EXPLOITING MOLECULAR TARGETING IN ANTICANCER CHEMOTHERAPY: IN SILICO STUDIES TO IDENTIFY NOVEL MOLECULES TARGETING KINASES IN CONVERGENT METABOLIC PATHWAYS IN CANCER THERAPY

In recent years, a convergence of scientific progress has allowed to identify specific molecular targets and signaling routes for cancer cells, leading to more selective, more effective, and less toxic treatments. The validation of compounds was originally based on the validation of the target, despite some of the most effective drugs often have effects outside their hypothetical mechanism. Protein kinases have become interesting molecular targets and considerable research has targeted drugs capable of inhibiting the pathogenic kinases. Clinical studies to date have validated the positive effects of kinase inhibitors in cancer therapy. The first part of this thesis essentially focused on the research of new selective inhibitors of serum and glucocorticoid protein kinase 1 (SGK1). Its role in human cancer has been extensively studied, identifying SGK1 as a key target in cancer progression, having regard to its ability to regulate processes such as cell cycle, invasion, migration, cellular apoptosis, autophagy and others. To date, there are no commercially available drugs against SGK1, and the available inhibitors still require further studies. In this study, a pharmacophore model was generated from the crystal structures of SGK1, through combined structure- and ligand-based approaches, using Phase software (Schrodinger suite). The hypotheses generated, based on docking poses of known inhibitors MMG (4-(5-phenyl-1H-pyrrolo[2,3-b]pyridin-3-yl)benzoic acid) and GMG ([4-(5-naphthalen-2-yl-1H-pyrrolo[2,3-b]pyridin-3-yl)phenyl]acetic acid), have been pruned according to the presence of some essential features for the interaction with the receptor and then were classified by survival score. Then, the selected hypothesis (thereafter reported as ADNRR_1, where A: hydrogen bond acceptor, D: hydrogen bond donor, N: negatively ionizable group, and R: aromatic ring) has been refined by adding excluded volumes. Since the validation process showed that the pharmacophore model was reliable, it was used to perform a virtual screening study. Starting from commercial databases, a multi-conformer optimized library was generated using Phase tools, which was subsequently screened on the validated pharmacophore model. The filtered molecules were subjected to molecular properties analysis. Only compounds that met the required parameters were analyzed through docking studies and selected based on an appropriate binding mode and extra-precision (XP) Glide-score value. Four compounds were available for purchase and were sent for biological tests. The results provided two hit compounds with the activity of 0.93 μM and 11.9 μM toward SGK1. Starting from the compound with activity of 0.93 μM, a similarity search was performed on several commercial databases, resulting in a library of 705 analogues. The latter was subjected to molecular docking studies using Glide SP mode (Schrodinger suite) that resulted in the prioritization of 5 compounds. Finally, they were evaluated by biological assays on SGK1, finding lower activity in comparison to the parent compound. However, the results obtained have allowed us to make useful observations to direct a future perspective of the study, towards the search for better compounds. In the second section, the focus is on tyrosine kinase Src. In recent years, a large number of Src family kinase (SFK) targeted compounds have been designed and tested in several preclinical models, confirming the ability of these inhibitors to block cancer progression. Simulations were performed as support to the research study conducted by the group of Professor Sabrina Dallavalle, integrating computational information into a work based on the research of Src inhibitors. Starting from a small internal library of structurally different compounds, the best structures examined had a common indolinone core, which was chosen as scaffold for further investigation. Several 3-(hetero)arylideneindolin-2-one substitutes have been designed and synthesized to identify the characteristics that determine activity. Molecular docking studies have helped to suggest a putative binding mode within the Src binding site and to direct future optimization studies.