Development and validation of antivirals against Flaviviruses

SUMMARY Flaviviruses cause hundreds of millions of infections annually and a range of clinical syndromes including hemorrhagic fever, encephalitis, liver failure, and congenital disease. Currently, and despite extensive screening campaigns by academic and pharmaceutical laboratories, there are no specific therapeutics against these viruses and a paucity of available vaccines. Our goal is to use innovative screening assays and novel viral protein targets to develop combinations of orally-formulated direct acting antivirals that can treat existing and emerging flaviviruses. We will develop antivirals against three essential proteins in flaviviruses. First, given that nucleoside analogs are an important class of antivirals we will develop orally bioavailable pan-antiflaviviral nucleoside analogs. We have in hand two scaffolds we are developing and will screen libraries of nucleosides for new scaffolds. As nucleosides can be broadly active, we will test the most active nucleosides against additional RNA viruses focusing on emerging viruses (e.g., SARS-CoV-2, EBOV, LASV and SFTSV) that are in our CAMPP consortium. Since flaviviruses are small RNA viruses and encode few proteins, we will develop antivirals against two of these essential protens with no known enzymatic activity: NS4A and NS1. Recently, clinically approved antiviral against the distantly related hepatitis C virus NS5B blocks infection of this non-enzymatic target. We have identified an inhibitor of ZIKV NS4A, an essential non-enzymatic viral protein, as a possible antiviral drug. As part of our program, we will use medicinal chemistry and SAR to optimize and broaden its activity against additional flaviviruses. NS1 serves a scaffold for replication complexes in the cytoplasm at the endoplasmic reticulum and also functions extracellularly to promote vascular leakage and central nervous system invasion by binding to endothelial cells and antagonizing innate immunity. We will use biochemical assays to identify drugs that bind flavivirus NS1 and then screen them for blockade of its intracellular and/or extracellular functions. Drugs that can block the functional activity of NS1 may impact viral replication and steps in pathogenesis. For those inhibitors against NS5, NS4A or NS1 that show optimal bioavailability and efficacy profiles, with in vivo levels that at several fold above their cellular EC90 values, we will advance into animal models of flavivirus infection. In addition, we will determine the barrier to resistance, test combinations of inhibitors first in vitro and ultimately in vivo to increase potency and prevent the emergence of resistance.