Spectral, electrochemical and molecular docking methods to get an understanding of supramolecular chemistry of sulfa drugs to biomolecules

Elucidating the binding mechanism of an antimigraine agent with a model protein: insights from molecular spectroscopic, calorimetric and computational approaches

Sumatriptan (SUM), a serotonin activator used to treat migraines and cluster headaches. Molecular spectroscopic methods including fluorescence quenching, time dependent fluorescence, FRET, absorption, circular dichroism, differential scanning calorimetric and computational approaches were employed to unravel the interaction between sumatriptan and bovine serum albumin (BSA). The fluorescence quenching studies suggested the interaction between SUM and BSA with a moderate binding with the binding constant (K_b) in the order of 10⁴. The findings of temperature and time dependent fluorescence quenching studies confirmed the role of static quenching mechanism. Thermodynamic parameters suggested the key role of electrostatic force in the interaction of SUM with BSA. Absorption and CD spectral studies revealed the bioenvironmental changes around the Trp in BSA upon binding of SUM. Calorimetric based thermal denaturation results confirmed that the thermal stability of BSA was improved in the presence of SUM. resulted in the this decreased flexibility of protein chain. Site competitive studies indicated SUM was located in the hydrophobic cavity of site I which was further confirmed by the docking and dynamic simulation studies. Additionally, molecular dynamics simulations inferred the microenvironmental condition around the SUM and the amino acids and forces involved in the binding of SUM with BSA.Communicated by Ramaswamy H. Sarma.

Interaction of cobalt(II) and copper(II) hydroxamates with polyriboadenylic acid: An insight into RNA based drug designing

The polyadenylic acid [poly(A)] tail of mRNA plays a noteworthy role in the initiation of the translation, maturation, and stability of mRNA. It also significantly contributes to the production of alternate proteins in eukaryotic cells. Hence, it has recently been recognized as a prospective drug target. Binding affinity of bis(N-p-tolylbenzohydroxamato)Cobalt(II), [N-p-TBHA-Co(II)] (1) and bis(N-p-naphthylbenzohydroxamato)Copper(II), [N-p-NBHA-Cu(II)] (2) complexes with poly(A) have been investigated by biophysical techniques namely, absorption spectroscopy, fluorescence spectroscopy, diffuse reflectance infrared Fourier transform spectroscopy, circular dichroism spectroscopy, viscometric measurements and through molecular docking studies. The intrinsic binding constants (Kb) of complexes were determined following the order of N-p-TBHA-Co(II)] > N-p-NBHA-Cu(II), along with hyperchromism and a bathochromic shift for both complexes. The fluorescence quenching method revealed an interaction between poly(A)-N-p-TBHA-Co(II)/poly(A)-N-p-NBHA-Cu(II). The mode of binding was also determined via the fluorescence ferrocyanide quenching method. The increase in the viscosity of poly(A) that occurred from increasing the concentration of the N-p-TBHA-Co(II)/N-p-NBHA-Cu(II) complex was scrutinized. The characteristics of the interaction site of poly(A) with N-p-TBHA-Co(II)/N-p-NBHA-Cu(II) were adenine and phosphate groups, as revealed by DRS-FTIR spectroscopy. Based on these observations, a partial intercalative mode of the binding of poly(A) has been proposed for both complexes. Circular dichroism confirmed the interaction of both the complexes with poly(A). The molecular docking results illustrated that complexes strongly interact with poly(A) via the relative binding energies of the docked structure as -259.39eV and -226.30eV for N-p-TBHA-Co(II) and N-p-NBHA-Cu(II) respectively. Moreover, the binding affinity of N-p-TBHA-Co(II) is higher in all aspects than N-p-NBHA-Cu(II) for poly(A).

Study of the Interaction of Ciprofloxacin and Sparfloxacin with Biomolecules by Spectral, Electrochemical and Molecular Docking Methods

Interactions of ciprofloxacin and sparfloxacin with different biomolecules (DNA, RNA and BSA) are investigated by UV–Visible spectroscopy, fluorescence spectroscopy, cyclic voltammetry and molecular docking methods. Upon increasing the concentration of the biomolecules, the absorption maxima of ciprofloxacin and sparfloxacin are red shifted in the aqueous solutions whereas red or blue shift noticed in the fluorescence spectra. The negative free energy changes suggest that the interaction processes are spontaneous. Cyclic voltammetry results suggested that when the drug concentration is increased, the anodic electrode potential increased. Molecular docking results showed that hydrophobic forces, electrostatic interactions, and hydrogen bonds played vital roles in the interaction drugs with biomolecules. The molecular docking calculation clarifies the binding mode and the binding sites are in good accordance with the experiment results.

Unraveling the thermodynamics, binding mechanism and conformational changes of HSA with chromolyn sodium: Multispecroscopy, isothermal titration calorimetry and molecular docking studies

Cromolyn sodium is an anti-allergic drug effective for treatment in asthma and allergic rhinitis. In this project, interaction of chromolyn sodium (CS) with human serum albumin (HSA) has been investigated by various techniques such as UV-vis, fluorescence, circular dichorism (CD), fourier transform infrared (FT-IR) spectroscopy, isothermal titration calorimetric (ITC) and molecular docking. The fluorescence quenching results revealed that there was static quenching mechanism in the interactions of CS with HSA. The binding constant (K_b), enthalpy change (ΔH°), entropy change (ΔS°) and Gibbs free energy change (ΔG°) were calculated. The negative values of TΔS° and ΔH° obtained from fluorescence spectroscopy and isothermal titration calorimetry, indicate that hydrogen bonding and van der Waal's forces played major role in the binding process and the reaction is exothermic in nature. The binding constant (K_b) was found to be in the order of 10⁴M^-1 which depicts a good binding affinity of CS towards HSA. The conformational changes in the HSA due to interaction of CS were investigated from CD and FT-IR spectroscopy. The binding site of CS in HSA was sub-domain IIA as evident from site probing experiment and molecular docking studies.