Journal of molecular graphics & modelling最新文献

{"title":"Exploring the capability of tetra-penta-octagonal (TPO) graphene as anode material for sodium storage via DFT and AIMD calculations","authors":"Nafis Ahmad ,&nbsp;Anjan Kumar ,&nbsp;Munther Kadheem ,&nbsp;Prakash Kanjariya ,&nbsp;Asha Rajiv ,&nbsp;Aditya Kashyap ,&nbsp;Helen Merina Albert ,&nbsp;Mehul Manu","doi":"10.1016/j.jmgm.2025.109077","DOIUrl":"10.1016/j.jmgm.2025.109077","url":null,"abstract":"<div><div>Batterie energy storage systems (BESSs) have a critical role in today's human society. Sodium-ion batteries (SIBs) have been introduced as potential BESSs for human demands. Herein, we probed the sodium storage characteristics of tetra-penta-octagonal (TPO) graphene for SIBs using DFT and Ab Initio Molecular Dynamics (AIMD) methods. The projected density of states (PDOS) profiles indicate a non-covalent interaction between sodium and host that is critical for reversible adsorption of sodium. Climbing image (CI-NEB) calculation reveals a low diffusion energy barrier of 0.037–0.058 eV, suggesting efficient sodium ion mobility for fast charge technology. Theoretical calculations predict a high capacity of 781 mAh/gr which is higher than many other 2D materials. An average open-circuit voltage (OCV) of 0.98 V shows that this structure works within the appropriate operating voltage range of SIBs. AIMD calculations illustrated that the fully adsorbed structure remains stable at 300 K.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"139 ","pages":"Article 109077"},"PeriodicalIF":2.7,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144072359","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 screening of peptide inhibitors targeting α-synuclein for Parkinson's disease","authors":"Gulsah Gul","doi":"10.1016/j.jmgm.2025.109079","DOIUrl":"10.1016/j.jmgm.2025.109079","url":null,"abstract":"<div><div>Parkinson's disease affects cognitive, motor, and autonomic functions due to nervous system degeneration. Though no cure exists, medications and therapies can help alleviate symptoms, but their effectiveness diminishes as the disease progresses, ultimately increasing the need for alternative treatments. α-Synuclein has long been one of the main targets in addressing Parkinson's through drug design studies, but no drugs are yet approved against α-Synuclein aggregation. Therefore, this study aims to develop potential inhibitors of fibrillization by screening thousands of peptides in terms of their binding abilities via Molecular Docking and Molecular Dynamics simulations. Our results show that peptides with Lysine and Arginine at terminal groups result in higher binding affinities to the C-terminal domain. Among the heptapeptides examined, RWRRKRL shows the highest binding free energy to the protein while KKRHKWR exhibits superior stabilizing effect, interacting with both N- and C-terminal regions of α-Synuclein. The inhibitory potential of peptides on the fibrillar structure of protein varies with concentration, and RWRRKRL at 1:3 protein-peptide monomer ratio shows promise as an inhibitor by reducing the internal H-bonds of the protein and increasing RMSD values. These results reveal that short-chain peptides can be designed against α-Synuclein oligomerization offering a potential therapeutic approach for preventing Parkinson's.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"139 ","pages":"Article 109079"},"PeriodicalIF":2.7,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144069055","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":"Harnessing computational tools for drug discovery: An integrated computational approach to identify potential BACE-1 inhibitors","authors":"Usman Shareef ,&nbsp;Muhammad Kazim Zargaham ,&nbsp;Ahsan Ibrahim ,&nbsp;Aisha Altaf ,&nbsp;Rohail Bhatti","doi":"10.1016/j.jmgm.2025.109076","DOIUrl":"10.1016/j.jmgm.2025.109076","url":null,"abstract":"<div><div>The hallmark of Alzheimer's disease (AD), a progressive neurodegenerative condition, is the buildup of amyloid-beta (Aβ) plaque, which is mainly caused by β-secretase 1 (BACE-1) activity. BACE-1 inhibition is a potentially effective treatment strategy to lower the progression of AD. In order to find possible BACE-1 inhibitors using a drug repurposing technique, this study uses an integrated computational approach that includes pharmacophore modelling, virtual screening, molecular docking, MM-GBSA, molecular dynamics (MD) simulations, in-silico ADMET profiling, and PBPK modelling. A pharmacophore model, was created with known BACE-1 inhibitors to enable virtual screening of both novel and FDA-approved chemical libraries. Top candidates with good free energy scores and strong binding affinities were found using molecular docking and MM-GBSA calculations. The stability of shortlisted Hits inside the BACE-1 active site was further validated using MD simulations, which showed that some of the important interactions were maintained across a period of 50ns. ADMET and PBPK studies predicted favorable pharmacokinetic and safety profiles for the shortlisted hits, particularly for B2 and B9. These findings identify potential candidates for future experimental validation, offering an inexpensive approach for identification of compounds as potential BACE-1 inhibitors.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"139 ","pages":"Article 109076"},"PeriodicalIF":2.7,"publicationDate":"2025-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143947067","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":"Supervised machine learning and molecular docking modeling to identify potential Anti-Parkinson's agents","authors":"Adib Ghaleb ,&nbsp;Adnane Aouidate ,&nbsp;Mohammed Aarjane ,&nbsp;Hafid Anane","doi":"10.1016/j.jmgm.2025.109073","DOIUrl":"10.1016/j.jmgm.2025.109073","url":null,"abstract":"<div><div>Parkinson's disease is a neurodegenerative condition that affects the brain's neurons, and causes malfunction of nerve cells and their death. A neurotransmitter called dopamine interacts with the part of the brain in charge of coordination and movement. In general, the brain produces less dopamine as Parkinson's disease worsens; therefore, it becomes harder to control the movements. In this study, a dataset collected from CHEMBL library was applied to build four machine learning models using three different descriptors functions to determine the best models with the best features and suggest the best adenosine inhibitors. Molecular docking of adenosine A2A (PDB ID: <span><span>3UZA</span><svg><path></path></svg></span>) receptor was applied to identify the potential inhibitors. The machine learning and molecular docking results indicate that XGBoost model with RDkit features is an excellent model for this dataset to explore new Anti-Parkinson's agents.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"139 ","pages":"Article 109073"},"PeriodicalIF":2.7,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143931324","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":"Elucidating OASL-RNA Interactions: Structural and energetic insights into vault RNAs binding","authors":"Erick Bahena-Culhuac ,&nbsp;Rodolfo Daniel Avila-Avilés ,&nbsp;José Manuel Hernández-Hernández ,&nbsp;Rodolfo Gamaliel Avila-Bonilla","doi":"10.1016/j.jmgm.2025.109071","DOIUrl":"10.1016/j.jmgm.2025.109071","url":null,"abstract":"<div><div>Oligoadenylate synthetase-like (OASL) proteins play an essential role in the innate immune response by detecting RNA molecules and modulating antiviral signalling pathways. This study investigated the structural and functional dynamics of OASL in its interaction with endogenous vault RNAs (vtRNAs) through computational analyses, including molecular docking and molecular dynamics simulations. Predicted 3D structures of vtRNAs revealed key interactions within the positively charged RNA-binding groove of OASL, involving residues such as Arg45, Lys63, and Arg196. Among the vtRNAs analysed, vtRNA 1-1 exhibited the highest binding affinity and stability, inducing conformational changes in OASL consistent with canonical activation mechanisms. In contrast, vtRNA 1–2 and 1–3 demonstrated moderate interactions, while vtRNA 2-1 had minimal impact on OASL conformation. Our results underscore the critical role of guanine- and cytosine-enriched regions in mediating binding stability and specificity, as corroborated by MM/GBSA calculations. The study highlights the molecular determinants of OASL-vtRNA interactions, offering structural insights into the mechanisms of nucleic acid recognition.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"139 ","pages":"Article 109071"},"PeriodicalIF":2.7,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143947068","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":"Investigation of the temperature effect on the properties of biological nanomembranes with different concentrations of cholesterol using molecular dynamics simulation","authors":"Armin Jarahi Khameneh ,&nbsp;Azadeh Kordzadeh ,&nbsp;Abbas Rastgoo ,&nbsp;Amin Hadi","doi":"10.1016/j.jmgm.2025.109074","DOIUrl":"10.1016/j.jmgm.2025.109074","url":null,"abstract":"<div><div>The cell membrane is the outermost boundary of the cell, and its role is to protect the cell. Drugs must first pass through the membrane to enter the cell; therefore, investigating the properties of the bilayer membrane is of great importance and can provide important information regarding drug delivery processes. In this study, the effect of increasing temperature on the properties of bilayer membranes with 0 %, 10 %, 30 %, and 50 % cholesterol was investigated using molecular dynamics simulation. Moreover, the phase transition temperature of the lipid bilayer was selected based on the percentages of cholesterol. The results indicated that with increasing temperature, the membrane changed from gel phase to fluid phase. Moreover, a rise in temperature led to an increase in the area per lipid and a decrease in the order parameter, the reason for which was the increase in the kinetic energy of the molecules. The fluid phase membrane, which is at a higher temperature, had a higher diffusion coefficient than the gel phase membrane. The increase in the temperature caused the membrane with 0 % cholesterol to experience a 24 % decrease in the order parameter, while the structural properties of the membrane with 50 % cholesterol are almost constant with increasing temperature, indicating the rigidity of the membrane. With the increase in cholesterol concentration from 0 % to 50 %, the time for pore formation under the electric field increased from 0.26 ns to 8.46 ns. These results will be helpful in the development of drug delivery and therapeutic processes.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"139 ","pages":"Article 109074"},"PeriodicalIF":2.7,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144070523","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":"A DFT study of physical properties of the new Cr2S2BrCl material","authors":"S. Dahri ,&nbsp;A. Jabar ,&nbsp;L. Bahmad ,&nbsp;L.B. Drissi ,&nbsp;R. Ahl Laamara","doi":"10.1016/j.jmgm.2025.109075","DOIUrl":"10.1016/j.jmgm.2025.109075","url":null,"abstract":"<div><div>Using first-principles calculations, this study comprehensively investigates the structural, magnetic, electronic, optical, and thermodynamic properties of the newly material Cr₂S₂BrCl compound. The crystal structure was optimized, and the exchange-correlation interactions were modeled using the GGA + SOC + U approximation to capture the material's electronic structure accurately. Our magnetic analysis reveals significant spin polarization, with Cr atoms contributing dominantly to the overall magnetic moment, further supported by computed partial and total magnetic moments. The electronic density of states (DOS) and band structure calculations show that Cr₂S₂BrCl possesses a spin-dependent band gap. The optical properties, including the dielectric function and absorption coefficient, were evaluated, demonstrating strong absorption in the visible range, making this compound a candidate for optoelectronic devices. Additionally, thermoelectric properties, including the Seebeck coefficient, electrical conductivity, electronic thermal conductivity, figure of merit, electronic specific heat, and Pauli magnetic susceptibility, were evaluated.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"139 ","pages":"Article 109075"},"PeriodicalIF":2.7,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143937800","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":"OH-initiated degradation of 2,2′,4,4′,5,6′-hexabrominated diphenyl ether (BDE-154) in the atmosphere and wastewater: Mechanisms, kinetics, and ecotoxicity","authors":"Yunju Zhang ,&nbsp;Meilian Zhao ,&nbsp;Cen Yao ,&nbsp;Yuxi Sun ,&nbsp;Huirong Li","doi":"10.1016/j.jmgm.2025.109070","DOIUrl":"10.1016/j.jmgm.2025.109070","url":null,"abstract":"<div><div>In the present work, the reaction mechanism and kinetics of 2,2′,4,4′,5,6′-hexabrominated diphenyl ether (BDE-154) with OH were researched by employing density functional theory (DFT) and transition state theory (TST). The gas-phase and aqueous solution reaction mechanisms and kinetic parameters were computed at the level of M06–2X/6–311++G (3df, 3pd)//M06–2X/6-311G (d,p). The OH-addition of the non-bromine replaced carbon atom of the aromatic ring in BDE-154 is superior to substitution and H-abstraction mechanisms. The secondary reaction referring to OH-addition adducts in the existence of O₂/NO will generate tribromophenol and OH-addition products. The majority of conversion products are still poisonous to hydrobiont. The KiSThelP program was applied to assess the overall rate coefficient and the individual rate coefficient at 258–328 K of 760 Torr. The overall rate coefficient at 298 K and 760 Torr are 9.40 × 10⁻¹⁴ cm³ molecule⁻¹ s⁻¹ and 3.60 × 10⁶ M⁻¹ s⁻¹ in atmosphere and wastewater. The half-lives are 123.1 days and 1.93 × 10²-1.93 × 10¹¹ s, respectively. These results elucidated the conversion mechanism, atmospheric fate and ecotoxicity of BDE-154 in advanced oxidation procedure.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"139 ","pages":"Article 109070"},"PeriodicalIF":2.7,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143929164","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":"A molecular modeling study of pristine and Li-doped B16N16 nanocages for sensing G-series nerve agents using DFT-D3","authors":"Hafiz Ali Rizwan ,&nbsp;Muhammad Usman Khan ,&nbsp;Abida Anwar ,&nbsp;Munazza Idrees ,&nbsp;Nasir A. Siddiqui","doi":"10.1016/j.jmgm.2025.109069","DOIUrl":"10.1016/j.jmgm.2025.109069","url":null,"abstract":"<div><div>The detection and removal of toxic warfare agents, such as G-series nerve agents, is a critical area of research for environmental safety and public health. This research uses density functional theory (DFT) to address the gap in understanding the molecular-level interactions of G-series nerve agents with boron nitride nanocages (BNNC) and lithium-doped boron nitride nanocages (Li-BNNC). The investigated nanostructures exhibited high negative adsorption energies, allowing the G-series nerve agents to adsorb strongly onto the BNNC and Li-BNNC surfaces. The Li-BNNC complexes undergo the chemisorption process with the adsorption energy, ranging from −31.819 kcal/mol to −33.635 kcal/mol. The findings of frontier molecular orbitals (FMOs) and density of states (DOS) indicated that the electronic characteristics of GS@BNNC and GS@Li-BNNC had been significantly changed, resulting in a smaller energy gap and higher conductivity. The Li-doping results in much lower energy gaps in Li-BNNC systems, such as 2.707 eV for Tabun@Li-BNNC, that cause higher electrical conductivity. Tabun@Li-BNNC has the highest electrical conductivity of 4.60 × 10¹² among Li-doped systems, and Tabun@BNNC has a high conductivity of 2.84 × 10¹² among undoped BNNC systems. Li-BNNC systems have higher electrical conductivity, which makes them good sensors for detecting G-series nerve agents. These findings provide a molecular-level understanding of the effect of Li-doping on BNNC-based nanomaterials and their potential for advancing nanotechnology-driven gas sensors.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"139 ","pages":"Article 109069"},"PeriodicalIF":2.7,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143901972","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":"Application of machine learning approaches for estimating carbon dioxide absorption capacity of a variety of blended imidazolium-based ionic liquids","authors":"Alexei Rozhenko ,&nbsp;Fahimeh Hadavimoghaddam ,&nbsp;Peyvand Valeh-e-Sheyda ,&nbsp;Mohsen Tamtaji ,&nbsp;Jafar Abdi","doi":"10.1016/j.jmgm.2025.109060","DOIUrl":"10.1016/j.jmgm.2025.109060","url":null,"abstract":"<div><div>Ionic liquids (ILs) have gained attention in recent times as potentially effective absorbents for CO₂ emissions owing to the number of their notable attributes, including reduced volatility, enhanced thermal consistency etc. Due to the number of challenges of thermodynamic models in forecasting CO₂ solubility in ILs under a variety of operating conditions, machine learning (ML) approaches have been developed as a result of the necessity for an alternate solution. Nevertheless, there are currently quite a few of forecasting techniques available for evaluating the solubility of CO₂, specifically in combinations of imidazolium-based ILs. For this reason, the present study focuses on the utilization of molecular structure-based descriptors as an alternative chemistry concept for predicting the CO₂ solubility in an imidazolium-based ILs mixture. This research utilized and contrasted 6 sophisticated machine learning models (AdaBoost-SVR, Extra trees, DT, CatBoost, LightGBM, XGBoost) to determine the most effective method for target parameter estimation. The study employed an exclusive and all-encompassing databank consisting of 43 imidazolium-based ILs, 26 input variables, and 4397 experimental data points in total. The remarkable 90 % overall accuracy consistently surpassed by all models serves as evidence of the ML methodologies' robustness and efficacy. The highest-performing approaches, XGBoost, exhibited a remarkable precision level of R² being equal to 0.999 and RMSE of 0.0077. A comprehensive trend analysis was performed to assess the XGBoost model's performance across different operational scenarios such as molecular weight, temperature, water content, and pressure. The developed model proved to be capable of accurately detecting patterns in various operating conditions. By employing sensitivity analysis with SHAP values, it was observed that pressure, temperature, and molecular weight were the most impactful factors influencing the XGBoost model's predictions.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"139 ","pages":"Article 109060"},"PeriodicalIF":2.7,"publicationDate":"2025-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143891082","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}