Biophysical insights on the interaction of anticoagulant drug dicoumarol with calf thymus-DNA: deciphering the binding mode and binding force with thermodynamics.

The biological activity of drugs is exhibited due to their interactions with bio-receptors. Dicoumarol (DIC) is a natural hydroxycoumarin and a well-known anticoagulant. DNA is the genetic material and one of the targets of numerous drugs. The interaction of DIC with calf-thymus DNA (ct-DNA) has been studied using different biophysical techniques and docking studies. The binding constant in the order of 103 to 104 M-1 was observed from spectroscopic studies. Thermodynamic studies at 4 different temperatures revealed the spontaneity of the interaction with the entropy-driven process. Marker displacement studies with competitive markers of intercalators (ethidium bromide) and groove binders (Hoechst 33258) confirmed the groove-binding nature of DIC in DNA. The groove-binding mode of DIC was complemented by different studies like viscosity measurements, DNA melting, and the effect of KI on the binding. A minor perturbation in the DNA viscosity and no significant change in the DNA melting temperature (Tm) after binding with DIC further confirms the groove binding mode. The effect of KI on the DIC and DIC-DNA system suggested the absence of DIC intercalation. The absence of significant electrostatic force was revealed from the ionic-strength effect study. Binding-induced conformational variation in ct-DNA was absent in circular dichroism studies. Molecular docking studies suggested the position of DIC within the minor groove of ct-DNA, covering three base pairs long. The outcome of this report may help in understanding the pharmacodynamics and pharmacokinetics of dicoumarol analogs and related molecules.Communicated by Ramaswamy H. Sarma.

Assessing Partial Inhibition of Ribonuclease A Activity by Curcumin through Fluorescence Spectroscopy and Theoretical Studies.

Molecular interactions and controlled expression of enzymatic activities are fundamental to all cellular functions in an organism. The active polyphenol in turmeric known as curcumin (CCM) is known to exhibit diverse pharmacological activities. Ribonucleases (RNases) are the hydrolytic enzymes that plays important role in ribonucleic acid (RNA) metabolism. Uncontrolled and unwanted cleavage of RNA by RNases may be the cause of cell death leading to disease states. The protein ribonuclease A (RNase A) in the superfamily of RNases cleaves the RNA besides its role in different diseases like autoimmune diseases, and pancreatic disorders. Interaction of CCM with RNase A have been reported along with the possible role of CCM to inhibit the RNase A enzymatic activity. The interaction strength was found to be 104 M-1 order from spectroscopic results. Quenching of RNase A fluorescence by CCM was 104 M-1 order. Non-radiative energy transfer from RNase A (donor) to CCM (acceptor) suggested a distance of 2.42 nm between the donor-acceptor pair. Circular dichroism studies revealed no structural changes in RNase A after binding. Binding-induced conformational variation in protein was observed from synchronous fluorescence studies. Agarose gel electrophoresis revealed a partial inhibition of the RNase A activity by CCM though not significant. Molecular docking and molecular dynamics studies suggested the residues of RNase A involved in the interaction with supporting the experimental finding for the partial inhibition of the enzyme activity. This study may help in designing new CCM analogues or related structures to understand their differential inhibition of the RNase A activity.

Binding of dicoumarol analog with DNA and its antioxidant studies: A biophysical insight by in-vitro and in-silico approaches.

DNA is the major target for a number of pharmaceutical drugs. The interaction of drug molecules with DNA plays a major role in pharmacokinetics and pharmacodynamics. Bis-coumarin derivatives have diverse biological properties. Here, we have explored the antioxidant activity of 3,3'-Carbonylbis (7-diethylamino coumarin) (CDC) using DPPH, H2O2, and superoxide scavenging studies followed by its binding mode in calf thymus-DNA (CT-DNA) using several biophysical methods including molecular docking. CDC exhibited comparable antioxidant activity to standard ascorbic acid. The UV-Visible and fluorescence spectral variations indicate the CDC-DNA complex formation. The binding constant in the range of 104 M-1 was obtained from spectroscopic studies at room temperature. The fluorescence quenching of CDC by CT-DNA suggested a quenching constant (KSV) of 103 to 104 M-1 order. Thermodynamic studies at 303, 308, and 318 K revealed the observed quenching as a dynamic process besides the spontaneity of the interaction with negative free energy change. Competitive binding studies with site markers like ethidium bromide, methylene blue, and Hoechst 33258 reflect CDC's groove mode of interaction. The result was complemented by DNA melting study, viscosity measurement, and KI quenching studies. The ionic strength effect was studied to interpret the electrostatic interaction and found its insignificant role in the binding. Molecular docking studies suggested the binding location of CDC within the minor groove of CT-DNA, complementing the experimental result.

DNA binding studies of antifungal drug posaconazole using spectroscopic and molecular docking methods.

The binding studies of DNA with small molecules have been an emerging field of research all the time since DNA as the genetic material is a major biological target for various drugs. Interpretation of small molecule-DNA binding helps in understanding their interactions with designing new drugs of greater medicinal activity. Posaconazole is an antifungal drug in the class of triazoles which are known to possess numerous pharmacological properties. In this work, the nature of the binding of posaconazole with calf-thymus DNA has been studied using spectroscopic techniques and molecular docking studies. A binding constant of the order of 103 M-1 was observed from UV-visible and fluorescence studies for the interaction between posaconazole and calf-thymus DNA. The fluorescence property of posaconazole was found to be quenched by calf-thymus DNA with a quenching constant of the order of 103 M-1. Competitive displacement of ethidium bromide and Hoechst 33258 by posaconazole using fluorescence technique suggested minor groove binding of posaconazole in calf-thymus DNA. Confirmation of the binding mode was further complemented by the viscosity measurement and DNA melting studies followed by KI quenching experiments. The studies on the effect of ionic strength on the binding suggested a possible role of electrostatic force in the interaction. Molecular docking studies reflected a crescent shape of the posaconazole within the minor groove of calf-thymus DNA validating the experimental findings showing the residues involved in the interaction.

Deciphering the nature of binding of dexlansoprazole with DNA: Biophysical and docking approaches.

Drugs, in general, exhibit their pharmacological activity in binding with intracellular targets. Numerous anticancer and antibacterial drugs target DNA as one of their primary intracellular targets. Dexlansoprazole (DLP) is a heterocyclic compound containing benzimidazole moiety and a proton pump inhibitor used to treat gastroesophageal reflux disease. The interaction of dexlansoprazole with calf thymus DNA (ct-DNA) has been studied using biophysical methods. The UV-Visible studies revealed a binding constant of 2.15 ± 0.3 × 104 M-1 which is close to the value of 2.44 ± 0.3 × 104 M-1 obtained from the fluorescence studies. Competitive displacement studies using the fluorescence spectroscopic method with ethidium bromide and Hoechst as DNA markers suggested the groove binding mode of DLP in ct-DNA. The groove binding mode of DLP in ct-DNA was complemented by the results of viscosity and DNA melting studies. Further studies on the effect of ionic strength and potassium iodide on DLP binding with ct-DNA supported the observed binding mode. Circular dichroism studies reflected no significant conformational variation in ct-DNA after the interaction. The binding mode obtained from the experimental studies was corroborated by the molecular docking studies that showed the position of DLP in the minor groove of ct-DNA along with the receptor interface restudies involved in the interaction.

An investigation of the molecular interactions of diacetylcurcumin with ribonuclease A.

Curcumin is a natural product with diverse pharmacological activities. Studies of curcumin and its structural derivatives have been a subject of growing interest as a result of their diverse biological activities. We report the interaction of diacetylcurcumin (DAC) with Ribonuclease A (RNase A). The binding constant of DAC with RNase A was found to be of the order of 10(4) M(-1). The intrinsic fluorescence of RNase A was quenched by DAC with a quenching constant of 2.2 x10(4) M(-1). The distance between the fluorophore of RNase A and DAC was found to be 2.6 nm, calculated from a Förster type fluorescence resonance energy transfer (FRET). Secondary structural changes of RNase A after binding were analyzed from circular dichroism and Fourier transform infrared studies. Protein-ligand docking studies were conducted to determine the residues involved in the interaction of RNase A with DAC and changes in the accessible surface of the interacting residues were calculated accordingly.

A spectroscopic investigation into the interactions of 3'-O-carboxy esters of thymidine with bovine serum albumin.

Binding studies of 3'-O-carboxy esters of thymidine, reported inhibitors of ribonucleases, with bovine serum albumin (BSA) have been explored in this report. Fluorescence spectroscopy in combination with Fourier transform infrared (FTIR) and circular dichroism (CD) spectroscopy have been used to determine the nature and mode of binding. The binding and quenching parameters were determined from tryptophan fluorescence quenching by Scatchard plots and modified Stern-Volmer plots. The association constants are of the order of 10(4) M(-1) for both the ligands. Thermodynamic parameters suggest that apart from an initial hydrophobic association, hydrogen bonding and van der Waals interactions play a decisive role during protein-ligand complex formation. Minor changes were observed in the secondary structures of human serum albumin (HSA) as revealed by FTIR and CD. Docking studies suggest that the ligands are close to Trp 213, which causes fluorescence quenching.

Molecular interactions of isoxazolcurcumin with human serum albumin: spectroscopic and molecular modeling studies.

Curcumin is a nontoxic natural product with diverse pharmacological potencies. We report the interaction of a potent synthetic derivative of curcumin, isoxazolcurcumin (IOC) with human serum albumin (HSA) using various biophysical methods. The observed fluorescence quenching of HSA by IOC is due to a complex formation by a static quenching process with a quenching constant of the order of 10(5) M(-1). The binding affinity and the number of binding sites were obtained from a Scatchard analysis. Thermodynamics reveals that the interaction is entropy driven with predominantly hydrophobic forces. From the observed Förster-type fluorescence resonance energy transfer (FRET), the donor (Trp 214 in HSA) to acceptor (IOC) distance is calculated to be 3.2 nm. The conformational changes of HSA due to the interaction were investigated qualitatively from synchronous fluorescence spectra along with a quantitative estimation of the secondary structure from Fourier Transform Infrared (FTIR) and circular dichroism (CD) spectroscopies. Molecular docking studies were performed to obtain information on the possible residues involved in the interaction process, and changes in accessible surface area of the interacting residues were calculated. The preferred binding site of IOC was analyzed by ligand displacement experiments with 1-anilino-8-naphthalenesulfonate (ANS) and warfarin-bound HSA.

Studies on the interaction of copper complexes of (-)-epicatechin gallate and (-)-epigallocatechin gallate with calf thymus DNA.

The interaction of copper complexes of (-)-epicatechin gallate (ECG) and (-)-epigallocatechin gallate (EGCG) with calf thymus DNA (ct-DNA) was investigated by UV-visible (UV-Vis), fluorescence and circular dichroism along with melting studies. It was observed that both copper complexes quench the fluorescence intensity of ethidium bromide bound ct-DNA upon binding, resulting in a ground state complex formation by a static quenching process. The binding constants evaluated from fluorescence data were supported by the UV-Vis study. The values ranged from 0.84 to 1.07x10(5)M(-1) and 1.14 to 1.04x10(5)M(-1) for Cu(II)-ECG and Cu(II)-EGCG, respectively for the temperature range 21-42 degrees C with two binding sites. Thermodynamic parameters obtained are suggestive of the involvement of different modes of interaction during binding for each complex although both were found to be intercalating in nature. Circular dichroism studies and variations in the melting temperature reveal unwinding of the ct-DNA helix with conformational changes due to binding.

Investigating the binding of curcumin derivatives to bovine serum albumin.

The interaction of bovine serum albumin (BSA) with isoxazolcurcumin (IOC) and diacetylcurcumin (DAC) has been investigated. Binding constants obtained were found to be in the 10(5) M(-1) range. Minor conformational changes of BSA were observed from circular dichroism (CD) and Fourier transformed infrared (FT-IR) studies on binding. Based on Förster's theory of non-radiation energy transfer, the average binding distance, r between the donor (BSA) and acceptors IOC and DAC was found to be 3.79 and 4.27 nm respectively. Molecular docking of isoxazolcurcumin and diacetylcurcumin with bovine serum albumin indicated that they docked close to Trp 213, which is within the hydrophobic subdomain.