Designing peptide inhibitors for the guanylate kinase domain of the MAGUK family scaffold proteins using computational approaches

Abstract

MAGUKs (membrane-associated guanylate kinases) are a family of scaffold proteins. They are distributed in both pre- and post-synaptic sides of excitatory synapses and function in diverse cellular processes. Dysfunction of MAGUKs and mutations of MAGUKs-binding proteins have been shown to play important roles in mental disorders, such as ASD (autism spectrum disorder) and Williams syndrome. GK (guanylate kinases like) domain is one of the conserved domains and acts as binding module to mediate the binding between MAGUKs and other synaptic proteins. As the regulation of the MAGUKs-associated synaptic protein complex is related to ASD and other mental illnesses, it is useful to design inhibitors against the GK domain that are effective and highly specific in cellular environment. In this thesis, we used computational biology and chemical biology approaches to design such inhibitor peptides. We have obtained dephosphorylated peptides that bind to the GK domain with comparable affinities of natural phosphorylated ligands. These dephosphorylated peptides are expected to be more stable and effective inhibitors in cellular environment than their natural phosphorylated counterpart. These peptides are first identified through a computational iterative sequence optimization protocol combining molecular dynamics simulations and MMPBSA (molecular mechanics energy combined with the Poisson-Boltzmann and surface area continuum solvation) binding free energy calculation method and then validated by biochemical experiments. Additional trials suggest that adding staples to the found peptides may further enhance their structural stability compared to non-stapled ones. We also showed that compounds with low molecular weights are not effect inhibitors of the GK domain because of their weak solubility.

Date of Award	2016
Original language	English
Awarding Institution	The Hong Kong University of Science and Technology