Mapping the Druggability of Complement C3 and its Derivatives, and Inhibitor Design

The complement system, consisting of several plasma proteins and cell-bound receptors, is an important part of innate immunity. Complement component C3 is central to the multiple complement pathways and its cleavage results in the activation of various cascades for the generation of effector proteins and complexes as a response to injury or infection. A lack of regulation in this response can result in adverse effects such as inflammatory and autoimmune diseases. Despite complement's role in several autoimmune and inflammatory diseases, there is a noted dearth of complement-targeted therapeutics on the marker. In this thesis, we outline a variety of studies in which we employ computational and experimental methods to characterize the mechanistic properties and dynamics of C3 and its derivatives in order to map their druggability. We explore the mechanisms driving the C3d:CR2 interaction using electrostatic analysis, molecular dynamics simulations (both steered and explicit solvent), and MM-GBSA calculations. We investigate the role of electrostatic steering in the C3d:CR2 interaction through Brownian Dynamics simulations and confirm the ionic strength-dependence of the interaction as well as gain additional insights into the amino acids driving the association of the C3d:CR2 complex. We utilize the insights into significant intermolecular interactions gained from the C3d:CR2 complex for the design of CR2-based peptides targeting C3d for biomarker and inhibitor development. In continuing with the pursuit of C3d-binding ligands, we implement a virtual screening workflow for the identification of small molecules with fluorescence properties for potential theranostic applications. In addition, we explore the dynamics of the C3d:CR3 complex to further characterize the structural and physicochemical properties of C3d and identify amino acids crucial to the interaction through molecular dynamics (both explicit and steered) and electrostatic analysis. We perform redesign of a compstatin family peptidic inhibitor targeting C3, and small molecule biomarker discovery at the site of compstatin-C3 binding using virtual screening. Our results provide a fundamental mechanistic understanding of the physicochemical, structural and dynamic properties of C3, and form the foundation for the development of potential diagnostic imaging molecular sensors and therapeutics