A NOVEL CLASS of ANTIVIRAL COMPOUNDS with POTENT ACTIVITY AGAINST SARS-CoV-2

ABSTRACT

Background: The SARS-CoV-2 pandemic has sickened over 245 million people, and has killed more than 5 million worldwide. Recent data proves that vaccinations are highly effective in preventing Covid-19 disease, however antigenic drift and other functional mutations in the virus genome reduce the efficacy of vaccines, indicating that the development of antiviral treatments remain a crucial priority. We report potent antiviral activity against SARS-CoV-2 for a promising, novel class of nitrogen-based heterocyclic compounds. Methods: 232 compounds based on the same class of nitrogen-based hetereocyclic molecules were synthesized to final purity of greater than 99%. This library was screened for antiviral phenotypes in a cytopathic effect (CPE) assay using VeroE6 cells and the SARS-CoV-2 WA1 isolate. Based on the results of the WA1 CPE screen, 47 lead candidates were structurally analyzed, and this information was utilized to design 56 additional compounds. A second antiviral CPE-based screen was performed using these 103 candidates in VeroE6 cells with the SARS-CoV-2 delta variant. Antiviral assays studying SARS-CoV-1 (Urbani) and MERS-CoV were performed in Vero 76 cells utilizing a Neutral Red cytopathic effect assay. Results: Within the same class of structurally related small molecules, we tested an initial set of 232 compounds using a CPE-based assay with VeroE6 cells and the USA/WA1 SARS-CoV-2 isolate. Of the compounds tested, 124 demonstrated potency 10 to 540-times higher than a Remdesivir control tested in parallel. Importantly, we observed no detectable toxicity for the vast majority of these compounds when tested up to a concentration of 30 μ M. The lead candidate in this screen displayed an IC50 of 0.02 μ M and a selectivity index of >1,500. Based on structural analysis of an initial 47 lead candidates, we synthesized 56 new molecules, and tested all 103 in a CPE-based assay using the delta variant, also observing efficacy against this variant of concern. Examples of this same class of compounds also display antiviral activity against SARS-CoV-1 (Urbani) and MERS-CoV in cell-based assays. Conclusion: We have identified a novel class of antiviral compounds with potent activity against SARS-CoV-2. High potency against both the early WA1 isolate and the more recent delta variant, as well as efficacy against SARS-CoV-1 and MERS-CoV, suggest that this class of antiviral compounds has pan-Coronavirus antiviral activity.