Accelerated discovery of cell-active SARS-CoV-2 polymerase inhibitors via molecular dynamic guided screening and optimization

Project Summary Significance: Worldwide spread of the SARS-CoV-2 virus has resulted in over 20 million confirmed human cases and 730,000 deaths from COVID-19, and cases continue to surge as there is no approved vaccine or other therapeutic modality broadly available to mitigate community spread. The virus has not only impacted human health but has also threatened national security, economic stability, and education. Broad, long term objectives: The research objectives described in this proposal will afford vetted, small molecule non-nucleoside-based inhibitors of the SARS-CoV-2 viral polymerase enzyme that will serve as lead compounds for future development and clinical evaluation targeting COVID-19 disease. Specific Aims/premise: The proposed aims are constructed to evaluate if potent, cell permeable, non-nucleot/side-based inhibitors of the SARS-CoV-2 RNA polymerase can be discovered using an integrated drug discovery pipeline. Specifically, we hypothesize that a highly efficient, dynamic computational screening method will reveal desirable hits that will be validated in antiviral assays to show target engagement and cellular efficacy. Further, medicinal chemistry optimization will tune the activity and property profiles of hits to make them suitable for evaluation in our established COVID-19 K18 hACE2 mouse models. Research design and methods: Aim 1 will identify competitive non-nucleot/side SARS-CoV-2 RdRp inhibitors from a strategically chosen compound collection using an efficient in silico screening approach developed and employed by Drs. Baudry and Smith. The hits will be ranked by binding energies and selected for confirmatory activity in the Jonsson's lab using established cellular SARS-CoV-2 assays, along with secondary assays that validate active site inhibition of the viral polymerase. The Golden lab will lead hit validation efforts and advance hits that meet defined criteria to Aim 2. The latter aim will prioritize and evaluate specific scaffolds by medicinal chemistry optimization (Golden lab), guided by the primary and secondary assays, computational models and tiered ADME and pharmacokinetic analyses, to refine compound activity profiles that are suitable for in vivo efficacy assessments performed in the Jonsson lab.