Computational methods applied to drug discovery: the rational design of dual inhibitors of FAAH and COX

The search for effective and safe drugs in pain-relief treatment represents a great challenge for medicinal chemists. Lipid derived mediators, such as endocannabinoids, may have different roles as agonists of cannabinoid receptors, relieving pain, or as substrates of cyclooxygenase (COX), generating the pro-inflammatory prostamides. Moreover, the tissue-protective endocannabinoid anandamide is metabolised by fatty acid amide hydrolase (FAAH). Therefore, a new challenging approach in pain-relief might be the development of dual action FAAH/COX inhibitors. The purpose of this thesis is to apply computational methods in drug discovery to assist medicinal chemistry studies targeting the rational design of novel FAAH/COX inhibitors, and to exploit structural studies relative to two side projects on other biological targets. The wider project of this thesis explores the mechanism of action and the rational design of novel FAAH/COX dual inhibitors. The reversible mixed type inhibitors Flu-AM1 and Ibu-AM5, derivatives of flurbiprofen and ibuprofen, respectively, retain similar COX inhibitory properties and are more potent FAAH inhibitors than the parent compounds. Applying a combination of molecular docking, MD simulations and free energy evaluation of the ligand-receptor complex, the binding mode of the enantiomer forms of Flu-AM1 and Ibu-AM5 has been found in the substrate access channel of FAAH and has been supported by studies of site-directed mutagenesis. The substitution of the isobutyl group of Ibu-AM5 with 4-(2-(trifluoromethyl)pyridin-4-yl)amino group led to the design of TPA5 derivative, which showed an inhibitory activity (IC50 = 0.59 μM) similar to the lead compound (Ibu-AM5, IC50 = 0.52 μM). Kinetic studies of TPA5 revealed that it is a pure competitive inhibitor of rat FAAH and molecular modeling studies supported a binding mode that overlap the anandamide analog MAFP. Among TPA5 derivatives, compound TPA27 exhibited a 10-fold enhancement in the inhibitory profile against FAAH (IC50 = 0.058 μM). ...