Journal of molecular graphics & modelling最新文献_第7页

Oxo-triaryl methyl (oxTAM) as targeted drug delivery vehicle for fludarabine and cytarabine anticancer drugs: A first-principles insight 氧三芳基甲基（oxTAM）作为氟达拉滨和阿糖胞苷抗癌药物的靶向药物递送载体：第一线原理的见解。

IF 3 4区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

Journal of molecular graphics & modelling

Pub Date : 2025-11-12 DOI: 10.1016/j.jmgm.2025.109224

Misbah Asif , Tariq Mahmood , Mazhar Amjad Gilani , Nadeem S. Sheikh , Imene Bayach , Khurshid Ayub

The design and development of efficient and responsive drug carriers always remain a challenge in targeted cancer treatment, where the traditional nanocarriers suffer the drawbacks of limited stability, a lack of selectivity, and slow release of the drug. In this perspective, the oxygenated triaryl methyl (oxTAM) nanocarrier is known for its tunability, and redox activity offers a promising alternative. In the present work, we hypothesize that the oxTAM carrier can function as an efficient and effective drug carrier for selected anticancer drugs like Fludarabine (Flu) and Cytarabine (Cyt) due to its ability to make stable noncovalent interactions and release of drugs in acidic conditions. The potential application of oxTAM as drug carrier is explored by using ωB97XD/6-31+G(d,p) functional. The interaction in energy analysis (E_int) and interacting distances (E_dis) reveal that oxTAM shows excellent interaction for Flu (−1.77 eV, 1.92 Å) drug. Non-covalent interaction index (NCI) indicates the existence of van der Waals interaction and hydrogen bonding (O—H bond) between the interacting moieties. The results of dipole moment and quantum chemical descriptors show the high reactivities of oxTAM for Flu and Cyt drugs. Electronic analysis including natural bond orbital (NBO) charge transfer demonstrates the higher response of Flu drug towards oxTAM. In addition, the reduced adsorption stability upon protonation in an acidic environment can quickly release drug molecules from the carrier. Short recovery time indicates easy drug delivery at the targeted site. From all these results, we concluded that oxTAM can be a potential candidate for further experimental exploration in drug delivery systems.

设计和开发高效、反应性强的药物载体一直是肿瘤靶向治疗中的一个挑战，传统的纳米载体存在稳定性有限、缺乏选择性、药物释放缓慢等缺点。从这个角度来看，氧化三芳基甲基（oxTAM）纳米载体以其可调性而闻名，氧化还原活性提供了一个有希望的替代方案。在目前的工作中，我们假设oxTAM载体可以作为一种高效的药物载体，用于某些抗癌药物，如氟达拉滨（Flu）和阿糖胞苷（Cyt），因为它能够在酸性条件下进行稳定的非共价相互作用和药物释放。通过ωB97XD/6-31+G（d,p）泛函探讨了oxTAM作为药物载体的潜在应用。相互作用能量分析（Eint）和相互作用距离（Edis）表明，oxTAM对流感药物具有良好的相互作用（-1.77 eV, 1.92 Å）。非共价相互作用指数（NCI）表明相互作用基团之间存在范德华相互作用和氢键（O-H键）。偶极矩和量子化学描述子的结果表明，oxTAM对流感和细胞药物具有较高的反应性。包括自然键轨道（NBO）电荷转移在内的电子分析表明，流感药物对oxTAM有更高的响应。此外，在酸性环境中质子化后的吸附稳定性降低，可以迅速从载体中释放药物分子。恢复时间短表明药物容易到达目标部位。综上所述，我们认为oxTAM有潜力在给药系统中进行进一步的实验探索。

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引用次数: 0

Mechanistic exploration of IGF2BP3-mediated m6A dynamics in diabetic retinopathy for therapeutic interventions through in silico approaches igf2bp3介导的m6A动态在糖尿病视网膜病变治疗干预中的机制探索

IF 3 4区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

Journal of molecular graphics & modelling

Pub Date : 2025-11-11 DOI: 10.1016/j.jmgm.2025.109222

Hemavathy Nagarajan , Nishath Fathima Majid , Sharada Ramasubramanyan , Sampathkumar Ranganathan

Insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3) is a crucial post-transcriptional regulator in mRNA localization, stability, and translation. While IGF2BP3 overexpression is widely studied in cancer, recent evidence highlights its role in diabetic retinopathy (DR), a significant cause of blindness. In DR, IGF2BP3 regulates pro-angiogenic and pro-inflammatory factors, such as VEGF, contributing to retinal vascular damage, neovascularization, and inflammation. These effects make IGF2BP3 a potential therapeutic target for DR. Henceforth, in this study, high-throughput virtual screening (HTVS) and molecular dynamics (MD) simulations were implemented to identify potential IGF2BP3 inhibitors, focusing on its KH3 and KH4 RNA-binding domains. The KH4 domain was selected as the optimal target with a higher druggability score. HTVS of the ChemDiv database identified three promising candidates: Y040–1954, C200-9224, and 1761-0723, which showed strong interactions with the GXXG motif within the KH4 domain, critical for RNA binding. Density Functional Theory (DFT) and molecular docking analysis confirmed these candidates' reactivity and binding affinity to IGF2BP3. MD simulations conducted over 200 ns showed that IGF2BP3-inhibitor complexes retained structural stability with consistent hydrogen bonding, particularly involving key residues Ser624, Ser627, and Thr628. These findings suggest that the identified compounds could disrupt IGF2BP3's interaction with m6A-modified RNA, potentially blocking its role in stabilizing pro-angiogenic and pro-inflammatory mRNAs in DR. With experimental validation and optimization, these compounds could significantly advance the treatment landscape for DR, offering hope for better outcomes in this leading cause of blindness.

胰岛素样生长因子2 mRNA结合蛋白3 （IGF2BP3）是mRNA定位、稳定和翻译的关键转录后调节因子。虽然IGF2BP3过表达在癌症中被广泛研究，但最近的证据强调了它在糖尿病视网膜病变（DR）中的作用，这是导致失明的重要原因。在DR中，IGF2BP3调节促血管生成和促炎症因子，如VEGF，促进视网膜血管损伤、新生血管和炎症。这些作用使IGF2BP3成为dr的潜在治疗靶点。因此，本研究采用高通量虚拟筛选（HTVS）和分子动力学（MD）模拟来鉴定潜在的IGF2BP3抑制剂，重点关注其KH3和KH4 rna结合域。KH4结构域被选为最佳靶点，具有较高的致药性评分。ChemDiv数据库的HTVS确定了三个有希望的候选者：Y040-1954， C200-9224和1761-0723，它们与KH4结构域内的GXXG基序具有强相互作用，对RNA结合至关重要。密度泛函理论（DFT）和分子对接分析证实了这些候选物与IGF2BP3的反应性和结合亲和力。超过200 ns的MD模拟表明，igf2bp3抑制剂复合物保持结构稳定性，具有一致的氢键，特别是涉及关键残基Ser624、Ser627和Thr628。这些发现表明，所鉴定的化合物可能会破坏IGF2BP3与m6a修饰RNA的相互作用，潜在地阻断其在DR中稳定促血管生成和促炎症mrna的作用。通过实验验证和优化，这些化合物可能会显著推进DR的治疗前景，为这一主要致盲原因带来更好的结果。

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引用次数: 0

In silico investigation of the efficacy of benzopyrazine derivatives on breast cancer by VEGFR2 inhibition using ML/DL based CADD software 基于ML/DL的CADD软件对苯并吡嗪衍生物对乳腺癌VEGFR2抑制作用的计算机研究

IF 3 4区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

Journal of molecular graphics & modelling

Pub Date : 2025-11-10 DOI: 10.1016/j.jmgm.2025.109219

İrem Bozbey Merde , Okan Aykaç , Ceylan Hepokur , Muzammil Kabi̇er , Ahmet Buğra Ortaakarsu

Angiogenesis is a critical pathway for cancer; The formation of new blood vessels is essential for the growth and metastasis of tumors. VEGF and its receptor VEGFR also play important roles in angiogenesis. VEGFR2 stands out as an important therapeutic target for breast cancer treatment. In this study, the interaction between benzopyrazine derivatives and VEGFR2 was evaluated using computer-based drug design (CADD) models, bioinformatics analyses and complementary computational methods. Biological activity predictions were made by developing the interaction data of 49 benzopyrazine-derived compounds in a virtual environment and by developing a QSAR model. Binding stability of proteins in newly designed structures was demonstrated with molecular dynamics simulations. ADMET predictions reveal that these tables have appropriate pharmacokinetic metabolism. Synthesizability of compounds with the best docking scores was calculated with artificial intelligence using the Retroscheme software. For compound number 46, which has the highest potential, molecular dynamics simulation data for 500 ns were calculated via the Desmond interface and its binding was interpreted. The study particularly shows that compound 46 may be an effective VEGFR2 inhibitor in the treatment of breast cancer.

血管生成是癌症的关键途径；新血管的形成对肿瘤的生长和转移至关重要。VEGF及其受体VEGFR在血管生成中也起重要作用。VEGFR2是乳腺癌治疗的重要靶点。本研究采用计算机药物设计（CADD）模型、生物信息学分析和互补计算方法评估苯并吡嗪衍生物与VEGFR2之间的相互作用。通过在虚拟环境中开发49种苯并吡嗪衍生化合物的相互作用数据并建立QSAR模型进行生物活性预测。通过分子动力学模拟证明了蛋白质在新设计结构中的结合稳定性。ADMET预测显示这些表具有适当的药代动力学代谢。利用Retroscheme软件，人工智能计算对接得分最高的化合物的可合成性。对于势最高的化合物46，通过Desmond界面计算了500 ns的分子动力学模拟数据，并对其结合进行了解释。该研究特别表明，化合物46可能是治疗乳腺癌的有效VEGFR2抑制剂。

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引用次数: 0

The first study of the organic solvents influence on the organo-halides compounds using a new theoretical approach of solvation properties 首次采用新的溶剂化性质理论方法研究了有机溶剂对有机卤化物化合物的影响。

IF 3 4区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

Journal of molecular graphics & modelling

Pub Date : 2025-11-08 DOI: 10.1016/j.jmgm.2025.109218

Ali Harchani

A first study of the organic solvents influence on the organo-halides such as chloromercurate, chlorostannate and chlorocadmate compounds by using a new theoretical method was reported in the present work. A lot of discussions concerning the solvation properties, sorption, adsorption simulation and blends mixing analysis have been presented in this paper to show the interesting role of the organic solvents and their impact in the chemistry of the organo-metal halides and organo-mercuric halides compounds. The results of chemical calculations leads to conclude that solvents such as water, dimethyl sulfoxide, acetonitrile, ethanol, methylene chloride and diethyl ether are very important for the solvation and chemical synthesis of the title compounds but to varying degrees.

本文首次用一种新的理论方法研究了有机溶剂对氯汞酸盐、氯锡酸盐和氯酸盐等有机卤化物的影响。本文就有机溶剂的溶剂化性质、吸附、吸附模拟和共混物混合分析等方面进行了大量的讨论，以表明有机溶剂在有机金属卤化物和有机汞卤化物化合物的化学反应中的重要作用及其影响。化学计算结果表明，水、二甲亚砜、乙腈、乙醇、二氯甲烷和乙醚等溶剂对上述化合物的溶剂化和化学合成非常重要，但程度不同。

引用次数: 0

Enhancing predictive modeling with XGBoost-engineered probabilities and deep neural networks: A hybrid approach for building reliable kinase inhibition QSAR models 利用xgboost工程概率和深度神经网络增强预测建模：建立可靠的激酶抑制QSAR模型的混合方法。

IF 3 4区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

Journal of molecular graphics & modelling

Pub Date : 2025-11-08 DOI: 10.1016/j.jmgm.2025.109216

Mohamed Oussama Mousser , Brahim Matougui , Fouad Chafaa , Mohamed Abdesselem Dems

Novel antineoplastic therapies focus on the inhibition of various protein kinases, creating an important need for new molecules capable of regulating their abnormal activity. Here, we introduce a specific hybrid Machine Learning (ML) architecture that combines an eXtreme Gradient Boosting (XGBoost) as a base model, and a deep neural network (DNN) to improve prediction accuracy in kinase inhibition QSARs. The approach utilizes XGBoost to process structured data features, while employing the DNN to refine and calibrate the probability estimates. The predictive probabilities from XGBoost are incorporated as new input features for a DNN to enhance classification performance. For the prediction of kinase inhibition, 40 reliable QSAR models were trained on large datasets (559–5675 compounds and

\sim

400–500 descriptors). As a result, the approach achieved a marked improvement in accuracy and robustness compared to the standalone XGBoost algorithm and various descriptors-based state-of-the-art methods, including Random Forest (RF) and Support Vector Machine (SVM). The accuracy enhancement reaches up to 14% for JAK2, BRAF and TRK-

α

, 13% for VEGFR2 and PIK3C

δ

, and ranges between 5 and 12% for 30 other kinase datasets. Performance is thus analyzed through the discussion of several evaluation metrics. The proposed method will be useful for building accurate prediction models, either specific to the neoplastic drug design or QSAR modeling in general. Models constructed in this study are available at GitHub.

新的抗肿瘤疗法集中于抑制各种蛋白激酶，这就产生了对能够调节其异常活性的新分子的重要需求。在这里，我们介绍了一种特定的混合机器学习（ML）架构，该架构结合了极端梯度增强（XGBoost）作为基础模型，以及深度神经网络（DNN）来提高激酶抑制QSARs的预测准确性。该方法利用XGBoost来处理结构化数据特征，同时使用DNN来改进和校准概率估计。来自XGBoost的预测概率被纳入DNN的新输入特征，以提高分类性能。为了预测激酶抑制，在大型数据集（559-5675个化合物和~ 400-500个描述符）上训练了40个可靠的QSAR模型。因此，与独立的XGBoost算法和各种基于描述符的最先进方法（包括随机森林（RF）和支持向量机（SVM））相比，该方法在准确性和鲁棒性方面取得了显着改善。JAK2、BRAF和TRK-α的准确性提高了14%，VEGFR2和PIK3Cδ的准确性提高了13%，其他30个激酶数据集的准确性提高了5%至12%。因此，通过对几个评估指标的讨论来分析性能。所提出的方法将有助于建立准确的预测模型，无论是针对肿瘤药物设计还是一般的QSAR建模。本研究中构建的模型可以在GitHub上获得。

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引用次数: 0

Photophysical and photochemical reactivity of 1,4-dihydropyrazine derivatives: A theoretical investigation using DFT and TDDFT 1,4-二氢吡嗪衍生物的光物理和光化学反应性：用DFT和TDDFT的理论研究。

IF 3 4区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

Journal of molecular graphics & modelling

Pub Date : 2025-11-08 DOI: 10.1016/j.jmgm.2025.109213

Changwei Ge , Haojing Li , Chaochun Wei , Xiaokun Zhang , Hong Yan

Eleven 1,4-dihydropyrazine derivatives were selected for theoretical investigation into the structural effects on photophysical properties and photochemical reactivity using Density Functional Theory (DFT) and Time-Dependent Density Functional Theory (TDDFT). They are divided into three distinct Series (1–3), each characterized by a unique substitution pattern: Series 1 features different acyl groups attached to the N,N′ - positions of the 1,4-dihydropyrazine ring; Series 2 includes various substituents on the 1,4-dihydropyrazine ring itself; and Series 3 combines modifications on both the nitrogen atoms and the 1,4-dihydropyrazine ring. All ground-state geometries were optimized at the M06-2XD3/def2-TZVP level to ensure structural stability, and vibrational frequency analysis was performed to confirm the absence of imaginary frequencies. Simulated ultraviolet–visible (UV–Vis) absorption spectra were used to characterize the electronic excitation behavior. Molecular orbital diagrams (HOMO–1, HOMO, LUMO, and LUMO+1) corresponding to the first singlet excited-state (S₁) were analyzed to elucidate the property of the electronic transitions. Electron-hole analysis was applied to qualitatively assess the direction of charge transfer upon excitation. Additionally, the electron localization function (ELF) was calculated to evaluate how substituents and conjugation affect electron distribution within the molecule. The root-mean-square deviation (RMSD) between the excited-state and ground-state geometries was also calculated to quantify structural changes induced by excitation. Collectively, these analyses provide valuable insights into how structural modifications affect the photophysical properties of 1,4-dihydropyrazines and their subsequent photochemical reactivity. All the findings are intended to provide theoretical basis for understanding the experimental observations related to the photocycloaddition reactions of 1,4-dihydropyrazines.

采用密度泛函理论（DFT）和时变密度泛函理论（TDDFT）对11个1,4-二氢吡嗪衍生物的光物理性质和光化学反应性的结构效应进行了理论研究。它们被分为三个不同的系列（1-3），每个系列都具有独特的取代模式：系列1的特征是不同的酰基连接到1,4-二氢吡嗪环的N，N' -位置；系列2包括1,4-二氢吡嗪环上的各种取代基；系列3结合了氮原子和1,4-二氢吡嗪环的修饰。在M06-2XD3/def2-TZVP水平上对所有基态几何形状进行了优化，以确保结构稳定性，并进行了振动频率分析以确认不存在虚频率。利用模拟紫外-可见（UV-Vis）吸收光谱来表征电子激发行为。分析了第一单重态激发态（S1）对应的分子轨道图（HOMO-1、HOMO、LUMO和LUMO+1），阐明了电子跃迁的性质。利用电子-空穴分析定性地评价了激发后电荷转移的方向。此外，计算了电子定位函数（ELF）来评估取代基和共轭作用如何影响分子内的电子分布。还计算了激发态和基态几何形状之间的均方根偏差（RMSD），以量化激发引起的结构变化。总的来说，这些分析为结构修饰如何影响1,4-二氢吡嗪的光物理性质及其随后的光化学反应性提供了有价值的见解。这些发现旨在为理解1,4-二氢吡嗪的光环加成反应的实验观察提供理论依据。

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引用次数: 0

In-silico identification of a Doxorubicin alternative with reduced cardiotoxicity informed by LLM-assisted modeling 通过llm辅助建模，降低心脏毒性的阿霉素替代品的硅鉴定。

IF 3 4区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

Journal of molecular graphics & modelling

Pub Date : 2025-11-08 DOI: 10.1016/j.jmgm.2025.109217

Debojyoti Das , Debdutta Chakraborty

Anthracyclines such as doxorubicin are potent anticancer agents but suffer from cardiotoxicity and poor clearance. We developed a hybrid pipeline integrating docking (2375 runs), molecular dynamics, and a large language model (LLM) to predict ADME/ADMET properties. Ligand-2 (CHEMBL1514139) showed strong affinity for UGT1A9 (−11.4 kcal/mol) and minimal interaction with topoisomerase IIβ. MD simulations confirmed stable binding. LLM-based regression predicted favorable ADME properties, including R² = 0.840 for clearance and R² > 0.89 for BBB and absorption. hERG II inhibition was classified using a random forest (RF) model, achieving 92 % accuracy and an R² score of 91 %. Model interpretability was further achieved using Shapley Additive Explanations (SHAP), which identified key molecular descriptors influencing pharmacokinetic and toxicity predictions. Ligand-2 demonstrated comparable or improved pharmacokinetics versus doxorubicin, supporting its potential as a safer anthracycline analog.

蒽环类药物如阿霉素是有效的抗癌药物，但有心脏毒性和清除率差。我们开发了一个集成对接（2375次运行）、分子动力学和大语言模型（LLM）的混合管道来预测ADME/ADMET的性质。配体-2 （CHEMBL1514139）对UGT1A9具有较强的亲和力（-11.4 kcal/mol），与拓扑异构酶i - β的相互作用最小。MD模拟证实了稳定的结合。基于llm的回归预测了良好的ADME性能，其中清除R2 = 0.840， BBB和吸收R2 = 0.89。使用随机森林（RF）模型对hERG II抑制进行分类，准确率为92%，R2评分为91%。使用Shapley加性解释（SHAP）进一步实现了模型的可解释性，该解释确定了影响药代动力学和毒性预测的关键分子描述符。配体-2表现出与阿霉素相当或改善的药代动力学，支持其作为更安全的蒽环类药物类似物的潜力。

引用次数: 0

Structural preferences and multiple bonding interactions in hetero-closo-dodecaborates of group-14 elements – A theoretical study 14族元素杂合十二烷基化合物的结构偏好和多键相互作用的理论研究。

IF 3 4区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

Journal of molecular graphics & modelling

Pub Date : 2025-11-05 DOI: 10.1016/j.jmgm.2025.109214

Brindha Veerappan, Krishnamoorthy Bellie Sundaram

The geometric and electronic structural features of group-14 hetero-closo-dodecaborates such as monomers [HEB₁₁H₁₁]^-, [EB₁₁H₁₁]^2- [E = C (1a), Si (2a), Ge (3a), Sn (4a) and Pb (5a)] and dimers [(EB₁₁H₁₁)₂]^2- [E = C (1), Si (2), Ge (3), Sn (4) and Pb (5)] analyzed using density functional theory (DFT) method at BP86/Def2-TZVP level of theory. The structural features such as the geometry, metrical parameters and bonding interactions are theoretically studied. The dispersion correction method has been used to get more insight which improves the metrical parameter of group-14 elements towards experimental parameters. The electronic structure of the clusters has been studied using frontier molecular orbital analysis (FMO). It shows the group-14 elements electronic contribution and possible electron delocalization between the cages to stabilize the dimeric clusters. DFT (BP86/Def2-TZVP) calculations on the clusters confirm the thermal stability of the newly modelled dimeric clusters (2–5) which could have diverse applications. The ¹³C, ¹H, ²⁹Si, and ¹¹B nmr chemical shift values computed at DFT (BP86/Def2-TZVP) level are highly useful in identifying and assigning the individual atoms of the monomeric and dimeric clusters. From the global reactivity descriptors and local descriptors analysis, an identification of reactive sites with respect to electrophilic and nucleophilic centers of the reactant has been reported.

采用密度泛函（DFT）方法在BP86/Def2-TZVP理论水平上分析了14族杂合十二硼酸盐单体[HEB11H11]-、[EB11H11]2- [E = C （1a）、Si （2a）、Ge （3a）、Sn （4a）、Pb (5a)]和二聚体[(EB11H11)2]2- [E = C(1)、Si(2)、Ge(3)、Sn(4)、Pb(5)]的几何和电子结构特征。从理论上研究了复合材料的几何形状、几何参数和键合作用等结构特征。利用色散校正方法使14族元素的测量参数与实验参数有了更深入的了解。利用前沿分子轨道分析（FMO）研究了簇的电子结构。它显示了14族元素的电子贡献和笼间可能的电子离域，以稳定二聚体簇。DFT （BP86/Def2-TZVP）计算证实了新模型二聚体簇的热稳定性（2-5），可以有多种应用。在DFT （BP86/Def2-TZVP）水平上计算的13C， 1H， 29Si和11B核磁共振化学位移值对于识别和分配单体和二聚体簇的单个原子非常有用。从全局反应性描述符和局部描述符分析中，已经报道了与反应物的亲电和亲核中心有关的反应位点的鉴定。

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引用次数: 0

Modification of graphenylene nanostructure as a promising material for adsorption and sensing of 5-fluorouracil: First-principles investigations 改性石墨烯纳米结构作为一种有前途的5-氟尿嘧啶吸附和传感材料：第一性原理研究。

IF 3 4区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

Journal of molecular graphics & modelling

Pub Date : 2025-11-01 DOI: 10.1016/j.jmgm.2025.109210

Ali B.M. Ali , A.A. Abdulazez , G. Padma Priya , Subhashree Ray , Amrita Pal , Renu Sharma , Sulton Usanov , Zukhra Atamuratova , Elyor Saitov , Aseel Smerat , Mohammad Y. Alshahrani

Studies aimed at developing materials with high efficacy for detecting the anticancer drug 5-fluorouracil (5FUL) are considered essential for both environmental protection and human health. However, practical utilization of such materials requires overcoming several challenges. In this study, the adhesion behavior of 5FUL on graphenylene (GrNL), a two-dimensional carbon nanostructure, as well as on Al-modified GrNL (Al@GrNL), was investigated using density functional theory (DFT) calculations. For Al@GrNL, various adhesion sites and distances from the GrNL nanosheet were thoroughly examined. The electronic and structural properties, adhesion energies, bandgap values, and adhesion energies of different complexes were analyzed and discussed in detail. The results indicate that the six-ring site (H2) is the most favorable adhesion site for the Al atom. Adhesion energy analysis reveals a strong interaction between 5FUL molecules and Al@GrNL (Ead = −1.253 eV), whereas the interaction with pure GrNL is relatively weak. Furthermore, Al@GrNL exhibits high sensitivity to 5FUL, as evidenced by significant changes in electrical conductance and magnetic properties upon adhesion. These DFT calculations provide valuable insights into the potential of Al@GrNL as an effective chemical sensor for 5FUL detection.

开发高效检测抗癌药物5-氟尿嘧啶（5-fluorouracil, 5FUL）的材料，对环境保护和人类健康都至关重要。然而，这些材料的实际利用需要克服几个挑战。在本研究中，利用密度泛函理论（DFT）计算研究了5FUL在二维碳纳米结构石墨烯（GrNL）以及al修饰的GrNL （Al@GrNL）上的粘附行为。对于Al@GrNL，各种粘附位点和距离GrNL纳米片被彻底检查。详细分析和讨论了不同配合物的电子和结构特性、粘附能、带隙值和粘附能。结果表明，六环位（H2）是Al原子最有利的粘附位。粘附能分析表明5FUL分子与Al@GrNL之间的相互作用较强（Ead = -1.253 eV），而与纯GrNL的相互作用相对较弱。此外，Al@GrNL对5FUL表现出很高的敏感性，这可以通过粘附后电导率和磁性能的显著变化来证明。这些DFT计算为Al@GrNL作为5FUL检测的有效化学传感器的潜力提供了有价值的见解。

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引用次数: 0

In silico investigation of molecular mechanisms underlying the function of NLuc and its variants NLuc及其变体功能的分子机制的计算机研究。

IF 3 4区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

Journal of molecular graphics & modelling

Pub Date : 2025-11-01 DOI: 10.1016/j.jmgm.2025.109212

Mina Oliayi, Rahman Emamzadeh, Mohamad Reza Ganjalikhany

Bioluminescence, the emission of light by living organisms, results from chemiluminescent reactions facilitated by enzymes like luciferases. Among these, NanoLuc (NLuc) stands out due to its exceptional brightness, stability, and compact structure, making it a valuable tool in bioassays and imaging applications. NLuc is a 19.1 kDa monomeric enzyme derived from the deep-sea shrimp Oplophorus gracilirostris. Its structure comprises eleven antiparallel β-strands forming a β-barrel, capped by four α-helices. To enhance its versatility, NLuc has been engineered into split forms. Despite the advancements in split NLuc applications, several impediments exist that can be addressed to improve these systems. Recently the spectacular allosteric mechanisms of NLuc has been reported. Based on that, the enzyme exhibits homotropic negative allostery, where product binding to an allosteric site inhibits substrate binding at the catalytic site. Ongoing research into its structural dynamics and allosteric behaviors continues to expand its potential applications, while efforts to enhance the efficiency of its split forms aim to broaden its utility in complex biological assays. In this in silico assay, we performed dynamic simulations for both the various forms of apo-NLuc and the docking complex with the substrate and product. As a result, we clarify the sources of malfunctions in split NLuc and explore various aspects of split NLuc technologies. We also examine some hypotheses of NLuc mechanisms that display the complex behavior of this luciferase.

生物发光是生物体发出的光，是由荧光素酶等酶促进的化学发光反应产生的。其中，NanoLuc （NLuc）因其卓越的亮度，稳定性和紧凑的结构而脱颖而出，使其成为生物分析和成像应用中的宝贵工具。NLuc是一种19.1 kDa的单体酶，来源于深海虾Oplophorus gracilirostris。它的结构包括11个反平行的β链，形成一个β桶，顶部有4个α-螺旋。为了增强其通用性，NLuc被设计成分裂的形式。尽管分离式NLuc应用取得了进步，但仍存在一些可以解决的障碍来改进这些系统。近年来，NLuc的变构机制得到了广泛的报道。基于此，酶表现出同向负变构，其中产物与变构位点的结合抑制了催化位点的底物结合。正在进行的对其结构动力学和变构行为的研究继续扩大其潜在的应用，同时努力提高其分裂形式的效率，旨在扩大其在复杂生物分析中的用途。在这个硅实验中，我们对各种形式的载脂蛋白nluc和对接配合物与底物和产物进行了动态模拟。因此，我们澄清了分裂NLuc故障的来源，并探讨了分裂NLuc技术的各个方面。我们还研究了NLuc机制的一些假设，这些机制显示了这种荧光素酶的复杂行为。

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引用次数: 0