Journal of molecular graphics & modelling最新文献

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Mangiferin as a potential inhibitor of transthyretin fibrillogenesis
IF 2.7 4区 生物学
Journal of molecular graphics & modelling Pub Date : 2025-03-08 DOI: 10.1016/j.jmgm.2025.109007
Grudinina N.A , Petukhov M.G , Sokolov A.V , Shaldzhyan A.A , Zabrodskaya Y.A , Gavrilova N.V , Morozkina S.N , Egorov V.V
{"title":"Mangiferin as a potential inhibitor of transthyretin fibrillogenesis","authors":"Grudinina N.A ,&nbsp;Petukhov M.G ,&nbsp;Sokolov A.V ,&nbsp;Shaldzhyan A.A ,&nbsp;Zabrodskaya Y.A ,&nbsp;Gavrilova N.V ,&nbsp;Morozkina S.N ,&nbsp;Egorov V.V","doi":"10.1016/j.jmgm.2025.109007","DOIUrl":"10.1016/j.jmgm.2025.109007","url":null,"abstract":"<div><div>By using <em>in silico</em> molecular docking, we predicted a high potential of mangiferin to inhibit transthyretin amyloidogenesis. Subsequently, we tested this prediction in an <em>in vitro</em> system. The study involved testing effect of mangiferrin in a system that included isolated and purified recombinant transthyretin under fibrillogenesis conditions and a detection assay based on the fluorescent dye thioflavin T, characteristic of amyloid fibrils. The conditions for fibrillogenesis of this protein at neutral pH values were established. Using the developed test system, it was shown that mangiferin is able to inhibit abnormal transthyretin fibrillogenesis.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"137 ","pages":"Article 109007"},"PeriodicalIF":2.7,"publicationDate":"2025-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143620890","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 impact of the fluorophore pyrrole, indole, furan, benzofuran, thiophene, benzothiophene, and pyrene attachments on the C7 atom of the isomorphic fluorescent thieno-guanine: A theoretical investigation
IF 2.7 4区 生物学
Journal of molecular graphics & modelling Pub Date : 2025-03-04 DOI: 10.1016/j.jmgm.2025.108999
Laibin Zhang, Yaping Zhang
{"title":"Unveiling the impact of the fluorophore pyrrole, indole, furan, benzofuran, thiophene, benzothiophene, and pyrene attachments on the C7 atom of the isomorphic fluorescent thieno-guanine: A theoretical investigation","authors":"Laibin Zhang,&nbsp;Yaping Zhang","doi":"10.1016/j.jmgm.2025.108999","DOIUrl":"10.1016/j.jmgm.2025.108999","url":null,"abstract":"<div><div>Thieno-guanine (thG) is a prominent emissive surrogate of natural guanine (G), which almost perfectly mimics G in nucleic duplexes. In this paper, to widen the utility of thG, the C7 attachment effects by aromatic pyrrole, indole, furan, benzofuran, thiophene, benzothiophene, and pyrene on the structural, electronic, and photophysical properties of thG were theoretically examined by using the density functional theory (DFT) and the time-dependent DFT (TD-DFT). Calculations were performed employing the hybrid B3LYP and the long-range corrected CAM-B3LYP density functionals in combination with the 6–311++G(d, p) basis set. Rigid scan calculations and optimizations were performed to obtain the most stable rotamers, and totally 14 bases (including thG) were studied. The hole-electron theory and the interfragment charge transfer (IFCT) method were applied to reveal the intrinsic characteristics of the low-lying electron excitation processes. In water solution, all the S<sub>1</sub> states of the thG-derivatives are highly allowed ππ∗ states dominated by HOMO (L)→LUMO (L) with some charges (0.028–0.193 e) been transferred from the introduced groups to the thG-moiety. The introduced groups can tune the photophysics of thG resulting in improved fluorescent properties, including visible excitation and emission wavelengths, greater absorption and emission intensities (oscillator strengths), and larger Stokes shifts. In water solution, all substituents display fluorescence wavelength longer than 500 nm and the Stokes shifts are larger than 100 nm. Also examined are the effects of base pairing with cytosine (C), and it was revealed that the S<sub>1</sub> states of all the studied base pairs (totally 14) are local excitations of the thG-derivatives. Both the S<sub>1</sub> state excitation energies and the fluorescence wavelengths are red-shifted to some extent after base pair with C, with a concomitantly decrease of the corresponding oscillator strength.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"137 ","pages":"Article 108999"},"PeriodicalIF":2.7,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143580007","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
The impact of increasing Zr dopant concentration in Ruddlesden Popper perovskite to enhance Resistive Random-Access Memory performance: Using the DFT method
IF 2.7 4区 生物学
Journal of molecular graphics & modelling Pub Date : 2025-03-04 DOI: 10.1016/j.jmgm.2025.109000
Fayyaz Hussain , Aqsa Arooj , Muhammad Imran , Ammar Mohamed Tighezza , Umbreen Rasheed , R.M.Arif Khalil , Muhammad Fahad Ehsan
{"title":"The impact of increasing Zr dopant concentration in Ruddlesden Popper perovskite to enhance Resistive Random-Access Memory performance: Using the DFT method","authors":"Fayyaz Hussain ,&nbsp;Aqsa Arooj ,&nbsp;Muhammad Imran ,&nbsp;Ammar Mohamed Tighezza ,&nbsp;Umbreen Rasheed ,&nbsp;R.M.Arif Khalil ,&nbsp;Muhammad Fahad Ehsan","doi":"10.1016/j.jmgm.2025.109000","DOIUrl":"10.1016/j.jmgm.2025.109000","url":null,"abstract":"<div><div>As Resistive Random- Access memory (RRAM) emerges as a promising solution for high-performance memory application, this study applies density functional theory (DFT) to analyze the structural, electronic, and optical properties of pure and Zr-doped Mg<sub>3</sub>Hf<sub>2</sub>O<sub>7</sub> at various doping concentrations (0, 0.25, 0.50, 0.75, and 1.0). The electronic analysis reveals that increasing Zr doping reduces the bandgap, thereby enhancing the conductivity of the composites. These findings highlight their potential for resistive switching memory applications. Iso-surface charge density plots revealed that the substitutional replacement of all Hf atoms by Zr atoms significantly increased the number of conducting channels, which enhanced the material's overall conductivity and increased the efficiency of non-volatile memory. Optical analysis showed that Mg<sub>3</sub>Zr<sub>2</sub>O<sub>7</sub> composite has significant conductivity and absorption over a wide range of photon energies and low reflectivity. In particular, Mg<sub>3</sub>Zr<sub>2</sub>O<sub>7</sub> exhibited the least formation energy and highest conductivity, suggesting it is the most stable composite. Mechanical properties confirm all studied materials' stability, anisotropic nature, and ductility. The analysis indicates that Mg<sub>3</sub>Zr<sub>2</sub>O<sub>7</sub> holds strong potential for Resistive Random- Access memory applications.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"137 ","pages":"Article 109000"},"PeriodicalIF":2.7,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143611361","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
Assessment of dynamic removal mechanism of non-steroidal anti-inflammatory biomolecules in the aqueous environments by a novel covalent organic framework
IF 2.7 4区 生物学
Journal of molecular graphics & modelling Pub Date : 2025-03-04 DOI: 10.1016/j.jmgm.2025.109006
Saeed Pourmand , Sara Zareei , Mohammad Pourmand , Sima Majidi , Hamid Erfan-Niya
{"title":"Assessment of dynamic removal mechanism of non-steroidal anti-inflammatory biomolecules in the aqueous environments by a novel covalent organic framework","authors":"Saeed Pourmand ,&nbsp;Sara Zareei ,&nbsp;Mohammad Pourmand ,&nbsp;Sima Majidi ,&nbsp;Hamid Erfan-Niya","doi":"10.1016/j.jmgm.2025.109006","DOIUrl":"10.1016/j.jmgm.2025.109006","url":null,"abstract":"<div><div>Covalent Organic Frameworks (COFs) are a new class of highly porous crystalline substances which have demonstrated excellent potential as novel adsorbents for efficient depollution of pharmaceutical compounds from wastewater. Herein, the molecular mechanism involved in the removal process of non-steroidal anti-inflammatory drug residues, Ibuprofen (IBP) and Naproxen (NPX), from polluted water by an emerging novel COF functionalized with vinyl groups (COF-V), is evaluated through molecular dynamics (MD) simulations under various external electric fields (EFs). MD analyses show that COF-V is efficient in drug loading capacity of % 100 with total interaction energy value of −519.66 and −415.21 kJ/mol for NPX and IBP in single-component systems. In addition, both drug molecules can be simultaneously and efficiently removed in NPX/IBP/COF-V binary system. The van der Waals (vdW) potential is the primary force during the removal mechanism of drug residues. The efficacy of removing biomolecules from wastewater using COF-V substrate is reduced as the strength of EF is intensified in such a way an enhancement of solvent-accessible surface area (SASA) value of the adsorbent and the decreasing of Drug/COF-V contact area are found. The changes in the interaction energy and the RDF patterns are well in agreement with the adsorption mechanism observed in the presence of EFs. This work highlights using of COF as an effective adsorbent for removing pollutant from aqueous solution.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"137 ","pages":"Article 109006"},"PeriodicalIF":2.7,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143580165","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
Las Vegas algorithm in the prediction of intrinsic solubility of drug-like compounds
IF 2.7 4区 生物学
Journal of molecular graphics & modelling Pub Date : 2025-03-04 DOI: 10.1016/j.jmgm.2025.109004
Aleksandar M. Veselinović , Alla P. Toropova , Andrey A. Toropov , Alessandra Roncaglioni , Emilio Benfenati
{"title":"Las Vegas algorithm in the prediction of intrinsic solubility of drug-like compounds","authors":"Aleksandar M. Veselinović ,&nbsp;Alla P. Toropova ,&nbsp;Andrey A. Toropov ,&nbsp;Alessandra Roncaglioni ,&nbsp;Emilio Benfenati","doi":"10.1016/j.jmgm.2025.109004","DOIUrl":"10.1016/j.jmgm.2025.109004","url":null,"abstract":"<div><div>A randomized algorithm that always succeeds in producing a correct output, but whose running time depends on random events is known as a Las Vegas algorithm. In this study, the Las Vegas algorithm aimed to improve QSPR models of intrinsic solubility of drug-like compounds obtained by the Monte Carlo method. Corresponding computational experiments were carried out with the CORAL software. The developed QSPR models were rigorously validated using a battery of statistical parameters, demonstrating excellent predictive ability and robustness. It has been shown, that the Las Vegas algorithm is a suitable way to improve the predictive potential of models obtained with the Monte Carlo technique. Additionally, the study identified key molecular fragments derived from the SMILES notation descriptors that influence the intrinsic solubility (increase or decrease). Overall, this work underscores the efficacy of the Monte Carlo method optimization with applied Las Vegas algorithm in constructing conformation-independent QSPR models with strong predictive power for prediction of intrinsic solubility of drug-like compounds.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"137 ","pages":"Article 109004"},"PeriodicalIF":2.7,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143551519","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
The ability of ZnO and MgO nanocages for adsorption and sensing performance of anticancer drug detection
IF 2.7 4区 生物学
Journal of molecular graphics & modelling Pub Date : 2025-03-04 DOI: 10.1016/j.jmgm.2025.109003
Mohamed J. Saadh , Ali B.M. Ali , Z. Hanoon , Vicky Jain , Piyus Kumar Pathak , Anjan Kumar , Abdulrahman A. Almehizia , Devendra Pratap Rao
{"title":"The ability of ZnO and MgO nanocages for adsorption and sensing performance of anticancer drug detection","authors":"Mohamed J. Saadh ,&nbsp;Ali B.M. Ali ,&nbsp;Z. Hanoon ,&nbsp;Vicky Jain ,&nbsp;Piyus Kumar Pathak ,&nbsp;Anjan Kumar ,&nbsp;Abdulrahman A. Almehizia ,&nbsp;Devendra Pratap Rao","doi":"10.1016/j.jmgm.2025.109003","DOIUrl":"10.1016/j.jmgm.2025.109003","url":null,"abstract":"<div><div>In recent years, researchers have carried out numerous research studies on the application of nanomaterials as tools for detecting various types of drugs within the field of pharmaceuticals, particularly for treating various cancer types such as Nitrosourea (NURS). Based on DFT calculations, the present study aims at examining the capability of the ZnO nanocage (ZnONC) and the MgO nanocage (MgONC) in detecting NURS. Different parameters such as the sensor mechanism, non-covalent interactions (NCIs), natural bond orbitals (NBOs), frontier molecular orbitals (FMOs) and adhesion energies were analyzed. The adhesion of NURS onto ZnO was accompanied by an energy of −45.01 kcal/mol. However, the adhesion energy of the complexes of MgONC was less. The bandgap of the complexes of ZnO and MgO decreased from 5.98 eV to 6.76 eV respectively for the pristine nanocage, which showed that these nanocages could be used for detecting NURS. Based on the analysis of FMOs, the complex of 6m-ZnONC@Nur had the lowest bandgap of 2.81 eV. Moreover, the recovery time of NURS from the MgONC was substantially shorter than its recovery time from the ZnONC. According to the topological analyses, the interactions between the ZnONC and MgONC were non-covalent. Following the adhesion process, there was an increase in the electrical conductance values. The complex of ZnO had the highest electrical conductance value. The analysis of the sensor mechanism revealed that the complexes of the ZnONC had the highest sensitivity since the bandgaps were narrow. Hence, the ZnONC can be used for detecting NURS and delivering NURS for treating cancers.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"137 ","pages":"Article 109003"},"PeriodicalIF":2.7,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143562107","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 the mixture composition of Acetonitrile/Benzene on excited state intramolecular proton transfer in 3-hydroxyflavone, theoretical insights: QTAIM, NBO, NLO behavior, thermodynamic and kinetic aspects
IF 2.7 4区 生物学
Journal of molecular graphics & modelling Pub Date : 2025-03-03 DOI: 10.1016/j.jmgm.2025.109001
Fatma Zohra Imene Yeddou , Mohamed Ali Benmensour , Anissa Amar
{"title":"Effect of the mixture composition of Acetonitrile/Benzene on excited state intramolecular proton transfer in 3-hydroxyflavone, theoretical insights: QTAIM, NBO, NLO behavior, thermodynamic and kinetic aspects","authors":"Fatma Zohra Imene Yeddou ,&nbsp;Mohamed Ali Benmensour ,&nbsp;Anissa Amar","doi":"10.1016/j.jmgm.2025.109001","DOIUrl":"10.1016/j.jmgm.2025.109001","url":null,"abstract":"<div><div>The effect of the Acetonitrile/Benzene mixture composition on excited state intramolecular proton transfer in 3-hydroxyflavone (3HF) was studied by means of density functional theory (DFT) and time-dependent DFT (TDDFT). The static dielectric constant ε<sub>m</sub> is considered as a polarity parameter to characterize the composition of the two mixed solvents. We used the B3LYP/6-31G(d) level of theory for all the calculations of various properties (structural, electronic, spectroscopic, photophysical) in both ground and excited states. Our initial findings show that the mixture composition has a negligible effect on the geometry parameters. The computation of the maximum absorption and fluorescence wavelengths for 3HF and its tautomer correlates well with their corresponding experimental counterparts. The QTAIM and NBO tools were employed to estimate the strength of intramolecular hydrogen bond IHB. It reveals that E<sub>HB</sub> is weakened with the increase of ε<sub>m</sub>, due to the existence of electrostatic interactions. The title molecule is prone to exhibit remarkable NLO response. Secondly, the kinetic and thermodynamic outcomes, together with all former results, strongly support the occurrence of ESIPT phenomenon. Meanwhile, they also highlight the limits of PCM model in accurately describing solute-solvent interactions. Finally, the estimated ESIPT time is very close to the experimental values, which validates our level of theory.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"137 ","pages":"Article 109001"},"PeriodicalIF":2.7,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143551517","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
Unravelling the effect of successive electron injection into the smallest cyclic boron cluster, B3n (n = +2, +1, 0, −1, −2, −3) through electronic structure analysis
IF 2.7 4区 生物学
Journal of molecular graphics & modelling Pub Date : 2025-03-03 DOI: 10.1016/j.jmgm.2025.108998
Sourav Ranjan Ghosh , Sasthi Charan Halder , Suranjana Mitra , Rohan Mondal , Atish Dipankar Jana
{"title":"Unravelling the effect of successive electron injection into the smallest cyclic boron cluster, B3n (n = +2, +1, 0, −1, −2, −3) through electronic structure analysis","authors":"Sourav Ranjan Ghosh ,&nbsp;Sasthi Charan Halder ,&nbsp;Suranjana Mitra ,&nbsp;Rohan Mondal ,&nbsp;Atish Dipankar Jana","doi":"10.1016/j.jmgm.2025.108998","DOIUrl":"10.1016/j.jmgm.2025.108998","url":null,"abstract":"<div><div>With an aim to study the effect of successive electron injection or abstraction on the electronic structure of the cyclic boron clusters; B<sub>3</sub><sup>n</sup> (where n = +2, +1, 0, −1, −2, −3) have been explored using DFT methodology. A total of nine clusters have been studied including the minimum energy ground states and a few closely lying ground states. Through real space functions like electron density, Electron Localization Function (ELF), Localized Orbital Locator (LOL), and Phase-space-defined Fisher Information Density (PS-FID) an in-depth study has been carried out to understand how the electronic character evolves with the successive electron injection into the cluster. Based on Atoms in Molecules (AIM) theory evolution of electron density at critical points and basins has also been studied. Global indices have also been calculated using Conceptual Density Functional Theory (CDFT) to understand cluster's reactivity and stability. IR spectrum has been computed for future experimental verification. B<sub>3</sub> clusters fall into two main symmetry classes: six of them have <em>D</em><sub><em>3h</em></sub> symmetry (B<sub>3</sub><sup>+2</sup>, both the singlet and triplet states of B<sub>3</sub><sup>+1</sup>, B<sub>3</sub><sup>0</sup>, B<sub>3</sub><sup>−1</sup> and the triplet state of B<sub>3</sub><sup>−3</sup>) and three have <em>C</em><sub><em>2v</em></sub> symmetry (B<sub>3</sub><sup>−2</sup> and two singlet states of B<sub>3</sub><sup>−3</sup>). It has been found that the B<sub>3</sub><sup>−1</sup> cluster has the minimum energy among all the structures with the most electron delocalization in the centre.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"137 ","pages":"Article 108998"},"PeriodicalIF":2.7,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143601726","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 tiopronin adsorption on pristine and Al/Ga-doped boron nitride nanoclusters: A DFT approach for enhanced drug delivery
IF 2.7 4区 生物学
Journal of molecular graphics & modelling Pub Date : 2025-03-03 DOI: 10.1016/j.jmgm.2025.109002
Ebtesam Khodayar , Behnaz Abyaz , Morteza Zare , Ehsan Shakerzadeh , Ernesto Chigo Anota
{"title":"Exploring tiopronin adsorption on pristine and Al/Ga-doped boron nitride nanoclusters: A DFT approach for enhanced drug delivery","authors":"Ebtesam Khodayar ,&nbsp;Behnaz Abyaz ,&nbsp;Morteza Zare ,&nbsp;Ehsan Shakerzadeh ,&nbsp;Ernesto Chigo Anota","doi":"10.1016/j.jmgm.2025.109002","DOIUrl":"10.1016/j.jmgm.2025.109002","url":null,"abstract":"<div><div>Tiopronin is a thiol-based medication recognized for its antioxidant properties, which may offer therapeutic benefits for various medical conditions. At present, it is utilized for the treatment of cystinuria and rheumatoid arthritis. However, its limited bioavailability poses a significant challenge for broader applications, necessitating high systemic doses to achieve localized therapeutic effects. The incorporation of a drug delivery system could help overcome this issue by allowing for controlled and targeted release. Functionalized B<sub>12</sub>N<sub>12</sub> fullerenes present a promising platform with substantial potential for biomedical applications, particularly in drug delivery. In this study, the effect of loading the tiopronin drug on the structural and electronic properties of pure B<sub>12</sub>N<sub>12</sub>, AlB<sub>11</sub>N<sub>12</sub> and GaB<sub>11</sub>N<sub>12</sub> fullerenes nano agent were evaluated using density functional theory in both gas and aqueous environments. The adsorption energy of tiopronin over the fullerenes has been studied through its nucleophilic sites (COOH, NH<sub>2</sub>, CO, and SH). Based on our analysis, the adsorption energies are about −1.69, −3.38 and −1.96 eV for the most stable complexes of B<sub>12</sub>N<sub>12</sub>, AlB<sub>11</sub>N<sub>12</sub> and GaB<sub>11</sub>N<sub>12</sub>, respectively. Electronic analysis showed that the HOMO-LUMO gaps decrease upon drug adsorption, resulting in significant changes in molecular orbital levels and quantum molecular descriptors. Additionally, quantum theory of atoms in molecules (QTAIM) analysis, electron localization function (ELF), and reduced density gradient (RDG) plots were explored to investigate interaction properties.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"137 ","pages":"Article 109002"},"PeriodicalIF":2.7,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143562106","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
Computational design and structural insights into quinazoline-based lead molecules for targeting PARP10 in cancer therapy
IF 2.7 4区 生物学
Journal of molecular graphics & modelling Pub Date : 2025-03-03 DOI: 10.1016/j.jmgm.2025.109005
Revathi Gnanavelou , Manikandan Jayaraman , Jeyakanthan Jeyaraman , Konda Reddy Girija
{"title":"Computational design and structural insights into quinazoline-based lead molecules for targeting PARP10 in cancer therapy","authors":"Revathi Gnanavelou ,&nbsp;Manikandan Jayaraman ,&nbsp;Jeyakanthan Jeyaraman ,&nbsp;Konda Reddy Girija","doi":"10.1016/j.jmgm.2025.109005","DOIUrl":"10.1016/j.jmgm.2025.109005","url":null,"abstract":"<div><div>Quinazoline scaffolds, a class of nitrogen-containing heterocyclic compounds, are considered a “privileged structure\" in drug development due to their broad physiological activities and significant therapeutic potential. Many anti-breast cancer therapies are designed using this pharmacophore. Structural modifications such as halogen substitution and aromatic amino group insertion have been explored to improve the anticancer efficacy of quinazoline derivatives. Breast cancer continues to be the primary cause of cancer-related mortality among women, approximately 670,000 deaths globally in 2022, emphasizing the need for novel therapies. To combat multidrug resistance in breast cancer, new drug candidates targeting the Poly (ADP-ribose) polymerase (PARP) enzyme are being developed to improve chemotherapeutic efficacy and reduce toxicity. In this study, computational screening of 365 quinazoline derivatives was conducted to identify potential PARP inhibitors. Docking based screening identified three quinazoline scaffolds (RFAP77, RISA30, and RISAC) as top hits, demonstrating docking scores ranging from −8.41 to −9.31 kcal/mol and MM-GBSA binding free energy scores between −52.08 and −55.99 kcal/mol, compared to the reference approved inhibitor. ADMET analysis revealed favorable predicted drug-likeness profiles for the identified scaffolds. The structural stability of the docked PARP-ligand complexes was further investigated using molecular dynamics simulations (MDS). The computational simulations revealed significant conformational changes upon ligand binding, as evidenced by RMSD, RMSF, and hydrogen bond analyses. Essential dynamics analysis, including PCA-based FEL mapping, demonstrated energy minima profiles for all top docked PARP complexes. These computational findings highlight the potential of these scaffolds as promising candidates for further development as PARP inhibitors.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"137 ","pages":"Article 109005"},"PeriodicalIF":2.7,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143657303","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
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