Rational targeting of FUS and TDP-43 protein assemblies for diagnostics and treatment of ALS
The project addresses a grand challenge in ALS, the integration of a multi-targeted and personalized approach to patients with a rational strategy focusing on a unifying pivotal mechanism of the disease. We seek to test the extended “prion hypothesis”, which suggests that ALS progression is driven by a self-propagating buildup of heterogeneous aberrant assemblies of key proteins implicated in the disease, such as FUS, TDP-43, and several others. Structural heterogeneity of the aberrant assemblies, which may include small unstructured oligomers, droplets of proteinaceous condensates, and beta-sheet rich fibrils; sensitivity of the assemblies to their biochemical environment; and their dependence on the presence or absence of certain mutations allow for a level of multi-targeting that is difficult or impossible to achieve within different conceptual frameworks taken separately.
As a hypothesis-testing strategy, we have adopted rational epitope matching via the development of conformation-specific monoclonal antibodies targeted against disease-specific protein conformers – an experimentally proven framework that may allow both interrogating patient-derived samples for the presence of the pathogenic state of ALS-linked proteins, and acting as potential disease modifying therapeutic agents against ALS. The rational development of assembly-specific antigens will rely upon the results of our computational predictions of the structure of proteinaceous assemblies, which we will conduct via an integration of coarse-grained and all-atom molecular dynamics simulations, and complement with our original and unique statistical-mechanical method of analysis.
Overall, the proposal builds upon our respective expertise in biochemical and biophysical experimental methods, computational structural biology, and physics of phase separation; and, importantly, our proof-of-principle work that allowed the rational design of a structure-based prion vaccine and resulted in a monoclonal antibody capable of specifically recognizing all prion isolates tested. Upon completion of the proposed research we expect to know which of the predicted surface epitopes in FUS and TDP-43 can be found in patient-derived samples and which of the novel monoclonal antibodies are capable of recognizing the disease-causing conformers of FUS and TDP-43. In addition, we expect to clarify which molecular-level structural and dynamical impacts affect the pathogenicity of these conformers. Moreover, we expect to develop improved simulation protocols to predict the structure of aberrant protein assemblies and identify supramolecular templates for epitope matching and/or drug binding.
Maria Stepanova , University of Alberta
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