Spectroscopic and molecular docking studies on chlorambucil interaction with DNA

Chlorambucil (CMB) is an anticancer drug used for the treatment of variety of cancers. Structural and conformational changes associated with DNA after binding with CMB were explored using spectroscopic techniques to get insight into the mechanism of action of CMB at molecular level. Different molar ratios of CMB-DNA complex were prepared with constant DNA concentration under physiological conditions. FTIR spectroscopy, UV-visible spectroscopy, CD spectroscopy and molecular docking studies were employed to determine the binding site and binding constant of CMB with DNA. The results show CMB binds DNA through nitrogenous bases (thymine, guanine and cytosine). The binding constant was calculated to be 1.3×10(3)M(-1), which suggests weak binding of CMB with DNA double helix. FTIR and CD results show that CMB do not disturb native B-conformation of DNA and it continues to remain in its B conformation even at higher concentrations of CMB. The molecular docking results are in corroboration with our experimental results and provides structural insight into the interaction site.     

Molecular interaction of human serum albumin with paracetamol: Spectroscopic and molecular modeling studies

The interaction between paracetamol and human serum albumin (HSA) under physiological conditions has been investigated by fluorescence, circular dichroism (CD) and docking. Fluorescence data revealed that the fluorescence quenching of HSA by paracetamol was the result of the formed complex of HSA–paracetamol, and the binding constant (K_a) and binding number obtained is 1.3 × 10⁴ at 298 K and 2, respectively for the primary binding site. Circular dichorism spectra showed the induced conformational changes in HSA by the binding of paracetamol. Moreover, protein–ligand docking study indicated that paracetamols (two paracetamols bind to HSA) bind to residues located in the subdomain IIIA.     

DNA condensation with polyamines I. Spectroscopic studies

The addition of polyamines with three or four positive charges to very dilute solutions of phage T7 DNA leads to a co-operative condensation. The reaction is very rapid and the DNA remains in the B-form as characterized by circular dichroism. The particles which are formed are roughly the size of a phage particle when they are prepared for electron microscopy. This aspect is discussed more completely in the accompanying paper (Chattoraj et al., 1978).Most of the experiments were performed at low ionic strength (roughly 0.002 m) with the triamine, spermidine. The reaction also occurs in 0.15 m-sodium chloride but here the experiments are accompanied by slow irreversible effects which are evidently due to aggregation since they are accompanied by a commensurate increase in turbidity. Consequently, most of the experiments have been done under the reversible low ionic strength conditions.Neither Mg²⁺ nor the diamine putrescine produce the reaction at concentrations similar to those found in bacterial cells. The tetramer spermine, on the other hand, which is not found in bacterial cells, is a very strong condensation agent in the μm region. The spermidine analog, bis-(3-aminopropyl)amine is very similar in behavior to spermidine.The role which polyamines might play in the condensation of DNA in phage heads is discussed.     

Spectroscopic and molecular modeling studies of the interaction between morin and polyamidoamine dendrimer

Interactions between the polyamidoamine (PAMAM) dendrimer and drug molecules are of interest for their potential biomedical applications. The goal of this work is to examine the interaction of PAMAM‐C₁₂ 25% dendrimer with morin. The ultraviolet–visible, fluorescence spectroscopic methods as well as molecular modeling were used to analyze drug‐binding mode, binding constants and binding sites, etc. The experimental data showed that the binding constant of morin‐PAMAM‐C₁₂ 25% is about 10⁵ L/mol. The interaction of morin with PAMAM‐C₁₂ 25% is mainly driven by the hydrophobic, electrostatic, hydrogen bonds and van der Waals forces. There are mainly three classes of binding site of morin at the interface of PAMAM‐C₁₂ 25%. These results provided some useful information for self‐assembling and disassembling the PAMAM dendrimer as well as efficient drug delivery and therapeutic applications. Copyright © 2013 John Wiley & Sons, Ltd.     

Nanosecond fluorescence studies of noncovalent interaction of monomeric and dimeric intercalators with DNA

The noncovalent interaction of 2-aminodipyrido[1,2-a:3',2'-d]imidazole (Glu-P-2) and its derivatives, which are potent mutagens isolated from L-glutamic acid pyrolysate, with calf thymus DNA was studied by steady-state and nanosecond fluorescence spectroscopies. The fluorescence of these compounds exhibits static quenching by noncovalent interaction with DNA. Fluorescence lifetimes of the free and intercalated states of these compounds were determined to be 9-10 and 0.5-1 ns, respectively. The bisintercalative effect of the dimeric analogue of Glu-P-2, bis(Glu-P-2)spermine (2GP-SP), to DNA was also investigated. This 2GP-SP, which has two Glu-P-2 moieties at each end of spermine, indicates a strong intramolecular interaction exhibiting remarkable quenching of fluorescence spectrum and lifetime (tau = 3.5 ns) in the absence of DNA. In the presence of DNA, however, the 3.5-ns lifetime component of fluorescence disappeared, and a two-exponential decay of fluorescence (t = approximately 10 and 1.5 ns) was observed at a DNA concentration of more than approximately 0.001 mM P, while the solution containing a very dilute DNA concentration (less than or equal to 0.001 mM P) exhibits a three-component decay of fluorescence (1.5, 3.5, and approximately 10 ns). The potent bis intercalation of two moieties in 2GP-SP with an identical DNA molecule was suggested by the DNA-concentration dependence of these fluorescence lifetimes and their intensity.     

Spectroscopic and molecular docking studies on interaction of two Schiff base complexes with bovine serum albumin

Abstract

This study was designed to examine interaction of two ternary copper (II) Schiff base complexes with bovine serum albumin (BSA), using spectroscopic and molecular docking techniques. The fluorescence quenching measurements revealed that the quenching mechanism was static and the binding site of both Schiff bases to BSA was singular. Förster energy transfer measurements, synchronous fluorescence spectroscopy, and docking study showed both Schiff bases bind to the Trp residues of BSA in short distances. Docking study showed that both Schiff base molecules bind with BSA by forming several hydrogen and van der Waals bonds. In addition, molecular docking study indicated that Schiff base A and Schiff base B were located within the binding pocket of subdomain IB and subdomain IIA of BSA, respectively. Results of Fourier transform-infrared spectroscopy demonstrated that bovine serum albumin interacts with both Schiff bases and the secondary structure of BSA was changed.

Communicated by Ramaswamy H. Sarma     

Spectroscopic and molecular docking studies on the interaction of antiviral drug nevirapine with calf thymus DNA

The interaction of calf thymus DNA with nevirapine at physiological pH was studied by using absorption, circular dichroism, viscosity, differential pulse voltammetry, fluorescence techniques, salt effect studies and computational methods. The drug binds to ct-DNA in a groove binding mode, as shown by slight variation in the viscosity of ct-DNA. Furthermore, competitive fluorimetric studies with Hoechst 33258 indicate that nevirapine binds to DNA via groove binding. Moreover, the structure of nevirapine was optimized by DFT calculations and was used for the molecular docking calculations. The molecular docking results suggested that nevirapine prefers to bind on the minor groove of ct-DNA.     

Spectroscopic studies of interaction of chlorobenzylidine with DNA

Electronic absorbance and fluorescence titrations are used to probe the interaction of chlorobenzylidine with DNA. The binding of chlorobenzylidine to DNA results in hypochromism, a small shift to a longer wavelength in the absorption spectra, and emission quenching in the fluorescence spectra. These spectral characteristics suggest that chlorobenzylidine binds to DNA by an intercalative mode. This conclusion is reinforced by fluorescence polarization measurements. Scatchard plots constructed from fluorescence titration data give a binding constant of 1.3 x 10(5) M(-1) and a binding site size of 10 base pairs. This indicates that chlorobenzylidine has a high affinity with DNA. The intercalative interaction is exothermic with a Van't Hoff enthalpy of -143 kJ/mol. This result is obtained from the temperature dependence of the binding constant. The interaction of chlorobenzylidine with DNA is affected by the pH value of the solution. The binding constant has its maximum at pH 3.0. Upon binding to DNA, the fluorescence from chlorobenzylidine is quenched efficiently by the DNA bases and the fluorescence intensity tends to be constant at high concentrations of DNA when the binding is saturated. The Stern-Volmer quenching constant obtained from the linear quenching plot is 1.6 x 10(4) M(-1) at 25 degrees C. The measurements of the fluorescence lifetime and the dependence of the quenching constant on the temperature indicate that the fluorescence quenching process is static. The fluorescence lifetime of chlorobenzylidine is 1.9 +/- 0.4 ns.     

Copper(II) complexes of diclofenac: Spectroscopic studies and DNA strand breakage

Copper(II) complexes of diclofenac with interesting anti-inflammatory profiles have been prepared and studied by infrared and electronic spectroscopy. In the solid state and in polar and coordinating solvents, all the complexes are solvated binuclear carboxylato-bridged complexes, [Cu(L)²(S)]², where L is monodeprotonated diclofenac and S is the axially bonded solvent. The effect of the copper(II) complexes on the in vitro DNA strand breakeage was studied by agarose gel electrophoresis. Relaxation or double stranded scissions of pDNA were observed leading to the formation of linear pDNA. Treatment of pDNA with high concentrations of these compounds caused a disappearance of pDNA. For the parent drug, sodium diclofenac, no effect on the pDNA was observed. This study presents some indications that the binuclear copper(II) complexes, [Cu(L)²(S)]², could have some relevance in the treatment of tumor cell lines.     

Spectroscopic studies of enantiomeric discrimination in jet-cooled chiral complexes.

Van der Waals complexes formed between chiral molecules in the isolated gas phase were studied by combining supersonic expansion techniques with laser spectroscopy. The weakly bound diastereoisomers formed between a chiral secondary alcohol, butan-2-ol, and a chiral aromatic derivative such as 2-naphthyl-1-ethanol or 1-phenylethanol used as a resolving agent were discriminated on the basis of the spectral shifts of the UV S(0)-S(1) transition of the chromophore. Ground-state depletion spectroscopy (hole burning) has shown that, while only one structure was detected for the 1-phenylethanol/butan-2-ol homochiral complex, the heterochiral complex is trapped in the jet under two different conformations. Two isomers have also been shown for each diastereoisomeric pair of the 2-naphthyl-1-ethanol/butan-2-ol complexes. Using a semiempirical potential model, these isomeric forms were related to calculated structures which exhibit a folded or extended geometry depending on the solvent conformation (anti or gauche). The relative binding energy of the complexes involving R-1-phenylethanol and R- or S-butan-2-ol were obtained from fragmentation threshold measurements following two-color photoionization. Comparison of the diastereoisomers exhibiting a similar spectral signature shows that the homochiral pair is more stable than the heterochiral one by about 0.7 kcal/mol. The fragmentation threshold has been shown to depend on the jet-cooled isomer and this result addresses the role of conformational control in enantioselective interactions.     

Molecular modeling of B-DNA site recognition by Ru intercalators: molecular shape selection

In this work, molecular modeling methods have been applied to the interaction characterization of polypyridyl transitional-metal complexes with the oligonucleotide (B-DNA fragment). In order to explore the factors governing the groove recognition and intercalative depth, we establish a simple and practical docking method (step-by-step docking operation) to obtain potential curves while making complexes inset into B-DNA along an assigned path. Energy values in the potential curve are obtained from energy minimization of binding geometries. Modeling results clearly show that the optimum binding conformation corresponding to the global minimum in the potential curve for each complex is found to correlate well with the experimental results. Our results also confirm that minor changes of the ligand structure can lead to profound influences on binding geometries, so the molecular shape of the complexes is a predominant factor in governing the binding mode. Moreover, we find that the vdW force and water molecular effect are strongly associated with molecular-shape selection in our model. These results complement and extend the knowledge of the nature of these complexes binding to B-DNA.Figure Schematic illustration of metal complexes bound to B-DNA. The complexes are intercalated into the A₅T₆/T₆A₅ base step via a head-on fashion     

Spectroscopic and molecular modeling studies on the binding of the flavonoid luteolin and human serum albumin

Luteolin (LUT) is a polyphenolic compound, found in a variety of fruits, vegetables, and seeds, which has a variety of pharmacological properties. In the present contribution, binding of LUT to human serum albumin (HSA), the most abundant carrier protein in the blood, was investigated with the aim of describing the binding mode and parameters of the interaction. The application of circular dichroism, UV‐Vis absorption, fluorescence, Raman and surface‐enhanced Raman scattering spectroscopy combined with molecular modeling afforded a clear picture of the association mode of LUT to HSA. Specific interactions with protein amino acids were evidenced. LUT was found to be associated in subdomain IIA where an interaction with Trp‐214 is established. Hydrophobic and electrostatic interactions are the major acting forces in the binding of LUT to HSA. The HSA conformations were slightly altered by the drug complexation with reduction of α‐helix and increase of β‐turns structures, suggesting a partial protein unfolding. Also the configuration of at least two disulfide bridges were altered. Furthermore, the study of molecular modeling afforded the binding geometry. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 917–927, 2009. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com     

Spectroscopic,electrochemical and molecular docking studies of dothiepin and doxepin with bovine serum albumin and DNA base

The interaction of dothiepin (DOT) and doxepin (DOX) with bovine serum albumin (BSA) and a DNA base (adenine) was studied using UV–visible, fluorescence, attenuated total reflection–infra‐red (ATR‐IR), cyclic voltammetry and molecular docking methods. Strong fluorescence quenching was observed upon interaction of DOT and DOX with BSA/adenine and the mechanism suggested static quenching. Hydrophobic and hydrogen bonding interactions were the predominant intermolecular forces needed to stabilize the copolymer. Upon addition of the drugs: (i) the tautomeric equilibrium structure of the adenine was changed; and (ii) the oxidation and the reduction peaks of the adenine/BSA interaction shifted towards high and low potentials, respectively. In ATR‐IR, the band shift of amides I and II indicated a change in secondary structure of BSA upon binding to DOT and DOX drugs. The reduction in voltammetric current in the presence of BSA/adenine was attributed to slow diffusion of BSA/adenine binding with DOX/DOT. The docking method indicated that the drug moiety interacted with the BSA molecule. Copyright © 2016 John Wiley & Sons, Ltd.     

Stability of triple helices containing RNA and DNA strands: experimental and molecular modeling studies.

UV-absorption spectrophotometry and molecular modeling have been used to study the influence of the chemical nature of sugars (ribose or deoxyribose) on triple helix stability. For the Pyrimidine.purine* Pyrimidine motif, all eight combinations were tested with each of the three strands composed of either DNA or RNA. The chemical nature of sugars has a dramatic influence on triple helix stability. For each double helix composition, a more stable triple helix was formed when the third strand was RNA rather than DNA. No stable triple helix was detected when the polypurine sequence was made of RNA with a third strand made of DNA. Energy minimization studies using the JUMNA program suggested that interactions between the 2'-hydroxyl group of the third strand and the phosphates of the polypurine strand play an important role in determining the relative stabilities of triple-helical structures in which the polypyrimidine third strand is oriented parallel to the polypurine sequence. These interactions are not allowed when the third strand adopts an antiparallel orientation with respect to the target polypurine sequence, as observed when the third strand contains G and A or G and T/U. We show by footprinting and gel retardation experiments that an oligoribonucleotide containing G and A or G and U fails to bind double helical DNA, while the corresponding DNA oligomers form stable triple-helical complexes.     

Design of copper DNA intercalators with leishmanicidal activity

The complexes [Cu(dppz)(NO(3))]NO(3) (1), [Cu(dppz)(2)(NO(3))]NO(3) (2), [Cu(dpq)(NO(3))]NO(3) (3), and [Cu(dpq)(2)(NO(3))]NO(3) (4) were synthesized and characterized by elemental analysis, FAB-mass spectrometry, EPR, UV, and IR spectroscopies, and molar conductivity. DNA interaction studies showed that intercalation is an important way of interacting with DNA for these complexes. The biological activity of these copper complexes was evaluated on Leishmania braziliensis promastigotes, and the results showed leishmanicidal activity. Preliminary ultrastructural studies with the most active complex (2) at 1 h revealed parasite swelling and binucleated cells. This finding suggests that the leishmanicidal activity of the copper complexes could be associated with their interaction with the parasitic DNA.     

Spectroscopic studies of pig kidney diamine oxidase-anion complexes

Complexes of pig kidney diamine oxidase with azide, thiocyanate, and cyanide have been characterized by EPR and circular dichroism spectroscopy. Cu(II) d-d bands are observed in the CD spectrum of the resting enzyme at ≈800 nm (12 500 cm⁻¹) and 575 nm (17 400 cm⁻¹). Anion binding produces characteristic changes in the CD spectra. N₃⁻/SCN⁻ → Cu(II) ligand-to-metal charge-transfer transitions are located at 390 nm (25 600 cm⁻¹) and 365 nm (27 400 cm⁻¹), respectively. In addition, an intense new band grew in at ≈500 nm (20 000 cm⁻¹) when azide or thiocyanate were added, which may be assigned as a Cu(II) electronic transition that gains rotational strength in the anion complex. EPR spectra established that the Cu(II)-anion complexes are tetragonal; however, the magnitudes of the anion-induced shifts in the EPR parameters were consistent with substantial perturbations of the Cu(II) electronic ground state in the thiocyanate and cyanide complexes. Prominent superhyperfine splitting was apparent in the EPR spectra of the diamine oxidase complexes with thiocyanate and cyanide. The superhyperfine structure is (at least) partially attributable to endogenous Cu(II) ligands, probably from imidazole.     

DNA interaction with low molecular weight ligands of different structure. III. DNA complexes with distactins

The DNA complexes with distactins have been investigated by means of spectrophotometry, viscosimetry and flow birefringence methods. The distactins are actinocin's derivatives containing in the 1,9 positions of the phenoxazone moiety oligopyrrolcarboxamide groups (like those of distamycin A), which have from one to three fragments of 1-methyl-4-amino-2-pyrrolic acid. The mode of DNA-distactins binding in water solution depends on the quantity of the methylpyrrole rings in the oligopeptide groups. The ligand with oligopeptide groups containing three methylpyrrole rings joins the DNA double helix only from outside by means of oligopeptide groups. The compounds with one and two methylpyrrole rings form two kinds of complexes with DNA: external binding and intercalation. In the latter case both chromophore and methylpyrrole fragments, interact with DNA.     

Spectroscopic and molecular modeling studies of the interaction between cytidine and human serum albumin and its analytical application

In this study, the interaction between cytidine and human serum albumin (HSA) was investigated for the first time by fluorescence spectroscopy in combination with UV absorption spectrum and molecular modeling under simulative physiological conditions. Experimental results indicated that cytidine had a strong ability to quench the intrinsic fluorescence of human serum albumin. The binding constants (K) at different temperatures, thermodynamic parameter enthalpy changes (DeltaH) and entropy changes (DeltaS) of HSA-cytidine had been calculated according to the relevant fluorescence data, which indicated that the hydrophobic and electrostatic interactions played a major role, which was in agreement with the results of molecular modeling study. In addition, the effects of other ions on the binding constants were also studied. Furthermore, synchronous fluorescence technology was successfully applied to the determination of human serum albumin added into the cytidine solution.     

Sugar complexes with neodymium nitrate. Spectroscopic and structural studies of two Nd(NO3)3-galactitol complexes

Two different Nd(NO3)3-galactitol complexes, 2Nd(NO3)3.C6H14O6.8 H2O and Nd(NO3)3.C6H14O6 have been obtained and were characterized by FT-IR and X-ray diffraction techniques. The spectral differences of the two complexes were consistent with the crystal-structure data.