Journal of molecular graphics & modelling最新文献

{"title":"Effect of isomerism, inter-ring torsion angle and chain length in structural and electronic properties of oligothiophenes: computational study","authors":"Belgacem Bezzina ,&nbsp;Safia Himri ,&nbsp;Mohamed Tayeb Abedghars ,&nbsp;Assia khelalfa ,&nbsp;Djameleddine Khatmi","doi":"10.1016/j.jmgm.2025.109085","DOIUrl":"10.1016/j.jmgm.2025.109085","url":null,"abstract":"<div><div>Density Functional Theory (DFT) and Time-Dependent DFT (TD-DFT) methods are employed to investigate the influence of isomerism and inter-ring torsion angle on the energetic, electronic, and structural properties of bithiophenes. Furthermore, the effect of the chain length of polythiophene (1–24 units) on their structural and electronic properties has been established.</div><div>The anti-gauche rotamer represents the most energetically favorable and reactive conformation in 2,2′-bithiophene, while the syn-gauche is the less stable rotamer in 3,3′-bithiophene. The inter-ring torsion energy profile for 2,2′-bithiophene reveals that the most stable conformer is twisted, exhibiting an optimized dihedral angle of 146.27° and a rotational barrier of approximately 1.48 kcal/mol. Increasing the length of the thiophene chain from one to 24 rings induces significant changes in their structural and electronic properties. The curvature behavior of oligothiophenes decreases as the oligomer size increases, from 0.0359 Å⁻¹ for T2 to 0.0270 Å⁻¹ for T24. The maximum absorption wavelengths of the oligothiophenes are red-shifted from 216.26 nm for T1 to 527.96 nm for T24. The orbital and optical band gaps of these oligothiophenes were calculated and plotted against 1/Tn. Linear relationships were obtained in both cases, with the optical band gap showing better agreement with experimental data. The extrapolated energy gap for infinitely long polythiophene is 2.15 eV in chloroform and 2.20 eV in the gas phase, consistent with the experimental values of 2.0–2.20 eV.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"140 ","pages":"Article 109085"},"PeriodicalIF":2.7,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144124233","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 pure and M-encapsulated (M=Na and K) B40 fullerenes as potential sensors for the flutamide drug","authors":"Zahra Bagherzadeh ,&nbsp;Sharieh Hosseini ,&nbsp;Mehdi Esrafili dizaji","doi":"10.1016/j.jmgm.2025.109084","DOIUrl":"10.1016/j.jmgm.2025.109084","url":null,"abstract":"<div><div>Recent research has illustrated that B40 fullerene can function as a sensor for detecting biological molecules, including drugs. This study examined the electron sensitivity of pure and metal-encapsulated (M = Na and K) B40 fullerenes about the anticancer drug flutamide (FLUT) by density functional theory (DFT). The findings revealed that the adsorption energy of FLUT on M@B40 fullerenes is −3.2 KCal/mol, slightly stronger than on the bare B40 fullerene in the gas phase. The dipole moment of the complexes increased significantly in both the gas and water phases. Thermodynamic parameters for the adsorption of FLUT indicated physical adsorption, which is exothermic and spontaneous at room temperature in both gas and water media. The energy gap of fullerenes after the adsorption of FLUT on B40 and Na@B40 decreased by 9 % and 3 %, respectively, resulting in increased electric conductivity and the generation of an electrical signal. Consequently, B40 and Na@B40 have the potential for sensing the FLUT anticancer drug.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"140 ","pages":"Article 109084"},"PeriodicalIF":2.7,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144124232","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 discovery of multi-target small molecules and efficient siRNA design to overcome drug resistance in breast cancer via local therapy","authors":"Seyed Mohammad Javad Hashemi ,&nbsp;Hossein Ghalehnoei ,&nbsp;Ali Barzegar ,&nbsp;Mehran Feizi-Dehnayebi ,&nbsp;Javad Akhtari ,&nbsp;Amir Mellati","doi":"10.1016/j.jmgm.2025.109086","DOIUrl":"10.1016/j.jmgm.2025.109086","url":null,"abstract":"<div><div>In this study, we designed an efficient siRNA for PKMYT1 gene knockdown and evaluated the binding affinity of various natural small molecules to key proteins associated with breast cancer through molecular docking and molecular dynamics (MD) simulations. Subsequently, among these molecules, The small molecule, SCHEMBL7562664, was introduced as a “golden ligand” that showed potent multi‐target activity as an antagonist for aromatase, estrogen receptor α, HER2, and PARP10, and as an agonist for MT2 and STING. Next, MD simulations of six protein‐ golden ligand complexes (PDB IDs: 4QXQ, 5GS4, 5JL6, 5LX6, 6ME6, and 7PCD), performed with GROMACS over 100 ns at 298.15 K, provided valuable information about their structural dynamics. Analysis of the radius of gyration (Rg) revealed that, while five complexes (7PCD, 5GS4, 5LX6, 4QXQ, and 5JL6) maintained compact structures (Rg between 1.7 and 2.3 nm), the 6ME6 complex exhibited a more extended and flexible conformation (average Rg ∼3.4 nm). Complementary RMSD analysis confirmed that most complexes rapidly stabilized with minimal deviations (generally &lt;0.3 nm), whereas the 6ME6 complex showed higher variability, reaching up to 0.67 nm. Furthermore, Binding free energy calculations using MM-GBSA and PBSA methods further supported these findings, with energies ranging from −21.45 ± 2.28 kcal/mol (5LX6) to −39.79 ± 1.34 kcal/mol (6ME6), indicating an optimal balance between intrinsic interactions and desolvation costs in the 6ME6 and 5JL6 systems. Based on DFT results, the golden ligand showed higher stability and lower reactivity compared to control ligands such as aromatase, tamoxifen, and dacomitinib, potentially leading to reduced off-target interactions and a more favorable safety profile. The integration of these data underscores the therapeutic potential of SCHEMBL7562664 as a multi-target agent for breast cancer, with promising pharmacokinetic properties that can be optimized for local treatment by incorporation into a 3D scaffold.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"140 ","pages":"Article 109086"},"PeriodicalIF":2.7,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144139292","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":"Adsorption of procarbazine anticancer drug over C24 and B12N12 nanocages: A comparative DFT study","authors":"Christian A. Celaya ,&nbsp;Carmen Martínez del Sobral Sinitsyna ,&nbsp;Luis Felipe Hernández-Ayala ,&nbsp;M. Solórzano ,&nbsp;Daniel G. Araiza ,&nbsp;Miguel Reina","doi":"10.1016/j.jmgm.2025.109087","DOIUrl":"10.1016/j.jmgm.2025.109087","url":null,"abstract":"<div><div>This research explores the interaction nature and adsorption energies of the anticancer agent procarbazine with C₂₄ and B₁₂N₁₂ nanocages using Density Functional Theory (DFT), A<em>b</em> <em>I</em><em>nitio</em> Molecular Dynamics simulations (AIMD), and docking studies. Both nanocages exhibited excellent structural stability and formed favorable interactions with procarbazine through chemisorption phenomena. These interactions ensure robust chemical attraction while preserving the structural integrity of the procarbazine. Thermodynamic analyses confirmed that the adsorption process is energetically favorable, and that B₁₂N₁₂ nanocage shows a stronger interaction compared to the C₂₄ system. Electronic property evaluations, including Density of States (DOS) and Molecular Electrostatic Potential (MEP), indicated that the nanocages do not negatively impact the electronic properties of procarbazine. Furthermore, HOMO-LUMO analyses revealed enhanced stability and change in the reactivity for the drug upon adsorption without compromising its anticancer efficacy. AIMD simulations at physiological temperature confirmed the structural stability of the procarbazine-nanocage complexes, with no dissociation observed. Additionally, the docking studies were conducted to evaluate the interaction potential of various compounds with a 16BP-DNA strand (CACTACAATGTTGCAAT) selected for its low guanine content (15 %). Blind docking of procarbazine revealed stable adducts with binding energies ranging from −4.08 to −5.95 kcal/mol. Procarbazine and other ligands demonstrated greater stability when forming adducts with guanine, suggesting that this interaction plays a critical role in stabilizing compound-DNA adducts. These findings underscore the potential of C₂₄ and B₁₂N₁₂ nanocages as promising candidates for biomedical applications.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"140 ","pages":"Article 109087"},"PeriodicalIF":2.7,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144147985","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":"Evaluating the binding potency of the carbapenem (T208) ligand and modelled non-halogen (NH2 and SH) and halogen (Br, Cl, F) derivatives in Mycobacterium tuberculosis L. D-transpeptidase","authors":"Duraisamy Thirumeignanam ,&nbsp;Palanisamy Deepa ,&nbsp;Balasubramanian Sundarakannan","doi":"10.1016/j.jmgm.2025.109082","DOIUrl":"10.1016/j.jmgm.2025.109082","url":null,"abstract":"<div><div>Improvements in medication are required because number of tuberculosis (TB)-related deaths increase during COVID-19 pandemic. Reducing efficiency of current therapeutic agents require creation of novel medications that aim specific targets and avoid existing resistance mechanisms. In this study, we had focused on tuberculosis, most deadly infection, which threatens humanity in the 20th century after COVID-19, and world's leading cause of infection-related mortality. Our main goal in this study was to understand the stability and potency of carbapenem (T208) ligands and their modelled derivatives (Br, Cl, F, NH₂, and SH) through hydrogen and halogen bond interactions that holds ligand-amino acid contact in the hinge region. This information will provide a clear picture of structural and binding characteristics of protein-ligand interactions. Further, this will aid chemists in creating new carbapenem ligands, which are expected to reduce the action of β-lactamase enzyme and serve as anti-TB drugs. The binding strength of carbapenem ligands with interacting hinge region amino acid side chains: tryptophan (Trp-340), histidine (His-336), histidine (His-352), cystine (Cys 354), and tyrosine (Tyr 318) were analyzed through interaction energies calculated at HF, M062X, M06HF, B3PW91, and MP2 level of theories for various basis sets (6-311G∗∗, SDD). Overall, derivatives of halogen atoms (Br, Cl, and F) and NH₂ enhanced the binding strength of T208 in β-lactamase enzymes. This opened up a new and unique pathway for derivatives preference on ligand that perfectly encloses amino acid in the hinge region.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"139 ","pages":"Article 109082"},"PeriodicalIF":2.7,"publicationDate":"2025-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144105707","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":"Electronic structures, bonding aspects and photophysical properties of N-heterocyclic carbene manganese complexes: DFT and TDDFT exploration","authors":"Mukhtar Ahmed ,&nbsp;Manjeet Kumar ,&nbsp;Subodh ,&nbsp;Sumit Sahil Malhotra ,&nbsp;Abdullah Saad Alsubaie ,&nbsp;Manoj Kumar Gupta ,&nbsp;Azaj Ansari","doi":"10.1016/j.jmgm.2025.109083","DOIUrl":"10.1016/j.jmgm.2025.109083","url":null,"abstract":"<div><div>Here we explored the influence of axial ligands on the structural, electronic, and photophysical properties of Mn(II)(TPP)(1,3-Me₂Imd)(L) complexes, where L = -NH₃, -OCH₃, -SH, -Cl, and -NO₂, using density functional theory (DFT) and time-dependent DFT (TDDFT) methods. Frontier molecular orbital analysis was performed to assess the reactivity behavior of the complexes which exhibit strong nonlinear optical properties due to their high polarizability. The nature of bonding and charge distribution was further investigated through electrostatic potential mapping, quantum theory of atoms in molecules, electron localization function and localized orbital locator analyses. Natural bond orbital analysis was also conducted to identify stabilizing interactions within the species. Our calculations reveal that the complex with an NH₃ axial ligand (species 1) possesses a larger HOMO-LUMO energy gap and a more negative electrostatic potential, suggesting lower reactivity due to the electron-donating character of the ligand. Furthermore, TDDFT results indicate strong light-harvesting efficiencies in the visible region (575–735 nm), with species 4 demonstrating the highest efficiency and species 5 the lowest. These findings provide insights into the design of Mn-based complexes for optoelectronic applications.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"139 ","pages":"Article 109083"},"PeriodicalIF":2.7,"publicationDate":"2025-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144105708","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":"Unveiling the role of Pt doping on the sensor behavior of graphene-based ternary (Boron)x-(Nitrogen)y-(Carbon)z for (x=y=1, z=2) monolayer for detection of NO2 and SO2 gases","authors":"Mustafa Habeeb Chyad ,&nbsp;Abdulrahman T. Ahmed ,&nbsp;Shoira Formanova ,&nbsp;Jayanti Makasana ,&nbsp;M.M. Rekha ,&nbsp;Aman Shankhyan ,&nbsp;T. Anand ,&nbsp;Kamal Kant Joshi ,&nbsp;Mustafa Shakir ,&nbsp;Ahmed M. Naglah","doi":"10.1016/j.jmgm.2025.109080","DOIUrl":"10.1016/j.jmgm.2025.109080","url":null,"abstract":"<div><div>Fabricating efficient sensors for detecting various gasses is one of the major challenges in environmental monitoring and safety. There has been extensive research in recent years into the applications of 2D nanomaterials as gas sensors thanks to their great surface-to-volume ratio as well as adjustable electronic characteristics. The current study, by employing DFT, aimed at examining the sensing capability of graphene-based ternary (Boron)_x-(Nitrogen)_y-(Carbon)_z for (x = y = 1, z = 2) (BNC₂) in detecting gasses, with a particular emphasis on the adhesion of H₂, H₂S, NO₂, and SO₂ onto both bare and platinum-doped BNC₂ (Pt@BNC₂). The findings indicated that the Pt atom exhibited a strong binding affinity to the BNC₂, albeit with a slight protrusion from the plane. The Pt@ BNC₂ demonstrated the most robust interaction with gasses, especially NO₂ and SO₂. The charge transport analysis revealed that the majority of gasses functioned as acceptors of charges, with NO₂ and SO₂ displaying considerable electron acquisition from the Pt@BNC₂. Furthermore, recovery time analyses indicated that doping the Pt atom significantly improved the capability of Pt@BNC₂ in sensing gasses in comparison to the bare BNC₂, particularly in detecting NO₂ and SO₂. The current study highlighted the adaptability of Pt@BNC₂ in both sensing and capturing gasses, being conducive to fabricating sophisticated sensing devices and preserving the environment.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"140 ","pages":"Article 109080"},"PeriodicalIF":2.7,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144134700","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":"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":"Generating a vast chemical space for high polar surface area triphenylamine polymers by machine learning-DFT calculations assisted reverse engineering for photovoltaics","authors":"Abrar U. Hassan ,&nbsp;Mamduh J. Aljaafreh","doi":"10.1016/j.jmgm.2025.109078","DOIUrl":"10.1016/j.jmgm.2025.109078","url":null,"abstract":"<div><div>The total polar surface area (TPSA) is a crucial parameter in photovoltaic (PV) materials, as it directly influences their solubility, processability, and device performance. This study leverages machine learning-assisted reverse engineering to generate a vast chemical space of high polar surface area triphenylamine (TPA) polymers for PV applications. By applying co-gradient boosted (xGBoost) and Random Forest algorithms to a dataset of 543 triphenylamine-based chromophores, high accuracy (R2 = 0.93–0.96) is achieved in predicting the TPSA of these chromophores. Feature importance analysis using the Shapley Additive eXplanation (SHAP) values reveals that the number of nitro groups (NOCount) has the highest impact on model performance. The generated model is rigorously evaluated using K-fold cross-validation and out-of-bag evaluation. 1000 new polymers are then generated with predicted TPSA values, including some with exceptionally high TPSA of up to 182. Further analysis of the charge transfer patterns in selected polymers shows that the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) are oriented in opposite directions, indicating a high potential for these materials in PV devices. The predicted PV performance of these polymers exhibits promising characteristics, with values of 54–79 % for the light-harvesting efficiency (LHIE), 1.63–1.68 V for the open-circuit voltage (V_oc), 0.54–0.92 for the fill factor (FF), and 21.99–32.43 mA/cm² for the short-circuit current density (J_sc).</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"139 ","pages":"Article 109078"},"PeriodicalIF":2.7,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144089019","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}