Machine Learning of Molecular Dynamics Simulations Provides Insights into the Modulation of Viral Capsid Assembly

An effective approach in the development of novel antivirals is to target the assembly of viral capsids by using capsid assembly modulators (CAMs). CAMs targeting hepatitis B virus (HBV) have two major modes of function: they can either accelerate nucleocapsid assembly, retaining its structure, or misdirect it into noncapsid-like particles. Previous molecular dynamics (MD) simulations of early capsid-assembly intermediates showed differences in protein conformations for the apo and bound states. Here, we have developed and tested several classification machine learning (ML) models to better distinguish between apo-tetramer intermediates and those bound to accelerating or misdirecting CAMs. Models based on tertiary structural properties of the Cp149 tetramers and their interdimer orientation, as well as models based on direct and inverse contact distances between protein residues, were tested. All models distinguished the apo states and the two CAM-bound states with high accuracy. Furthermore, tertiary structure models and residue-distance models highlighted different tetramer regions as being important for classification. Both models can be used to better understand structural transitions that govern the assembly of nucleocapsids and to assist in the development of more potent CAMs. Finally, we demonstrate the utility of classification ML methods in comparing MD trajectories and describe our ML approaches, which can be extended to other systems of interest.