Tesi di Dottorato
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Item Molecular simulation of transport proteins in interaction with physiological and pharmacological ligands(2014-11-13) Evoli, Stefania; Bartolino, Roberto; Carbone, Vincenzo; Guzzi, Rita; Rizzuti, BrunoMolecular complexes of transport proteins with small compounds have been studied by using docking techniques and molecular dynamics simulations. The macromolecules considered are β- lactoglobulin and albumin, i.e. the most abundant proteins in bovine milk and human blood serum, respectively. The ligands are long-chain fatty acids of different length and ibuprofen, a molecule of pharmaceutical interest. Simulations of β-lactoglobulin with fatty acids, ranging from caprylic to stearic acid, revealed the key protein residues that contribute to the binding process. In particular, a rationale was found for the high binding affinity of both stearic and palmitic acid compared to shorter lipids. Moreover, the location of two low-affinity external binding sites was predicted for palmitic acid, by comparing docking results with those obtained for vitamin D3, for which an external site has already been identified in crystallography. For human serum albumin, docking results suggest different candidate binding locations for both charged and neutral ibuprofen. An alchemical free energy approach has been used to estimate the binding affinity for each pose. The results show that charged ibuprofen has a greater affinity for albumin compared to the ligand in the neutral form, suggesting that the former corresponds to the physiological binding state. The simulation findings were compared to experimental results and show an overall good agreement, predicting details of the protein-ligand interaction that include binding geometries and contacts with specific amino acid residues. The overall findings reveal significant features of the binding of well-known ligands to two extensively investigated transport proteins, and show how computational tools can be used to support experimental techniques in a variety of cases.Item Different medicinal chemistry approaches towards the identification of novel targets in breast cancer(2013-12-02) Pisano, Assunta; Bartolino, Roberto; Gabriele, Bartolo; Sindona, Giovanni; Maggiolini, MarcelloG protein-coupled receptors (GPCRs) belong to the largest family of cellsurface molecules representing the targets of approximately 40% of current medicinal drugs (Overington, J.P et al 2006). GPCRs are ubiquitous in mammalian (Bockaert, J. et al. 1999), regulate several physiological processes and play an important role in multiple diseases ranging from cardiovascular dysfunction, depression, pain, obesity to cancer (Rosenbaum D.M. et al. 2011). One member of this superfamily, named GPR30/GPER, mediates estrogen signaling in different cell contexts, leading to gene expression changes and relevant biological responses (Filardo E.J et al. 2000, Bologa C.G.et al. 2006, Maggiolini M. and Picard D. 2010). GPER acts by transactivating the Epidermal Growth Factor Receptor (EGFR), which thereafter induces the increase of intracellular cyclic AMP (cAMP), calcium mobilization and the activation of the phosphatidylinositol 3-kinase (PI3K) and the mitogen-activated protein kinases (MAPKs) (Maggiolini M. and Picard D. 2010). Moreover, the GPER-mediated transduction pathways activated by estrogens trigger the expression of a typical gene signature, including the expression of cfos and the gene encoding the connective tissue growth factor (CTGF), which are involved in the proliferation and migration of diverse cell types (Lappano R. et al 2012a, Madeo A. and Maggiolini M. 2010). On the basis of these findings, the first objective of the present study was the characterization of GPER from different points of view: GPERmediated signaling pathways and biological functions, selective ligands and molecular characterization of the receptors. In particular, the research project focused on:1. the transduction pathways by which the environmental contaminant Bisphenol A (BPA) influences cell proliferation and migration of human breast cancer cells and cancer-associated fibroblasts (CAFs); 2. the characterization of novel carbazole derivatives as GPER agonists in ER-negative breast cancer cells; 3. the isolation and characterization of GPER in estrogen-sensitive cancer cells by Mass Spectrometry. Additionally, the second section of this doctoral thesis was focused on the evaluation of the cytotoxic activity of novel synthesized compounds, given the interest and the need to discover new molecules against cancer. In particular, novel titanocene-complexes were studied evaluating their ability to elicit repressive effects on the growth of estrogen-sensitive breast cancer cells.