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Strategically designed carboxylated acyclonucleosides have been probed as a new class of RNase A inhibitors. Several experimental and theoretical studies have been performed to compile relevant qualitative and quantitative information regarding the nature and extent of inhibition. The inhibition constant (Ki) values were determined using a UV-based kinetics experiment. The changes in the secondary structure of the enzyme upon binding with the inhibitors were obtained from circular dichroism studies. The binding constants for enzyme-inhibitor interactions were determined with the help of fluorescence spectroscopy. Docking studies were performed to reveal the possible binding sites of the inhibitors within the enzyme. The cytosine analogues were found to possess better inhibitory properties in comparison to the corresponding uracil derivatives. An increment in the number of carboxylic acid groups (-COOH) in the inhibitor backbone was found to result in better inhibition. [ABSTRACT FROM AUTHOR]

Highlights: [•] Amino and carboxy functionalized nucleosides. [•] Competitive inhibition of the ribonucleolytic activity of angiogenin. [•] Fluorescence based enzyme kinetics. [•] Inhibition of angiogenin induced angiogenesis. [•] Better activity of the nucleosidic molecules compared with phosphate analogues. [ABSTRACT FROM AUTHOR]

A new series of (E)-pyrene oxime ester conjugates of carboxylic acids including amino acids were synthesized by coupling with an environment sensitive fluorophore 1-acetylpyrene. (E)-Pyrene oxime esters exhibited strong fluorescence properties and interestingly their fluorescence properties were found to be highly sensitive to the surrounding environment. Direct irradiation of the (E)-pyrene oxime esters by UV light (≥350 nm) resulted in both the photo-Beckmann rearrangement product and products resulting from N–O bond homolysis. Photoproduct formation and their distribution were found to be solvent dependent. Further, we also showed (E)-pyrene oxime esters intercalated into DNA efficiently and photo-cleaved DNA. Finally we also showed these oxime esters can permeate cells efficiently and may cause cytotoxicity upon irradiation of light. [ABSTRACT FROM AUTHOR]

Abstract: The ribonuclease (RNase) activity of ribonucleases has been assayed by observing the change in fluorescence intensity of ethidium bromide on binding with yeast RNA. The binding of EtBr with RNA was monitored via UV–vis and fluorimetric methods. The degradation of RNA by RNase A was monitored by the change in fluorescence emission intensity of ethidium bromide at 600nm on excitation at 510nm. The ribonucleolytic activity of RNase A and angiogenin at various pH values was determined by this method. From this technique we have also determined the macroscopic pK a values of active site residues of these enzymes. This assay permits the evaluation of the catalytic efficiency of enzymatic proteins ranging from high ribonucleolytic activity to low ribonucleolytic activity toward the natural substrate RNA. [Copyright &y& Elsevier]

Abstract: The protein, hen egg white lysozyme, on photoexcitation undergoes electron transfer with menadione (2-methyl-1,4-naphthoquinone), a widely known anticancer drug. With the addition of menadione the fluorescence of lysozyme is quenched with the simultaneous formation of an excited state charge-transfer complex in the longer wavelength and a ground state complex. The former is further evident from laser flash photolysis studies, which indicate a tryptophan to menadione electron transfer. From fluorescence quenching studies the binding constant is found to be ∼1.7×104 M−1 with the corresponding changes in enthalpy (ΔH°) and entropy (ΔS°) as 12.24kJmol−1 and 124.12Jmol−1 K−1, respectively, indicative of an entropy-driven process. The circular dichroism studies also show some structural changes with increase in α-helical content in the protein on interaction with menadione. Finally, docking studies give some insight into the role of Trp 108 of lysozyme in the interaction. [Copyright &y& Elsevier]

Abstract: The interactions of two stereoisomeric antioxidant flavonoids, catechin (C) and epicatechin (EC) with bovine serum albumin (BSA) and human serum albumin (HSA), have been investigated by steady state and time resolved fluorescence, phosphorescence, circular dichroism (CD), FTIR and protein–ligand docking studies. The steady-state fluorescence studies indicate a single binding site for both the ligands. FTIR spectra suggest that in both the albumins, C and EC stabilize the α-helix at the cost of a corresponding loss in the β-sheet structure. CD studies have been carried out using (±)C, and both the epimers (+)C and (−)C. The low temperature phosphorescence and protein–ligand [(+), (−) and (±) forms of C and EC] docking studies indicate that the ligands bind in the proximity of Trp 134 of BSA and Trp 214 of HSA, thereby changing their solvent accessible surface areas (ASA). Asn 158 and Glu 130 side chains are found to be within the hydrogen bonding distance from the phenolic –OH groups of C and EC in the case of BSA complex. C and EC are located within the binding pocket of sub-domain IIa of HSA. [Copyright &y& Elsevier]

Abstract: The enhanced fluorescence and anisotropy of the ESIPT emission of 3-hydroxy-2-naphthoic acid (3HNA) in the complexes of 3HNA with bovine serum albumin (BSA) and human serum albumin (HSA) showed the formation of 1:1 complex [binding constant=5.3×105 M−1 for BSA and =2.2×105 M−1 for HSA]. The ESIPT emission of the probe in non-polar, polar protic, polar aprotic and mixed solvents indicate that the position and the quantum yield of the emission are governed by the intermolecular hydrogen bonding ability and the polarity/polarizability of the solvents. Rotational correlation time of 3HNA (2.4ns and 5.2ns in BSA and HSA, respectively) obtained from the time resolved anisotropy decay of the ESIPT emission suggests motional restriction of the probe. Docking studies reveal H-bonding of some residues with the probe and loss of accessible surface area of several residues located near binding site. [Copyright &y& Elsevier]

Abstract: Ongoing research on curcumin and its structural derivatives are a subject of growing interest because of their demonstrated biological properties. Diacetylcurcumin (DAC), a synthetic derivative of natural non-toxic curcumin has been shown to affect a host of activities ranging from wound healing to life threatening diseases like AIDS, cancer etc. The interaction of diacetylcurcumin (DAC) with calf thymus-DNA (ct-DNA) has been investigated by spectroscopic and viscometric techniques. The fluorescence intensity of DAC was quenched by ct-DNA. The mean binding constant obtained from the spectroscopic techniques was 3.97±0.31×105 M−1. Circular dichroism studies did not reveal any unwinding of the DNA helix on interaction with DAC, implying no conformational changes. The binding mode was analyzed by competitive binding between ethidium bromide (EB) and DAC for ct-DNA and also by viscometric studies. DAC was found to be a minor groove binder with a preference for the A-T region compared to the G-C region. This was substantiated by displacement studies with Hoechst 33258, a known minor groove binder. Docking studies were found to corroborate the experimental results. [Copyright &y& Elsevier]

Abstract: Silibinin is a well-known naturally occurring compound used for the treatment of a wide range of hepatitic diseases. In this study, we report the binding of silibinin to the carrier protein, human serum albumin (HSA) under physiological conditions. UV–Vis and fluorescence quenching methods in combination with Fourier transformed infrared (FT-IR) and circular dichroism (CD) spectroscopy have been used to study the nature and mode of binding. The binding parameters were determined from tryptophan fluorescence quenching by a Scatchard plot and the results were found to be consistent with those obtained from a modified Stern–Volmer equation. The association constant is of the order of 105. The change in enthalpy (ΔH°) and entropy (ΔS°) due to the interaction were found to be −6.76kJmol−1 and 73.69Jmol−1 K−1, respectively. These values suggest that apart from an initial hydrophobic association, electrostatic interactions play a decisive role during complexation of silibinin with HSA. Observations from FT-IR and CD spectra upon ligand binding indicate changes in the secondary structure of HSA. Docking studies that corroborate our experimental results reveal that the silibinin molecule lies within hydrogen bonding distance of Trp 214 and Asp 451 residues of subdomains IIa and IIIa of HSA, respectively. [Copyright &y& Elsevier]

Abstract: The interaction of isoxazolcurcumin (IOC), a synthetic derivative of curcumin, with calf thymus-DNA (ct-DNA) has been investigated by UV–Vis, fluorescence, circular dichroism spectroscopies, viscosity measurements and docking studies. From these analyses, the binding constant, number of binding sites and mode of binding of IOC to ct-DNA has been determined. The binding constant of IOC to DNA calculated from both UV–Vis and CD spectra was found to be in the 104 M−1 range. Analyses of fluorescence spectra, viscosity measurements and molecular modeling of IOC–DNA interactions indicate that IOC is a minor groove binder of ct-DNA and preferentially binds to AT rich regions. Ethidium bromide displacement studies revealed that IOC did not have any effect on ethidium bromide bound DNA which is indicative of groove binding. To elucidate the preferred region of binding of IOC to DNA, docking studies have been performed and changes in accessible surface area (ΔASA) of nucleobases determined due to IOC–DNA complexation. [Copyright &y& Elsevier]

Abstract: All-trans retinoic acid derived from vitamin A is an essential component for the modulation of angiogenesis, the process of blood vessel formation. We have investigated the binding of all-trans retinoic acid to the carrier protein, human serum albumin (HSA) under physiological conditions. Fluorescence quenching methods in combination with Fourier transform infrared (FT-IR) spectroscopy and circular dichroism (CD) spectroscopy were used for the biophysical studies. The binding parameters were determined by a Scatchard plot and the results found to be consistent with those obtained from a modified Stern–Volmer equation. From the thermodynamic parameters calculated according to the van’t Hoff equation, the enthalpy change ΔH 0 and entropy change ΔS 0 are found to be 106.17 and 106.14J/molK, respectively. These values suggest that apart from hydrophobic interactions electrostatic interactions are present. Changes in the CD spectra and FT-IR spectra were observed upon ligand binding along with a significant degree of tryptophan fluorescence quenching on complex formation. Docking studies performed substantiated our experimental findings and it was observed that all-trans retinoic acid hydrogen bonded with Trp 214 and Asp 451 residues of subdomain IIA and IIIA of HSA, respectively. [Copyright &y& Elsevier]