Investigations of drug–DNA interactions using molecular docking, cyclic voltammetry and UV–Vis spectroscopy

Perveen, Fouzia; Qureshi, Rumana; Ansari, Farzana Latif; Kalsoom, Saima; Ahmed, Safeer

doi:10.1016/j.molstruc.2011.07.027

Cited by 49 publications

(23 citation statements)

References 22 publications

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“…■ REFERENCES 36 fish sperm Tris 1.98 × 10 5 absorption/fluorescence 20,[26][27][28]32,34 calf-thymus phosphate 1.96 × 10 5 to 7.0 × 10 5 absorption 37 chicken blood McIlvain 1.8 × 10 5 cyclic voltammetry 45 calf-thymus phosphate 2.35 × 10 5 H 1 -NMR 46,47,51,52 4-and 6-mers deuterated phosphate 4.3 × 10 5 to 1.7 × 10 6 scanning force microscopy 53 pBluBacHis b ammonium acetate 1.2 × 10 5…”

Section: ■ Acknowledgmentsmentioning

confidence: 99%

Binding of the Anti-Cancer Drug Daunomycin to DNA Probed by Second Harmonic Generation

et al. 2013

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Second harmonic generation (SHG) was used to selectively probe DNA−drug interactions without the need for chemical labels or invasive detection methods. In particular, the binding constant of the anticancer drug daunomycin to a recognition triplet sequence in a 33-mer of double stranded DNA was determined. The SHG method, which is interface selective, probed the binding of daunomycin to DNA that was tethered to the surface of colloidal microparticles suspended in aqueous solution. Probing biomolecule coated colloids is expected to yield larger SH signals and provides experimental flexibility as compared to experiments performed at planar interfaces. The change in SHG intensity as daunomycin was added to the microparticle solution was fit to a Langmuir binding model, which yielded an equilibrium constant of 2.3 (±0.7) × 10 5 M −1 ; the corresponding Gibbs free energy change at 20°C is −7.2 ± 0.2 kcal/mol. Control experiments established that daunomycin preferentially binds to DNA at the recognition sequence. The equilibrium was found to be unaffected by the presence of free DNA in solution, and hyper-Rayleigh scattering from bulk molecules did not change with increasing daunomycin concentration. The extracted equilibrium constants are in agreement with the range of reported values found in the literature. ■ INTRODUCTIONThis work presents a sensitive method for determining equilibrium binding constants for biomolecular interactions in a label free and noninvasive way. The experiments used second harmonic generation (SHG) to probe the binding of a drug to DNA tethered to the surface of colloidal microparticles suspended in aqueous solution. Biomolecule coatings on nano-and microparticle surfaces have opened up a broad field of self-assembling superstructured materials; 1−7 some biomolecule coated particles have found applications in drug delivery systems and in vivo detection schemes. 8,9 The present work also builds on interface specific nonlinear optical experiments that have measured the electronic and vibrational spectra of DNA covalently bound to planar fused quartz surfaces immersed in aqueous media, 10−13 and recent work that tracked in real time the cleavage of DNA by the restriction enzyme EcoR1 and the subsequent rehybridization of DNA attached to colloidal polymer microparticles without labeled reporter molecules or invasive detection methods. 14 Using SHG to study biomolecular reactions, with one of the reactants attached to a colloidal interface, can yield larger signals than analogous experiments performed at planar interfaces due to the larger number of molecules that can be accommodated in the laser focus. Additionally, the number of particles in solution can be changed without changing the density of the DNA that is attached to the individual particles, allowing for flexibility in experimental design.The class of anthracycline chemotherapeutic drugs has long been studied due to their potent anticancer properties. 15−20 Daunomycin (structure given in Figure 1a) is a member of this class ...

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Section: ■ Acknowledgmentsmentioning

confidence: 99%

Binding of the Anti-Cancer Drug Daunomycin to DNA Probed by Second Harmonic Generation

et al. 2013

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“…These docking programs, when used prior to experimental screening, can be considered as powerful computational filters to reduce labor and cost for the development of effective medicinal compounds. When they are used after experimental screening, they can help in better understanding bioactivity mechanisms [75]. The docking is important in the study of various properties associated with DNA-ligand interactions, such as binding energy, geometry complementarily, electron 1396 N. Shahabadi et al distribution, hydrogen bond, donor acceptor properties, hydrophobicity, and polarizability [76].…”

Section: Molecular Docking Analysismentioning

confidence: 99%

Synthesis, characterization, molecular modeling, and DNA interaction studies of a Cu(II) complex containing drug of chronic hepatitis B: adefovir dipivoxil

Shahabadi

Falsafi

Fili

2015

Journal of Coordination Chemistry

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A new copper(II) complex [Cu(adefovir) 2 Cl 2 ], where adefovir = adefovir dipivoxil drug, was synthesized and characterized by using different physicochemical methods. Binding interaction of this complex with calf thymus DNA (ct-DNA) has been investigated by multi-spectroscopic techniques and molecular modeling study. The complex displays significant binding properties of ct-DNA. The results of fluorescence and UV-vis absorption spectroscopy indicated that, this complex interacted with ct-DNA in a groove-binding mode, and the binding constant was 4.3(±0.2) × 10 4 M −1 . The fluorimeteric studies showed that the reaction between the complex and ct-DNA is exothermic (ΔH = 73.91 kJ M −1 ; ΔS = 357.83 J M −1 K −1 ). Furthermore, the complex induces detectable changes in the CD spectrum of ct-DNA and slightly increases its viscosity which verified the groove-binding mode. The molecular modeling results illustrated that the complex strongly binds to the groove of DNA by relative binding energy of the docked structure −5.74 kcal M −1 . All experimental and molecular modeling results showed that the Cu(II) complex binds to DNA by a groove-binding mode.

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“…Molecular docking plays an important role in drug designing by placing a ligand molecule into the binding site of the target molecule in a non-covalent fashion [11]. Flexible docking programs like DOCK [12], Molecular Operating Environment (MOE), and AutoDock [13] enable user to predict favorable biological target-ligand complex structures with reasonable accuracy and speed.…”

Section: Figure 1 Drug Designing Schemementioning

confidence: 99%

In silico Molecular Docking and Design of Anti-Hepatitis B Drugs

Arooj¹

2012

IOSJPBS

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Investigations of drug–DNA interactions using molecular docking, cyclic voltammetry and UV–Vis spectroscopy

Cited by 49 publications

References 22 publications

Binding of the Anti-Cancer Drug Daunomycin to DNA Probed by Second Harmonic Generation

Binding of the Anti-Cancer Drug Daunomycin to DNA Probed by Second Harmonic Generation

Synthesis, characterization, molecular modeling, and DNA interaction studies of a Cu(II) complex containing drug of chronic hepatitis B: adefovir dipivoxil

In silico Molecular Docking and Design of Anti-Hepatitis B Drugs

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