Journal of molecular graphics & modelling最新文献

{"title":"Computational modeling of novel perovskite oxides InXO3 (Be, Ca): Phase stable and sustainable materials for optoelectronic devices","authors":"Maaz Azeem ,&nbsp;Muhammad Khuram Shahzad ,&nbsp;Bekzod Matyakubov ,&nbsp;Ghulam Abbas Ashraf ,&nbsp;Vineet Tirth ,&nbsp;Ali Algahtani ,&nbsp;N. Sfina ,&nbsp;Naoufel Ben Hamadi","doi":"10.1016/j.jmgm.2025.109177","DOIUrl":"10.1016/j.jmgm.2025.109177","url":null,"abstract":"<div><div>Optoelectronics devices need improved performance, and there are challenges in achieving high efficiency. The perovskite compounds have become the center of attraction for their properties and characteristics. The studies on the double perovskite have gained attention due to its adjustable bandgap, better properties, and best optoelectronics applications. This study investigates the novel perovskite InXO₃ (X = Be, Ca) for structural, electronic, mechanical, phonon, and optical properties by using DFT simulations. We calculated the characteristics of perovskite using the CASTEP simulations technique and LDA-CAPZ approximation. Achieved the cubic structure, negative formation energy (InBeO₃ is −1.68 eV/atom &amp; InCaO₃ is −1.92 eV/atom), and tolerance factors (InBeO₃ is 0.84 &amp; InCaO₃ is 0.88) of both perovskite compounds predicting the stability of the materials. The electronic property disclosed that the compounds have a metallic nature. For the electronic properties, the band gap of the InBeO3 compound is 4.05 eV. After elemental substitution, the band gap of the InCaO₃ compound is reduced to 2.67 eV, which falls within the visible range and is most suitable for optoelectronics devices. The mechanical properties calculated on the positive values of coordinates C₄₄, C_11, and C₁₂ show the stability of both structures of the compounds. The excellent optical properties are calculated by full polarization for absorption, conductivity, loss function, refractive index, dielectric function &amp; loss function from the energy range that varies for both InBeO₃ and InCaO₃. The proposed results of novel perovskite InXO₃ (X = Be, Ca) oxides are a potential candidate for optoelectronics applications such as photodetectors and LEDs devices.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"142 ","pages":"Article 109177"},"PeriodicalIF":3.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145119051","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}

{"title":"In silico investigation of molecular mechanisms underlying the function of NLuc and its variants","authors":"Mina Oliayi,&nbsp;Rahman Emamzadeh,&nbsp;Mohamad Reza Ganjalikhany","doi":"10.1016/j.jmgm.2025.109212","DOIUrl":"10.1016/j.jmgm.2025.109212","url":null,"abstract":"<div><div>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 <em>Oplophorus gracilirostris</em>. 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 <em>in silico</em> 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.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"142 ","pages":"Article 109212"},"PeriodicalIF":3.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145470942","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}

{"title":"Synthesis, characterization and biological evaluation of a novel chalcone derivative: Spectroscopic, DFT, docking, ADMET and MD Studies","authors":"Manikandan Anandhan ,&nbsp;Vijayaraj Venkatachalam ,&nbsp;D. Karthikeyan ,&nbsp;Sebastian Anand ,&nbsp;A.R. Prabakaran ,&nbsp;Mysoon M. Al-Ansari ,&nbsp;Sandhanasamy Devanesan","doi":"10.1016/j.jmgm.2025.109161","DOIUrl":"10.1016/j.jmgm.2025.109161","url":null,"abstract":"<div><div>E)-3-(2-hydroxy-6-methoxyphenyl)-1-(1OH-Pheno thiazin-2-yl) prop 2-en-1-one (3HM1P) was synthesized by condensing 2-acetyl phenothiazine and 2-hydroxy-3-methoxy benzaldehyde. The molecular structure of 3HM1P was confirmed by analysis and well supported by FT-IR spectrum. The compound's geometry was optimized using the B3LYP method at the 6–311++G(d,p) level, and theoretical calculations were compared to experimental data. Linear optical absorption spectra were analyzed to study solvent effects on 3HM1P, with HOMO-LUMO analysis revealing a highest energy gap of 3.27 eV in hexane. Molecular electrostatic potential (MEP) analysis identified electron-rich and electron-deficient regions, crucial for enzyme interactions. Natural bond orbital (NBO) analysis indicated a maximum stabilization energy of 392.59 kJ/mol from π→π∗ orbital overlap. Antibacterial potential was assessed through molecular docking studies against the 2JIU protein, supported by early drug-likeness evaluations and ADMET virtual screening. Molecular dynamics simulations confirmed successful docking of 3HM1P-3JUV, while normal mode analysis indicated stable and flexible molecular mobility at the binding site, with a low eigenvalue of 2.6383 × 10⁻⁰⁴.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"142 ","pages":"Article 109161"},"PeriodicalIF":3.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145106255","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}

{"title":"Ricci-GraphDTA: A graph neural network integrating discrete Ricci curvature for drug–target affinity prediction","authors":"Xiangxiang Zheng ,&nbsp;Zhongrong Zhang ,&nbsp;Xiaona Zhang ,&nbsp;Nengzhi Jin ,&nbsp;Yunyun Zhang","doi":"10.1016/j.jmgm.2025.109170","DOIUrl":"10.1016/j.jmgm.2025.109170","url":null,"abstract":"<div><div>Drug–target affinity (DTA) prediction facilitates accelerated drug screening and reduces development costs. To enhance prediction performance and generalization capability, this paper proposes a DTA prediction model based on discrete curvature, named Ricci-GraphDTA, which integrates molecular graph and protein sequence modeling for efficient and accurate DTA prediction. The model consists of three parts: feature encoding, input representation learning, and affinity prediction. In the feature encoding stage, drug molecules are modeled as graphs, where Forman curvature is introduced to adjust the weights of neighbor information aggregation. A GIN residual network is then used to capture the local geometric and topological features of molecules. Protein sequences are modeled using BiLSTM to extract global dependency features, enhanced by an attention mechanism to capture long-range dependencies and key residue interactions—overcoming the limitations of traditional CNNs in handling long-range dependencies. In the input representation learning stage, the high-level representations of drugs and proteins are concatenated and passed through multiple nonlinear transformations to extract cross-modal interaction features, which are then used for affinity prediction. Experimental results demonstrate that Ricci-GraphDTA exhibits significant performance across various evaluation metrics on the Davis and KIBA datasets. Further cold-start experiments demonstrate the strong generalization ability of Ricci-GraphDTA in scenarios involving unseen drugs or targets, highlighting its potential in real-world drug discovery applications. On average, it achieves a 22.5% reduction in MSE across three cold-start tasks, with over 42% reduction in the dual cold-start setting, showcasing excellent structural modeling capability and robustness.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"142 ","pages":"Article 109170"},"PeriodicalIF":3.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145086332","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}

{"title":"Discovery of potential attention deficit and hyperactivity disorder (ADHD) drug molecules from natural compounds: In silico studies with Tanimoto similarity","authors":"Onur Ertik","doi":"10.1016/j.jmgm.2025.109200","DOIUrl":"10.1016/j.jmgm.2025.109200","url":null,"abstract":"<div><div>Attention deficit and hyperactivity disorder (ADHD) is a neurological disorder that prevents individuals from developing their potential and causes an inability to focus, especially in children, and the prevalence of ADHD in adults has been increasing. There is a very limited group of drugs for treatment of ADHD, the most important of which is methylphenidate. Therefore, the discovery of new drug molecules becomes very important because of limited drugs. In this study, methylphenidate molecule was compared with 790096 molecules by utilizing Tanimoto similarity of natural compounds and molecules were identified by second filtering according to blood-brain barrier penetration. Then, molecules were docked with dopamine transporter (DAT) and compounds with better binding scores than methylphenidate were identified and molecular dynamics simulation studies were done for the best pose and validated conformation. In addition, molecular docking and dynamic simulations were performed for monoamine oxidase A and B (MAO-A and MAO-B) in order to control the state of depression frequently encountered in ADHD individuals. The results suggest the compound 3706153 ((octahydro-1H-quinolizin-1-yl)methyl 2-(naphthalen-1-yl)acetate) has potentially inhibitory molecule for DAT, MAO-A and MAO-B and have a potential of the main structure in the development of alternative drug molecule for ADHD from the natural compounds.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"142 ","pages":"Article 109200"},"PeriodicalIF":3.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145362975","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}

{"title":"First-principles study of toxic industrial gases adsorption on magnesium (4,4)-Porphyrin nanoballs: Electronic structure, dipole moment modulation, and high-sensitivity gas sensing performance","authors":"Amirhassan Moallem ,&nbsp;Sattar Arshadi ,&nbsp;Mohammad Reza Sarmasti Emami ,&nbsp;Ahad Khaghani ,&nbsp;Mina Salary ,&nbsp;Omid Marvi","doi":"10.1016/j.jmgm.2025.109198","DOIUrl":"10.1016/j.jmgm.2025.109198","url":null,"abstract":"<div><div>The adsorption behavior of five Toxic industrial gases (TI_Gas) - cyanogen chloride (CNCl), cyanogen (C₂N₂), dichloroacetylene (C₂Cl₂), hydrogen cyanide (HCN), and phosgene (COCl₂) - on a Mg-porphyrin nanoball was investigated using density functional theory (DFT). The gases interacted with the nanoball via their primary functional groups, exhibiting negative, physical, and reversible adsorption. In all configurations, gas adsorption induced a significant increase (approximately 134 %) in the nanoball's band gap, leading to a substantial reduction in conductivity. Equilibrium distances between the gases and the central magnesium ions ranged from 2.25 to 3.9 Å, confirming physisorption. The recovery times were in the microsecond, nanosecond, and picosecond ranges, respectively, indicating rapid adsorption-desorption dynamics. Natural Bond orbital (NBO) analysis revealed electron transfer from the highest occupied molecular orbital (HOMO) of the gases to the lowest unoccupied molecular orbital (LUMO) of the nanoball, reducing the positive charge on magnesium ions while increasing the gas molecules' positive charge. Within the porphyrin rings, nitrogen atoms lost electron density, whereas carbon atoms gained electrons from the nanoball's wings. Frontier molecular orbital (FMO) and charge transfer analyses further supported electron donation from the gases to the nanoball. The Mg-porphyrin nanoball's six adsorption sites enable saturation-free detection of toxic industrial (TI) gases, even in the presence of oxygen, nitrogen, or humidity.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"142 ","pages":"Article 109198"},"PeriodicalIF":3.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145390466","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}

{"title":"Vanalyzer: an open-source tool for automated statistical analysis and continuous updating of vanadate-binding sites in the Protein Data Bank","authors":"Alexander Trachtenberg,&nbsp;Barak Akabayov","doi":"10.1016/j.jmgm.2025.109223","DOIUrl":"10.1016/j.jmgm.2025.109223","url":null,"abstract":"<div><div>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.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"142 ","pages":"Article 109223"},"PeriodicalIF":3.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145564194","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}

{"title":"Design and evaluation of hole transporting molecules for flexible perovskite solar cells: Enhancing efficiency and optoelectronic properties","authors":"Shanza Hameed ,&nbsp;Shaukat Ali ,&nbsp;Ijaz Ahmad Bhatti ,&nbsp;Muhammad Yasin Naz","doi":"10.1016/j.jmgm.2025.109205","DOIUrl":"10.1016/j.jmgm.2025.109205","url":null,"abstract":"<div><div>Flexible perovskite solar cells (PSCs) are emerging as a promising photovoltaic technology for portable and wearable electronics, offering excellent power conversion efficiencies (PCEs) and ease of processing. In this work, we present five newly designed foldable hole transport materials (HTMs), labeled C1M1-C1M5, engineered by thiophene-bridged acceptor modifications of the reference CM molecule. Using density functional theory (DFT), we explore the structural, electronic, optical, and photovoltaic properties of these molecules.</div><div>The results show that the newly designed HTMs exhibit narrow band gaps (1.65–2.32 eV), significantly lower than the CM reference (3.75 eV). Notably, the extended conjugation length of the molecules contributes to their red-shifted absorption (up to 832 nm), enhanced dipole moments (ranging from 6.37 to 19.14 D), and improved exciton dissociation, particularly for C1M5, with an exciton binding energy of 0.22 eV. Furthermore, the charge transport characteristics were found to be promising, with C1M4 exhibiting the highest charge transmission (λe = 0.036577, λh = 0.050162), where electron transport was slightly more favorable than hole transport. In conclusion, these newly engineered HTMs are highly promising for next-generation solar devices due to their excellent solution processability, efficient light harvesting, and charge transport capabilities.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"142 ","pages":"Article 109205"},"PeriodicalIF":3.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145444880","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}

{"title":"Interpretable support vector classifier for reliable prediction of antibacterial activity of modified peptides against Escherichia coli","authors":"Remmer L. Salas ,&nbsp;Portia Mahal G. Sabido ,&nbsp;Ricky B. Nellas","doi":"10.1016/j.jmgm.2025.109188","DOIUrl":"10.1016/j.jmgm.2025.109188","url":null,"abstract":"<div><div>Antimicrobial peptides (AMPs) are promising alternatives to traditional antibiotics, whose effectiveness is declining due to rising antimicrobial resistance (AMR). To accelerate AMP discovery, we developed ISCAPE (<strong>I</strong>nterpretable <strong>S</strong>upport Vector <strong>C</strong>lassifier of <strong>A</strong>ntibacterial Activity of <strong>P</strong>eptides against <strong><em>E</em></strong><em>scherichia coli</em>), a machine learning (ML) model that addresses the limitations of current AMP predictors. ISCAPE requires only a Simplified Molecular-Input Line-Entry System (SMILES) string as input and can predict the activity of both natural and chemically modified peptides against <em>E. coli</em> ATCC 25922. Activity is defined by a minimum inhibitory concentration (MIC) threshold of ≤16 μg/mL. To ensure reliability, only MIC values obtained under comparable experimental conditions were included in our curated dataset. ISCAPE outperformed the state-of-the-art AntiMPmod, achieving an area under the receiver operating characteristic curve (AUROC) of 91.83% and a Matthew's correlation coefficient (MCC) of 71.86%. Features driving this performance include the fraction of carbon-carbon pairs and feature- and count-based extended connectivity fingerprints (ECFPs). Model interpretability is enhanced through SHapley Additive exPlanations (SHAP), which identifies the molecular features most critical for AMP activity. To our knowledge, ISCAPE is the first interpretable ML predictor capable of predicting antibacterial activity for both natural and modified peptides against a specific <em>E. coli</em> strain. It is a user-friendly tool that allows experimentalists to pinpoint key molecular features, reducing the need for extensive structure-activity relationship (SAR) studies and guiding the design of novel AMPs.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"142 ","pages":"Article 109188"},"PeriodicalIF":3.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145267854","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}

{"title":"Computer-based discovery of SIRT7 inhibitors from Nigella sativa for cancer treatment","authors":"Ashik Sharfaraz ,&nbsp;Aysha Ferdoushi ,&nbsp;Md Arju Hossain ,&nbsp;Abida Sultana Nupur ,&nbsp;Umme Salma ,&nbsp;Md. Fazlul Karim","doi":"10.1016/j.jmgm.2025.109176","DOIUrl":"10.1016/j.jmgm.2025.109176","url":null,"abstract":"<div><h3>Background</h3><div>SIRT7, a nicotinamide adenine dinucleotide (NAD+)-dependent deacetylase, is implicated in tumorigenesis, making it a promising therapeutic target for cancer treatment.</div></div><div><h3>Aim</h3><div>This study aims to identify potent and selective bioactive candidate inhibitors of SIRT7 by virtually screening small-molecule compounds derived from <em>Nigella sativa</em> (<em>N. sativa</em>) and evaluating their drug-likeness and physical stability using computational methods.</div></div><div><h3>Methods</h3><div>The structure of SIRT7 was retrieved from the RCSB Protein Data Bank (PDB), and <em>N. sativa</em>-derived small molecules were obtained from the PubChem database. Molecular docking was performed using PyRx 0.8 and PyMOL version 2.3.3. Pharmacokinetic parameters and antitumor effects were assessed using SwissADME, pkCSM, and PASS analysis. Furthermore, binding stability was checked through Molecular Dynamics (MD) Simulationusing Schrödinger's Desmond v3.6 program for 100 ns.</div></div><div><h3>Results</h3><div>From 159 <em>N. sativa</em>-derived compounds, Chrysin, Pinocembrin, Nigellidine, Nigellicine, and Epicatechin showed high binding affinities (−9.3 to −8.7 kcal/mol) and favorable oral bioavailability with low toxicity. Chrysin (CID: 5281607) exhibited the strongest binding score (−9.3 kcal/mol), stable hydrogen bonding, and robust pharmacokinetic properties. PASS analysis highlighted predicted anticancer activities including TP53 activation, apoptosis induction, and antimutagenic effects, particularly for Chrysin, Pinocembrin, and Epicatechin. MD simulation confirmed stable SIRT7–Chrysin interactions, supported by favorable MM/GBSA free energy (−77.11 kcal/mol).</div></div><div><h3>Conclusion</h3><div>This study highlights <em>N. sativa</em> phytochemicals as potential SIRT7 inhibitors, with Chrysin as the lead candidate and Pinocembrin and Nigellidine as additional promising compounds. The findings offer a computational framework for future validation and development of selective SIRT7-targeted anticancer therapeutics.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"142 ","pages":"Article 109176"},"PeriodicalIF":3.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145080806","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}