Journal of Biomolecular Structure & Dynamics最新文献

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Structural investigation of vitamin K epoxide reductase domain-containing protein in Leptospira species: a potential target for the development of new leptospirosis treatments as an alternative to antibiotics. 钩端螺旋体中含维生素 K 环氧化物还原酶结构域蛋白的结构研究:开发可替代抗生素的新型钩端螺旋体病治疗方法的潜在目标。
IF 2.7 3区 生物学
Journal of Biomolecular Structure & Dynamics Pub Date : 2025-05-01 Epub Date: 2024-01-10 DOI: 10.1080/07391102.2024.2302925
Sionfoungo Daouda Soro, Virginie Lattard, Angeli Kodjo, Etienne Benoît, Nolan Chatron
{"title":"Structural investigation of vitamin K epoxide reductase domain-containing protein in <i>Leptospira</i> species: a potential target for the development of new leptospirosis treatments as an alternative to antibiotics.","authors":"Sionfoungo Daouda Soro, Virginie Lattard, Angeli Kodjo, Etienne Benoît, Nolan Chatron","doi":"10.1080/07391102.2024.2302925","DOIUrl":"10.1080/07391102.2024.2302925","url":null,"abstract":"<p><p>Leptospirosis is a worldwide zoonosis caused by the motile bacterium <i>Leptospira</i>. This disease can cause hemorrhagic symptoms, multi-visceral and renal failures, resulting in one million cases and approximately 60,000 deaths each year. The motility of <i>Leptospira</i> is highly involved in its virulence and is ensured by the presence of two flagella in the periplasm. Several proteins that require the formation of disulfide bridges are essential for flagellar function. In <i>Leptospira</i>, these redox reactions are catalysed by the vitamin K epoxide reductase domain-containing protein (VKORdcp). The aim of the present work was to study the conservation of VKORdcp among <i>Leptospira</i> species and its interactions with putative substrates and inhibitor. Our results evidenced the presence of ten amino acids specific to either pathogenic or saprophytic species. Furthermore, structural studies revealed a higher affinity of the enzyme for vitamin K1 quinone, compared to ubiquinone. Finally, characterisation of the binding of a potential inhibitor revealed the involvement of some VKORdcp amino acids that have not been present in the human enzyme, in particular the polar residue D114. Our study thus paves the way for the future development of <i>Leptospira</i> VKORdcp inhibitors, capable of blocking bacterial motility. Such molecules could therefore offer a promising therapeutic alternative to antibiotics, especially in the event of the emergence of antibiotic-resistant strains.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"4274-4286"},"PeriodicalIF":2.7,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139403048","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
Investigating the effects of four medicinal plants against dengue virus through QSAR modeling and molecular dynamics studies. 通过QSAR建模和分子动力学研究探讨四种药用植物对登革热病毒的作用
IF 2.7 3区 生物学
Journal of Biomolecular Structure & Dynamics Pub Date : 2025-05-01 Epub Date: 2024-01-10 DOI: 10.1080/07391102.2024.2301744
Faisal Alotaibi, Faris F Aba Alkhayl, Ahmed I Foudah, Mohammad Azhar Kamal, Ehssan H Moglad, Shamshir Khan, Zia Ur Rehman, Mohiuddin Khan Warsi, Talha Jawaid, Aftab Alam
{"title":"Investigating the effects of four medicinal plants against dengue virus through QSAR modeling and molecular dynamics studies.","authors":"Faisal Alotaibi, Faris F Aba Alkhayl, Ahmed I Foudah, Mohammad Azhar Kamal, Ehssan H Moglad, Shamshir Khan, Zia Ur Rehman, Mohiuddin Khan Warsi, Talha Jawaid, Aftab Alam","doi":"10.1080/07391102.2024.2301744","DOIUrl":"10.1080/07391102.2024.2301744","url":null,"abstract":"<p><p>The Dengue virus (DENV) has been increasingly recognized as a prevalent viral pathogen responsible for global transmission of infection. It has been established that DENV's NS5 methyltransferase (MTase) controls viral replication. As a result, NS5 MTase is considered a potentially useful drug target for DENV. In this study, the two phases of virtual screening were conducted using the ML-based QSAR model and molecular docking to identify potential compounds against NS5 of DENV. Four medicinal plants [<i>Aloe vera</i>, <i>Cannabis sativa</i> (Hemp), <i>Ocimum sanctum</i> (Holy Basil; Tulsi), and <i>Zingiber officinale</i> (Ginger)] that showed anti-viral properties were selected for sourcing the phytochemicals and screening them against NS5. Additionally, re-docking at higher exhaustiveness and interaction analysis were performed which resulted in the identification of the top four hits (<b>135398658</b>, <b>5281675</b>, <b>119394</b>, and <b>969516</b>) which showed comparable results with the control Sinefungin (SFG). Post molecular dynamics simulation, <b>135398658</b> showed the lowest RMSD (0.4-0.5 nm) and the maximum number of hydrogen bonds (eight hydrogen bonds) after the control while <b>5281675</b> and <b>969516</b> showed comparable hydrogen bonds to the control. These compounds showed direct interactions with the catalytic site residues GLU111 and ASP131, in addition to this these compounds showed stable complex formation as depicted by principal component analysis and free energy landscape. <b>135398658</b> showed lower total binding free energy (Δ<i>G</i><sub>Total</sub> = -36.56 kcal/mol) than the control, while <b>5281675</b> had comparable values to the control (Δ<i>G</i><sub>Total</sub> = -34.1 kcal/mol). Overall, the purpose of this study was to identify phytochemicals that inhibit NS5 function, that could be further tested experimentally to treat dengue virus (DENV).</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"4063-4080"},"PeriodicalIF":2.7,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139403045","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
Structural and functional analysis of engineered antibodies for cancer immunotherapy: insights into protein compactness and solvent accessibility. 用于癌症免疫疗法的工程抗体的结构和功能分析:对蛋白质致密性和溶剂可及性的见解。
IF 2.7 3区 生物学
Journal of Biomolecular Structure & Dynamics Pub Date : 2025-05-01 Epub Date: 2024-01-03 DOI: 10.1080/07391102.2023.2300129
Samvedna Saini, Yatender Kumar
{"title":"Structural and functional analysis of engineered antibodies for cancer immunotherapy: insights into protein compactness and solvent accessibility.","authors":"Samvedna Saini, Yatender Kumar","doi":"10.1080/07391102.2023.2300129","DOIUrl":"10.1080/07391102.2023.2300129","url":null,"abstract":"<p><p>Antibodies are crucial tools in various biomedical applications, including immunotherapy. In this study, we focused on designing and engineering antibodies to enhance their structural dynamics and functional properties. By employing advanced computational techniques and experimental validation, we gained crucial insights into the impact of specific mutations on the engineered antibodies. This study investigates the design and engineering of antibodies to improve their structural dynamics and functional properties. Structural attributes, such as protein compactness and solvent accessibility, were assessed, revealing interesting trends in anti-CD3 and anti-HER2 antibodies. Mutations in CD3 antibodies resulted in a more stable conformation, while mutant HER2 antibodies exhibited altered interaction with the target. Analysis of secondary structure assignments demonstrated significant changes in the folding and stability of the mutant antibodies compared to the wild-type counterparts. The conformational landscape of the engineered antibodies was explored, providing insights into folding pathways and binding mechanisms. Overall, the current study highlights the significance of antibody design and engineering in modulating structural dynamics and functional properties. The findings contribute to developing improved immunotherapeutic strategies by optimising antibody-based therapeutics for targeted diseases with enhanced efficacy and precision.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"3859-3872"},"PeriodicalIF":2.7,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139087024","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
Identification, characterization, and CADD analysis of Plasmodium DMAP1 reveals it as a potential molecular target for new anti-malarial discovery. 疟原虫 DMAP1 的鉴定、表征和 CADD 分析揭示了它是新抗疟药物发现的潜在分子靶标。
IF 2.7 3区 生物学
Journal of Biomolecular Structure & Dynamics Pub Date : 2025-05-01 Epub Date: 2024-01-12 DOI: 10.1080/07391102.2024.2302923
Merlyne Lawrence, Juhi Khurana, Ashish Gupta
{"title":"Identification, characterization, and CADD analysis of Plasmodium DMAP1 reveals it as a potential molecular target for new anti-malarial discovery.","authors":"Merlyne Lawrence, Juhi Khurana, Ashish Gupta","doi":"10.1080/07391102.2024.2302923","DOIUrl":"10.1080/07391102.2024.2302923","url":null,"abstract":"<p><p>Developing drug resistance in the malaria parasite is a reason for apprehension compelling the scientific community to focus on identifying new molecular targets that can be exploited for developing new anti-malarial compounds. Despite the availability of the <i>Plasmodium</i> genome, many protein-coding genes in <i>Plasmodium</i> are still not characterized or very less information is available about their functions. DMAP1 protein is known to be essential for growth and plays an important role in maintaining genomic integrity and transcriptional repression in vertebrate organisms. In this study, we have identified a homolog of DMAP1 in <i>P. falciparum</i>. Our sequence and structural analysis showed that although PfDMAP1 possesses a conserved SANT domain, parasite protein displays significant structural dissimilarities from human homolog at full-length protein level as well as within its SANT domain. PPIN analysis of PfDMAP1 revealed it to be vital for parasite and virtual High-throughput screening of various pharmacophore libraries using BIOVIA platform-identified compounds that pass ADMET profiling and showed specific binding with PfDMAP1. Based on MD simulations and protein-ligand interaction studies two best hits were identified that could be novel potent inhibitors of PfDMAP1 protein.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"4258-4273"},"PeriodicalIF":2.7,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139466531","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
Design, synthesis, molecular modeling, and biological evaluations of novel chalcone based 4-Nitroacetophenone derivatives as potent anticancer agents targeting EGFR-TKD. 新型查尔酮基 4-硝基苯乙酮衍生物作为靶向表皮生长因子受体-TKD 的强效抗癌剂的设计、合成、分子建模和生物学评价。
IF 2.7 3区 生物学
Journal of Biomolecular Structure & Dynamics Pub Date : 2025-05-01 Epub Date: 2024-01-28 DOI: 10.1080/07391102.2024.2301746
Showkat Ahmad Mir, Narayan Murmu, Rajesh Kumar Meher, Iswar Baitharu, Binata Nayak, Andleeb Khan, Mohammad Imran Khan, Wesam H Abdulaal
{"title":"Design, synthesis, molecular modeling, and biological evaluations of novel chalcone based 4-Nitroacetophenone derivatives as potent anticancer agents targeting EGFR-TKD.","authors":"Showkat Ahmad Mir, Narayan Murmu, Rajesh Kumar Meher, Iswar Baitharu, Binata Nayak, Andleeb Khan, Mohammad Imran Khan, Wesam H Abdulaal","doi":"10.1080/07391102.2024.2301746","DOIUrl":"10.1080/07391102.2024.2301746","url":null,"abstract":"<p><p>A series of chalcone-based 4-Nitroacetophenone derivatives were designed and synthesized by the single-step condensation method. These compounds were identified by <sup>1</sup>H NMR,<sup>13</sup>C NMR, MS, and FTIR analysis. Further, the derivatives were evaluated against four cancer cell lines H1299, MCF-7, HepG2, and K526. The IC<sub>50</sub> value of potent compounds NCH-2, NCH-4, NCH-5, NCH-6, NCH-8, and NCH-10 was 4.5-11.4 μM in H1299, 4.3-15.7 μM in MCF-7, 2.7-4.1 μM in HepG2 and 4.9-19.7 μM in K562. To assess the toxicity against healthy cells all potent molecules were evaluated against the HEK-293T cell line, and IC<sub>50</sub> values exhibited by NCH-2, and NCH-3 were 77.8, 74.3, and other molecules showed IC<sub>50</sub> values > 100 μM. The EGFR expression was determined by using rabbit anti-EGFR monoclonal antibody and significant EGFR expression was knocked down observed in H1299 treated with NCH-10 as well as erlotinib. The underlying mechanism behind cell death was investigated through bioinformatics. First, the molecules were optimized and docked to the binding site of the EGFR kinase domain. The best complexes were simulated for 100-ns and compounds NCH-2, NCH-4, and NCH-10 achieved stability similar to the erlotinib bound kinase domain. The free energy binding (Δ<i>G</i><sub>bind</sub>) of NCH-10 was found to be more negative -226.616 ± 2.148 kJ/mol calculated by Molecular Mechanics Poisson Boltzmann's Surface Area (MM-PBSA) method. Both <i>in vitro</i> and <i>in silico</i> results conclude that the present class of chalcone-based 4-Nitroacetophenone derivatives are potent anti-cancer agents targeting EGFR-TKD and are 39 folds more effective against H1299, MCF-7, HepG2, and K562 carcinoma cell lines than healthy HEK-293T cell lines.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"4095-4110"},"PeriodicalIF":2.7,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139570069","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
Antipyretic effects of Xiangqin Jiere granules on febrile young rats revealed by combining pharmacodynamics, metabolomics, network pharmacology, molecular biology experiments and molecular docking strategies. 结合药效学、代谢组学、网络药理学、分子生物学实验和分子对接策略揭示湘秦艽颗粒对发热幼鼠的解热作用
IF 2.7 3区 生物学
Journal of Biomolecular Structure & Dynamics Pub Date : 2025-05-01 Epub Date: 2024-01-10 DOI: 10.1080/07391102.2024.2301761
Xiying He, Jieqiong Cui, Huayan Li, Yang Zhou, Xinchen Wu, Chunrong Jiang, Zhichang Xu, Ruirui Wang, Lei Xiong
{"title":"Antipyretic effects of Xiangqin Jiere granules on febrile young rats revealed by combining pharmacodynamics, metabolomics, network pharmacology, molecular biology experiments and molecular docking strategies.","authors":"Xiying He, Jieqiong Cui, Huayan Li, Yang Zhou, Xinchen Wu, Chunrong Jiang, Zhichang Xu, Ruirui Wang, Lei Xiong","doi":"10.1080/07391102.2024.2301761","DOIUrl":"10.1080/07391102.2024.2301761","url":null,"abstract":"<p><p>Xiangqin Jiere granules (XQJRG) is a proprietary Chinese medicine treating children's colds and fevers, but its mechanism of action is unclear. The aim of this study was to explore the antipyretic mechanisms of XQJRG based on pharmacodynamics, non-targeted metabolomics, network pharmacology, molecular biology experiments, molecular docking, and molecular dynamics (MD) simulation. Firstly, the yeast-induced fever model was constructed in young rats to study antipyretic effect of XQJRG. Metabolomics and network pharmacology studies were performed to identify the key compounds, targets and pathways involved in the antipyretic of XQJRG. Subsequently, MetScape was used to jointly analyze targets from network pharmacology and metabolites from metabolomics. Finally, the key targets were validated by enzyme-linked immunosorbent assay (ELISA), and the affinity and stability of key ingredient and targets were evaluated by molecular docking and MD simulation. The animal experimental results showed that after XQJRG treatment, body temperature of febrile rats was significantly reduced, 13 metabolites were significantly modulated, and pathways of differential metabolite enrichment were mainly related to amino acid and lipid metabolism. Network pharmacology results indicated that quercetin and kaempferol were the key active components of XQJRG, <i>TNF</i>, <i>AKT1</i>, <i>IL6</i>, <i>IL1B</i> and <i>PTGS2</i> were core targets. ELISA confirmed that XQJRG significantly reduced the plasma concentrations of IL-1β, IL-6, and TNF-α, and the hypothalamic concentrations of COX-2 and PGE2. Molecular docking demonstrated that the binding energies of kaempferol to the core targets were all below -5.0 kcal/mol. MD simulation results showed that the binding free energies of TNF-kaempferol, IL6-kaempferol, IL1B-kaempferol and PTGS2-kaempferol were -87.86 kcal/mol, -70.41 kcal/mol, -69.95 kcal/mol and -106.67 kcal/mol, respectively. In conclusion, XQJRG has antipyretic effects on yeast-induced fever in young rats, and its antipyretic mechanisms may be related to the inhibition of peripheral pyrogenic cytokines release by constituents such as kaempferol, the reduction of hypothalamic fever mediator production, and the amelioration of disturbances in amino acid and lipid metabolism.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"4183-4200"},"PeriodicalIF":2.7,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139403027","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
Discovery of hematopoietic progenitor kinase 1 inhibitors using machine learning-based screening and free energy perturbation. 利用基于机器学习的筛选和自由能扰动发现造血祖细胞激酶 1 抑制剂。
IF 2.7 3区 生物学
Journal of Biomolecular Structure & Dynamics Pub Date : 2025-05-01 Epub Date: 2024-01-10 DOI: 10.1080/07391102.2024.2301754
Dazhi Feng, Bo Liu, Zhiwei Chen, Jinyi Xu, Meiyu Geng, Wenhu Duan, Jing Ai, Hefeng Zhang
{"title":"Discovery of hematopoietic progenitor kinase 1 inhibitors using machine learning-based screening and free energy perturbation.","authors":"Dazhi Feng, Bo Liu, Zhiwei Chen, Jinyi Xu, Meiyu Geng, Wenhu Duan, Jing Ai, Hefeng Zhang","doi":"10.1080/07391102.2024.2301754","DOIUrl":"10.1080/07391102.2024.2301754","url":null,"abstract":"<p><p>Hematopoietic progenitor kinase 1 (HPK1) is a key negative regulator of T-cell receptor (TCR) signaling and a promising target for cancer immunotherapy. The development of novel HPK1 inhibitors is challenging yet promising. In this study, we used a combination of machine learning (ML)-based virtual screening and free energy perturbation (FEP) calculations to identify novel HPK1 inhibitors. ML-based screening yielded 10 potent HPK1 inhibitors (IC<sub>50</sub> < 1 μM). The FEP-guided modification of the in-house false-positive hit, <b>DW21302</b>, revealed that a single key atom change could trigger activity cliffs. The resulting <b>DW21302-A</b> was a potent HPK1 inhibitor (IC<sub>50</sub> = 2.1 nM) and potently inhibited cellular HPK1 signaling and enhanced T-cell function. Molecular dynamics (MD) simulations and ADME predictions confirmed <b>DW21302-A</b> as candidate compound. This study provides new strategies and chemical scaffolds for HPK1 inhibitor development.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"4152-4164"},"PeriodicalIF":2.7,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139417200","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
Diphenolic boldine, an aporphine alkaloid: inhibitory effect evaluation on α-glucosidase by molecular dynamics integrating enzyme kinetics. 一种卟吩生物碱--二苯呋啶:通过分子动力学整合酶动力学评估对α-葡萄糖苷酶的抑制作用。
IF 2.7 3区 生物学
Journal of Biomolecular Structure & Dynamics Pub Date : 2025-05-01 Epub Date: 2024-01-08 DOI: 10.1080/07391102.2024.2301769
Yuexiu Si, Jiabo Zhu, Xia Xu, Yueyuan Xu, Jinhyuk Lee, Yong-Doo Park
{"title":"Diphenolic boldine, an aporphine alkaloid: inhibitory effect evaluation on α-glucosidase by molecular dynamics integrating enzyme kinetics.","authors":"Yuexiu Si, Jiabo Zhu, Xia Xu, Yueyuan Xu, Jinhyuk Lee, Yong-Doo Park","doi":"10.1080/07391102.2024.2301769","DOIUrl":"10.1080/07391102.2024.2301769","url":null,"abstract":"<p><p>Screening α-glucosidase inhibitors with novel structures is an important field in the development of anti-diabetic drugs due to their application in postprandial hyperglycemia control. Boldine is one of the potent natural antioxidants with a wide range of pharmacological activities. Virtual screening and biochemical inhibition kinetics combined with molecular dynamics simulations were conducted to verify the inactivation function of boldine on α-glucosidase. A series of inhibition kinetics and spectrometry detections were conducted to analyze the α-glucosidase inhibition. Computational simulations of molecular dynamics/docking analyses were conducted to detect boldine docking sites' details and evaluate the key binding residues. Boldine displayed a typical reversible and mixed-type inhibition manner. Measurements of circular dichroism and fluorescence spectrum showed boldine changed the secondary structure and loosened the tertiary conformation of target α-glucosidase. The computational molecular dynamics showed that boldine could block the active pocket site through close interaction with binding key residues, and two phenolic hydroxyl groups of boldine play a core function in α-glucosidase inhibition <i>via</i> ligand binding. This investigation reveals the boldine function on interaction with the α-glucosidase active site, which provides a new inhibitor candidate.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"4227-4239"},"PeriodicalIF":2.7,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139377684","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 phenanthroline-based erbium (III) complex: molecular docking, DNA/BSA -binding and biological evaluation. 基于菲罗啉的铒 (III) 复合物:分子对接、DNA/BSA 结合和生物学评价。
IF 2.7 3区 生物学
Journal of Biomolecular Structure & Dynamics Pub Date : 2025-05-01 Epub Date: 2024-01-04 DOI: 10.1080/07391102.2023.2300130
Faisal F Albaqami, Ameer S Sahib, Khalid M Alharthy, Ali Altharawi, Mohammad Y Alshahrani, Mohammed Abed Jawad, Muath Suliman, Irfan Ahmad
{"title":"A phenanthroline-based erbium (III) complex: molecular docking, DNA/BSA -binding and biological evaluation.","authors":"Faisal F Albaqami, Ameer S Sahib, Khalid M Alharthy, Ali Altharawi, Mohammad Y Alshahrani, Mohammed Abed Jawad, Muath Suliman, Irfan Ahmad","doi":"10.1080/07391102.2023.2300130","DOIUrl":"10.1080/07391102.2023.2300130","url":null,"abstract":"<p><p>With the help of both theoretical as well as experimental research, <i>in vitro</i> binding research with CT-DNA (calf thymus) and BSA (bovine serum albumin) were carefully examined to figure out the chemotherapeutic and pharmacokinetic facets of the Erbium complex, which contains 1,10-phenanthroline (Phen). The binding characteristics and the mechanism of complex's interaction with DNA as well as the protein were determined utilizing fluorescence quenching method. Findings indicated that the complex's interaction with DNA <i>via</i> groove binding into DNA's minor grooves, with their binding constants falling within the 10<sup>4</sup> M<sup>-1</sup> range. Furthermore, thermodynamic characteristics and the fluorescence emission of the tryptophan residues of the protein were obtained through fluorescence quenching studies at different temperatures. According to the results of the binding constants, the protein's interactions with the Er- complex were moderate, demonstrating that the compound may be transported effectively by the protein. Molecular docking results supported that of the experimental research. The HeLa and MCF-7 cancer cell lines, along with the normal human fibroblast cell line, were used in an MTT assay evaluation of the Er-complex cytotoxicity. The Er-complex displayed a selective inhibitory effect on the proliferation of different cancer cells.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"3873-3885"},"PeriodicalIF":2.7,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139087027","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
Assessing the potential of Psidium guajava derived phytoconstituents as anticholinesterase inhibitor to combat Alzheimer's disease: an in-silico and in-vitro approach. 评估从番石榴中提取的植物成分作为抗胆碱酯酶抑制剂防治阿尔茨海默氏症的潜力:一种体内和体外方法。
IF 2.7 3区 生物学
Journal of Biomolecular Structure & Dynamics Pub Date : 2025-05-01 Epub Date: 2024-01-11 DOI: 10.1080/07391102.2024.2301930
Kunal Bhattacharya, Atanu Bhattacharjee, Manodeep Chakraborty
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