Journal of Biomolecular Structure & Dynamics最新文献

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Conformational variants of the ternary complex of C5a, C5aR1, and G-protein. C5a、C5aR1 和 G 蛋白三元复合物的构象变异。
IF 2.7 3区 生物学
Journal of Biomolecular Structure & Dynamics Pub Date : 2025-07-01 Epub Date: 2024-01-21 DOI: 10.1080/07391102.2024.2305698
Pulkit Kr Gupta, Aditi Singh, Soumendra Rana
{"title":"Conformational variants of the ternary complex of C5a, C5aR1, and G-protein.","authors":"Pulkit Kr Gupta, Aditi Singh, Soumendra Rana","doi":"10.1080/07391102.2024.2305698","DOIUrl":"10.1080/07391102.2024.2305698","url":null,"abstract":"<p><p>The complement component fragment 5a (C5a) binds and activates two complement receptors like C5aR1 and C5aR2, which play a significant role in orchestrating the proinflammatory function of C5a in tissues through the recruitment of heterotrimeric G-proteins and β-arrestins. Dysregulation of the complement induces excessive production of C5a, which triggers aberrant activation of the C5a-C5aR1-G-protein and C5a-C5aR2-β-arrestin signalling axes in tissues, contributing to the pathology of numerous immune-inflammatory diseases. Thus, understanding the interaction of C5a with C5aR1 and C5aR2, as well as the interaction of G-protein and β-arrestins, respectively, with C5a-C5aR1 and C5a-C5aR2, holds tremendous therapeutic value. In the absence of structural data, we have previously elaborated the binary complexes of C5a-C5aR1 and C5a-C5aR2, as well as the ternary complex of C5a-C5aR2-β-arrestin1, in highly refined model structures. While our ternary model complex of C5a-C5aR1-G-protein was in progress, two cryo-electron microscopy-based ternary structural complexes of C5aR1 were made available by others. However, it is observed that the interaction of the crucial NT-peptide of C5aR1 with C5a, including the portion of the G⍺<sub>i</sub>-subunit that harbors the switch-I region, is not fully resolved in both complexes. The current study addresses the issues and provides two highly refined alternative model ternary complexes of C5a-C5aR1-G-protein. The study highlights the conformational heterogeneity in C5aR1 by comparing the two conformational variants of the model ternary complex in the context of C5a-C5aR2-β-arrestin1 for further devising methods and molecules targeting both surface and intracellular C5aR1/C5aR2 for effectively mitigating the proinflammatory role of C5a in various disease settings.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"4885-4900"},"PeriodicalIF":2.7,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139511787","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Rational design for novel heterocyclic based Donepezil analogs for Alzheimer's disease: an in silico approach. 治疗阿尔茨海默病的新型杂环类多奈哌齐类似物的合理设计:一种硅学方法。
IF 2.7 3区 生物学
Journal of Biomolecular Structure & Dynamics Pub Date : 2025-07-01 Epub Date: 2024-01-23 DOI: 10.1080/07391102.2024.2306200
Sunandini Swain, Anik Sen, Atanu K Metya
{"title":"Rational design for novel heterocyclic based Donepezil analogs for Alzheimer's disease: an in silico approach.","authors":"Sunandini Swain, Anik Sen, Atanu K Metya","doi":"10.1080/07391102.2024.2306200","DOIUrl":"10.1080/07391102.2024.2306200","url":null,"abstract":"<p><p>Alzheimer's disease (AD) is a progressive neurodegenerative disease and has devastating impacts on the elderly population. During the last two decades, there has been a significant focus on developing effective and safe treatments for AD. Acetylcholinesterase (AChE) has been identified as one of the primary therapeutic targets for developing drug candidates for AD. However, there is still a need for more efficient therapies. In this study, our aim is to design a new series of heterocyclic-based AChE inhibitors inspired by a standard drug. Here, we carried out molecular docking, drug-likeliness characteristics, and molecular dynamics (MD) to predict important pharmacophore features and understand the inhibitory mechanism of the designed inhibitors towards the AChE. We have designed 112 new derivatives by replacing the piperidine moiety of Donepezil with the different five and six-membered heterocyclic rings and selected 15 compounds that show higher or comparable docking scores as compared to standard Donepezil and pose no risk for carcinogenicity. Furthermore, MD results imply the structural stability of the selected docked complexes and seven exhibit a stronger binding affinity towards the AChE than Donepezil. Thus, heterocyclic-based derivatives based on oxazole, pyrazole, and tetrahydropyran may be potential therapeutic candidates for AD. Our structure-based drug design approach allows us to identify and gain insight into the structural stability of the inhibitor-protein complex and the inhibition mechanism of the newly designed inhibitors. The present finding might be an initial selection for developing a new inhibitor for AD and provide a direction for further experiments on its biological activities.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"4985-4996"},"PeriodicalIF":2.7,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139521127","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Targeting PDE4A for therapeutic potential: exploiting drug repurposing approach through virtual screening and molecular dynamics. 针对 PDE4A 的治疗潜力:通过虚拟筛选和分子动力学利用药物再利用方法。
IF 2.7 3区 生物学
Journal of Biomolecular Structure & Dynamics Pub Date : 2025-07-01 Epub Date: 2024-01-29 DOI: 10.1080/07391102.2024.2308764
Anas Shamsi, Mohd Shahnawaz Khan, Nojood Altwaijry, Nageeb Hassan, Moyad Shahwan, Dharmendra Kumar Yadav
{"title":"Targeting PDE4A for therapeutic potential: exploiting drug repurposing approach through virtual screening and molecular dynamics.","authors":"Anas Shamsi, Mohd Shahnawaz Khan, Nojood Altwaijry, Nageeb Hassan, Moyad Shahwan, Dharmendra Kumar Yadav","doi":"10.1080/07391102.2024.2308764","DOIUrl":"10.1080/07391102.2024.2308764","url":null,"abstract":"<p><p>cAMP-specific 3',5'-cyclic phosphodiesterase 4 A (PDE4A) holds a pivotal role in modulating intracellular levels of cyclic adenosine monophosphate (cAMP). Targeting PDE4A with novel therapeutic agents shows promise in addressing neurological disorders (e.g. Alzheimer's and Parkinson's diseases), mood disorders (depression, anxiety), inflammatory conditions (asthma, chronic obstructive pulmonary disease), and even cancer. In this study, we present a comprehensive approach that integrates virtual screening and molecular dynamics (MD) simulations to identify potential inhibitors of PDE4A from the existing pool of FDA-approved drugs. The initial compound selection was conducted focusing on binding affinity scores, which led to the identification of several high-affinity compounds with potential PDE4A binding properties. From the refined selection process, two promising compounds, Fluspirilene and Dihydroergocristine, emerged as strong candidates, displaying substantial affinity and specificity for the PDE4A binding site. Interaction analysis provided robust evidence of their binding capabilities. To gain deeper insights into the dynamic behavior of Fluspirilene and Dihydroergocristine in complex with PDE4A, we conducted 300 ns MD simulations, principal components analysis (PCA), and free energy landscape (FEL) analysis. These analyses revealed that Fluspirilene and Dihydroergocristine binding stabilized the PDE4A structure and induced minimal conformational changes, highlighting their potential as potent binders. In conclusion, our study systematically explores repurposing existing FDA-approved drugs as PDE4A inhibitors through a comprehensive virtual screening pipeline. The identified compounds, Fluspirilene and Dihydroergocristine, exhibit a strong affinity for PDE4A, displaying characteristics that support their suitability for further development as potential therapeutic agents for conditions associated with PDE4A dysfunction.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"5423-5435"},"PeriodicalIF":2.7,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139575889","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Investigation of natural compounds as methyltransferase inhibitors against dengue virus: an in silico approach. 研究作为登革热病毒甲基转移酶抑制剂的天然化合物:一种硅学方法。
IF 2.7 3区 生物学
Journal of Biomolecular Structure & Dynamics Pub Date : 2025-07-01 Epub Date: 2024-01-30 DOI: 10.1080/07391102.2024.2309647
Mohd Imran, Abida, Nawaf M Alotaibi, Hamdy Khamees Thabet, Jamal Alhameedi Alruwaili, Lina Eltaib, Ahmed Alshehri, Mehnaz Kamal
{"title":"Investigation of natural compounds as methyltransferase inhibitors against dengue virus: an <i>in silico</i> approach.","authors":"Mohd Imran, Abida, Nawaf M Alotaibi, Hamdy Khamees Thabet, Jamal Alhameedi Alruwaili, Lina Eltaib, Ahmed Alshehri, Mehnaz Kamal","doi":"10.1080/07391102.2024.2309647","DOIUrl":"10.1080/07391102.2024.2309647","url":null,"abstract":"<p><p>The global challenge posed by Dengue virus (DENV) infection persists, exacerbated by the absence of specific antiviral therapies. The viral methyltransferase (MTase) enzyme, crucial for viral RNA methylation and immune system evasion, has emerged as a promising drug target for combating Dengue fever. In this study, a comprehensive exploration of natural compounds derived from the COCONUT database was conducted, selecting 224 compounds based on their structural similarity to the native substrate of the MTase enzyme, S-adenosyl-L-methionine (SAM). Employing virtual screening techniques, four natural compounds (CNP0307160, CNP0082902, CNP0449158, and CNP0296775) with acceptable docking scores were selected for further re-docking after geometry optimization by the DFT method. Re-docking analyses unveiled significant interactions, including hydrogen bonds and hydrophobic interactions, between these selected ligands and the MTase protein. To gain deeper insights into the dynamic stability of these complexes, we conducted molecular dynamics simulations which showed lower RMSD values for CNP0307160, CNP0082902, and CNP0296775 when compared to the reference molecule. Furthermore, we assessed the structural and dynamic stability of the protein-ligand complexes through free binding energy calculations and Principal Component Analysis (PCA) of the simulation trajectories. In these analyses, the CNP0296775 compound exhibited promising results compared to the other three compounds. The cumulative findings of these investigations underscore the potential of CNP0296775 as a strong inhibitor of DENV MTase, thus offering a promising starting point for its further experimental validation and optimization.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"5577-5592"},"PeriodicalIF":2.7,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139575827","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A close-up shot of protein-protein docking, from experiment to theory and reverse with the PROTAC performers. 从实验到理论,再到使用 PROTAC 执行器进行反向操作的蛋白质-蛋白质对接特写镜头。
IF 2.7 3区 生物学
Journal of Biomolecular Structure & Dynamics Pub Date : 2025-07-01 Epub Date: 2024-01-29 DOI: 10.1080/07391102.2024.2308778
Khanh Quynh Thi Nguyen, Hieu Hien Nguyen, Huong Thi Thu Phung, Khanh Linh Chung, Thien Y Vu
{"title":"A close-up shot of protein-protein docking, from experiment to theory and reverse with the PROTAC performers.","authors":"Khanh Quynh Thi Nguyen, Hieu Hien Nguyen, Huong Thi Thu Phung, Khanh Linh Chung, Thien Y Vu","doi":"10.1080/07391102.2024.2308778","DOIUrl":"10.1080/07391102.2024.2308778","url":null,"abstract":"<p><p>PROTACs (Proteolysis Targeting Chimeras), heterobifunctional molecules, exhibit selectivity in degrading target proteins through E3 ubiquitin ligases. Designing effective PROTACs requires a deep understanding of the intricate binding interactions in the ternary complex (POI/PROTAC/E3 ligase), crucial for efficient target protein degradation. To address this challenge, we introduce a novel computational virtual screening method that considers essential amino acid interactions between the protein of interest and the chosen E3 ligase. This approach enhances accuracy and reliability, facilitating the strategic development of potent PROTACs. Utilizing a crystallized model of the VHL:PROTAC:SMARCA2<sup>BD</sup> ternary complex (PDB: 7Z6L), we assessed the effectiveness of our method. Our study reveals that increasing the number of essential restraints between the two proteins reduces the generated docking poses, leading to closer alignment with the experimental ternary complex. Specifically, utilizing three restraints showed the closest resemblance to the published complex, highlighting crucial interactions such as an H-bond between A:Gln 89 and B:Asn 67, along with two hydrophobic interactions: A:Gly 22 with B:Arg 69 and A:Glu 37 with B:Pro 99. This resulted in a significant decrease in the mean RMSD value from 31.8 and 31.0 Å to 24.4 Å, respectively. This underscores the importance of incorporating multiple essential restraints to enhance docking accuracy. Building on this progress, we introduce a systematic approach to design potential PROTACs between the Estrogen receptor and the E3 ligase, utilizing bridging intermediates with 4, 6, or 7 carbon atoms. By providing a more accurate and efficient means of identifying optimal PROTAC candidates, this approach has the potential to accelerate the development of targeted therapies and reduce the time and costs associated with drug discovery.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"5260-5267"},"PeriodicalIF":2.7,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139569998","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A comprehensive integrated gene network construction to explore the essential role of Notch 1 in lung adenocarcinoma (LUAD). 构建全面整合的基因网络,探索 Notch 1 在肺腺癌(LUAD)中的重要作用。
IF 2.7 3区 生物学
Journal of Biomolecular Structure & Dynamics Pub Date : 2025-07-01 Epub Date: 2024-01-28 DOI: 10.1080/07391102.2024.2306501
Pearl John, C Sudandiradoss
{"title":"A comprehensive integrated gene network construction to explore the essential role of Notch 1 in lung adenocarcinoma (LUAD).","authors":"Pearl John, C Sudandiradoss","doi":"10.1080/07391102.2024.2306501","DOIUrl":"10.1080/07391102.2024.2306501","url":null,"abstract":"<p><p>The heterogeneous biological landscape of non-small cell lung cancer (NSCLC) is largely attributed to the activation of Notch signalling pathway. Among the Notch family transmembrane proteins, neurogenic locus notch homolog protein1 (NOTCH1) is a putative oncogene in NSCLC which activates the pathway as negative prognostic factor. This study aims to explore integrated network approach in lung adenocarcinoma (LUAD) especially linked to the notch pathway and its receptors. Our gene set enrichment analysis reveals the key Notch pathway genes are predominantly down regulated in LUAD. There were 675 genes with a total of 6517 functional interactions and 6 densely connected clusters of 38 miRNAs, 84 transcription factors with 156 edges identified through network construction. Here we report five key genes namely NOTCH1, CDH1, ERBB2, GAPDH and COL1A1 significantly enriched in Notch pathway which are further validated through the KM plot, box plots, stage plots and TIMER analysis. In addition, the NOTCH1 receptor is strongly linked to the immune checkpoint inhibitor CD274 (PD-L1) and can be considered as prognostic marker and tumour suppressor gene in LUAD which surely provide the basis for early diagnosis and futuristic immunotherapeutic targets for LUAD.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"5097-5109"},"PeriodicalIF":2.7,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139570000","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Molecular dynamics of α-helix inside a protein with single helix. 单螺旋蛋白质内部α-螺旋的分子动力学。
IF 2.7 3区 生物学
Journal of Biomolecular Structure & Dynamics Pub Date : 2025-07-01 Epub Date: 2024-01-30 DOI: 10.1080/07391102.2024.2308755
Y N Chirgadze, I V Likhachev, N K Balabaev, E V Brazhnikov
{"title":"Molecular dynamics of α-helix inside a protein with single helix.","authors":"Y N Chirgadze, I V Likhachev, N K Balabaev, E V Brazhnikov","doi":"10.1080/07391102.2024.2308755","DOIUrl":"10.1080/07391102.2024.2308755","url":null,"abstract":"","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"5290-5295"},"PeriodicalIF":2.7,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139575777","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
2,4,6-Trimethoxy chalcone derivatives: an integrated study for redesigning novel chemical entities as anticancer agents through QSAR, molecular docking, ADMET prediction, and computational simulation. 2,4,6-三甲氧基查尔酮衍生物:通过QSAR、分子对接、ADMET预测和计算模拟重新设计作为抗癌剂的新型化学实体的综合研究。
IF 2.7 3区 生物学
Journal of Biomolecular Structure & Dynamics Pub Date : 2025-07-01 Epub Date: 2024-02-07 DOI: 10.1080/07391102.2024.2309644
Trupti S Chitre, Aayush M Mandot, Ramali D Bhagwat, Nikhil D Londhe, Atharva R Suryawanshi, Purvaj V Hirode, Aniket L Bhatambrekar, Somdutta Y Choudhari
{"title":"2,4,6-Trimethoxy chalcone derivatives: an integrated study for redesigning novel chemical entities as anticancer agents through QSAR, molecular docking, ADMET prediction, and computational simulation.","authors":"Trupti S Chitre, Aayush M Mandot, Ramali D Bhagwat, Nikhil D Londhe, Atharva R Suryawanshi, Purvaj V Hirode, Aniket L Bhatambrekar, Somdutta Y Choudhari","doi":"10.1080/07391102.2024.2309644","DOIUrl":"10.1080/07391102.2024.2309644","url":null,"abstract":"<p><p>QSAR, an efficient and successful approach for optimizing lead compounds in drug design, was employed to study a reported series of compounds derived from 2,4,6-trimethoxy chalcone derivatives. The ability of these compounds to inhibit CDK1 was examined, with the help of QSARINS software for model development. The generated QSAR model revealed three significant descriptors, exhibiting strong correlations with impressive statistical values: cross-validation leave-one-out correlation coefficient (<i>Q</i><sup>2</sup>LOO) = 0.6663, coefficient of determination (<i>R</i><sup>2</sup>) = 0.7863, external validation coefficient (<i>R</i><sup>2</sup><sub>ext</sub>) = 0.7854, cross-validation leave-many-out correlation coefficient (<i>Q</i><sup>2</sup>LMO) = 0.6256, Concordance Correlation Coefficient for cross-validation (CCC<sub>cv</sub>) = 0.8150, CCC<sub>tr</sub> = 0.8804, and CCC<sub>ext</sub> = 0.8750. From the key structural findings and the insights gained from the descriptors, ETA_dPsi_A, WTPT-5, and GATS7s, new lead molecules were designed. The designed molecules were then evaluated for their CDK1 inhibitory activity using the three-descriptor model developed in this study. To evaluate their drug likeliness, <i>in-silico</i> ADMET predictions were made using Schrodinger's Software. Molecular docking was carried out to determine the interactions of designed compounds with the target protein. The designed compounds having excellent binding pocket molecular stability and anticancer effectiveness was substantiated by the findings of the molecular dynamics simulation. The results of this work point out important properties and crucial interactions necessary for efficient protein inhibition, suggesting lead candidates for further development as novel anticancer agents.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"5512-5535"},"PeriodicalIF":2.7,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139697569","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Development of a highly sensitive fluorescent probe using Delonix regia (Gulmohar) tree pod shell for precise sarcosine detection in human urine samples: advancing prostate cancer diagnosis. 利用 Delonix regia(Gulmohar)树荚壳开发高灵敏度荧光探针,用于精确检测人体尿液样本中的肌氨酸:推进前列腺癌诊断。
IF 2.7 3区 生物学
Journal of Biomolecular Structure & Dynamics Pub Date : 2025-07-01 Epub Date: 2024-01-23 DOI: 10.1080/07391102.2024.2306196
Mustafa Zeyadi, Komal G Chaudhari, Pravin O Patil, Fahad A Al-Abbasi, Naif A R Almalki, May M Alqurashi, Imran Kazmi, Shaktipal Patil, Zamir G Khan
{"title":"Development of a highly sensitive fluorescent probe using <i>Delonix regia</i> (Gulmohar) tree pod shell for precise sarcosine detection in human urine samples: advancing prostate cancer diagnosis.","authors":"Mustafa Zeyadi, Komal G Chaudhari, Pravin O Patil, Fahad A Al-Abbasi, Naif A R Almalki, May M Alqurashi, Imran Kazmi, Shaktipal Patil, Zamir G Khan","doi":"10.1080/07391102.2024.2306196","DOIUrl":"10.1080/07391102.2024.2306196","url":null,"abstract":"<p><p>We designed a highly sensitive fluorescent sensor for the early detection of sarcosine, a potential biomarker for prostate cancer. This sensor was based on surface-cobalt-doped fluorescent carbon quantum dots (Co-CD) using a FRET-based photoluminescent sensing platform. Blue luminescent carbon quantum dots (CQD) were synthesised through a hydrothermal approach, utilizing <i>Delonix regia</i> tree pod shells. Cobalt was employed to functionalize the CQD, enhancing the quantum-entrapped effects and minimizing surface flaws. To optimize Co-CD preparation, we employed a Box-Behnken design (BBD), and response surface methodology (RSM) based on single-factor experiments. The Co-CD was then used as a fluorescent probe for selective Cu<sup>2+</sup> detection, with Cu<sup>2+</sup> quenching Co-CD fluorescence through an energy transfer process, referred to as 'turn-off'. When sarcosine was introduced, the fluorescence intensity of Co-CD was restored, creating a 'turn-on' response. The sensor exhibited a Cu<sup>2+</sup> detection limit (LOD) of 2.4 µM with a linear range of 0 μM to 10 µM. The sarcosine detection in phosphate buffer saline (PBS, pH 7.4) resulted in an LOD of 1.54 μM and a linear range of 0 to 10 µM. Importantly, the sensor demonstrated its suitability for clinical analysis by detecting sarcosine in human urine. In summary, our rapid and highly sensitive sensor offers a novel approach for the detection of sarcosine in real samples, facilitating early prostate cancer diagnosis.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"4928-4941"},"PeriodicalIF":2.7,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139521090","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
epi-Magnolin, a tetrahydrofurofuranoid lignan from the oleo-gum resin of Commiphora wightii, as inhibitor of pancreatic cancer cell proliferation, in-vitro and in-silico study. 作为胰腺癌细胞增殖抑制剂的表马格诺林(epi-Magnolin)的体外和体内研究
IF 2.7 3区 生物学
Journal of Biomolecular Structure & Dynamics Pub Date : 2025-07-01 Epub Date: 2024-01-24 DOI: 10.1080/07391102.2024.2308767
Mohamed H Abd El-Razek, Ibrahim H Eissa, Ahmed A Al-Karmalawy, Ahmed A Elrashedy, Ahmed H El-Desoky, Mohamed Aboelmagd, Tarik A Mohamed, Mohamed-Elamir F Hegazy
{"title":"<i>epi</i>-Magnolin, a tetrahydrofurofuranoid lignan from the oleo-gum resin of <i>Commiphora wightii</i>, as inhibitor of pancreatic cancer cell proliferation, <i>in-vitro</i> and <i>in-silico</i> study.","authors":"Mohamed H Abd El-Razek, Ibrahim H Eissa, Ahmed A Al-Karmalawy, Ahmed A Elrashedy, Ahmed H El-Desoky, Mohamed Aboelmagd, Tarik A Mohamed, Mohamed-Elamir F Hegazy","doi":"10.1080/07391102.2024.2308767","DOIUrl":"10.1080/07391102.2024.2308767","url":null,"abstract":"<p><p>Five known furofuran lignans, <i>dia</i>-sesamin (<b>1</b>), 5-methoxysesamin (<b>2</b>), <i>epi</i>-magnolin (<b>3</b>), kobusin (<b>4</b>) and yangambin (<b>5</b>) were isolated for the first-time from the oleo-gum resin of <i>Commiphora wightii</i>. This is the first report on the <sup>13</sup>C NMR assignments for <i>epi</i>-magnolin (<b>3</b>). Each of the isolated compounds was evaluated for its ability to inhibit MIA PaCa-2 pancreatic cancer cell line. Among them, <i>epi</i>-magnolin (<b>3</b>) displayed potential activity (IC<sub>50</sub> = 29 nM) compared to colchicine (IC<sub>50</sub> = 56 nM). 3D-flexible alignment revealed that <i>epi</i>-magnolin (<b>3</b>) has great matching with the tubulin polymerization inhibitor, colchicine. Meanwhile, docking studies exhibited that compounds <b>1</b>-<b>5</b> displayed good binding free energies against colchicine binding site (CBS) of tubulin with binding modes that were highly comparable to that of colchicine. Compounds <b>2</b>, <b>3</b>, and <b>5</b> showed superior binding free energies than colchicine (-24.37 kcal/mol). <i>epi</i>-Magnolin (<b>3</b>) showed the highest binding score against CBS. MD simulation studies confirmed the stability of <i>epi</i>-magnolin (<b>3</b>) in the active site for 200 ns. Furthermore, four online servers (Swiss ADME, pkCSM pharmacokinetics, AdmetSAR, and ProTox-II) were utilized to predict the ADMET parameters. The <i>in-silico</i> pharmacokinetics predictions reveled that <i>epi</i>-magnolin (<b>3</b>) has significant oral bioavailability and drug-like capabilities.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"5151-5163"},"PeriodicalIF":2.7,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139546491","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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