Discovery of Novel Adenosine Receptor Antagonists through a Combined Structure- and Ligand-Based Approach Followed by Molecular Dynamics Investigation of Ligand Binding Mode

An intense effort is made by pharmaceutical and academic research laboratories to identify and develop selective antagonists for each adenosine receptor (AR) subtype as potential clinical candidates for “soft” treatment of various diseases. Crystal structures of subtypes A_2A and A₁ARs offer exciting opportunities for structure-based drug design. In the first part of the present work, Maybridge HitFinder library of 14400 compounds was utilized to apply a combination of structure-based against the crystal structure of A_2AAR and ligand-based methodologies. The docking poses were rescored by CHARMM energy minimization and calculation of the desolvation energy using Poisson–Boltzmann equation electrostatics. Out of the eight selected and tested compounds, five were found positive hits (63% success). Although the project was initially focused on targeting A_2AAR, the identified antagonists exhibited low micromolar or micromolar affinity against A_2A/A₃, ARs, or A₃AR, respectively. Based on these results, 19 compounds characterized by novel chemotypes were purchased and tested. Sixteen of them were identified as AR antagonists with affinity toward combinations of the AR family isoforms (A_2A/A₃, A₁/A₃, A₁/A_2A/A₃, and A₃). The second part of this work involves the performance of hundreds of molecular dynamics (MD) simulations of complexes between the ARs and a total of 27 ligands to resolve the binding interactions of the active compounds, which were not achieved by docking calculations alone. This computational work allowed the prediction of stable and unstable complexes which agree with the experimental results of potent and inactive compounds, respectively. Of particular interest is that the 2-amino-thiophene-3-carboxamides, 3-acylamino-5-aryl-thiophene-2-carboxamides, and carbonyloxycarboximidamide derivatives were found to be selective and possess a micromolar to low micromolar affinity for the A₃ receptor

Identification of New Fyn Kinase Inhibitors Using a FLAP-Based Approach

The abnormal activity of Fyn tyrosine kinase has been shown to be related to various human cancers. Furthermore, its involvement in signaling pathways that lead to severe pathologies, such as Alzheimer’s and Parkinson’s diseases, has also been demonstrated, thus making Fyn an attractive target for the discovery of potential novel therapeutics for brain pathologies and tumors. In this study we evaluated the reliability of various screening approaches based on the FLAP software. By the application of the best procedure, the virtual screening workflow was used to filter the Gold and Platinum database from Asinex to identify new Fyn inhibitors. Enzymatic assays revealed that among the eight top-scoring compounds five proved to efficiently inhibit Fyn activity with IC₅₀ values in the micromolar range. These results demonstrate the validity of the methodologies we followed. Furthermore, the five active compounds herein described may be considered as interesting leads for the development of new and more efficient Fyn inhibitors