{"title":"从抗癌剂 VCp2Cl2 中提取的钒(IV)和钒(V)络合物对 DNA 作用的全新理解方法","authors":"Luis Soriano-Agueda , Alfredo Guevara-García","doi":"10.1016/j.jinorgbio.2024.112705","DOIUrl":null,"url":null,"abstract":"<div><p>A computational study based on derivatives of the anticancer <span><math><msub><mi>VCp</mi><mn>2</mn></msub><msub><mi>Cl</mi><mn>2</mn></msub></math></span> compound and their interaction with representative models of deoxyribonucleic acid (DNA) is presented. The derivatives were obtained by substituting the cyclopentadienes of <span><math><msub><mi>VCp</mi><mn>2</mn></msub><msub><mi>Cl</mi><mn>2</mn></msub></math></span> with <span><math><msub><mi>H</mi><mn>2</mn></msub><mi>O</mi></math></span>, <span><math><msub><mi>NH</mi><mn>3</mn></msub></math></span>, <span><math><msup><mi>OH</mi><mo>−</mo></msup></math></span>, <span><math><msup><mi>Cl</mi><mo>−</mo></msup></math></span>, <span><math><msup><mi>O</mi><mrow><mn>2</mn><mo>−</mo></mrow></msup></math></span> and <span><math><msub><mi>C</mi><mn>2</mn></msub><msubsup><mi>O</mi><mn>4</mn><mrow><mn>2</mn><mo>−</mo></mrow></msubsup></math></span> ligands. The oxidation states IV and V of vanadium were considered, so a total of 20 derivative complexes are included. The complexes interactions with DNA were studied using two different models, the first model considers the interactions of the complexes with the pair Guanine-Cytosine (G-C) and the second involves the interaction of the complexes with adjacent pairs, that is, d(GG). This study compares methodologies based on density functional theory with coupled cluster like calculations (DLPNO-CCSD(T)), the gold standard of electronic structure methods. Furthermore, the change in the electron density of the hydrogen bonds that keep bonded the G-C pair and d(GG) pairs, due to the presence of vanadium (IV) and (V) complexes is rationalize. To this aim, quantities obtained from the topology of the electron densities are inspected, particularly the value of the electron density at the hydrogen bond critical points. The approach allowed to identify vanadium complexes that lead to significant changes in the hydrogen bonds indicated above, a key aspect in the understanding, development, and proposal of mechanisms of action between metal complexes and DNA.</p></div>","PeriodicalId":364,"journal":{"name":"Journal of Inorganic Biochemistry","volume":null,"pages":null},"PeriodicalIF":3.8000,"publicationDate":"2024-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"A refreshing approach to understanding the action on DNA of vanadium (IV) and (V) complexes derived from the anticancer VCp2Cl2\",\"authors\":\"Luis Soriano-Agueda , Alfredo Guevara-García\",\"doi\":\"10.1016/j.jinorgbio.2024.112705\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p>A computational study based on derivatives of the anticancer <span><math><msub><mi>VCp</mi><mn>2</mn></msub><msub><mi>Cl</mi><mn>2</mn></msub></math></span> compound and their interaction with representative models of deoxyribonucleic acid (DNA) is presented. The derivatives were obtained by substituting the cyclopentadienes of <span><math><msub><mi>VCp</mi><mn>2</mn></msub><msub><mi>Cl</mi><mn>2</mn></msub></math></span> with <span><math><msub><mi>H</mi><mn>2</mn></msub><mi>O</mi></math></span>, <span><math><msub><mi>NH</mi><mn>3</mn></msub></math></span>, <span><math><msup><mi>OH</mi><mo>−</mo></msup></math></span>, <span><math><msup><mi>Cl</mi><mo>−</mo></msup></math></span>, <span><math><msup><mi>O</mi><mrow><mn>2</mn><mo>−</mo></mrow></msup></math></span> and <span><math><msub><mi>C</mi><mn>2</mn></msub><msubsup><mi>O</mi><mn>4</mn><mrow><mn>2</mn><mo>−</mo></mrow></msubsup></math></span> ligands. The oxidation states IV and V of vanadium were considered, so a total of 20 derivative complexes are included. The complexes interactions with DNA were studied using two different models, the first model considers the interactions of the complexes with the pair Guanine-Cytosine (G-C) and the second involves the interaction of the complexes with adjacent pairs, that is, d(GG). This study compares methodologies based on density functional theory with coupled cluster like calculations (DLPNO-CCSD(T)), the gold standard of electronic structure methods. Furthermore, the change in the electron density of the hydrogen bonds that keep bonded the G-C pair and d(GG) pairs, due to the presence of vanadium (IV) and (V) complexes is rationalize. To this aim, quantities obtained from the topology of the electron densities are inspected, particularly the value of the electron density at the hydrogen bond critical points. The approach allowed to identify vanadium complexes that lead to significant changes in the hydrogen bonds indicated above, a key aspect in the understanding, development, and proposal of mechanisms of action between metal complexes and DNA.</p></div>\",\"PeriodicalId\":364,\"journal\":{\"name\":\"Journal of Inorganic Biochemistry\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":3.8000,\"publicationDate\":\"2024-08-24\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of Inorganic Biochemistry\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S0162013424002290\",\"RegionNum\":2,\"RegionCategory\":\"化学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"BIOCHEMISTRY & MOLECULAR BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Inorganic Biochemistry","FirstCategoryId":"99","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S0162013424002290","RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
引用次数: 0
摘要
本文介绍了基于抗癌 VCp2Cl2 化合物衍生物及其与脱氧核糖核酸(DNA)代表模型相互作用的计算研究。这些衍生物是用 H2O、NH3、OH-、Cl-、O2- 和 C2O42- 配体取代 VCp2Cl2 的环戊二烯而得到的。考虑到钒的氧化态 IV 和 V,共包括 20 种衍生物配合物。使用两种不同的模型研究了络合物与 DNA 的相互作用,第一种模型考虑了络合物与鸟嘌呤-胞嘧啶(G-C)配对的相互作用,第二种模型涉及络合物与相邻配对(即 d(GG))的相互作用。本研究比较了基于密度泛函理论的方法和电子结构方法的黄金标准--类簇耦合计算(DLPNO-CCSD(T))。此外,由于钒 (IV) 和 (V) 复合物的存在,使 G-C 对和 d(GG) 对保持结合的氢键的电子密度发生了变化。为此,对从电子密度拓扑结构中获得的量进行了检验,特别是氢键临界点的电子密度值。这种方法可以识别出导致上述氢键发生重大变化的钒络合物,而这正是理解、开发和提出金属络合物与 DNA 作用机制的一个关键方面。
A refreshing approach to understanding the action on DNA of vanadium (IV) and (V) complexes derived from the anticancer VCp2Cl2
A computational study based on derivatives of the anticancer compound and their interaction with representative models of deoxyribonucleic acid (DNA) is presented. The derivatives were obtained by substituting the cyclopentadienes of with , , , , and ligands. The oxidation states IV and V of vanadium were considered, so a total of 20 derivative complexes are included. The complexes interactions with DNA were studied using two different models, the first model considers the interactions of the complexes with the pair Guanine-Cytosine (G-C) and the second involves the interaction of the complexes with adjacent pairs, that is, d(GG). This study compares methodologies based on density functional theory with coupled cluster like calculations (DLPNO-CCSD(T)), the gold standard of electronic structure methods. Furthermore, the change in the electron density of the hydrogen bonds that keep bonded the G-C pair and d(GG) pairs, due to the presence of vanadium (IV) and (V) complexes is rationalize. To this aim, quantities obtained from the topology of the electron densities are inspected, particularly the value of the electron density at the hydrogen bond critical points. The approach allowed to identify vanadium complexes that lead to significant changes in the hydrogen bonds indicated above, a key aspect in the understanding, development, and proposal of mechanisms of action between metal complexes and DNA.
期刊介绍:
The Journal of Inorganic Biochemistry is an established international forum for research in all aspects of Biological Inorganic Chemistry. Original papers of a high scientific level are published in the form of Articles (full length papers), Short Communications, Focused Reviews and Bioinorganic Methods. Topics include: the chemistry, structure and function of metalloenzymes; the interaction of inorganic ions and molecules with proteins and nucleic acids; the synthesis and properties of coordination complexes of biological interest including both structural and functional model systems; the function of metal- containing systems in the regulation of gene expression; the role of metals in medicine; the application of spectroscopic methods to determine the structure of metallobiomolecules; the preparation and characterization of metal-based biomaterials; and related systems. The emphasis of the Journal is on the structure and mechanism of action of metallobiomolecules.