The binding modes of cationic porphyrin-anthraquinone hybrids to DNA duplexes: in silico study.

نویسندگان

  • Muhammad Arba
  • Daryono H Tjahjono
چکیده

Cationic porphyrin-anthraquinone hybrids bearing peripheral substituents, either pyridine, imidazole, or pyrazole rings have been investigated for their binding mode to DNA duplexes. The four kinds of DNA duplexes were used, which represent intercalation and groove binding modes. AutoDock 4.2 was used to dock nine hybrid compounds to four DNA duplexes, while monitoring of conformational changes of four best hybrid-DNA complexes during 2 ns was performed by Amber9 molecular dynamics package. The binding energy calculation of best four complexes was then carried out using MMPBSA method. The hybrid compounds interacted to DNA duplexes through intercalation and groove binding modes. The minor groove binding of DNA was energetically preferred by cationic porphyrin hybrids due to favorable electrostatic and van der Waals interactions. Both electrostatic and van der Waals contributions were able to distinguish the binding mode of porphyrin hybrid to DNA duplexes.

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

DNA groove binding of an asymmetric cationic porphyrin and its Cu(II) complex: Resolved by spectroscopic, viscometric and molecular docking studies

In the present study, the interaction between water-soluble cationic asymmetric porphyrin, 5-(1-Hexadecyl pyridinium-4-yl)-10, 15, 20-tris (1-Butyl pyridinium-4-yl) Porphyrin Chloride, and its copper (II) derivative with calf thymus DNA (CT-DNA) were studied by means of spectroscopic techniques, viscosity measurements and molecular docking. The monitoring of the changes in visible absorbance sp...

متن کامل

Spectroscopic study on the interaction of three water-soluble porphyrins with calf thymus DNA

Porophyrins and their metal derivatives are strong DNA binders with association constant of  to  . Some of these compounds have been used for the radiations sensitization therapy of cancer and are targeted to interact with cellular DNA. Binding of porphyrins to DNA changes the expectral and other physic chemical characteristic of porphyrins, The mode of binding can be extracted from inspection ...

متن کامل

Thermodynamics Binding of Tetrakis (2,3,5,6-Tetrafluoro-N,N′,Nʺ-Trimethyl Ammonium Phenyl) Porphyrin Nickel(II) With Calf Thymus DNA

In this study, aggregation behavior of a water soluble cationic metalloporphyrin, meso-tetrakis (2,3,5,6-tetrafluoro-N,N´,N´´-trimethyl ammonium phenyl) porphyrin nickel(II) [Ni(II)(TF4TMAPP)]4+ is investigated in 5 mM aqueous phosphate buffer of pH 7.0 at 25.0 °C and various ionic strengths using optical absorption and resonance light scattering spectroscopic methods. The...

متن کامل

Thermodynamic of Interaction between Some Water-Soluble Porphyrins and DNA by Titration Microcalorimetry

In the present work, the interaction of three water soluble porphyrins, tetra (p-trimethyle) ammoniumphenyl porphyrin iodide (TAPP) as a cationic porphyrin, tetra sodium meso-tetrakis (p-sulphonatophenyle) porphyrin (TSPP) as an anionic porphyrin and manganese tetrakis (p-sulphonato phenyl)porphinato acetate (MnTSPP) as a metal porphyrin, with DNA have been studied by isothermaltitration microc...

متن کامل

Physicochemical Study of the Interaction of some Water Soluble Porphyrins with Calf Thymus DNA

In order to shed more light on the effect of peripheral groups of porphyrin core intophysicochemical properties and DNA binding behavior of porphyrins, we have chosen toinvestigate solution properties and calf thymus DNA binding behavior of meso-tetrakis (4-Nbenzyl-pyridyl) porphyrin (TBZPyP) and its Mn (III), Co (III), Ni (II) and Cu (II) complexesderivatives have been studied in thermodynamic...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

عنوان ژورنال:
  • Journal of biomolecular structure & dynamics

دوره 33 3  شماره 

صفحات  -

تاریخ انتشار 2015