Journal of molecular graphics & modelling最新文献

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Manipulating high Curie temperature of Sm/Ag doped ZnO monolayers by first-principles GGA+U study 用第一性原理GGA+U研究Sm/Ag掺杂ZnO单层膜的高居里温度
IF 2.7 4区 生物学
Journal of molecular graphics & modelling Pub Date : 2025-06-02 DOI: 10.1016/j.jmgm.2025.109101
Hao Yuan , Yanfang Zhao , Yuanbin Xiao , Bing Yang , Wei Ding , Jian Lv
{"title":"Manipulating high Curie temperature of Sm/Ag doped ZnO monolayers by first-principles GGA+U study","authors":"Hao Yuan ,&nbsp;Yanfang Zhao ,&nbsp;Yuanbin Xiao ,&nbsp;Bing Yang ,&nbsp;Wei Ding ,&nbsp;Jian Lv","doi":"10.1016/j.jmgm.2025.109101","DOIUrl":"10.1016/j.jmgm.2025.109101","url":null,"abstract":"<div><div>This work studies the electronic structure, and magnetic properties of Sm/Ag doped ZnO monolayer by first-principles GGA + U calculations. The results show Sm-doped ZnO monolayer exhibits stable room temperature ferromagnetism with a high magnetic moment of 5.91 μB per unit. The total magnetic moment of the system is mainly contributed by Sm-4f, and the high Curie temperature results from the strong ferromagnetic coupling between the adjacent Sm atoms. The Ag-doped ZnO monolayers undergo magnetic quenching with the Ag doping concentration from 6.25 at.% to 12.5 at.%, which is extremely advantageous for designing and manufacturing magnetic switches. The ZnO monolayer shifts between the non-magnetic to the antiferromagnetic as the distance between neighboring two Ag atoms changes. In Sm-Ag co-doped ZnO monolayer, the Sm atom and Ag atom spin in opposite directions, and the magnetic moments partially cancel out, and the total magnetic moment of the system decreases. In addition, Sm/Ag mono-doped and Sm-Ag co-doped ZnO monolayer exhibited half-metallic behavior due to the impurity energy levels introduced in the bandgap by Sm/Ag dopant, and calculations of the formation energy show that dopants are prone to aggregate. This research may provide a reference for modifying the material properties of ZnO monolayers and designing nano-electronic and spintronic devices.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"140 ","pages":"Article 109101"},"PeriodicalIF":2.7,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144204613","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
Combinatorial chemistry-driven In silico design and computational evaluation of covalent peptidomimetic SARS-CoV-2 main protease inhibitors via structure-based virtual screening and multivariate analysis 基于结构的虚拟筛选和多变量分析,组合化学驱动的共价拟肽SARS-CoV-2主要蛋白酶抑制剂的计算机设计和计算评估
IF 2.7 4区 生物学
Journal of molecular graphics & modelling Pub Date : 2025-06-01 DOI: 10.1016/j.jmgm.2025.109100
Alessia Bono , Gabriele La Monica , Federica Alamia , Francesco Mingoia , Annamaria Martorana , Antonino Lauria
{"title":"Combinatorial chemistry-driven In silico design and computational evaluation of covalent peptidomimetic SARS-CoV-2 main protease inhibitors via structure-based virtual screening and multivariate analysis","authors":"Alessia Bono ,&nbsp;Gabriele La Monica ,&nbsp;Federica Alamia ,&nbsp;Francesco Mingoia ,&nbsp;Annamaria Martorana ,&nbsp;Antonino Lauria","doi":"10.1016/j.jmgm.2025.109100","DOIUrl":"10.1016/j.jmgm.2025.109100","url":null,"abstract":"<div><div>The COVID-19 pandemic has underscored the urgent need for specific pharmacological treatments beyond existing vaccines. One of the most attractive targets for antiviral therapies development is the SARS-CoV-2 Main Protease (M<sup>PRO</sup>), a key enzyme in viral life. The lack of M<sup>PRO</sup> human homologs and its conservation rate among coronaviruses make this enzyme strategically important. Considering its mechanism of action, the catalytic cysteine residue (Cys<sup>145</sup>) presents a prime target for covalent inhibition. Electrophilic warhead inhibitors, designed to react with this catalytic site, mimic the amide peptide bonds of the viral polyproteins, thereby facilitating their binding and subsequent inactivation of the enzyme. Their activity is further potentiated when incorporated into peptidomimetic structures. <em>In silico</em> approaches are gaining increasing importance in the search for effective COVID-19 treatments. In this view, this study focuses on developing an innovative <em>in silico</em> protocol for identifying anti-SARS-CoV-2 agents covalently targeting M<sup>PRO</sup>. To this purpose, a combinatorial library of 450 peptidomimetic compounds with aldehydic warheads was generated, refined to 388 compounds through docking studies, and further evaluated for covalent binding capabilities, revealing that compounds <strong>9</strong>–<strong>14</strong>, <strong>16</strong>, and <strong>20</strong> exhibited significantly higher affinities compared to known inhibitors, even during a 200 ns dynamics simulation, thus affirming the validity of the adopted design strategy. Furthermore, this work takes the advantages of our in-house ligand-based tool, the Biotarget Predictor Tool, available in DRUDIT, integrated with both structure-based techniques and, interestingly, multivariate statistical analysis.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"140 ","pages":"Article 109100"},"PeriodicalIF":2.7,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144196115","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
A new insight of structures, bonding and electronic properties for 6-mercaptopurine adsorbed on M@Au12 (M=Au, Ag, Pd and Pt) Nanoclusters: a theoretical perspective 6-巯基嘌呤在M@Au12 (M=Au, Ag, Pd和Pt)纳米团簇上吸附的结构、键和电子性质的新认识:理论视角
IF 2.7 4区 生物学
Journal of molecular graphics & modelling Pub Date : 2025-05-31 DOI: 10.1016/j.jmgm.2025.109097
Hongjiang Ren , Panpan Wang , Gang Zhu , Liuchang Wang , Gang Wang , Yaping He
{"title":"A new insight of structures, bonding and electronic properties for 6-mercaptopurine adsorbed on M@Au12 (M=Au, Ag, Pd and Pt) Nanoclusters: a theoretical perspective","authors":"Hongjiang Ren ,&nbsp;Panpan Wang ,&nbsp;Gang Zhu ,&nbsp;Liuchang Wang ,&nbsp;Gang Wang ,&nbsp;Yaping He","doi":"10.1016/j.jmgm.2025.109097","DOIUrl":"10.1016/j.jmgm.2025.109097","url":null,"abstract":"<div><div>The metal complexes M@Au<sub>12</sub>-6MP (M = Au, Ag, Pd and Pt) have been investigated theoretically using B3LYP//6–311++G (d, p) and M06-L//def2-TZVP methods. The electronic and energy properties were analyzed. The results show that either in the gas phase or aqueous phase, the stability of four complexes for the tautomer 6MP-7 with metal clusters is higher than that of 6MP-9. The adsorption energy <em>E</em><sub>ad</sub> including BSSE for Pt@Au<sub>12</sub>-6MP-7 is the lowest with −1.41eV in the gas phase and that for Pd@Au<sub>12</sub>-6MP-7 is the lowest with −1.12 eV in the aqueous phase. The electronic property, molecular orbital analysis, density of states, the second order perturbation energy in NBO explicit that Pt@Au<sub>12</sub>-6MP-7 and Pd@Au<sub>12</sub>-6MP-7 are better potential candidate for 6 MP drug delivery.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"140 ","pages":"Article 109097"},"PeriodicalIF":2.7,"publicationDate":"2025-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144204612","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
Unveiling the chlorinated aliphatic hydrocarbon contaminants sensing properties of the biphenylene network through DFT calculations 通过DFT计算揭示了联苯网络对氯代脂肪烃污染物的感知特性
IF 2.7 4区 生物学
Journal of molecular graphics & modelling Pub Date : 2025-05-30 DOI: 10.1016/j.jmgm.2025.109099
Erwin García-Hernández
{"title":"Unveiling the chlorinated aliphatic hydrocarbon contaminants sensing properties of the biphenylene network through DFT calculations","authors":"Erwin García-Hernández","doi":"10.1016/j.jmgm.2025.109099","DOIUrl":"10.1016/j.jmgm.2025.109099","url":null,"abstract":"<div><div>Biphenylene, a recently synthesized graphene allotrope, has demonstrated potential for pollutant adsorption and sensing applications. In this study, we investigate the interactions between biphenylene and three chlorinated aliphatic hydrocarbons: dichloroethylene, trichloromethane, and tetrachloroethylene, utilizing density functional theory calculations. Geometrical analysis shows that all complexes exhibit interaction distances above 3.3 Å, indicating physisorption governed by van der Waals forces. The complex with tetrachloroethylene exhibits the strongest interaction (adsorption energy of −0.48 eV) due to π–π stacking, while the systems with trichloromethane and dichloroethylene exhibit weaker adsorption (−0.30 eV and −0.35 eV, respectively). Solvent effects slightly diminish adsorption stability by up to ∼6 %. Electronic analysis reveals that biphenylene retains its intrinsic properties upon complexation, with minimal changes in the HOMO-LUMO gap (1.00 eV) and chemical potential (−3.92 eV). However, the dipole moment increases significantly (up to 1.40 D for the trichloromethane complex), enhancing solubility. Rapid recovery times for the complexes with trichloromethane (1.33 × 10<sup>−7</sup> s) and dichloroethylene (8.41 × 10<sup>−7</sup> s) suggest excellent sensing capabilities, while the tetrachloroethylene system's longer desorption time (1.42 × 10<sup>−4</sup> s) indicates potential for pollutant adsorption. These findings highlight biphenylene as a promising material for environmental applications, including the sensing and removal of chlorinated pollutants.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"140 ","pages":"Article 109099"},"PeriodicalIF":2.7,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144189547","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 the capabilities of metal-doped phthalocyanine (MPC, M = Co, Cu, Fe, Ni, Zn) for adsorption of CO2: A DFT study 探索金属掺杂酞菁(MPC, M = Co, Cu, Fe, Ni, Zn)吸附CO2的能力:DFT研究
IF 2.7 4区 生物学
Journal of molecular graphics & modelling Pub Date : 2025-05-26 DOI: 10.1016/j.jmgm.2025.109088
Khalida Abaid Samawi , Shaimaa Imad Ali , Taghried A. Salman , Belal A. Alshekhly
{"title":"Exploring the capabilities of metal-doped phthalocyanine (MPC, M = Co, Cu, Fe, Ni, Zn) for adsorption of CO2: A DFT study","authors":"Khalida Abaid Samawi ,&nbsp;Shaimaa Imad Ali ,&nbsp;Taghried A. Salman ,&nbsp;Belal A. Alshekhly","doi":"10.1016/j.jmgm.2025.109088","DOIUrl":"10.1016/j.jmgm.2025.109088","url":null,"abstract":"<div><div>Phthalocyanine-based covalent organic frameworks (PC-COFs) are a novel subclass of COFs that integrate phthalocyanine units to enhance electronic, optical, and catalytic properties. These frameworks are particularly effective in CO<sub>2</sub> adsorption due to their high surface area, tunable porosity, and exceptional stability. In this study, we have employed density functional theory (DFT) calculations to explore the electronic properties of phthalocyanine doped with various metal centers (Co, Cu, Fe, Ni, Zn) and their impact on CO<sub>2</sub> adsorption. The geometries of metal-doped phthalocyanines and their CO<sub>2</sub> complexes were optimized using the B3PW91 functional with the LANL2DZ basis set. Adsorption energies, electronic structures, and reactivity indices such as HOMO-LUMO gaps, ionization potentials, and electron affinities were analyzed. The findings revealed that Fe-doped phthalocyanines exhibited the highest reactivity and strongest CO<sub>2</sub> adsorption due to favorable charge transfer interactions. Additionally, aromaticity indices (HOMA and Bird) indicated enhanced aromatic character upon CO<sub>2</sub> adsorption. These insights provide a foundation for designing more efficient PC-COF materials for CO<sub>2</sub> capture, emphasizing the crucial role of electronic properties and metal center selection in optimizing adsorption performance.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"140 ","pages":"Article 109088"},"PeriodicalIF":2.7,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144168064","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
Thermal decomposition mechanism of HMX/DNAN at high temperatures by reactive molecular dynamics simulations 反应分子动力学模拟HMX/DNAN在高温下的热分解机理
IF 2.7 4区 生物学
Journal of molecular graphics & modelling Pub Date : 2025-05-26 DOI: 10.1016/j.jmgm.2025.109096
Tianhao Li , Fang Chen , Guoqi Guo , Ling Dong , Xiaofeng Yuan , Linxiu Zhao , Duanlin Cao
{"title":"Thermal decomposition mechanism of HMX/DNAN at high temperatures by reactive molecular dynamics simulations","authors":"Tianhao Li ,&nbsp;Fang Chen ,&nbsp;Guoqi Guo ,&nbsp;Ling Dong ,&nbsp;Xiaofeng Yuan ,&nbsp;Linxiu Zhao ,&nbsp;Duanlin Cao","doi":"10.1016/j.jmgm.2025.109096","DOIUrl":"10.1016/j.jmgm.2025.109096","url":null,"abstract":"<div><div>This work investigated the thermal decomposition process of the HMX/DNAN melt-cast explosive system at high temperatures using reactive molecular dynamics. The initial reaction paths of the system and the effects of DNAN on the thermal decomposition of HMX were revealed. The findings indicated that the H atoms and nitro groups produced by the decomposition of DNAN were reacted with HMX and its intermediates, which in turn promoted the pyrolysis of HMX, while the OH radicals produced by the decomposition of HNO<sub>2</sub> continued to induce the decomposition of HMX. Calculations of activation energies showed that the addition of DNAN enhanced the sensitivity of HMX to thermal stimuli. In terms of products, the addition of DNAN significantly impacted the final product H<sub>2</sub>O of HMX, while its impact on CO<sub>2</sub> is relatively small. At 2000 K–3500 K, the maximum number of clusters in mixed system showed a general decreased trend with increased temperature.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"140 ","pages":"Article 109096"},"PeriodicalIF":2.7,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144168062","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
Effect of isomerism, inter-ring torsion angle and chain length in structural and electronic properties of oligothiophenes: computational study 异构、环间扭角和链长对寡硫吩结构和电子性质的影响:计算研究
IF 2.7 4区 生物学
Journal of molecular graphics & modelling Pub Date : 2025-05-21 DOI: 10.1016/j.jmgm.2025.109085
Belgacem Bezzina , Safia Himri , Mohamed Tayeb Abedghars , Assia khelalfa , Djameleddine Khatmi
{"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<sup>−1</sup> for T2 to 0.0270 Å<sup>−1</sup> 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}
引用次数: 0
A DFT study of pure and M-encapsulated (M=Na and K) B40 fullerenes as potential sensors for the flutamide drug 纯和M包封(M=Na和K) B40富勒烯作为氟他胺类药物潜在传感器的DFT研究
IF 2.7 4区 生物学
Journal of molecular graphics & modelling Pub Date : 2025-05-20 DOI: 10.1016/j.jmgm.2025.109084
Zahra Bagherzadeh , Sharieh Hosseini , Mehdi Esrafili dizaji
{"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}
引用次数: 0
In silico discovery of multi-target small molecules and efficient siRNA design to overcome drug resistance in breast cancer via local therapy 发现多靶点小分子和高效siRNA设计,通过局部治疗克服乳腺癌耐药
IF 2.7 4区 生物学
Journal of molecular graphics & modelling Pub Date : 2025-05-20 DOI: 10.1016/j.jmgm.2025.109086
Seyed Mohammad Javad Hashemi , Hossein Ghalehnoei , Ali Barzegar , Mehran Feizi-Dehnayebi , Javad Akhtari , Amir Mellati
{"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}
引用次数: 0
Adsorption of procarbazine anticancer drug over C24 and B12N12 nanocages: A comparative DFT study 异丙卡嗪抗癌药物在C24和B12N12纳米笼上的吸附:比较DFT研究
IF 2.7 4区 生物学
Journal of molecular graphics & modelling Pub Date : 2025-05-20 DOI: 10.1016/j.jmgm.2025.109087
Christian A. Celaya , Carmen Martínez del Sobral Sinitsyna , Luis Felipe Hernández-Ayala , M. Solórzano , Daniel G. Araiza , Miguel Reina
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