Journal of molecular graphics & modelling最新文献

{"title":"Dispersion-corrected DFT calculations and dynamic molecular simulations to investigate conformational stability of Lidocaine towards β-CD and HP-β-CD","authors":"Amira Kadri ,&nbsp;Ouassila Attoui Yahia ,&nbsp;Belgacem Bezzina ,&nbsp;Djamel Eddine Khatmi ,&nbsp;Amel Bouzitouna","doi":"10.1016/j.jmgm.2024.108910","DOIUrl":"10.1016/j.jmgm.2024.108910","url":null,"abstract":"<div><div>Lidocaine (LDC) is one of the most important local anaesthesia compounds (LAs), designated to treat acute and chronic pain, especially in clinical applications. In the purpose to improve its lower solubility and bioavailability, numerous researches have been conducted to study the exact mode of association between the LDC molecule and cyclodextrins as drug carriers. Although, the reported structural details on LDC/β-CD and LDC/HP-β-CD inclusion complexes remain largely unexplored. The LDC molecule presents different spatial arrangements inside the hydrophobic cavities of the above-mentioned hosts; either the phenyl moiety or the diethylamino part is totally inserted. Hence, in the present work, we attempt to deepen our understanding about conformational preferences on the binding modes of LDC by investigating the quantum mechanical approach results.</div><div>The PM3 method combined with the pure corrected functional B97D3 revealed the tendency of LDC to enter its diethylamino inside the host, leaving the rest of molecule externally, and consequently form an inclusion complex with HP-β-CD more stable than with the native β-CD by approximately 12 kcal mol⁻¹.</div><div>The probability of partial insertion of LDC is further ascertained by MD simulations investigation running for 500 ns. The trajectory analysis of MD process showed that the diethyl amino fragment is accommodated inside the HP-β-CD's cavity for a significant period (82 % of the simulation time), while it is estimated to be 78 % in the case of LDC/β-CD complex.</div><div>Moreover, the wave function analysis, based on QTAIM, Reduced Density Gradient (RDG) and 2D Fingerprint, illustrated NCIs interactions and sustained the contribution of numerous van der Waals forces and weaker H-bonds interactions in the stability of studied ICs.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"134 ","pages":"Article 108910"},"PeriodicalIF":2.7,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142687185","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":"Recent advancements in mechanical properties of graphene-enhanced polymer nanocomposites: Progress, challenges, and pathways forward","authors":"Amir Hamed Mashhadzadeh ,&nbsp;Amin Hamed Mashhadzadeh ,&nbsp;Boris Golman ,&nbsp;Christos Spitas ,&nbsp;Salah A. Faroughi ,&nbsp;Konstantinos V. Kostas","doi":"10.1016/j.jmgm.2024.108908","DOIUrl":"10.1016/j.jmgm.2024.108908","url":null,"abstract":"<div><div>The versatile properties of graphene-based polymers have captured substantial interest in recent years, making them a topic of significant research focus. This review paper aims to provide an in-depth analysis of the reported mechanical properties of graphene polymer nanocomposites, a highly promising class of materials for diverse industrial applications. Within this review, we emphasize the role of interactions between graphene and the polymer matrix in achieving uniform dispersion to prevent agglomeration and mitigate adverse effects on mechanical properties. Furthermore, we focus on functionalization as the main method of enhancing graphene physicochemical properties, highlighting its capacity to enhance homogeneous dispersion and significantly improve mechanical properties. These enhancements are contingent on factors such as the type and quantity of functionalization agents and the chosen technique. Additionally, we comprehensively examine recent experimental and theoretical research pertaining to the mechanical properties of graphene/polymer nanocomposites. Our analysis contains two primary polymer categories, namely thermoset and thermoplastic matrices, while also considering graphene loading type and volume fraction, as well as the influence of functionalization agents. This review uniquely addresses the existing gap in a comparative analysis between thermoset and thermoplastic matrices, offering insights into how different loading and functionalization methods influence mechanical properties. Moreover, we emphasize the need for further research in optimizing functionalization techniques and understanding the long-term stability of these composites, an area underexplored in current literature. This work stands out by highlighting future directions for refining synthesis techniques and expanding applications of graphene/polymer nanocomposites across industries such as aerospace, automotive, and electronics. Future endeavors may focus on addressing the challenges, refining synthesis techniques, and exploring novel applications, thereby contributing to the continued growth and evolution of graphene/polymer nanocomposites in the field of materials science.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"135 ","pages":"Article 108908"},"PeriodicalIF":2.7,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142695349","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":"Effects of carbon nanotube and alumina doping on the properties of para-aramids: A DFT and molecular dynamics study","authors":"Chunxin Wang ,&nbsp;Longyin Qiao ,&nbsp;Jun Xie ,&nbsp;Xiaoyu Shi ,&nbsp;Bobin Xu ,&nbsp;Guowei Xia ,&nbsp;Qing Xie ,&nbsp;Shifang Yang","doi":"10.1016/j.jmgm.2024.108909","DOIUrl":"10.1016/j.jmgm.2024.108909","url":null,"abstract":"<div><div>Because of its superior mechanical and electrical insulation qualities, paramamid insulating paper is frequently used in the electrical industry. However, a significant barrier preventing it from taking a more prominent role is its low heat conductivity. This research modifies aramid by doping it with carbon nanotubes and alumina to balance its insulating qualities and increase its thermal conductivity. Materials Studio uses molecular dynamics (MD) computations to examine the thermodynamic parameters of the composite system, such as modulus, glass transition temperature, and thermal conductivity. the system's cohesive energy density, free volume fraction, mean square displacement, and other structural characteristics. The relative dielectric constant is used to calculate the insulating characteristics. The Density Functional Theory (DFT) is then used to calculate the fluctuation of the electrostatic potential with Mulliken charge on the electrical properties. According to the findings, a single doped carbon nanotube significantly raises its mechanical and thermal conductivity while completely destroying its insulation. While single alumina doping increases the insulating properties of the system and yields improved structural parameters and tighter intermolecular bonding, it has minimally positive effects on its thermal conductivity. When mixed doping is used, the system's thermodynamics will be significantly enhanced without compromising its insulating qualities.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"134 ","pages":"Article 108909"},"PeriodicalIF":2.7,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142681645","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":"Estimating AChE inhibitors from MCE database by machine learning and atomistic calculations","authors":"Quynh Mai Thai ,&nbsp;Trung Hai Nguyen ,&nbsp;George Binh Lenon ,&nbsp;Huong Thi Thu Phung ,&nbsp;Jim-Tong Horng ,&nbsp;Phuong-Thao Tran ,&nbsp;Son Tung Ngo","doi":"10.1016/j.jmgm.2024.108906","DOIUrl":"10.1016/j.jmgm.2024.108906","url":null,"abstract":"<div><div>Acetylcholinesterase (AChE) is one of the most successful targets for the treatment of Alzheimer's disease (AD). Inhibition of AChE can result in preventing AD. In this context, the machine-learning (ML) model, molecular docking, and molecular dynamics calculations were employed to characterize the potential inhibitors for AChE from MedChemExpress (MCE) database. The trained ML model was initially employed for estimating the inhibitory of MCE compounds. Atomistic simulations including molecular docking and molecular dynamics simulations were then used to confirm ML outcomes. In particular, the physical insights into the ligand binding to AChE were clarified over the calculations. Two compounds, PubChem ID of 130467298 and 132020434, were indicated that they can inhibit AChE.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"134 ","pages":"Article 108906"},"PeriodicalIF":2.7,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142675957","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 interaction between Fe3+ and REGLE motif of the high-affinity iron permease (Ftr1): An in silico approach","authors":"Ahana Roy Choudhury,&nbsp;Ayaluru Murali","doi":"10.1016/j.jmgm.2024.108907","DOIUrl":"10.1016/j.jmgm.2024.108907","url":null,"abstract":"<div><div>Mucormycosis is an invasive fungal infection with high mortality rate in immunocompromised individuals. Due to COVID-19 pandemic, the disease has resurfaced recently and lack of appropriate antifungals resulted in a poor outcome in patients. The iron uptake mechanism in Rhizopus delemar, the predominant causal agent, is crucial for its survival and pathogenesis in human host. The current study is first of its kind to focus on structural dynamics of high affinity iron permease (Ftr1), a virulence factor for Mucormycosis. Ftr1 is a transmembrane protein which is responsible for transport of Fe3+ ion from extracellular milieu to cytoplasm under iron starving conditions in Rhizopus. In this work, the three-dimensional modelling of Ftr1 was carried out. The Ftr1 possessed seven transmembrane helices with N- &amp; C-termini in extracellular and intracellular regions respectively. Moreover, the present study delineates interaction of glutamic acid residues, found in the REGLE motif of fourth transmembrane helix with Fe3+. The molecular dynamics simulation study revealed that the glycine present in the motif destabilizes the helix thereby bringing E157 closer to positively charged ion. Understanding the interaction between Fe3+ ion and Ftr1 would be helpful in designing effective small molecule drugs against this novel therapeutic target for treating mucormycosis.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"134 ","pages":"Article 108907"},"PeriodicalIF":2.7,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142648320","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":"Boron nitride nanoslits for water desalination via forward osmosis: A molecular dynamics study","authors":"Amin Hamed Mashhadzadeh ,&nbsp;Maryam Zarghami Dehaghani ,&nbsp;Narges Vafa ,&nbsp;Bahar Firoozabadi ,&nbsp;Boris Golman ,&nbsp;Christos Spitas ,&nbsp;Konstantinos V. Kostas","doi":"10.1016/j.jmgm.2024.108905","DOIUrl":"10.1016/j.jmgm.2024.108905","url":null,"abstract":"<div><div>The global shortage of freshwater resources has spurred significant interest among scientists in the development of cost-effective and highly efficient water desalination methods. The forward osmosis (FO) membrane has become well-known for its various advantages, such as its low energy usage, cost-effective performance, high efficiency in desalination, and minimal fouling. Herein, the desalination performance of an FO system containing a boron-nitride slit membrane (BNSM) was investigated using molecular dynamics (MD) simulations. The effects of parameters, including slit width, temperature, draw solution (DS) concentration, and its types (MgCl₂, CaCl₂, and KCl), on salt ion rejections and water flow rate were explored. The rejection percentages of Na⁺ and Mg²⁺ ions decreased from 100 % to 94 % and 96 %, respectively, as the slit width increased from 6 Å to 9 Å. Additionally, the water flow rate increased significantly, from 17.305 to 80.92 molecules/ns, with the same increase in slit width. The temperature elevation led to a decrease in ion rejection percentage and increased the water flow rate, since, according to the Stokes-Einstein equation, the diffusion coefficient of spherical particles increases with increasing temperature. The changes in DS concentration did not affect the ion rejection performance due to the small size of the slit width as well as the dominant effect of size exclusion. The increase in the DS concentration caused concentration polarization and a decrease in osmotic pressure resulting in a drop in the water flow rate. Due to the highest hydration radius of K⁺ ions, the rejection percentages of Mg²⁺ and Ca²⁺ ions were higher, while the Na ⁺ ion rejection percentages had the highest and lowest values in systems having DS of CaCl₂ and KCl, respectively, which was in accordance with the trend of water flow rate.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"134 ","pages":"Article 108905"},"PeriodicalIF":2.7,"publicationDate":"2024-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142622236","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":"Dynamics of AKAP/Calmodulin complex is largely driven by ionic occupancy state","authors":"Gauri Thapa ,&nbsp;Akash Bhattacharya ,&nbsp;Swati Bhattacharya","doi":"10.1016/j.jmgm.2024.108904","DOIUrl":"10.1016/j.jmgm.2024.108904","url":null,"abstract":"<div><div>AKAP79/150 is a scaffold protein found in dendritic spines and other neuronal compartments. It localizes and regulates phosphorylation by protein kinase A and C and is, in turn regulated by <span><math><mrow><mi>C</mi><msup><mi>a</mi><mrow><mn>2</mn><mo>+</mo></mrow></msup></mrow></math></span>, mediated by Calmodulin (CaM). Thus, the interaction of AKAP79/150 with CaM is of biological interest. A 2017 study used a peptide cross linking coupled to mass spectrometry (XLMS) to identify the CaM binding site on AKAP79/150 and subsequently solved an X-ray crystallography structure of CaM in complex with a short helical AKAP79/150 peptide. The XRD structure revealed an unusual mixed ionic occupancy state of CaM as bound to the AKAP79/150 peptide. In this molecular dynamics-based study, we have explored the motional modes of the CaM-AKAP helix complex under three ionic occupancy conditions. Our results indicate that the dynamics of this CaM backbone is largely dominated by the ionic occupancy state. We find that binding of the AKAP79/150 peptide to CaM is not preferentially stabilized in energetic terms in the Ca²⁺ state as compared to apo. However, the Mg²⁺ state is destabilized energetically as compared to the apo state. In addition, in the Ca²⁺ state, the AKAP79/150 peptide appears to be preferentially stabilized by additional hydrogen bonds. Our simulations suggest that further structural biology studies should be carried out, with a focus on driving the system equilibrium to full <span><math><mrow><mi>C</mi><msup><mi>a</mi><mrow><mn>2</mn><mo>+</mo></mrow></msup></mrow></math></span> occupancy. NMR studies may be able to capture conformational states which are not seen in crystals.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"134 ","pages":"Article 108904"},"PeriodicalIF":2.7,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142638837","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 drug encapsulation using 2-hydroxypropyl-β-CD, tyrosine kinase and tyrosinase inhibition of dinuclear Cu(II) carboxylate complexes","authors":"Amir Karim ,&nbsp;Najeeb Ullah ,&nbsp;Muhammad Iqbal ,&nbsp;Rahime Eshaghi Malekshah ,&nbsp;Saqib Ali ,&nbsp;Sodio C.N. Hsu","doi":"10.1016/j.jmgm.2024.108903","DOIUrl":"10.1016/j.jmgm.2024.108903","url":null,"abstract":"<div><div>In recent years, copper carboxylate complexes have garnered significant interest for biological applications. This study focuses on 20 Cu(II) carboxylate complexes selected from our previous research. Due to the hydrophobic nature of these complexes, the 2-hydroxypropyl-<em>β</em>-cyclodextrin (2HPβCD) was employed as a carrier to reduce toxicity and increase solubility for controlling drug delivery. Monte Carlo calculations were performed to confirm the interaction between the optimized structures of Cu(II) complexes and 2HPβCD, forming a host-guest system. All the structures were simulated and optimized using DFT-D calculations in Material Studio 2017. The results indicated that a neutral medium is more favorable for the adsorption of these complexes into 2HPβCD. More negative binding energy values suggested strong and energetically favorable adsorption on 2HPβCD. Complexes <strong>4</strong>, <strong>5</strong>, and <strong>7</strong> exhibited the highest interaction, making them excellent candidates for drug delivery systems. DFT-D calculations were also used to investigate the release of complexes, revealing that complexes <strong>5</strong>, <strong>14,</strong> and <strong>19</strong> were difficult to release due to their lowest energy. In contrast, complexes <strong>8</strong>, <strong>9</strong>, and <strong>16</strong> were found to be most efficient to release due to weak non-covalent interactions with 2HPβCD as we can predict from binding energy obtained by DFT-D. No specific trend was observed in the interaction of the complexes with 2HPβCD. Additionally, the effects of these complexes on c-kit tyrosine kinase and Mushroom tyrosinase were studied by molecular docking. The results demonstrated that all the complexes interacted with the active site of respective receptors through hydrophobic interactions. Complexes containing 1,10-phenanthroline and 2,2-bipyrdine were identified as having a strong, spontaneous binding ability with receptors.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"134 ","pages":"Article 108903"},"PeriodicalIF":2.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142622240","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":"Shape-dependent CO chemisorption on Pt13 nanocluster deposited on reduced TiO2(110)","authors":"Abel S. Maldonado ,&nbsp;Susana B. Ramos ,&nbsp;Gabriela F. Cabeza","doi":"10.1016/j.jmgm.2024.108902","DOIUrl":"10.1016/j.jmgm.2024.108902","url":null,"abstract":"<div><div>This article delves into the impact of nanoparticle shape on CO chemisorption and the reactivity of Pt₁₃ nanocatalysts supported on reduced TiO₂(110). Distinct reactivity in carbon monoxide adsorption is observed among nanoparticles, all composed of 13 platinum atoms but varying in shape. The calculated formation and CO adsorption energies are correlated to the electronic properties of the system and the oxidation states of the Pt atoms involved. Through an analysis of band shifting during the deposition of Pt clusters onto the oxide, and a comparison of the valence band maximum with the measured oxidation potential for the CO to CO₂ reaction, we make predictions about the system's oxidation capability in this reaction. Our findings suggest that Pt₁₃ clusters with cuboid, double triangle DT2 and octahedral Oh shapes, supported on the surface, are particularly advantageous for catalyzing the conversion of CO to CO₂. Within these geometries, several configurations for CO adsorption are evaluated, focusing on the ratio between anionic and cationic Pt sites. This ratio appears to govern the activity for CO oxidation, aligning with recent experimental reports.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"134 ","pages":"Article 108902"},"PeriodicalIF":2.7,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142603823","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":"Thermal unfolding of alpha-lactalbumin at acidic pH: Insights from molecular dynamics simulations","authors":"Elena Ermakova ,&nbsp;Rauf Kurbanov ,&nbsp;Igor Sedov ,&nbsp;Yuriy Zuev","doi":"10.1016/j.jmgm.2024.108900","DOIUrl":"10.1016/j.jmgm.2024.108900","url":null,"abstract":"<div><div>The transformation of globular proteins into fibrils passes through several stages, including the formation of partially expanded conformational states different from the native or fully unfolded forms. Here we used molecular dynamics simulations to characterize the thermal unfolding of alpha-lactalbumin on the microsecond timescale in the range of temperatures of 300–440 K. Comparative analysis of structural changes, mobility of different parts of protein, and pathways through the free energy landscape during the unfolding of alpha-lactalbumin at different temperatures reveals the existence of several intermediate states separated by small energy barriers. The lifetime of these intermediates depends on temperature and varies from nanoseconds to microseconds.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"134 ","pages":"Article 108900"},"PeriodicalIF":2.7,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142568950","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}