Small-Molecule Inhibitors of ERGIC-53

Emerging zoonotic viruses from several RNA virus families will continue to pose risks for human populations in the future. Our Discovery project aims to obtain hits and leads for the development of broad-spectrum antiviral compounds against emerging RNA viruses with outbreak potential. The project directly addresses the FY21 PRMRP Topic Area, "Emerging Viral Diseases." We plan to target a unique host protein, ERGIC-53, which is packaged and carried in the lipid bilayer of a large set of emerging RNA viruses and required for virus attachment and entry into cells. An important feature of this particular target is that the protein is dispensable for the host, making transient or even prolonged treatment with an inhibitor feasible. An additional attribute is that targeting a host protein, rather than a viral protein, theoretically obviates the problems of rapid evolution and the selection of viral variants resistant to the antiviral therapeutic. The rationale outlined above leads us to hypothesize that identification of small molecules that block the pro-viral activity ERGIC-53 will lead to a broad-spectrum inhibitor against a constellation of emerging pathogenic viruses from the arena-, hanta-, corona-, orthomyxo-, and filovirus families. This would be of obvious high impact. The inhibitor could be made primarily available for use by military and medical personnel responding to localized outbreaks of diverse known and unknown RNA viruses. Such an inhibitor could also be used in civilian populations to attenuate virus spread and to mitigate pathogenic effects of virus infection. The study design of our project synthesizes artificial intelligence (AI)-based protein-small molecule interaction with empirical cellular and virology. AI-based molecule identification will be carried out using deep learning (DL) with a set of convolutional neural networks (CNNs). This approach enables bioactivity prediction using three-dimensional convolutional filters trained on biological protein and small molecule structural information in conjunction with ligand-based features in a deep neural net architecture. Importantly, this approach has a demonstrated high success rate. There is also a suite of virus and cell assays in place for empirical validation of potential hits affecting virus replication and ERGIC-53 function. These include assays for directly screening small molecules on species from multiple RNA virus families as well as complementary assays that evaluate the effect of small molecules on intermolecular interaction with its binding partner. There are several innovative and impactful features of our project. The CNN that serves as the basis of the DL is different from other virtual approaches and has been successful in a multitude of projects. The use of DL to identify small molecule inhibitors of a human host protein required for virus replication is further innovative. ERGIC-53 is a target with high potential, dispensable in the human host, but necessary for the efficient replication of a large set of emerging pathogenic RNA viruses. Hits and leads facilitating the development of such a broad-spectrum drug against a legion of diverse RNA viruses would be of high impact. Expected results from the project include identification of a concrete set of hits and leads that can subsequently be taken through preclinical and clinical development. We have the expertise to manage small molecule development through this pipeline. Consequently, following completion of this Discovery project, we will pursue a Level 1 or 2 PRMRP Expansion project toward developing a broad-spectrum antiviral drug specifically targeting ERGIC-53. Less