Spectroscopic insights with molecular docking and molecular dynamic simulation studies of anticancer drug 5-Fluorouracil targeting human pyruvate kinase m2.

This study was conducted to test the efficacy of 5-fluorouracil (5-FU) as an anticancer drug against the human pyruvate kinase isozyme M2 (PKM2) using spectroscopic, molecular docking and molecular dynamic simulation studies. PKM2 fluorescence quenching studies in the presence of 5-FU performed at three different temperatures indicates dynamic quenching processes with single-set of binding (n ≈ 1) profile. The biomolecular quenching constants (kq) and the effective binding constants (Kb) obtained are shown to increase with temperature. The calculated enthalpy (ΔH) and entropy changes (ΔS) are estimated to be -118.06 kJ/mol and 146.14 kJ/mol/K respectively, which suggest the possible mode of interaction as electrostatic and hydrogen bonding. Further, these values were used to estimate the free energy changes (ΔG) and that increases with temperature. The negative ΔG values clearly indicates spontaneous binding process that stabilizes the complex formed between 5-FU and PKM2. Far-UV CD spectra of PKM2 in the presence of 5-FU shows decrease in α-helix contents which point towards the destabilization of secondary structure that weakens the biological activity of PKM2. The intrinsic fluorescence study and circular dichroism (CD) spectra showed minor conformational changes of PKM2 in the presence of 5-FU. Additionally, the results obtained from molecular docking and all-atom molecular dynamic simulation study supports the insight of the spectroscopic binding studies, and strengthens the dynamic stability of the complex between 5-FU and PKM2 through H-bonding. This study establishes a paradigm of 5-FU-PKM2 complexation and the efficacy of 5-FU that compromises the biological activity of the targeted PKM2.Communicated by Ramaswamy H. Sarma.

Kanamycin-Mediated Conformational Dynamics of Escherichia coli Outer Membrane Protein TolC.

TolC is a member of the outer membrane efflux proteins (OEPs) family and acts as an exit duct to export proteins, antibiotics, and substrate molecules across the Escherichia coli cell membrane. Export of these molecules is evidenced to be brought about through the reversible interactions and binding of substrate-specific drug molecules or antibiotics with TolC and by being open for transport, which afterward leads to cross-resistance. Hence, the binding of kanamycin with TolC was monitored through molecular docking (MD), the structural fluctuations and conformational changes to the atomic level. The results were further supported from the steady-state fluorescence binding and isothermal titration calorimetry (ITC) studies. Binding of kanamycin with TolC resulted in a concentration dependent fluorescence intensity quenching with 7 nm blue shift. ITC binding data maintains a single binding site endothermic energetic curve with binding parameters indicating an entropy driven binding process. The confirmational changes resulting from this binding were monitored by a circular dichroism (CD) study, and the results showed insignificant changes in the α-helix and ß-sheets secondary structure contents, but the tertiary structure shows inclusive changes in the presence of kanamycin. The experimental data substaintially correlates the RMSD, R g, and RMSF results. The resulting conformational changes of the TolC-kanamycin complexation was stabilized through H-bonding and other interactions.

Oxidative stress generated at nickel oxide nanoparticle interface results in bacterial membrane damage leading to cell death.

Metal oxide nanoparticles (NPs) have shown enhanced antibacterial effects against many bacteria. Thus, understanding the potential antibacterial effects of nickel oxide nanoparticles (NiO NPs) against Gram-positive and Gram-negative pathogenic bacteria is an urgent need to enable the exploration of NiO NP use in biomedical sciences. To this end, NiO NPs were synthesized by microwave assisted hydrothermal synthesis method. The synthesized NPs were characterized by X-ray diffraction (XRD) and Fourier Transfer Infrared (FT-IR) and UV-visible spectroscopy. The morphological features of the synthesized NiO NPs were analysed using Transmission Electron Microscopy (TEM) and FE-SEM analysis. The antibacterial activity of NiO NP was explored using different antimicrobial and biophysical studies. The obtained data reveals that the NiO NP has stronger antibacterial activity against Gram-positive bacteria compared to Gram-negative bacteria. The mechanism behind the antibacterial activity of the NiO NP was explored by evaluating the amount of ROS generation at the NiO NP interface. The effect of ROS generation on the bacterial membrane was evaluated by BacLight assay and morphological analysis of the bacterial membrane using FE-SEM. The data altogether suggested that the oxidative stress generated at the NiO NP interface resulted in membrane damage leading to bacterial cell death.