Pronab Kundu

Binding of an anionic fluorescent probe with calf thymus DNA and effect of salt on the probe–DNA binding: a spectroscopic and molecular docking investigation

Binding interaction of a biologically relevant anionic probe molecule, 8-anilino-1-naphthalene sulfonate (ANS) with calf-thymus deoxyribonucleic acid (ctDNA) has been investigated exploiting vivid spectroscopic techniques together with molecular docking study. Significant modifications in the absorption and emission profiles, the determined binding constant, micropolarity analysis, circular dichroism (CD) spectral study, comparative binding study with ethidium bromide (EtBr)—an intercalative binder, thermometric experiment relating to the helix melting of ctDNA and blind molecular docking simulation confirm the groove binding of ANS with ctDNA. Furthermore, a remarkable enhancement is observed in the fluorescence intensity as well as in the fluorescence lifetime of the DNA-bound probe with the addition of salts. Reduction in the electrostatic repulsion between the ANS and DNA at high salt concentration has been assigned responsible for this observation. Besides providing an insight into the probe–DNA interaction, the work implies that the binding interaction of a negatively charged probe with DNA can be enhanced considerably by the addition of salts.

DNA induced sequestration of a bioactive cationic fluorophore from the lipid environment: A spectroscopic investigation.

The effect of calf-thymus DNA (ctDNA) on the lipid bound probe, formed by the cationic phenazinium dye phenosafranin (PSF) and the anionic lipid dimyristoyl-L-α-phosphatidylglycerol (DMPG), has been unearthed exploiting various spectroscopic techniques. Steady state and time-resolved fluorometric studies and measurements of circular dichroism and DNA helix melting temperature reveal that in the presence of DNA the probe is dislodged from the lipid environment and gets intercalated within the DNA helix. The work qualitatively illustrates that the anionic lipid can be used as a potential nanocarrier for delivering the cationic drugs to the most relevant biomacromolecular target, DNA.

Interaction of a bioactive pyrazole derivative with calf thymus DNA: Deciphering the mode of binding by multi-spectroscopic and molecular docking investigations

Deoxyribonuclic acid (DNA) is the most relevant intracellular target for a wide variety of anticancer and antibiotic drugs. Elucidating the binding interaction of small bioactive molecules with DNA provides a structural guideline for designing new drugs with improved selectivity and superior clinical efficacy. In the present work interaction of a newly synthesized biologically relevant fluorophore, namely, (E)-1,5-diphenyl-3-styryl-4,5-dihydro-1H-pyrazole (DSDP) with calf thymus DNA (ctDNA) has been investigated vividly through a number of in vitro studies. Noteworthy modifications in the UV-Vis absorption and emission spectra reveal the formation of the probe-ctDNA complex. Several other spectroscopic experiments such as circular dichromism (CD), iodide induced quenching, competitive binding assay with known groove binder probe, 3-hydroxyflavone (3HF), time resolved fluorescence decay measurements, thermometric experiment in connection with the helix melting of ctDNA etc. unequivocally ascertain the groove binding interaction of DSDP with ctDNA. Determination of the thermodynamic parameters through temperature variation study implies the dominant role of hydrophobic interaction in the probe-DNA binding process. Inappreciable change in the CD spectrum of ctDNA with the addition of DSDP suggests that binding of the probe with the DNA does not lead to a significant modification in the DNA conformation. In-silico molecular docking simulation corroborates the experimental findings and depicts that DSDP favorably binds to the minor groove region of the biomacromolecule.

Impact of Structural Modification on the Photophysical Response of Benzoquinoline Fluorophores

Structural influence on the photophysical behavior of two pairs of molecular systems from the biologically potent benzoquinoline family, namely, dimethyl-3-(4-chlorophenyl)-3,4-dihydrobenzo[f]-quinoline-1,2-dicarboxylate, dimethyl-3-(2,6-dichlorophenyl)-3,4-dihydrobenzo[f]quinoline-1,2-dicarboxylate and their corresponding dehydrogenated analogues has been investigated exploiting experimental as well as computational techniques. The study unveils that dehydrogenation in the heterocyclic rings of the studied quinoline derivatives modifies their photophysics radically. Experimental observations imply that the photophysical behavior of the dihydro analogues is governed by the intramolecular charge transfer (ICT) process. However, the ICT process is restricted significantly by the dehydrogenation of the heterocyclic rings. Computational exertion leads to the proposition that the change in the electronic distribution in these molecular systems on dehydrogenation is the rationale behind the dramatic modification of their photophysics.

Binding interaction of differently charged fluorescent probes with egg yolk phosphatidylcholine and the effect of β-cyclodextrin on the lipid–probe complexes: A fluorometric investigation

Interaction of cationic phenosafranin (PSF), anionic 8-anilino-1-naphthalene sulfonate (ANS) and non-ionic nile red (NR) have been studied with the zwitterionic phospholipid, egg yolk L-α-phosphatidylcholine (EYPC). The study reveals discernible binding interactions of the three fluorescent probes with the EYPC lipid vesicle. Once the binding of the probes with the lipid is established, the effect of cyclic oligosaccharide, β-cyclodextrin (β-CD), on these lipid bound probes has been investigated. Different fluorometric techniques suggest that addition of β-CD to the probe-lipid complexes leads to the release of the probes from the lipid medium through the formation of probe-β-CD inclusion complexes. A competitive binding of the probes between β-cyclodextrin and the lipid is ascribed to be responsible for the effect. This provides an easy avenue for the removal of the probe molecules from the lipid environment. Extension of this work with drug molecules in cell membranes is expected to give rise to a strategy for the removal of adsorbed drugs from the cell membranes by the use of non-toxic β-cyclodextrin.

Unraveling the binding interaction of a bioactive pyrazole-based probe with serum proteins: Relative concentration dependent 1:1 and 2:1 probe-protein stoichiometries

Molecular interactions and binding of probes/drugs with biomacromolecular systems are of fundamental importance in understanding the mechanism of action and hence designing of proactive drugs. In the present study, binding interactions of a biologically potent fluorophore, (E)-1,5-diphenyl-3-styryl-4,5-dihydro-1H-pyrazole (DSDP) with two serum transport proteins, human serum albumin and bovine serum albumin, have been investigated exploiting multi-spectroscopic techniques. The spectrophotometric and fluorometric studies together with fluorescence quenching, fluorescence anisotropy, urea induced denaturation studies and fluorescence lifetime measurements reveal strong binding of DSDP with both the plasma proteins. Going beyond the vast literature data mostly providing 1:1 probe-protein complexation, the present investigation portrays 2:1 probe-protein complex formation at higher relative probe concentration. A newer approach has been developed to have an estimate of the binding constants varying the concentration of the protein, instead of the usual practice of varying the probe. The binding constants for the 2:1 DSDP-protein complexes are determined to be 1.37 × 1010 M-2 and 1.47 × 1010 M-2 for HSA and BSA respectively, while those for the 1:1 complexation process come out to be 1.85 × 105 M-1 and 1.73 × 105 M-1 for DSDP-HSA and DSDP-BSA systems respectively. Thermodynamic analysis at different temperatures implies that the forces primarily involved in the binding process are hydrogen bonding and hydrophobic interactions. Competitive replacement studies with known site markers and molecular docking simulations direct to the possible locations and binding energies of DSDP with the two serum proteins, corroborating well with the experimental results.

A promising strategy for improved solubilization of ionic drugs simply by electrostatic pushing

A simple and prospective strategy has been employed to enhance the solubility of a cationic bioactive photosensitizer, namely, phenosafranin (PSF), within the anionic sodium dodecyl sulfate (SDS) micellar nanocavity using soluble salts. Electrostatic repulsion between the cationic probe trapped at the micelle–water interface and the cation of the added salt plays an important role in effective pushing of probe inside the hydrophobic micellar nanocage. Vivid steady state and time resolved spectroscopic techniques divulge a notable improvement in the fluorescence yield, fluorescence anisotropy as well as the fluorescence lifetime of the SDS-bound probe in the presence of the added salts. Comparative spectral studies using various cations imply that higher charge density on the cation imparts a greater pushing effect on the cationic drug. The present study displays an encouraging demonstration of salt induced increased solubilization of the cationic drugs in the biomimicking target region, providing a promising strategy to a more effective delivery of ionic therapeutics.