Hydration change on complexation of aromatic ligands with DNA: molecular dynamics simulations

Aim. Analysis of the hydration changes at formation of DNA complexes with biologically active aromatic compounds (BAC): antibiotics actinomycin D, daunomycin, nogalamycin, novantrone and mutagens ethidium bromide and proflavine. Methods. Molecular dynamics simulations. Results. The hydration indexes for double-helical DNA and ligands in a free and complexed states were calculated. A critical analysis of modern ideas about changing water environment at binding of aromatic ligands to DNA was performed. Conclusions. It is shown that upon binding of aromatic BAC with DNA a significant (from 2.6 for novantrone to 13.1 for actinomycin D) liberation of water molecules out of hydration shells with the disruption of hydrogen bonds takes place.Цель. Исследование изменения гидратации при образовании комплексов с ДНК ароматических биологически активных соединений (БАС): антибиотиков актиномицина D, дауномицина, ногаламицина, новантрона и мутагенов бромистого этидия и профлавина. Методы. Молекулярная динамика. Результаты. Вычислены гидратационные индексы для двуспиральной ДНК и лигандов в свободном состоянии и в составе комплекса. Проведен критический анализ современных представлений об изменении водного окружения при связывании с ДНК ароматических лигандов. Выводы. Показано, что при взаимодействии ароматических БАС с ДНК происходит значительное (от 2,6 для новантрона до 13,1 для актиномицина D) высвобождение молекул воды гидратных оболочек с разрывом водородных связей.Мета. Дослідження зміни гідратації при утворенні комплексів з ДНК ароматичних біологічно активних сполук (БАС): антибіотиків актиноміцину D, дауноміцину, ногаламіцину, новантрону і мутагенів бромистого етидію і профлавіну. Методи. Молекулярна динаміка. Результати. Обчислено гідратаційні індекси для двоспіральної ДНК і лігандів у вільному стані та у складі комплексу. Проведено критичний аналіз сучасних уявлень щодо зміни водного оточення при зв’язуванні з ДНК ароматичних лігандів. Висновки. Показано, що при взаємодії ароматичних БАС з ДНК відбувається значне (від 2,6 для новантрону до 13,1 для актиноміцину D) вивільнення молекул води гідратних оболонок з розривом водневих зв’язків

Hetero-association of aromatic molecules in aqueous solution

Knowledge of the physical chemistry of small molecules complexation (the hetero-association) in aqueous solution is increasingly important in view of the rapidly emerging branch of supramolecular chemistry dealing with the formation of heterogeneous polymeric structures having specific functional roles. In this paper, the 50-year history of scientific studies of hetero-association of heterocyclic aromatic molecules in aqueous solution has been reviewed. Some important correlations of structural and thermodynamic parameters of complexation have been reported based on large data-set of hetero-association parameters accumulated to date. The fundamental problem of ‘energetic composition’ of π-stacking is extensively discussed. The review has shown that there are some gaps in our understanding of heteroassociation, which provides a challenge for further studies in this are

The first record of the genus Anaprostocetus Graham, 1987 (Hymenoptera: Eulophidae: Tetrastichinae) from Transcaucasia (Georgia)

European species of the genus Anaprostocetus Graham, 1987 – A. acuminatus (Ratzeburg, 1848) is reported as a new record for Transcaucasia (Georgia)

On the origin of the decrease in stability of the DNA hairpin d(GCGAAGC) on complexation with aromatic drugs

Molecular dynamics simulations of drug–DNA complexes have been carried out in order to explain the experimentally observed decrease in thermal stability of the DNA hairpin d(GCGAAGC) on binding the aromatic drug molecules, daunomycin, ethidium bromide, novantrone and proflavine. This complexation behavior is in contrast to the stabilizing effect of the same aromatic drug molecules on DNA duplexes. Analysis of the energy parameters and the hydration properties of the complexes shows that the main factor correlating with the decrease in melting temperatures of the drug–hairpin complexes is the number of water bridges, with a reduction of at least 40% on ligand binding

Investigation of the complexation of the anti-cancer drug novantrone with the hairpin structure of the deoxyheptanucleotide 5'-d(GpCpGpApApGpC)

In aqueous solution the deoxyheptanucleotide, 5′-d(GpCpGpApApGpC), exists as a very stable hairpin structure in equilibrium with small proportions of the single-stranded and duplex forms. Complexation of the anti-cancer drug novantrone (mitoxantrone) with the DNA heptamer was investigated by one- and two-dimensional 500 MHz 1H NMR spectroscopy (2M-TOCSY, 2M-NOESY) and molecular dynamics simulations. The proton chemical shifts of NOV in mixed solutions with the heptamer were measured as a function of concentration and temperature and the equilibrium association parameters were determined for complexation of NOV with the three forms of the heptamer. The spatial structure of the complex of the antibiotic with the hairpin form of the heptamer was built on the basis of 2D-NOE data. The conformational dynamics of the complex and its interaction with the water environment were investigated by molecular dynamics methods. The results suggest that NOV complexes with the hairpin form of the heptamer in solution by intercalation. Complexation of NOV with the hairpin stem results in a disruption of about one half of the intramolecular water bridges of the hairpin, which is considered to be the main reason for the observed decrease in the thermodynamical stability of the hairpin on binding with the ligand

Relation between structure and enthalpy for stacking interactions of aromatic molecules

An approximately linear correlation has been found between the enthalpy of complexation and the area of overlap of the chromophores using published structural and thermodynamical data on the self- and hetero-association of aromatic molecules measured under similar solution conditions. This finding is consistent with the assumption that short-range van-der-Waals forces dominate over other contributions to the enthalpy of stacking of aromatic molecules. It provides a 'model-independent' approach for a priori estimation of the enthalpy of aromatic-aromatic stacking interactions from knowledge of the structural properties or vice versa