Journal of molecular graphics & modelling最新文献_第9页

Comparison of electronic and magnetic properties of armchair and zigzag Ψ-graphene nanoribbons 扶手椅和之字形Ψ-graphene纳米带的电子和磁性比较

IF 3 4区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

Journal of molecular graphics & modelling

Pub Date : 2025-11-25 DOI: 10.1016/j.jmgm.2025.109232

Vahid Afsharnia, Ali Mohammad Yadollahi

This study investigates the effects of edge hydrogenation and length changes on the electronic and magnetic properties of armchair PSI (Ψ)-graphene nanoribbons (AΨGNRBs) and zigzag PSI (Ψ)- graphene nanoribbons (ZΨGNRBs) with changing the length and a repetition number from 1 to 10. Density Functional Theory (DFT) and Generalized Gradient Approximation (GGA-1/2) were used for this purpose. The Perdew-Burke-Ernzerhof (PBE) method was used to calculate the exchange-correlation energy. Results demonstrated that hydrogenation of AΨGNRBs causes a band gap of about 0.73 eV with slight changes due to the varied length of the nanoribbon (NRB), but with a constant value of 0.7366 in repetitions from 4 to 10. They are utilized in the fields of optoelectronics, photonics, LEDs, lasers, sensors, and photonic devices. This NRB is a non-magnetic N-type semiconductor. It is used in transistors, and quantum devices that require precise electronic (rather than spintronic) control. However, ZΨGNRBs with changing the length and a repetition number from 1 to 10 are non-magnetic conductors, and edge hydrogenation does not cause a band gap. These nanostructures are compatible with conventional electronic (non-spintronic) devices. The formation energy of hydrogen-passivated AΨGNRBs and ZΨGNRBs is lower than that of the non-passivated counterparts, indicating greater stability of the passivated NRBs. Moreover, the formation energy of AΨGNRBs from 1 to 10 repetitions is lower than that of ZΨGNRBs. This significant reduction in the formation energy indicates greater stability and a more optimal structure of AΨGNRBs compared to ZΨGNRBs. This issue is of critical importance in the design of nanomaterials.

本研究考察了边加氢和长度变化对扶手型PSI （Ψ）-石墨烯纳米带（AΨGNRBs）和之字形PSI （Ψ）-石墨烯纳米带（ZΨGNRBs）的电子和磁性能的影响，并改变了长度和重复次数从1到10。密度泛函理论（DFT）和广义梯度近似（GGA-1/2）用于此目的。采用PBE （Perdew-Burke-Ernzerhof）方法计算交换相关能。结果表明：AΨGNRBs加氢产生的带隙约为0.73 eV，且随着纳米带长度的变化而略有变化，但在4 ~ 10次重复中，带隙保持恒定值0.7366。它们被用于光电子、光子学、led、激光、传感器和光子器件等领域。该NRB是一种非磁性n型半导体。它被用于晶体管和需要精确电子（而不是自旋电子）控制的量子设备。但是，ZΨGNRBs改变长度和重复数从1到10是非磁性导体，边缘氢化不会引起带隙。这些纳米结构与传统的电子（非自旋电子）器件兼容。氢钝化后的AΨGNRBs和ZΨGNRBs的生成能比未钝化的低，表明钝化后的NRBs具有更大的稳定性。而且，AΨGNRBs在1 ~ 10次重复时的生成能低于ZΨGNRBs。地层能量的显著降低表明，与ZΨGNRBs相比，AΨGNRBs具有更高的稳定性和更优的结构。这个问题在纳米材料的设计中是至关重要的。

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引用次数: 0

Molecular dynamics insights into dimerization-dependent catalysis and thermal adaptation of mesophilic ketosteroid isomerase from Pseudomonas putida 恶臭假单胞菌嗜中温酮类固醇异构酶二聚化依赖性催化和热适应的分子动力学研究。

IF 3 4区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

Journal of molecular graphics & modelling

Pub Date : 2025-11-21 DOI: 10.1016/j.jmgm.2025.109230

Yi-Zhe Wang , Tzu-En Lin , Yu-Shan Tsai , Hsuan-Hsuan Lo , Chia-Ning Yang

Ketosteroid isomerase (KSI), a highly conserved enzyme in the β-ketoacyl metabolic pathway, exhibits temperature-dependent functional adaptations across species. In this study, we investigated the temperature sensitivity of mesophilic KSI from Pseudomonas putida using molecular dynamics simulations. Since KSI functions as a dimer, we simulated both monomeric and dimeric forms at its optimal catalytic temperature (303 K) and at an elevated, non-optimal temperature (338 K) to evaluate how temperature and dimerization affect activation. We focused on the dynamics of three catalytically important residues—Y16, D40, and D103—where Y16 is located on the mobile α1-helix not involved in the dimer interface, D40 lies at the edge of the dimer interface, and D103 resides at the center of the core β-sheet structure that remains static in both monomeric and dimeric states. In the monomeric form at 303 K, the Y16–D40, Y16–D103, and D40–D103 pairs exhibit broader and longer separation distances than the optimal range for catalysis. Dimerization stabilizes D40, resulting in a narrower D40–D103 separation that falls within the catalytically competent range. The relatively unchanged mobility of Y16 upon dimerization suggests that Y16 undergoes an induced-fit adjustment upon substrate binding. At 338 K, although dimerization partially corrects the D40–D103 geometry, the increased conformational flexibility of Y16 indicates a reduced likelihood of achieving the substrate-induced active-site reorganization. Together, our results demonstrate that dimerization is essential for achieving the geometric organization required for catalytic activity and that elevated temperature disrupts this coordination, rendering KSI inactive.

酮类固醇异构酶（KSI）是β-酮酰基代谢途径中的一种高度保守的酶，在物种间表现出温度依赖的功能适应性。在这项研究中，我们利用分子动力学模拟研究了恶臭假单胞菌中温性KSI的温度敏感性。由于KSI作为二聚体起作用，我们在最佳催化温度（303 K）和较高的非最佳温度（338 K）下模拟了单体和二聚体形式，以评估温度和二聚体如何影响活化。我们重点研究了三个催化重要残基——Y16、D40和D103的动力学，其中Y16位于不参与二聚体界面的α1-螺旋上，D40位于二聚体界面的边缘，D103位于核心β-片结构的中心，在单体和二聚体状态下都保持静态。在303 K时，单体形式的Y16-D40、Y16-D103和D40-D103比最佳催化范围更宽、更长的分离距离。二聚化稳定D40，使D40- d103的分离范围更窄，落在催化能力范围内。Y16在二聚化过程中相对不变的迁移率表明，Y16在底物结合时经历了诱导配合调节。在338 K时，虽然二聚化部分纠正了D40-D103的几何形状，但Y16构象灵活性的增加表明实现底物诱导的活性位点重组的可能性降低。总之，我们的研究结果表明，二聚化对于实现催化活性所需的几何组织是必不可少的，而升高的温度破坏了这种协调，使KSI失活。

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引用次数: 0

Atomic density distributions in proteins: structural and functional implications 蛋白质中的原子密度分布：结构和功能意义

IF 3 4区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

Journal of molecular graphics & modelling

Pub Date : 2025-11-19 DOI: 10.1016/j.jmgm.2025.109228

Sotirios Touliopoulos, Nicholas M. Glykos

Atomic packing is an important metric for characterizing protein structures, as it significantly influences various features including the stability, the rate of evolution and the functional roles of proteins. Packing in protein structures is a measure of the overall proximity between the proteins’ atoms and it can vary notably among different structures. However, even single domain proteins do not exhibit uniform packing throughout their structure. Protein cores in the interior tend to be more tightly packed compared to the protein surface and the presence of cavities and voids can disrupt that internal tight packing too.

Many different methods have been used to measure the quality of packing in proteins, identify factors that influence it, and their possible implications. In this work, we examine atomic density distributions derived from 21,255 non-redundant protein structures and show that statistically significant differences between those distributions are present. The biomolecular assembly unit was chosen as a representative for these structures. Addition of hydrogen atoms and solvation was also performed to emulate a faithful representation of the structures in vitro.

Several protein structures deviate significantly and systematically from the average packing behavior. Hierarchical clustering indicated that there are groups of structures with similar atomic density distributions. Search for common features and patterns in these clusters showed that some of them include proteins with characteristic structures such as coiled-coils and cytochromes. Certain classification families such as hydrolases and transferases have also a preference to appear more frequently in dense and loosely-packed clusters respectively.

Regarding factors influencing packing, our results support knowledge that larger structures have a smaller range in their density values, but tend to be more loosely packed, compared to smaller proteins. We also used indicators, like crystallographic water molecules abundance and B-factors as estimates of the stability of the structures to reveal its relationship with packing.

原子填充是表征蛋白质结构的重要指标，因为它对蛋白质的稳定性、进化速度和功能作用等多种特征具有重要影响。蛋白质结构中的包装是衡量蛋白质原子之间总体接近程度的一种方法，它可以在不同的结构中发生显著变化。然而，即使是单域蛋白也不会在其整个结构中表现出均匀的包装。与蛋白质表面相比，内部的蛋白质核心往往包裹得更紧密，而空腔和空隙的存在也会破坏内部的紧密包裹。许多不同的方法被用来测量蛋白质包装的质量，确定影响它的因素，以及它们可能的含义。在这项工作中，我们研究了来自21,255个非冗余蛋白质结构的原子密度分布，并表明这些分布之间存在统计学上的显着差异。选择生物分子组装单元作为这些结构的代表。添加氢原子和溶剂化也进行了模拟一个忠实的表示的结构在体外。一些蛋白质结构明显地和系统地偏离了平均的包装行为。分层聚类表明存在具有相似原子密度分布的结构群。对这些簇的共同特征和模式的搜索表明，其中一些包括具有特征结构的蛋白质，如卷曲线圈和细胞色素。某些分类家族，如水解酶和转移酶，也倾向于更频繁地出现在密集和松散排列的簇中。关于影响包装的因素，我们的结果支持这样的知识：与较小的蛋白质相比，较大的结构具有较小的密度值范围，但往往更松散地包装。我们还使用了一些指标，如晶体水分子丰度和b因子作为结构稳定性的估计，以揭示其与填料的关系。

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引用次数: 0

Quantum chemical engineering of enhanced nonlinear optical responses in alkali metal-doped diazadioxacirculenes for molecular photonics 分子光子学中碱金属掺杂重氮二氧环烯增强非线性光学响应的量子化学工程。

IF 3 4区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

Journal of molecular graphics & modelling

Pub Date : 2025-11-19 DOI: 10.1016/j.jmgm.2025.109229

Sabir Ali Siddique , Shanza Fatima , Muhammad Bilal Ahmed Siddique , Ejaz Ahmed , Rahman Shah Zaib Saleem , Muhammad Arshad

The pursuit of high-performance nonlinear optical (NLO) materials remains central to advancing optical communication, photonic circuitry, and laser-based technologies. In this study, we theoretically designed and evaluated a new class of alkali metal-doped diazadioxa[8]circulene complexes, denoted as M@C8 (M = Li, Na, K), using density functional theory. Metal doping induces profound structural and electronic reorganization, with interaction energies ranging from −0.25 to −11.21 kcal mol⁻¹, affirming both favorable metal binding and thermodynamic stability. Remarkably, these modifications lead to dramatic enhancements in NLO performance. The pristine C8 molecule exhibits a negligible static first hyperpolarizability (β₀) of just 0.03 au; however, upon doping, β₀ surges to an exceptional 470074.83 au for 3-Li@C8, an increase of nearly 1.57 × 10⁷-fold. Under dynamic conditions (λ = 1064 nm), the first-order hyperpolarizability β(−ω, ω, 0) reaches 104948.80 au for 3-Na@C8, while the hyper-Rayleigh scattering hyperpolarizability (β_HRS) peaks at 2837379.65 au for 5-K@C8, showcasing outstanding frequency-dependent NLO activity. Complementary UV–Vis analysis reveals pronounced redshifts in absorption (from 199.39 nm for C8 to 773.60 nm for 6-K@C8), indicating enhanced π-electron delocalization and efficient intramolecular charge transfer. Taken together, these findings position M@C8 complexes as compelling molecular platforms for next-generation NLO materials with exceptional static and dynamic optical responses.

对高性能非线性光学（NLO）材料的追求仍然是推进光通信、光子电路和基于激光的技术的核心。在本研究中，我们利用密度泛函理论，从理论上设计并评价了一类新的碱金属掺杂重氮二氧嘧啶[8]环烯配合物，表示为M@C8 （M = Li, Na， K）。金属掺杂引起了深刻的结构和电子重组，相互作用能在-0.25到-11.21 kcal mol-1之间，证实了良好的金属结合和热力学稳定性。值得注意的是，这些修改显著提高了NLO的性能。原始C8分子的静态第一超极化率（β0）仅为0.03 au，可以忽略不计；然而，在掺杂后，3-Li@C8的β0异常飙升至470074.83 au，增加了近1.57 × 107倍。在动态条件下（λ = 1064 nm）， 3-Na@C8的一阶超极化率β(-ω, ω, 0)达到104948.80 au，而5-K@C8的超瑞利散射超极化率（β hrs）峰值为2837379.65 au，表现出明显的频率相关NLO活性。互补紫外-可见分析显示C8的吸收红移明显（从199.39 nm到6-K@C8的773.60 nm），表明π-电子离域增强和有效的分子内电荷转移。综上所述，这些发现将M@C8配合物定位为下一代NLO材料的引人注目的分子平台，具有出色的静态和动态光学响应。

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引用次数: 0

Density functional modelling of lead-free Sn-based AmSnX3 (Am=Rb, Cs; X=Cl, Br, I) perovskites as sustainable materials for optoelectronics and solar cell applications 无铅sn基AmSnX3 （Am=Rb, Cs； X=Cl, Br， I）钙钛矿作为光电子和太阳能电池应用的可持续材料的密度泛函建模

IF 3 4区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

Journal of molecular graphics & modelling

Pub Date : 2025-11-18 DOI: 10.1016/j.jmgm.2025.109227

Zia ur Rehman , Ayesha Saddiqa , A.F. Abd El-Rehim , Amna Parveen , Heba Y. Zahran , Zeesham Abbas

This research uses density functional theory to examine the structural, electronic, optical, mechanical, thermodynamic, thermoelectric, magnetic, and photovoltaic properties of Sn-based AmSnX₃ (Am = Rb, Cs; X = Cl, Br, I) perovskites. The tolerance factor (0.71–1.04) and the negative cohesive energy confirm the materials’ structural and thermodynamic stability. The electronic properties show semiconducting behavior, with energy band gaps of 0.42 eV for RbSnBr3 and 1.02 eV for CsSnCl₃. The maximum absorption values (7.16 × 10⁴ cm⁻¹ to 8.11 × 10⁴ cm⁻¹) in the visible region indicate efficient light harvesting for solar cell applications. Mechanical properties suggest mechanical stability and ductility. The Debye temperature (146.08–190.78 K) offers insights into heat capacity and thermal behavior at different temperatures. The Seebeck coefficient at room temperature classifies RbSnBr₃, RbSnI₃, and CsSnCl₃ as p-type materials, while RbSnCl₃, CsSnBr₃, and CsSnI₃ are n-type. The calculated power conversion efficiencies, from 12.47 % for CsSnI₃ to 29.54 % for CsSnCl₃, emphasize the novelty of this work, which combines structural, mechanical, electronic, and optical analyses for the first time to thoroughly evaluate the potential of RbSnX₃ and CsSnX₃ perovskites in optoelectronic and energy applications.

本研究利用密度泛函理论研究了sn基AmSnX3 （Am = Rb, Cs; X = Cl, Br， I）钙钛矿的结构、电子、光学、机械、热力学、热电、磁性和光伏性能。公差系数（0.71-1.04）和负内聚能证实了材料的结构和热力学稳定性。RbSnBr3的能带隙为0.42 eV， CsSnCl3的能带隙为1.02 eV。可见光区的最大吸收值（7.16 × 104 cm-1至8.11 × 104 cm-1）表明太阳能电池应用的有效光收集。机械性能表明机械稳定性和延展性。德拜温度（146.08-190.78 K）提供了不同温度下的热容量和热行为的见解。室温下的塞贝克系数将RbSnBr3、RbSnI3和CsSnCl3归类为p型材料，而RbSnCl3、CsSnBr3和CsSnCl3归类为n型材料。计算的功率转换效率，从12.47%的cssn3到29.54%的CsSnCl3，强调了这项工作的新颖性，首次将结构，机械，电子和光学分析结合起来，全面评估了RbSnX3和CsSnX3钙钛矿在光电和能源应用中的潜力。

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引用次数: 0

Tailoring adsorption properties of Kekulene nanoring via functionalization for pharmaceutical pollutant removal 基于功能化的克库林纳米环对药物污染物去除的裁剪吸附性能。

IF 3 4区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

Journal of molecular graphics & modelling

Pub Date : 2025-11-18 DOI: 10.1016/j.jmgm.2025.109231

Hazem Abdelsalam , Mohamed Abdel Rafea , Mahmoud A.S. Sakr , Qinfang Zhang

Pharmaceutical pollutants such as Diclofenac and Naproxen are emerging environmental contaminants due to their persistence and potential biological hazards. In this study, pristine and functionalized Kekulene nanorings (KNRs) were theoretically explored as novel adsorbents using density functional theory (DFT). Various functional groups (–COOH, –NO₂, –NO, –N, –O, –S) were introduced to modulate the interaction with drug molecules. Adsorption energy (E_a) calculations confirmed spontaneous physisorption across all systems, with values ranging from −2.473 to −0.441 eV. Notably, the KNR–NO₂–N system in aqueous phase exhibited the lowest E_a (−0.441 eV) and shortest recovery time (τ = 2.864 × 10⁻⁵ s), making it the most promising candidate for rapid desorption and recyclability. Non-covalent interaction (NCI) analysis revealed that van der Waals forces and weak electrostatic interactions dominate the adsorption mechanism. Natural Bond Orbital (NBO) analysis of the oxygen atom (O6) confirmed variable charge transfer behaviour, reflecting the influence of surface functionalization. HOMO–LUMO analysis showed frontier orbital localization patterns that shifted upon functionalization, especially in Naproxen complexes, indicating enhanced electronic interactions. Compared to benchmark materials such as PTX@rGO and FPV@GN, KNR-based adsorbents demonstrated competitive or superior tunability and desorption potential. These results suggest that functionalized KNRs—particularly KNR–NO₂–N—are promising candidates for efficient, reversible pharmaceutical pollutant capture in both gas and aqueous environments.

药物污染物如双氯芬酸和萘普生由于其持久性和潜在的生物危害是新兴的环境污染物。本研究利用密度泛函理论（DFT）从理论上探讨了原始和功能化的Kekulene纳米颗粒作为新型吸附剂的可行性。引入各种官能团（-COOH, -NO2, -NO, -N, -O, -S）来调节与药物分子的相互作用。吸附能（Ea）计算证实了所有体系的自发物理吸附，其值范围为-2.473至-0.441 eV。值得注意的是，水溶液中的KNR-NO2-N体系具有最低的Ea （-0.441 eV）和最短的回收时间（τ = 2.864 × 10-5 s），是最有希望快速解吸和可循环利用的候选体系。非共价相互作用（NCI）分析表明，范德华力和弱静电相互作用主导了吸附机理。氧原子（O6）的自然键轨道（NBO）分析证实了可变电荷转移行为，反映了表面功能化的影响。HOMO-LUMO分析显示，前沿轨道定位模式随着功能化而改变，特别是在萘普生配合物中，表明电子相互作用增强。与PTX@rGO和FPV@GN等基准材料相比，基于knr的吸附剂表现出竞争性或优越的可调节性和解吸潜力。这些结果表明功能化的knr -特别是knr - no2 - n -是在气体和水环境中高效、可逆的药物污染物捕获的有希望的候选者。

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引用次数: 0

Vanalyzer: an open-source tool for automated statistical analysis and continuous updating of vanadate-binding sites in the Protein Data Bank Vanalyzer：一个开源工具，用于自动统计分析和持续更新蛋白质数据库中的钒酸结合位点。

IF 3 4区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

Journal of molecular graphics & modelling

Pub Date : 2025-11-17 DOI: 10.1016/j.jmgm.2025.109223

Alexander Trachtenberg, Barak Akabayov

The rapidly growing number of protein structures in the Protein Data Bank (PDB) offers opportunities to derive biological insights from proteins with common features. Taking advantage of this “big data” resource, we developed an automated open-source Python script designated “Vanalyzer” that performs statistical analysis on vanadate-binding sites across the PDB. Vanalyzer evaluates the structural properties of proteins containing vanadium-based oxyanions by comparing binding interfaces and geometries across a diverse array of proteins. Additionally, it allows a focused analysis on specific enzyme classes, facilitating direct comparisons between them. The newly developed tool will contribute to the understanding of vanadate recognition within protein binding sites and will serve as a valuable, up-to-date resource for analyzing both current and newly submitted vanadate structures in the PDB.

蛋白质数据库（PDB）中蛋白质结构数量的快速增长为从具有共同特征的蛋白质中获得生物学见解提供了机会。利用这个“大数据”资源，我们开发了一个自动化的开源Python脚本，名为“Vanalyzer”，用于对PDB上的钒酸盐结合位点进行统计分析。Vanalyzer通过比较多种蛋白质的结合界面和几何形状来评估含有钒基氧离子的蛋白质的结构特性。此外，它允许对特定酶类进行集中分析，促进它们之间的直接比较。新开发的工具将有助于理解蛋白质结合位点内的钒酸盐识别，并将作为分析PDB中当前和新提交的钒酸盐结构的有价值的最新资源。

引用次数: 0

Targeting HDAC3 dynamics: Allosteric role of Phe200 in inhibitor binding and breast cancer therapy 靶向HDAC3动力学：Phe200在抑制剂结合和乳腺癌治疗中的变构作用。

IF 3 4区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

Journal of molecular graphics & modelling

Pub Date : 2025-11-17 DOI: 10.1016/j.jmgm.2025.109226

Erick Bahena-Culhuac , Rodolfo Daniel Ávila-Avilés , Martiniano Bello

Histone deacetylase 3 (HDAC3) is a key epigenetic regulator implicated in breast cancer progression and represents a promising therapeutic target. Here, we investigated 14 HDAC3–ligand complexes using molecular dynamics (MD) simulations and binding free energy calculations (MM/GBSA) to identify the determinants of inhibitor binding. Key residues consistently engaged across ligands included Gly132, His134–135, Phe144, Asp170, His172, Phe200, Asp259, Leu266, Gly296, Tyr298, and the catalytic Zn²⁺ ion. Among the compounds, domatinostat and entinostat exhibited the strongest affinities (ΔGbind ≈ −70 kcal/mol), in reasonable agreement with experimental data (r = 0.60). Both ligands also showed small Highest Occupied Molecular Orbital–Lowest Unoccupied Molecular Orbital (HOMO–LUMO) gaps, high softness, and elevated electrophilicity indices, providing chemical cues for the design of next-generation HDAC3 inhibitors. Notably, ligand binding stabilized regions surrounding Phe200 and Asn370, restricting the conformational flexibility required for enzymatic activation. This supports an allosteric inhibition mechanism in which ligands lock HDAC3 into inactive conformations. Collectively, these findings offer mechanistic insights into HDAC3 regulation and highlight structural hot spots for the rational design of selective inhibitors with potential applications in targeted breast cancer therapy.

组蛋白去乙酰化酶3 （HDAC3）是参与乳腺癌进展的关键表观遗传调控因子，是一个有前景的治疗靶点。本文采用分子动力学（MD）模拟和结合自由能（MM/GBSA）计算方法研究了14种hdac3配体复合物，以确定抑制剂结合的决定因素。在配体上一致的关键残基包括Gly132、His134-135、Phe144、Asp170、His172、Phe200、Asp259、Leu266、Gly296、Tyr298和催化Zn2+离子。其中，domatinostat和entinostat的亲和力最强（ΔGbind≈-70 kcal/mol），与实验结果吻合较好（r = 0.60）。这两种配体还显示出较小的最高占据分子轨道-最低未占据分子轨道（HOMO-LUMO）间隙、高柔软度和高亲电性指数，为设计下一代HDAC3抑制剂提供了化学线索。值得注意的是，配体结合稳定了Phe200和Asn370周围的区域，限制了酶激活所需的构象灵活性。这支持了一种变构抑制机制，其中配体将HDAC3锁定为非活性构象。总的来说，这些发现提供了HDAC3调控的机制见解，并突出了合理设计选择性抑制剂的结构热点，这些抑制剂有可能应用于靶向乳腺癌治疗。

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引用次数: 0

Machine Learning–Driven discovery of mushroom-derived inhibitors targeting InhA of Mycobacterium tuberculosis: An integrated QSAR, molecular docking and molecular dynamic simulation approach 机器学习驱动下发现针对结核分枝杆菌InhA的蘑菇源抑制剂：综合QSAR，分子对接和分子动力学模拟方法

IF 3 4区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

Journal of molecular graphics & modelling

Pub Date : 2025-11-15 DOI: 10.1016/j.jmgm.2025.109220

Karma Wangchuk , Mudassar Fareed Awan , Syeda Nazish Sohaib , Abdul Basit , Biniyam Prince Danan , Laiba Nadeem , Guendouzi Abdelkrim , Aisha Khalid , Khursheed Muzammil

Mycobacterium tuberculosis causes tuberculosis (TB), which remains a significant health problem worldwide. The rise of multidrug-resistant bacteria has worsened the situation, and current treatments are becoming less effective. InhA, a key enzyme involved in mycolic acid biosynthesis, is a validated therapeutic target in anti-TB therapy. This study aimed to explore the chemical diversity of natural substances from mushrooms against TB. Experimentally validated inhibitors from ChEMBL were retrieved to generate machine learning–based QSAR models combining nine chemical fingerprints and rigorous feature selection. The optimal RF–SVM-RFE model displayed high prediction performance (accuracy = 0.953, ROC_AUC = 0.971) and led virtual screening of mushroom metabolites. Six top-ranked compounds, including Inoscavin A and Schizine A, displayed substantial binding affinities (−11.7 to −10.5 kcal/mol) and stable interaction networks in molecular docking and MD simulations. Explainable AI (SHAP and LIME) showed fundamental structural motifs that drive activity and enhance chemical interpretability. These findings suggest promising natural scaffolds for anti-TB drug development and underscore the importance of AI-driven strategies in accelerating natural product–based therapeutics.

结核分枝杆菌引起结核病（TB），这仍然是世界范围内的一个重大健康问题。耐多药细菌的增加使情况更加恶化，目前的治疗方法正在变得不那么有效。InhA是参与霉菌酸生物合成的关键酶，是抗结核治疗的有效靶点。本研究旨在探讨蘑菇抗结核天然物质的化学多样性。从ChEMBL中检索经过实验验证的抑制剂，生成基于机器学习的QSAR模型，该模型结合了9种化学指纹和严格的特征选择。优化后的RF-SVM-RFE模型具有较高的预测精度（准确率= 0.953,ROC_AUC = 0.971），可对蘑菇代谢产物进行虚拟筛选。在分子对接和分子动力学模拟中，Inoscavin A和Schizine A的结合亲和力（- 11.7 ~ - 10.5 kcal/mol）较高，具有稳定的相互作用网络。可解释的AI （SHAP和LIME）显示出驱动活性和增强化学可解释性的基本结构基序。这些发现为抗结核药物开发提供了有希望的天然支架，并强调了人工智能驱动战略在加速基于天然产品的治疗方面的重要性。

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引用次数: 0

CNT as a robust delivery vehicle for anti-breast cancer drugs: A combined DFT and in-silico study 碳纳米管作为抗乳腺癌药物的强大递送载体：一项DFT和计算机联合研究。

IF 3 4区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

Journal of molecular graphics & modelling

Pub Date : 2025-11-14 DOI: 10.1016/j.jmgm.2025.109215

Sumanta Pal , Narendra Nath Ghosh , Soumen Kumar Pati , Manab Mandal

Nanomedicine has transformed cancer therapy by introducing and developing nanocarriers to enhance drug delivery. Herein, we have executed a computational investigation of the efficiency of two anti-breast cancer drugs viz. Exemestane (EXE) and Ruxolitinib (RUX) are delivered through armchair CNT (10,10). The encapsulation process of drugs in CNTs has been investigated through an analysis of various structural and electrical parameters viz. atom centered density matrix(ADMP), adsorption energy, electrostatic potential map(ESPM), molecular orbital(MO) analysis, natural bond orbital (NBO) analysis, non-covalent index (NCI) plot, and projected density of state (PDOS). The higher adsorption value of RUX -72.42 kcal/mol(-3.14 eV) with CNT and CNT-EXE -63.29 kcal/mol(-2.75 eV) indicates a stronger binding affinity of RUX and EXE. The electronic properties of the CNT were examined and compared before and after the adsorption process.Study of several thermodynamic parameters revealed that the whole encapsulation process is exothermic and spontaneous in nature. The stabilizing interaction of drugs and CNT has been established and validated from ADMP molecular dynamics simulation and NCI analysis was performed through the encapsulation procedure of the drugs within CNT at room temperature. The best docking score showed the CNT with EXE (−7.6 kcal/mol) followed by CNT with RUX (−7.5 kcal/mol), higher than the studied drugs i.e. EXE (−7.3 kcal/mol) and RUX (−7.2 kcal/mol). The docking score indicates that the inclusion complex has a better interaction and pave the way for unlimited opportunities for the delivery vehicle of CNT for the studied drugs within the biological systems.

纳米医学通过引入和开发纳米载体来增强药物传递，已经改变了癌症治疗。在此，我们对两种抗乳腺癌药物即依西美坦（EXE）和鲁索利替尼（Ruxolitinib）通过扶手椅CNT输送的效率进行了计算研究（10,10）。通过分析各种结构和电学参数，即原子中心密度矩阵（ADMP）、吸附能、静电势图（ESPM）、分子轨道（MO）分析、自然键轨道（NBO）分析、非共价键指数（NCI）图和投影态密度（PDOS），研究了药物在CNTs中的包封过程。RUX -72.42 kcal/mol（-3.14 eV）对CNT和CNT-EXE -63.29 kcal/mol（-2.75 eV）的吸附值较高，表明RUX和EXE的结合亲和力较强。对碳纳米管吸附前后的电子性能进行了检测和比较。对几个热力学参数的研究表明，整个包封过程是放热自发的。通过ADMP分子动力学模拟验证了药物与碳纳米管的稳定相互作用，并通过室温下药物在碳纳米管内的包封过程进行了NCI分析。最佳的对接分数是碳纳米管与EXE (-7.6 kcal/mol)，其次是碳纳米管与RUX (-7.5 kcal/mol)，高于所研究的药物EXE （-7.3 kcal/mol）和RUX （-7.2 kcal/mol）。对接分数表明，包合物具有更好的相互作用，为碳纳米管在生物系统内作为研究药物的递送载体铺平了无限的机会。

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