Application of computational methods for the design and optimization of Src family kinase inhibitors

Kinases constitute a family of enzymes involved in many cellular signalling pathways thanks to their ability to catalyse the transfer of a phosphate group from a donor, ATP or GTP, to an acceptor, a protein or a lipid. Src family kinases (SFKs), that represent the topic of this PhD work, belong to the cytosolic tyrosine kinases group and act by transferring the phosphate group to a tyrosine of the acceptor protein. SFKs play a key role in controlling cellular processes such as proliferation, apoptosis, angiogenesis, and invasion. Hyperactivation of SFKs was observed in many human cancers, which makes these enzymes very attractive targets for the treatment of these diseases. In this PhD work, the application of molecular modelling techniques allowed the design and optimization of SFK inhibitors. In a first project, the ability of the pyrazolo[3,4-d]pyrimidine ALM4-23 to stabilize c-Src in the three different conformational states, was evaluated by computational techniques. The resulting insights were used to design ALM4-23 derivatives with potentially improved inhibitory activity against c-Src. In a second project, a structure-based virtual screening procedure was applied to a database of commercially available compounds to identify new c-Src inhibitors. The 3D structure of the kinase in an inactive conformation was used because potential advantages in terms of selectivity and drug residence time. In the last project, the pyrazolo[3,4-d]pyrimidine Fyn inhibitor, Si308, was studied to evaluate its ability to inhibit other SFK members, such as Lyn and Blk. Once confirmed the ability of Si308 to act as a multitarget SFKs inhibitor, a library of its derivatives was synthesized and tested against B- and T-cell lymphoma cell lines, in which Fyn, Lyn and Blk play a pivotal role.