The interaction between three isoquinoline alkaloids, berberine, palmatine and coralyne, and the protein lysozyme was studied using fluorescence, absorption, circular dichroism and isothermal titration calorimetry under physiological conditions. The three alkaloids caused strong quenching of the fluorescence of lysozyme by a static quenching mechanism, but with differing quenching efficiencies. The binding constants (K) at 25 °C are 5.37 × 10⁴, 4.22 × 10⁴, and 1.15 × 10⁵ M⁻¹, respectively, for berberine, palmatine and coralyne with binding sites (n) of approximately 1. We have demonstrated strong conformational changes in the secondary structure of the lysozyme molecule on alkaloid binding using synchronous fluorescence spectra, 3D fluorescence results and circular dichroism spectroscopic measurements. Interestingly, binding of the positively charged lysozyme to the positively charged alkaloid was endothermic and entropy driven. The negative standard molar Gibbs energy change (ΔG^o) in all the cases revealed that the binding process was spontaneous. The corresponding ΔH^o and TΔS^o values were 0.58 ± 0.03, 7.09 and 2.37 ± 0.03, 8.67 and 4.31 ± 0.03, 11.23 kcal mol⁻¹, respectively, for berberine, palmatine and coralyne. The thermodynamic parameters (ΔH^o and TΔS^o) of the reaction further indicated that both van der Waals forces and hydrogen bonds play a key role in the interaction. Spectroscopic evidence suggests that Trp62 and Trp63 in the β-domain of the protein are closer to the binding site of the alkaloids. Based on the Forster's theory of non-radiation energy transfer, the binding distances (r) between donor (protein) and acceptor (berberine, palmatine and coralyne) are 3.30, 3.09 and 3.06 nm, respectively. The results provide some valuable information on the interaction of these ligands with the protein.

The binding of the known DNA intercalators methylene blue and quinacrine with four sequence specific polynucleotides, viz. poly(dG-dC).poly(dG-dC), poly(dG).poly(dC), poly(dA-dT).poly(dA-dT) and poly(dA).poly(dT), have been compared using absorbance, fluorescence, competition dialysis and thermal melting and the thermodynamic aspects of the interaction studied. In all the cases, non-cooperative binding phenomena obeying neighbor exclusion principle was observed though the affinity was remarkably higher for quinacrine and the nature of the binding was characterized to be true intercalation. The data on the salt dependence of binding derived from the plot of log Kvs. log[Na⁺ ] revealed a slope of around 1.0, consistent with the values predicted by the theories for the binding of monovalent cations, and contained contributions from polyelectrolytic and non-polyelectrolytic forces. The bindings were characterized by strong stabilization of the polynucleotides against thermal strand separation in both optical melting as well as differential scanning calorimetry studies. The data analyzed from the thermal melting and isothermal titration calorimetry studies were in close proximity to those obtained from absorption spectral titration data. Isothermal titration calorimetry results revealed the bindings to poly(dG-dC).poly(dG-dC), poly(dG).poly(dC) and poly(dA-dT).poly(dA-dT) to be exothermic and favoured by both negative enthalpy and large favourable positive entropy changes, while that to poly(dA).poly(dT) was endothermic and entropy driven. The heat capacity changes obtained from temperature dependence of enthalpy gave negative values to all polynucleotides. New insights on the molecular aspects of interaction of these molecules to DNA have emerged from these studies.

Berberine, palmatine and coralyne, the isoquinoline alkaloids distributed in many botanical families, are extensively investigated due to their potential therapeutic actions and clinical utilities. In this work, their binding characteristics to hemoglobin (Hb) were studied by UV-vis absorption spectroscopy, fluorescence spectroscopy, circular dichroism spectroscopy, isothermal calorimetric titration and differential scanning calorimetric techniques. The results indicated that all the three alkaloids caused strong fluorescence quenching of Hb by the static quenching mechanism, but with differing quenching efficiencies. There was a single binding site on Hb for these alkaloids. According to the theory of Förster resonance energy transfer, the binding distances between β-Trp37 of Hb and berberine, palmatine and coralyne were evaluated to be 2.78 nm, 2.64 nm and 3.29 nm, respectively. The result of synchronous fluorescence, circular dichroism and 3D fluorescence revealed that the polarity around Trp residues experienced a significant increase in the presence of alkaloids. The binding was favoured by enthalpy and entropy changes. Results of circular dichroism, 3D and synchronous fluorescence studies confirmed that the binding of the alkaloids significantly changed the secondary structure of Hb. The studies revealed that berberine and palmatine bound to a site near to the α1β2 interface on Hb different than coralyne but the affinity of coralyne was one order higher than that of berberine and palmatine.