Multi-spectroscopic and free energy landscape analysis on the binding of antiviral drug remdesivir with calf thymus DNA

Structural Insight into Groove Binding of Yohimbine with Calf Thymus DNA: A Spectroscopic, Calorimetric, and Computational Approach

“…53 As presented in Table 2, the thermodynamic profiling of the interaction, indicate the binding of both the complex formation in favor of negative enthalpy, ΔH°= −13.05 kJ mol −1 (YH to CT-DNA), and a strong positive entropy contribution, with ΔS°= 16.04 kJ mol −1 indicating electrostatic interactions in the ligand and DNA complex formation, thus suggesting entropy driven exothermic binding process. 54,55 The origin of a strong positive entropy term is an indication of the disruption and release of water molecule and condensed sodium ions on the interaction of YH into the DNA helix as postulated in many previous ligand−DNA interaction studies. 56,57 A hallmark of such an association between a ligand and DNA that normally has a significant hydrophobic impact is the positive entropy and negative sign of enthalpy.…”

“…By the report, the primary force includes electrostatic when Δ H ° < 0 and Δ S ° > 0; the essential factor is hydrogen bonding and van der Waals when Δ H ° < 0 and Δ S ° < 0, and the major force is the hydrophobic association when Δ H ° > 0 and Δ S ° > 0 . As presented in Table , the thermodynamic profiling of the interaction, indicate the binding of both the complex formation in favor of negative enthalpy, Δ H ° = −13.05 kJ mol –1 (YH to CT-DNA), and a strong positive entropy contribution, with Δ S ° = 16.04 kJ mol –1 indicating electrostatic interactions in the ligand and DNA complex formation, thus suggesting entropy driven exothermic binding process. , The origin of a strong positive entropy term is an indication of the disruption and release of water molecule and condensed sodium ions on the interaction of YH into the DNA helix as postulated in many previous ligand–DNA interaction studies. , A hallmark of such an association between a ligand and DNA that normally has a significant hydrophobic impact is the positive entropy and negative sign of enthalpy . According to the results obtained, the Gibbs energy changes from −29.09 kJ mol –1 at 288.15 K to −30.21 kJ mol –1 at 308.15 K. Therefore, the binding process was spontaneous as a result of the change in negative free energy throughout all temperatures (Δ G ° < 0).…”

“…The shift in the emission spectra of such dye–DNA complex formation is monitored when the dye–DNA complex would be enabled to bind to YH; its binding mechanism needs to be determined. As YH competes with the dyes bound to DNA, it is therefore expected that it would interact with the DNA double helix in a manner that is similar to that of the dye it replaces. , Fluorescence spectra were obtained while the dyes to CT-DNA combination were determined by titration with increasing amounts of YH in various sets of assays. Quenching in fluorescence was perceived upon titration of YH in the case of CT-DNA complex with rhodamine-B (Figure A), whereas no such effect was seen in the case of ethidium bromide (Figure B).…”

“…Thus, YH's groove binding mechanism with CT-DNA is implemented. 55,66 Urea Denaturation Assay. This assay is often carried out to confirm the mode of interaction of small molecules with natural polymeric DNA.…”

N,N′,N′′-Trisubstituted guanidine derivatives as DNA-intercalators: synthesis, crystal structures and biophysical investigations

“…The simulation analysis was carried out as reported by us earlier. 42 The docked structure with the minimum binding free energy was selected as an input file in an orthorhombic box with a TIP4P water model. The box contains 12 403, 12 412 and 12 394 atoms for L1 , L2 and L3 , respectively.…”