The interaction between citronellol and bovine serum albumin: Spectroscopic, computational and thermal imaging studies

In silico approaches for the identification of novel ULK1 inhibitors: pharmacophore model, molecular docking and molecular dynamics simulations

The serine/threonine kinase unc-51-like autophagy activating kinase 1 (ULK1) has been regarded as an attractive target for tumor therapy. In this study, in silico approaches, such as the pharmacophore-based virtual screening strategy, molecular docking and molecular dynamics (MD) simulations, were applied to develop novel potential ULK1 inhibitors. The pharmacophore models based on known aminopyrimidine ULK1 inhibitors were constructed to screen the dataset of 1.68 million compounds, which were obtained via screening the 2.30 million compounds in ChEMBL database by Lipinski's rule of five. Seven novel compounds and 1 known ULK1 inhibitor stand out for the strong virtual biological activity by molecular docking, cluster analysis, Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) calculation and Absorption Distribution Metabolism Excretion Toxicity (ADMET) prediction. Their results of MD included principal component analysis (PCA) and Free Energy Landscapes surface (FELs) indicated that the protein-ligand complex was stable in simulated trajectories of 100 ns. The binding free energy (BFE) calculations showed that a total of 6 novel compounds (CL130, CL834, CL961, CL966, CL163 and CL329) with the stable binding state and stronger BFE (-61.17 to -37.01 kcal/mol) than that of original ligand 3RF (-36.66 kcal/mol). With reference to the ULK1 inhibition of 3RF (IC50 = 160 nM), it can be inferred that these compounds could be used as a new type of potential ULK1 inhibitors and be worthy of further investigation for tumor treatments.Communicated by Ramaswamy H. Sarma.

Albumin/Thiacalix[4]arene Nanoparticles as Potential Therapeutic Systems: Role of the Macrocycle for Stabilization of Monomeric Protein and Self-Assembly with Ciprofloxacin

The therapeutic application of serum albumin is determined by the relative content of the monomeric form compared to dimers, tetramers, hexamers, etc. In this paper, we propose and develop an approach to synthesize the cone stereoisomer of p-tert-butylthiacalix[4]arene with sulfobetaine fragments stabilization of monomeric bovine serum albumin and preventing aggregation. Spectral methods (UV-vis, CD, fluorescent spectroscopy, and dynamic light scattering) established the influence of the synthesized compounds on the content of monomeric and aggregated forms of BSA even without the formation of stable thiacalixarene/protein associates. The effect of thiacalixarenes on the efficiency of protein binding with the antibiotic ciprofloxacin was shown by fluorescence spectroscopy. The binding constant increases in the presence of the macrocycles, likely due to the stabilization of monomeric forms of BSA. Our study clearly shows the potential of this macrocycle design as a platform for the development of the fundamentally new approaches for preventing aggregation.