Investigating molecular recognition of small molecules by spleen tyrosine kinase (Syk) implicated in autoimmune disorders via multiscale simulations

Abstract

Spleen Tyrosine Kinase (Syk), a non-receptor protein tyrosine kinase, is involved with immune cell signal transduction in B cell receptors, T cell receptors, Fc receptors and its inhibition can help treat the immune system overactivity in autoimmune diseases. While fostamatinib, an Syk inhibitor, has been approved by FDA for treating immune thrombocytopenia (ITP), the quest to find drugs with better Syk affinity and lesser side effects to treat the various immune dysregulations and autoimmune diseases is still ongoing. The aim of the project was to provide structural and dynamics analyses of Syk, investigate the effects of mutation and phosphorylation in the Syk kinase domain and also to discover novel Syk inhibitors in silico. The crystal structure of Syk complexed with R406 (active metabolite of fostamatinib) (PDB ID – 3FQS) was taken as control. Three mutations, Met450Ile, Ser550Tyr and Ser550Phe, and phosphorylation on the Tyr525 and Tyr526 residues were performed in silico to prepare different systems followed by conventional replica molecular dynamic simulations. Virtual screening of ligands were performed from the small molecule databases ‘AnalytiCon Discovery’ and kinase inhibitory library’ using the ‘Glide’ module of Schrödinger in HTVS (30%), SP (20%) and XP (10%) modes. A total of 17 molecules having docking score better than -9 kcal/mol were selected for ADMET profiling. 6 ligands showing favourable ADMET properties were further considered for conventional replica molecular dynamic simulation. Structural and dynamic properties were characterized by analysing the trajectories. The Molecular Mechanics Poisson-Boltzmann Surface Area (MM/PBSA) scheme was used to calculate the binding free energy. The results indicated no change in ligand binding affinity of Syk due to phosphorylation and mutations. Of the novel lead molecules, lead 1 showed the strongest affinity towards Syk, being comparable to that of our control ligand R406, which is already FDA approved. Overall, these studies would be helpful for understanding the structural and dynamic changes of Syk due to mutation and phosphorylation and help in developing a broad range of anti-Syk therapy.