Amir Karim , Najeeb Ullah , Muhammad Iqbal , Rahime Eshaghi Malekshah , Saqib Ali , Sodio C.N. Hsu
{"title":"利用 2-hydroxypropyl-β-CD 进行药物包囊、双核羧酸铜(II)配合物的酪氨酸激酶和酪氨酸酶抑制作用的硅学研究。","authors":"Amir Karim , Najeeb Ullah , Muhammad Iqbal , Rahime Eshaghi Malekshah , Saqib Ali , Sodio C.N. Hsu","doi":"10.1016/j.jmgm.2024.108903","DOIUrl":null,"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":2.7000,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"In silico drug encapsulation using 2-hydroxypropyl-β-CD, tyrosine kinase and tyrosinase inhibition of dinuclear Cu(II) carboxylate complexes\",\"authors\":\"Amir Karim , Najeeb Ullah , Muhammad Iqbal , Rahime Eshaghi Malekshah , Saqib Ali , Sodio C.N. Hsu\",\"doi\":\"10.1016/j.jmgm.2024.108903\",\"DOIUrl\":null,\"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\":2.7000,\"publicationDate\":\"2024-11-05\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of molecular graphics & modelling\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S1093326324002031\",\"RegionNum\":4,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"BIOCHEMICAL RESEARCH METHODS\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of molecular graphics & modelling","FirstCategoryId":"99","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S1093326324002031","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"BIOCHEMICAL RESEARCH METHODS","Score":null,"Total":0}
In silico drug encapsulation using 2-hydroxypropyl-β-CD, tyrosine kinase and tyrosinase inhibition of dinuclear Cu(II) carboxylate complexes
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-β-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 4, 5, and 7 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 5, 14, and 19 were difficult to release due to their lowest energy. In contrast, complexes 8, 9, and 16 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.
期刊介绍:
The Journal of Molecular Graphics and Modelling is devoted to the publication of papers on the uses of computers in theoretical investigations of molecular structure, function, interaction, and design. The scope of the journal includes all aspects of molecular modeling and computational chemistry, including, for instance, the study of molecular shape and properties, molecular simulations, protein and polymer engineering, drug design, materials design, structure-activity and structure-property relationships, database mining, and compound library design.
As a primary research journal, JMGM seeks to bring new knowledge to the attention of our readers. As such, submissions to the journal need to not only report results, but must draw conclusions and explore implications of the work presented. Authors are strongly encouraged to bear this in mind when preparing manuscripts. Routine applications of standard modelling approaches, providing only very limited new scientific insight, will not meet our criteria for publication. Reproducibility of reported calculations is an important issue. Wherever possible, we urge authors to enhance their papers with Supplementary Data, for example, in QSAR studies machine-readable versions of molecular datasets or in the development of new force-field parameters versions of the topology and force field parameter files. Routine applications of existing methods that do not lead to genuinely new insight will not be considered.