunska, Michal Karynski","doi":"10.3389/fchem.2025.1536858","DOIUrl":"10.3389/fchem.2025.1536858","url":null,"abstract":"<p><strong>Background: </strong>The term post-cycle therapy (PCT) often appears in bodybuilding forums in the context of anabolic-androgenic steroids (AAS) cessation. To reduce the negative impact of AAS on the hormonal system, unapproved PCT is used, which consist of medications that help restore hormonal balance. The most used medicinal products are selective estrogen receptor modulators (SERMs), aromatase inhibitors (AIs), and preparations containing human chorionic gonadotropin (hCG). These substances are prohibited in sports by the World Anti-Doping Agency.</p><p><strong>Methods: </strong>Between January 2020 and the end of August 2024, 601 samples seized by the police and prosecutor's office from the illegal market, intended for use as performance-enhancing drugs (PEDs), were tested at the Polish Official Medicines Control Laboratory. Samples were analyzed using accredited methods, including liquid chromatography coupled with high-resolution hybrid mass spectrometry and X-ray powder diffraction, to estimate PCT drug prevalence among other PED samples. In total, 411 (68.4%) samples declaring to contain AAS, 63 (10.5%) declaring to contain substances used in PCT, and 127 (21.1%) other PEDs were tested.</p><p><strong>Results: </strong>Among the PCT drug samples, 33.3%, 25.4%, and 41.3% indicated the presence of SERMs (tamoxifen and clomiphene), AIs (anastrozole, letrozole, and exemestane), and other substances (hCG, cabergoline, and mesterolone), respectively according to the label. However, not all samples were consistent with the declarations. In 65.1% of the samples, the declared active pharmaceutical ingredients (APIs) were present, whereas in 34.9%, they were not. Furthermore, among the samples in which the declared API was found, 58.7% contained only the declared API, while 6.4% included an additional undeclared API. Conversely, among the samples without the declared API, 20.6% contained neither a declared API nor any API, while 14.3% had other undeclared APIs.</p><p><strong>Conclusion: </strong>We have shown that illicit drugs used in PCT may be substituted, adulterated, or contain no active ingredients. Our results indicate that in view of the high prevalence of illicit AAS use, the self-administration of unapproved PCT using illegal and falsified medicines is dangerous and can be considered a potential threat to consumer health.</p>","PeriodicalId":12421,"journal":{"name":"Frontiers in Chemistry","volume":"13 ","pages":"1536858"},"PeriodicalIF":3.8,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11962791/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143771922","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":"Iron ore pellets based-Ag₂O nanoparticles as efficient Bi-functional heterogeneous catalyst for the synthesis tetrahydrobenzo[α]xanthens in green media.","authors":"Ehsan Faryabi, Enayatollah Sheikhhosseini, Mahdieh Yahyazadehfar","doi":"10.3389/fchem.2025.1413080","DOIUrl":"10.3389/fchem.2025.1413080","url":null,"abstract":"<p><p>Through the use of a microwave, iron ore pellets (IOP)-based Ag₂O nanoparticles were successfully synthesized. They were then characterized by means of a vibrating sample magnetometer (VSM), Brunauer-Emmett-Teller (BET) surface area analysis, energy-dispersive X-ray (EDX) analysis, powder X-ray diffraction (XRD) analysis, EDX elemental mapping, and field emission scanning electron microscopy (FESEM). High quantities of tetrahydrobenzo[a]xanthen derivatives were obtained in a brief amount of time by the newly prepared nanocomposite, known as Ag₂O NP@IOP, in a one-pot, three-component reaction involving different aryl aldehydes, naphthol, and dimedone. There is no appreciable loss of catalytic activity when the catalyst is recycled and utilized several times, and it can be easily retrieved using an external magnet. The reason for functionality of designed hybrid catalyst can be related to textural properties such as desirable specific surface area and significant porosity as well as the structural nature of the Ag₂O NP@IOP catalyst.</p>","PeriodicalId":12421,"journal":{"name":"Frontiers in Chemistry","volume":"13 ","pages":"1413080"},"PeriodicalIF":3.8,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11962902/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143771924","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":"DNA delivery into plant tissues using carbon dots made from citric acid and β-alanine.","authors":"Kuber Shivashakarappa, Sureshbabu Marriboina, Zeinab Yadegari, Vikas Reddy Paduri, Ritesh Sachan, Korsi Dumenyo, Ali Taheri","doi":"10.3389/fchem.2025.1542504","DOIUrl":"10.3389/fchem.2025.1542504","url":null,"abstract":"<p><p>Agriculture and food security face significant challenges due to population growth, climate change, and biotic and abiotic stresses. Enhancing crop productivity and quality through biotechnology is crucial in addressing these challenges. Genome engineering techniques, including gene cassette delivery into plant cells, aim to meet these demands. However, conventional biomolecule delivery methods have limitations such as poor efficacy, low regeneration capability, and potential cell damage. Nanoparticles, known for their success in drug delivery in animals, hold promise as DNA nanocarriers in plant sciences. This study explores the efficacy of carbon dots (CDs), synthesized rapidly and cost-effectively from citric acid monohydrate and β-alanine using a microwave-assisted method, as carriers for plasmid DNA delivery into plant tissues. The detailed characterization of carbon dots, evaluation of their binding ability with plasmid DNA, and phytotoxicity assessments were systematically conducted. The delivery and expression of plasmid DNA were successfully demonstrated in canola leaves via needleless syringe infiltration and in soybean root cells and protoplasts through passive diffusion. Additionally, the particle bombardment method facilitated the efficient delivery of plasmid DNA of varying sizes (4 kb, 11 kb, and 17 kb) into onion epidermal cells, as well as the successful delivery of plasmid DNA containing the GUS reporter gene into soybean embryos, using carbon dots as a binding agent between plasmid DNA and tungsten microcarrier. To our knowledge, this is the first study to report the use of carbon dots as a substitute for spermidine in such applications. Overall, our research presents a rapidly synthesized, cost-effective platform for efficient plasmid DNA delivery, establishing a foundation for using carbon dots as carriers for CRISPR and RNAi constructs in gene knockout and knockdown applications in plant tissues, with a comparison of their transformation efficiency against traditional delivery techniques.</p>","PeriodicalId":12421,"journal":{"name":"Frontiers in Chemistry","volume":"13 ","pages":"1542504"},"PeriodicalIF":3.8,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11961904/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143771921","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":"Development of the TSR-based computational method to investigate spike and monoclonal antibody interactions.","authors":"Tarikul I Milon, Titli Sarkar, Yixin Chen, Jordan M Grider, Feng Chen, Jun-Yuan Ji, Seetharama D Jois, Konstantin G Kousoulas, Vijay Raghavan, Wu Xu","doi":"10.3389/fchem.2025.1395374","DOIUrl":"10.3389/fchem.2025.1395374","url":null,"abstract":"<p><strong>Introduction: </strong>Monoclonal antibody (mAb) drug treatments have proven effective in reducing COVID-19-related hospitalizations or fatalities, particularly among high-risk patients. Numerous experimental studies have explored the structures of spike proteins and their complexes with ACE2 or mAbs. These 3D structures provide crucial insights into the interactions between spike proteins and ACE2 or mAb, forming a basis for the development of diagnostic tools and therapeutics. However, the field of computational biology has faced substantial challenges due to the lack of methods for precise protein structural comparisons and accurate prediction of molecular interactions. In our previous studies, we introduced the Triangular Spatial Relationship (TSR)-based algorithm, which represents a protein's 3D structure using a vector of integers (keys). These earlier studies, however, were limited to individual proteins.</p><p><strong>Purpose: </strong>This study introduces new extensions of the TSR-based algorithm, enhancing its ability to study interactions between two molecules. We apply these extensions to gain a mechanistic understanding of spike - mAb interactions.</p><p><strong>Method: </strong>We expanded the basic TSR method in three novel ways: (1) TSR keys encompassing all atoms, (2) cross keys for interactions between two molecules, and (3) intra-residual keys for amino acids. This TSR-based representation of 3D structures offers a unique advantage by simplifying the search for similar substructures within structural datasets.</p><p><strong>Results: </strong>The study's key findings include: (i) The method effectively quantified and interpreted conformational changes and steric effects using the newly introduced TSR keys. (ii) Six clusters for CDRH3 and three clusters for CDRL3 were identified using all-atom keys. (iii) We constructed the TSR-STRSUM (TSR-STRucture SUbstitution Matrix), a matrix that represents pairwise similarities between amino acid structures, providing valuable applications in protein sequence and structure comparison. (iv) Intra-residual keys revealed two distinct Tyr clusters characterized by specific triangle geometries.</p><p><strong>Conclusion: </strong>This study presents an advanced computational approach that not only quantifies and interprets conformational changes in protein backbones, entire structures, or individual amino acids, but also facilitates the search for substructures induced by molecular binding across protein datasets. In some instances, a direct correlation between structures and functions was successfully established.</p>","PeriodicalId":12421,"journal":{"name":"Frontiers in Chemistry","volume":"13 ","pages":"1395374"},"PeriodicalIF":3.8,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11962798/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143771920","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}