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On QSPR analysis for predicting efficacy of physicochemical properties of antibiotics drugs via topological indices and regression models 基于拓扑指数和回归模型预测抗菌药物理化性质疗效的QSPR分析
IF 3 4区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2026-01-13 DOI: 10.1016/j.jmgm.2026.109280
Yingxuan Huang , W. Eltayeb Ahmed , Muhammad Farhan Hanif , Saba Hanif , Muhammad Imran , Muhammad Kamran Siddiqui
Quantitative structure property relationship(QSPR) has emerged as an indispensable tool for the estimation of physicochemical properties in drug molecules using mathematical and computational methods. Here, we introduce novel reverse degree based topological indices to see their applicability in case of selected antibiotic compounds property prediction. Reliable models to predict properties such as the boiling point, molar refractivity and enthalpy of vaporization exist to correlate molecular structure with experimentally reported physicochemical parameters. We have analyzed structurally different antibiotics with regression models developed in Python and SPSS in order to guarantee the robustness and reproducibility. We note here that predictive measures of cubic regression models seem to perform better, as observed through generally greater correlation coefficients. The results show that the reverse topological indices are efficient for recording structural differences in antibiotic molecules and they can be excellent descriptors for predicting their physical and chemical properties. It also stresses that, the use of reverse degree based descriptors on antibiotic compounds is new, providing a basis for further QSPR modeling for more general drug families. This work is part of a growing trend to study the interfaces between graph theory and cheminformatics where new indices help to improve our understanding over molecular properties with importance for drug design.
定量结构性质关系(QSPR)已成为利用数学和计算方法估计药物分子物理化学性质的重要工具。在这里,我们引入了新的基于逆度的拓扑指标,以观察它们在选定抗生素化合物性质预测中的适用性。存在可靠的模型来预测诸如沸点、摩尔折射率和汽化焓等性质,从而将分子结构与实验报告的物理化学参数联系起来。为了保证稳健性和可重复性,我们使用Python和SPSS开发的回归模型对结构不同的抗生素进行分析。我们在这里注意到,三次回归模型的预测措施似乎表现得更好,正如通过普遍较大的相关系数观察到的那样。结果表明,反向拓扑指数可以有效地记录抗生素分子的结构差异,并可作为预测其物理和化学性质的良好描述符。它还强调,在抗生素化合物上使用基于反向度的描述符是新的,为进一步对更一般的药物家族进行QSPR建模提供了基础。这项工作是研究图论和化学信息学之间接口的一个日益增长的趋势的一部分,其中新的指标有助于提高我们对分子特性的理解,对药物设计具有重要意义。
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引用次数: 0
Repurposing drugs for EGFR-targeted cancer therapy: An in silico and in vitro study with pharmacophore-based insights 重新利用药物用于egfr靶向癌症治疗:基于药物团的计算机和体外研究。
IF 3 4区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2026-01-13 DOI: 10.1016/j.jmgm.2026.109288
Pınar Siyah , Firat Baris Barlas
Cancer is the second leading cause of death globally and remains a priority due to its impact on life quality, treatment complexity, and high costs. To expedite drug development, researchers are increasingly repurposing FDA-approved drugs and clinical candidates, reducing time and costs through in silico methods. In this study, 3235 FDA-approved and clinical molecules were screened for EGFR inhibition, a significant target due to its role in cancer progression and treatment resistance. A pharmacophore model was generated based on erlotinib's co-crystallized structure and quantitative structure-activity relationships. Molecules meeting the pharmacophoric criteria underwent SP and XP docking, with thresholds of −6.00 kcal/mol and −7.00 kcal/mol, respectively, followed by anti-cancer potential analysis via MetaCore/MetaDrug and MD simulations at 1, 10, and 100 ns to assess EGFR-binding stability. For the molecule Ticagrelor, which demonstrated particularly promising results, and Erlotinib cell culture viability assays were conducted across three cell lines—cancerous A549, U87, and healthy BEAS-2B— (IC50) of, 8.2576 μM, 9.4058 μM, and 15.893 μM, respectively for Ticagrelor and 11.708 μM, 12.747 μM and 14.6709 μM, respectively for Erlotinib. In silico results highlight Ticagrelor's significant EGFR-inhibiting potential with enhanced binding stability compared to the reference.
癌症是全球第二大死亡原因,由于其对生活质量的影响、治疗的复杂性和高昂的费用,癌症仍然是一个优先事项。为了加快药物开发,研究人员越来越多地重新利用fda批准的药物和临床候选药物,通过计算机方法减少时间和成本。在这项研究中,筛选了3235个fda批准的和临床的EGFR抑制分子,这是一个重要的靶点,因为它在癌症进展和治疗耐药中起作用。基于厄洛替尼共晶结构和定量构效关系建立药效团模型。符合药效标准的分子进行SP和XP对接,阈值分别为-6.00 kcal/mol和-7.00 kcal/mol,然后通过MetaCore/ metdrug和MD模拟在1、10和100 ns进行抗癌潜力分析,以评估egfr结合稳定性。对于表现出特别有希望的结果的分子替格瑞洛,和厄洛替尼的细胞培养活力测定在三种细胞系-癌变的A549、U87和健康的BEAS-2B中进行,替格瑞洛的IC50分别为8.2576 μM、9.4058 μM和15.893 μM,厄洛替尼的IC50分别为11.708 μM、12.747 μM和14.6709 μM。与参考药物相比,硅实验结果突出了替格瑞洛显著的egfr抑制潜力和增强的结合稳定性。
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引用次数: 0
Investigating the anti-Alzheimer potential of biogenic compounds from Zinc15 database as NMDA antagonist: An in-silico approach 研究Zinc15数据库中生物源性化合物作为NMDA拮抗剂的抗阿尔茨海默病潜力:一种计算机方法。
IF 3 4区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2026-01-13 DOI: 10.1016/j.jmgm.2026.109277
Somdatta Chaudhari , Asavari Shinde , Mukund Salunke , Shriram Bairagi , Azad Dhage , Pinkal Patel , Vivek Rathod , Sandeep Pathare , Nojood Altwaijry , Mohd Shahnawaz Khan
Alzheimer's disease is an unavoidable neurological disorder in which the death of brain cells brings on memory loss, cognitive decline, and eventual dementia. There is no recognized treatment for Alzheimer's illness. By the year 2050, it is expected that the global population will witness approximately 100 million cases of Alzheimer's disease (AD). Despite recognizing AD as a formidable illness for over a century, no effective cure has been discovered thus far. Synaptic dysfunction could result from disturbed synaptic calcium handling caused by excessive activation of glutamate receptors, particularly the N-methyl-D-aspartate receptors (NMDARs). Glutamate serves as the brain's primary excitatory neurotransmitter, acting on ionotropic and metabotropic glutamate receptors. In recent years, several pharmacologically active substances derived from plants, animals, and microbes have shown promise in treating AD by focusing on various pathogenic processes. Initially, we used virtual screening to assess natural product-like compounds against NMDA receptors. In this research study, we have screened a natural compound database derived from zinc15. The best candidate was then validated through molecular dynamics simulation (MDS). The results revealed that out of 4221 compounds tested, only 165 showed superior binding interactions compared to native ligands, making them inhibitors for protein. Further analysis using ADMET indicates favorable drug-like properties, particularly for CNS drug-likeness. The MDS results, including RMSD, RMSF, Rg, and residue interactions, indicated a strong and stable association between top molecules and target protein. This confirms that top molecules can effectively remain within the binding pockets of the target proteins, forming stable protein-ligand complexes.
阿尔茨海默病是一种不可避免的神经系统疾病,脑细胞死亡会导致记忆丧失、认知能力下降,最终导致痴呆。阿尔茨海默病目前还没有公认的治疗方法。到2050年,预计全球人口将见证约1亿阿尔茨海默病(AD)病例。尽管一个多世纪以来人们就认识到阿尔茨海默病是一种可怕的疾病,但迄今为止还没有发现有效的治疗方法。突触功能障碍可能是由于谷氨酸受体,特别是n -甲基- d -天冬氨酸受体(NMDARs)的过度激活引起的突触钙处理紊乱。谷氨酸是大脑的主要兴奋性神经递质,作用于嗜离子性和代谢性谷氨酸受体。近年来,从植物、动物和微生物中提取的一些药理活性物质通过关注各种致病过程,在治疗AD方面显示出了希望。最初,我们使用虚拟筛选来评估抗NMDA受体的天然产物样化合物。在本研究中,我们筛选了一个来源于zinc15的天然化合物数据库。然后通过分子动力学模拟(MDS)验证最佳候选物。结果显示,在测试的4221种化合物中,只有165种与天然配体相比表现出更好的结合相互作用,使其成为蛋白质的抑制剂。进一步的ADMET分析显示了良好的药物样性质,特别是对中枢神经系统药物相似。MDS结果包括RMSD、RMSF、Rg和残基相互作用,表明顶分子与靶蛋白之间存在强而稳定的关联。这证实了顶部分子可以有效地留在靶蛋白的结合口袋内,形成稳定的蛋白质-配体复合物。
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引用次数: 0
A first-principles study of hydrogen storage on MXene Mo2C monolayer MXene Mo2C单层储氢的第一性原理研究
IF 3 4区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2026-01-12 DOI: 10.1016/j.jmgm.2026.109283
Mohamed Bakhit, Sina Karimzadeh, Tien-Chien Jen
This study investigates the potential of Mo2C MXene as a hydrogen storage material using density functional theory (DFT) and molecular dynamics (MD) simulations to examine its structural stability, electronic properties, and hydrogen adsorption behavior. The optimized Mo2C structure exhibits a hexagonal lattice with favorable adsorption sites over Mo atoms and shows a surface area expansion of approximately 4 % after hydrogen loading while maintaining lattice symmetry. Thermodynamic stability is confirmed through adsorption energy calculations, which reveal a clear relationship between energy levels and hydrogen concentration. The results indicate that H2 adsorption on Mo2C is a thermodynamically favorable and exothermic process, with adsorption energies ranging from −0.184 to −0.528 eV, satisfying the criteria for practical hydrogen storage applications. Charge transfer analysis identifies Mo atoms as electron acceptors. Density of States (DOS) calculations reveal a near-zero band gap, confirming the metallic nature of Mo2C, while Projected DOS (PDOS) and orbital maps show significant hybridization and electronic polarization among H, Mo, and C atoms. Charge density difference maps highlight effective charge redistribution with strong electric fields around Mo atoms. MD simulations further confirm the structural stability of the Mo2C–H2 system, showing minimal deformation during a 100 ps simulation and supporting efficient hydrogen adsorption. Overall, these findings establish Mo2C MXene as a promising candidate for hydrogen storage applications and provide valuable insights for experimental validation and further development of sustainable energy storage technologies.
本研究利用密度泛函理论(DFT)和分子动力学(MD)模拟研究了Mo2C MXene作为储氢材料的潜力,以研究其结构稳定性、电子性能和氢吸附行为。优化后的Mo2C结构呈现六边形晶格,具有对Mo原子有利的吸附位点,并且在保持晶格对称性的情况下,氢负载后表面面积扩大了约4%。通过吸附能计算证实了热力学稳定性,揭示了能级与氢浓度之间的明确关系。结果表明,H2在Mo2C上的吸附是一个热力学有利的放热过程,吸附能在−0.184 ~−0.528 eV之间,满足实际储氢应用的标准。电荷转移分析确定Mo原子为电子受体。态密度(DOS)计算显示Mo2C的带隙接近于零,证实了Mo2C的金属性质,而投影态密度(PDOS)和轨道图显示H、Mo和C原子之间存在明显的杂化和电子极化。电荷密度差图突出了Mo原子周围强电场下的有效电荷重分布。MD模拟进一步证实了Mo2C-H2体系的结构稳定性,在100 ps的模拟中显示出最小的变形,并支持高效的氢吸附。总的来说,这些发现确立了Mo2C MXene作为储氢应用的有前途的候选者,并为实验验证和可持续储能技术的进一步发展提供了有价值的见解。
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引用次数: 0
Unveiling the potential of π-conjugated 2TT-R non-fullerene alternatives for multifunctional optoelectronic applications: A first-principles study 揭示π共轭2TT-R非富勒烯替代品在多功能光电应用中的潜力:第一性原理研究。
IF 3 4区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2026-01-12 DOI: 10.1016/j.jmgm.2026.109285
Sidra Manzoor , Nadeem Raza , Faheem Abbas
Organic solar cells (OSCs) offer lightweight, flexible, and cost−effective energy solutions. However, fullerene−based systems face limitations in stability, tunability, and absorption, prompting the exploration of non−fullerene alternatives to enhance efficiency and scalability. In this work, five newly designed molecules (2TT−1A to 2TT−5A) were systematically studied using Density Functional Theory (DFT) and Time−Dependent DFT (TD−DFT) at the B3LYP/6−311G (d, p) level in both gas and solvent (chloroform) phases. Key optoelectronic properties, including HOMO−LUMO gaps, absorption spectra, dipole moments, and excitation energies, were analyzed to evaluate their photovoltaic performance. All compounds demonstrated strong light−harvesting abilities, with a notable redshift in the absorption spectra observed in the solvent phase. Among them, 2TT−5A stood out with the narrowest energy gap (1.35 eV), the longest absorption wavelength (861 nm), the highest dipole moment (12.17 D), and the lowest excitation energy (1.43 eV), indicating efficient charge transfer and exciton dissociation. Open−circuit voltages (Voc) ranging from 0.54 to 1.38 V also suggest good photovoltaic potential. Additionally, the nonlinear optical (NLO) and organic light−emitting diodes (OLED) properties of 2TT−5A were explored, revealing significant hyperpolarizability and a favorable emission profile. These results suggested that 2TT−5A is an exceptional multifunctional candidate, encouraging experimental synthesis and validating this material's stability, potentially accelerating the development of multifunctional organic optoelectronic devices.
有机太阳能电池(OSCs)提供了轻便、灵活、经济的能源解决方案。然而,基于富勒烯的系统在稳定性、可调性和吸收方面存在局限性,这促使人们探索非富勒烯替代品,以提高效率和可扩展性。本文采用密度泛函理论(DFT)和时间依赖DFT (TD-DFT)在B3LYP/6-311G (d, p)水平上对5种新设计的分子(2TT-1A至2TT-5A)在气相和溶剂(氯仿)相中进行了系统的研究。分析了关键光电性能,包括HOMO-LUMO间隙、吸收光谱、偶极矩和激发能,以评估其光伏性能。所有化合物都表现出很强的光收集能力,在溶剂相的吸收光谱中观察到明显的红移。其中,2TT-5A具有最窄的能隙(1.35 eV)、最长的吸收波长(861 nm)、最高的偶极矩(12.17 D)和最低的激发能(1.43 eV),表明其具有高效的电荷转移和激子解离。开路电压(Voc)范围从0.54到1.38 V也表明良好的光伏潜力。此外,研究了2TT-5A的非线性光学(NLO)和有机发光二极管(OLED)特性,揭示了显著的超偏振性和良好的发射分布。这些结果表明,2TT-5A是一种特殊的多功能候选材料,鼓励实验合成并验证该材料的稳定性,有可能加速多功能有机光电器件的发展。
{"title":"Unveiling the potential of π-conjugated 2TT-R non-fullerene alternatives for multifunctional optoelectronic applications: A first-principles study","authors":"Sidra Manzoor ,&nbsp;Nadeem Raza ,&nbsp;Faheem Abbas","doi":"10.1016/j.jmgm.2026.109285","DOIUrl":"10.1016/j.jmgm.2026.109285","url":null,"abstract":"<div><div>Organic solar cells (OSCs) offer lightweight, flexible, and cost−effective energy solutions. However, fullerene−based systems face limitations in stability, tunability, and absorption, prompting the exploration of non−fullerene alternatives to enhance efficiency and scalability. In this work, five newly designed molecules <strong>(2</strong><strong>TT−1A to 2</strong><strong>TT−5A)</strong> were systematically studied using Density Functional Theory (DFT) and Time−Dependent DFT (TD−DFT) at the B3LYP/6−311G (d, p) level in both gas and solvent (chloroform) phases. Key optoelectronic properties, including HOMO−LUMO gaps, absorption spectra, dipole moments, and excitation energies, were analyzed to evaluate their photovoltaic performance. All compounds demonstrated strong light−harvesting abilities, with a notable redshift in the absorption spectra observed in the solvent phase. Among them, <strong>2</strong><strong>TT−5A</strong> stood out with the narrowest energy gap (1.35 eV), the longest absorption wavelength (861 nm), the highest dipole moment (12.17 D), and the lowest excitation energy (1.43 eV), indicating efficient charge transfer and exciton dissociation. Open−circuit voltages (<em>V</em><sub>oc</sub>) ranging from 0.54 to 1.38 V also suggest good photovoltaic potential. Additionally, the nonlinear optical (NLO) and organic light−emitting diodes (OLED) properties of <strong>2</strong><strong>TT−5A</strong> were explored, revealing significant hyperpolarizability and a favorable emission profile. These results suggested that <strong>2</strong><strong>TT−5A</strong> is an exceptional multifunctional candidate, encouraging experimental synthesis and validating this material's stability, potentially accelerating the development of multifunctional organic optoelectronic devices.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"144 ","pages":"Article 109285"},"PeriodicalIF":3.0,"publicationDate":"2026-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146018703","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Exploring traditional Chinese medicine for antiviral drug discovery: A computational approach to combat human metapneumovirus (HMPV) 利用中药开发抗病毒药物:一种对抗人偏肺病毒(HMPV)的计算方法
IF 3 4区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2026-01-12 DOI: 10.1016/j.jmgm.2026.109290
Amit Dubey , Manish Kumar , Aisha Tufail , Vivek Dhar Dwivedi
Human metapneumovirus (HMPV) remains a major respiratory pathogen without approved antivirals, highlighting the urgent need for novel therapeutics. This study implemented an integrative computational pipeline combining virtual screening, molecular docking, 2 μs molecular dynamics (MD) simulations, density functional theory (DFT), pharmacophore modeling, and ADMET profiling to identify potent HMPV inhibitors from Traditional Chinese Medicine. Among 180 screened phytoconstituents, glycyrrhizin (–9.3 kcal mol−1), hesperidin (–9.1 kcal mol−1), and saikosaponins (–9.0 kcal mol−1) exhibited strong binding affinities toward the HMPV matrix protein (PDB ID: 5WB0). Extended MD simulations confirmed complex stability with RMSD 0.170.22 nm, average of 35 persistent H-bonds, and DCCM correlation coefficient = 0.86 for glycyrrhizin. MM-PBSA binding free energies (ΔG_bind) of –46.2 ± 2.5, –44.7 ± 2.8, and –43.9 ± 2.2 kJ mol−1 for glycyrrhizin, hesperidin, and oseltamivir respectively, validated strong and stable interactions. DFT results indicated favorable electronic reactivity (HOMO–LUMO gap = 3.86 eV; electrophilicity = 2.74 eV), enhancing ligand-target complementarity. ADMET analysis predicted low systemic toxicity (LD50 = 380530 mg kg−1) but revealed moderate CYP3A4/CYP2C9 inhibition, suggesting the need for metabolic stability evaluation. Compared with reported fusion inhibitors such as EGCG and rutin, this matrix-targeted strategy introduces a distinct therapeutic mechanism. Overall, these findings establish a robust computational foundation for developing and experimentally validating potent natural inhibitors against HMPV.
人偏肺病毒(HMPV)仍然是一种主要的呼吸道病原体,尚未获得批准的抗病毒药物,这表明迫切需要新的治疗方法。本研究采用虚拟筛选、分子对接、2 μs分子动力学(MD)模拟、密度泛函数理论(DFT)、药效团建模和ADMET谱分析相结合的综合计算流程,鉴定中药中有效的HMPV抑制剂。在筛选的180种植物成分中,甘草酸(-9.3 kcal mol−1)、橙皮苷(-9.1 kcal mol−1)和柴草皂苷(-9.0 kcal mol−1)与HMPV基质蛋白(PDB ID: 5WB0)具有较强的结合亲和力。扩展的MD模拟证实了甘草酸配合物的稳定性,RMSD为0.17-0.22 nm,平均有3-5个持久氢键,DCCM相关系数为0.86。甘草酸、橙皮苷和奥司他韦的MM-PBSA结合自由能(ΔG_bind)分别为-46.2±2.5、-44.7±2.8和-43.9±2.2 kJ mol−1,证实了强而稳定的相互作用。DFT结果表明,良好的电子反应性(HOMO-LUMO间隙= 3.86 eV,亲电性= 2.74 eV),增强了配体-靶标的互补性。ADMET分析预测低全身毒性(LD50 = 380-530 mg kg - 1),但显示中度CYP3A4/CYP2C9抑制,提示需要代谢稳定性评估。与已有报道的融合抑制剂如EGCG和芦丁相比,这种基质靶向策略引入了一种独特的治疗机制。总的来说,这些发现为开发和实验验证抗HMPV的有效天然抑制剂建立了强大的计算基础。
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引用次数: 0
Y- and Zr-modified boron nitride nanosheets as efficient sensors for formamide: A first-principles approach Y和zr修饰的氮化硼纳米片作为甲酰胺的高效传感器:第一性原理方法
IF 3 4区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2026-01-12 DOI: 10.1016/j.jmgm.2026.109278
Meryem Derdare, Abdel-Ghani Boudjahem, Nedjoua Cheghib
This study employs DFT calculations to investigate the structural stability and electronic properties of pristine and transition-metal-doped boron nitride (BN) nanosheets, using yttrium (Y) and zirconium (Zr) as dopants, as well as their gas-sensing response toward formamide (FO). The findings show that introducing Y or Zr atoms leads to notable modifications in the electronic structure of the BN nanosheet, substantially improving its chemical reactivity and adsorption performance. In the aqueous phase, the interaction between FO and Y/Zr-doped BN nanosheets becomes moderately weaker, with adsorption energies decreasing to – 4.23 to – 24.97 kcal mol−1; however, the most stable complexes still exhibit comparatively strong binding. Solvation also alters the electronic structure of the nanosheets, leading to noticeable variations in their energy gaps. Despite this reduction in interaction strength, both doped materials retain high sensitivity toward FO in water, with ZrBN reaching 99.9 %/1.43 × 103 % and YBN achieving 55.9 %/86.5 %. Moreover, the nanosheets exhibit extremely short recovery times in the liquid phase, with values of 1.27 × 10−15 s for ZrBN and 2.06 s for YBN, enabling rapid FO desorption and efficient restoration of active metal sites. These combined features confirm the strong potential of Y- and Zr-doped BN nanosheets as reusable and high-performance sensors for formamide detection in aqueous environments.
本研究采用DFT计算研究了原始和过渡金属掺杂的氮化硼(BN)纳米片的结构稳定性和电子性能,使用钇(Y)和锆(Zr)作为掺杂剂,以及它们对甲酰胺(FO)的气敏响应。研究结果表明,引入Y或Zr原子可以显著改变BN纳米片的电子结构,显著提高其化学反应性和吸附性能。在水相中,FO与掺杂Y/ zr的BN纳米片的相互作用变弱,吸附能降至- 4.23 ~ - 24.97 kcal mol−1;然而,最稳定的配合物仍然表现出相对强的结合。溶剂化也会改变纳米片的电子结构,导致其能隙的显著变化。尽管相互作用强度降低,但两种掺杂材料对水中FO的灵敏度都很高,ZrBN达到99.9% /1.43 × 103%, YBN达到55.9% / 86.5%。此外,纳米片在液相中表现出极短的恢复时间,ZrBN的值为1.27 × 10−15 s, YBN的值为2.06 s,能够快速解吸FO并有效恢复活性金属位。这些综合特性证实了Y和zr掺杂BN纳米片作为可重复使用的高性能传感器在水环境中检测甲酰胺的强大潜力。
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引用次数: 0
Structure-based discovery of novel TAOK3 inhibitor via virtual screening, molecular dynamics simulations, and MM/GBSA analysis 通过虚拟筛选、分子动力学模拟和MM/GBSA分析,发现基于结构的新型TAOK3抑制剂
IF 3 4区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2026-01-12 DOI: 10.1016/j.jmgm.2026.109286
Ali M. Alaseem , Glowi Alasiri , Mohamed M. El-Wekil , Al-Montaser Bellah H. Ali , Ahmed K. Hamdy
Cancer persists as a leading cause of global mortality, and the mitogen-activated protein kinase (MAPK) pathway plays a pivotal role in tumor progression and drug resistance. Among MAPK regulators, TAOK3 has emerged as a promising therapeutic target due to its oncogenic role in various cancers. Despite its significance, no clinically approved TAOK3 inhibitors exist. In this study we implemented a structure-based virtual screening approach to identify potential TAOK3 inhibitors from a library of 10,000 lead-like compounds. Molecular docking identified ten top-ranked candidates, with compound Z1 (ZINC ID: 77585305) demonstrating the strongest binding affinity (ΔG = −8.42 kcal/mol), outperforming reported inhibitors NCGC00188382 and SBI-581. ADMET profiling confirmed Z1's favorable drug-like properties, including high gastrointestinal absorption and minimal toxicity risks. Molecular dynamics simulations (100 ns) confirmed stable binding of Z1 to TAOK3, as indicated by low RMSD (<0.25 nm), consistent RMSF profiles, and compact radius of gyration. End-state free energy calculations using MM/GBSA also supported favorable binding, with Z1 showing excellent van der Waals interactions (−39.82 kcal/mol). Dynamic cross-correlation matrices and free energy landscape analysis further validated the stability of the TAOK3-Z1 complex. Collectively, these findings highlight Z1 as a promising TAOK3 inhibitor and a potential lead compound for further experimental validation in anticancer drug development.
癌症一直是全球死亡的主要原因,而丝裂原活化蛋白激酶(MAPK)途径在肿瘤进展和耐药性中起着关键作用。在MAPK调节因子中,TAOK3由于其在多种癌症中的致癌作用而成为一个有希望的治疗靶点。尽管具有重要意义,但尚未有临床批准的TAOK3抑制剂存在。在这项研究中,我们实施了一种基于结构的虚拟筛选方法,从10,000种铅样化合物的文库中鉴定潜在的TAOK3抑制剂。分子对接鉴定出10个排名前十位的候选化合物,其中化合物Z1(锌ID: 77585305)表现出最强的结合亲和力(ΔG =−8.42 kcal/mol),优于已报道的抑制剂NCGC00188382和SBI-581。ADMET分析证实了Z1有利的药物样特性,包括高胃肠道吸收和最小的毒性风险。分子动力学模拟(100 ns)证实了Z1与TAOK3的稳定结合,显示出低RMSD (<0.25 nm)、一致的RMSF分布和紧凑的旋转半径。用MM/GBSA计算的终态自由能也支持良好的结合,Z1表现出良好的范德华相互作用(- 39.82 kcal/mol)。动态互相关矩阵和自由能景观分析进一步验证了TAOK3-Z1配合物的稳定性。总的来说,这些发现突出了Z1作为一种有前途的TAOK3抑制剂和潜在的先导化合物在抗癌药物开发中的进一步实验验证。
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引用次数: 0
RLBindDeep: A ResNet-LSTM based novel framework for protein–ligand binding affinity prediction RLBindDeep:一个基于ResNet-LSTM的蛋白质配体结合亲和力预测新框架
IF 3 4区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2026-01-12 DOI: 10.1016/j.jmgm.2026.109282
Ekarsi Lodh , Shalini Majumder , Tapan Chowdhury , Manashi De
The prediction of the binding affinity of proteins and ligands in computational drug discovery with high accuracy is critical when evaluating the effectiveness of potential therapeutic compounds. This research work introduces RLBindDeep, a novel deep learning architecture based on the amalgamation of the ResNet and LSTM architectures, for improved accuracy in predicting protein–ligand binding affinities. Most traditional methodologies utilizing conventional molecular docking techniques suffer from poor accuracy owing to semi-flexible modeling approaches and limited considerations of complex interactions. On the other hand, RLBindDeep, which is formulated as a pose-independent binding affinity regression model that directly predicts experimental protein–ligand binding affinities from fixed complex structures, without performing docking or rescoring multiple poses, has performed well in extracting important features of the protein–ligand interaction. Specifically, the extracted features encompass ligand physicochemical descriptors (e.g., molecular weight, LogP, TPSA), protein-level features such as amino acid composition, and detailed interaction features including van der Waals, electrostatic, and hydrogen-bond energies. The model has been tested rigorously over the CASF-2016 benchmark dataset and has returned Pearson’s coefficient R=0.875, Spearman’s coefficient ρ=0.864, and Root Mean Square Error RMSE=0.993. This significantly outperforms existing state-of-the-art models, such as HAC-Net and AutoDock Vina. Improved accuracy and robustness in RLBindDeep further highlight the possibility of deep learning to revolutionize computational drug discovery processes, making strategies for drug development more efficient and targeted.
在计算药物发现中,高精度地预测蛋白质和配体的结合亲和力对于评估潜在治疗化合物的有效性至关重要。本研究引入了RLBindDeep,这是一种基于ResNet和LSTM架构融合的新型深度学习架构,用于提高预测蛋白质-配体结合亲和力的准确性。由于半灵活的建模方法和对复杂相互作用的考虑有限,大多数利用传统分子对接技术的传统方法精度较差。另一方面,RLBindDeep是一种不依赖于姿态的结合亲和力回归模型,它可以直接预测固定复杂结构中实验蛋白与配体的结合亲和力,而不需要进行对接或重新记录多个姿态,在提取蛋白质与配体相互作用的重要特征方面表现良好。具体来说,提取的特征包括配体的物理化学描述符(如分子量、LogP、TPSA)、蛋白质水平特征(如氨基酸组成)和详细的相互作用特征(包括范德华、静电和氢键能)。该模型已在CASF-2016基准数据集上进行了严格测试,并返回Pearson系数R=0.875, Spearman系数ρ=0.864,均方根误差RMSE=0.993。这明显优于现有的最先进的模型,如HAC-Net和AutoDock Vina。RLBindDeep提高了准确性和鲁棒性,进一步强调了深度学习在彻底改变计算药物发现过程中的可能性,使药物开发策略更高效、更有针对性。
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引用次数: 0
Discovery of a novel PI3Kα inhibitor for breast cancer therapy via virtual screening method, molecular dynamics simulation and biological evaluation 通过虚拟筛选方法、分子动力学模拟和生物学评价发现一种新的乳腺癌治疗PI3Kα抑制剂
IF 3 4区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2026-01-12 DOI: 10.1016/j.jmgm.2026.109289
Thitiya Boonma , Bodee Nutho , Phongthon Kanjanasirirat , Chananya Rajchakom , Nadtanet Nunthaboot
Phosphatidylinositol-4,5-bisphosphate 3-kinase alpha (PI3Kα) is a central signaling enzyme driving cell proliferation and growth in cancers including breast cancer. Selective inhibition of PI3Kα isoform has become a promising therapeutic approach. In this work, 2000 in-house natural compounds were virtually screened against the ATP-binding site of PI3Kα. Of these, 618 compounds were predicted to have acceptable drug-likeness, pharmacokinetic, and toxicity properties based on in silico ADMET screening. Docking analysis highlighted four candidates forming stable hydrogen bonds with key residues V851, S854, and Q859 in the PI3Kα binding pocket. Molecular dynamics simulations were then used to assess their structural features and dynamic stability. Hit 2 was found to form strong hydrogen bonds with E849 and V851 of the PI3Kα protein. MM/GBSA-based binding free energy analysis supported that Hit 2 possessed the most favorable binding affinity to PI3Kα among the identified candidates. In vitro cytotoxicity assays were then performed in MCF-7 and MDA-MB-231 breast cancer cell lines, with alpelisib as a reference compound. Hit 2 reduced cell viability in both cell lines, but its effect was particularly pronounced in MDA-MB-231 cells, a model of triple-negative breast cancer (TNBC). These results suggest that Hit 2 represents a promising natural scaffold for further design and development in breast cancer therapy, with particular relevance for aggressive TNBC.
磷脂酰肌醇-4,5-二磷酸3-激酶α (PI3Kα)是驱动包括乳腺癌在内的癌症细胞增殖和生长的中心信号酶。选择性抑制PI3Kα异构体已成为一种很有前途的治疗方法。在这项工作中,2000种内部天然化合物对PI3Kα的atp结合位点进行了虚拟筛选。其中,618种化合物预测具有可接受的药物相似性、药代动力学和基于计算机ADMET筛选的毒性。对接分析显示,在PI3Kα结合口袋中,有4个候选分子与关键残基V851、S854和Q859形成稳定的氢键。然后用分子动力学模拟来评估它们的结构特征和动态稳定性。Hit 2与PI3Kα蛋白的E849和V851形成强氢键。基于MM/ gbsa的结合自由能分析结果表明,Hit 2与PI3Kα的结合亲和力最强。然后在MCF-7和MDA-MB-231乳腺癌细胞系中进行体外细胞毒性测定,以alpelisib为参比化合物。Hit 2降低了两种细胞系的细胞活力,但其作用在三阴性乳腺癌(TNBC)模型MDA-MB-231细胞中尤为明显。这些结果表明,Hit 2代表了一种有前途的天然支架,可以进一步设计和开发乳腺癌治疗,特别是与侵袭性TNBC相关。
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Journal of molecular graphics & modelling
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