Development of Host- Oriented Therapeutics Targeting Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2),

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The ultimate goal of this Phase I application is to discover and develop host-oriented small molecule compounds targeting Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection. SARS-CoV-2 is a novel coronavirus driving the current global pandemic of severe respiratory syndrome in humans. Antiviral therapeutics are urgently needed to combat infection by SARS-CoV-2 and new variants that are continuing to emerge. We have discovered several chemical series that target modular interactions between specific host proteins containing WW-domains (e.g. Nedd4) and viral proteins containing PPxY motifs (e.g. Ebola VP40). Notably, emerging RNA virus pathogens such as Ebola, Marburg, Lassa, and rabies viruses all encode PPxY motifs that recruit host WW-domain containing proteins to facilitate efficient virus egress, spread, and transmission. Interestingly, the surface-exposed Spike glycoprotein (S) of SARS-CoV-2 also has a putative WW-domain binding motif (25PPAY28), that is not present in the S protein of SARS-CoV-1 or more attenuated coronavirus strains. The acquisition of this PPAY motif in the major surface protein of SARS-CoV-2 virions raises the intriguing possibility that it may contribute to the unique pathogenicity and/or transmission of SARS-CoV-2 via interactions with specific host WW-domain bearing proteins. In our ongoing studies on filoviruses and arenaviruses, we have used extensive SAR to identify a lead compound series capable of blocking egress and spread of live EBOV, MARV, and LAFV in cell culture, as well as blocking disease progression in vivo in a live MARV challenge model. Here, we hypothesize that “informed” SAR analyses of our in-hand PPxY/WW-domain inhibitors (e.g. lead candidate FC-10696) will lead to the discovery of analogs capable of blocking egress and disease progression of SARS-CoV-2, as well as related PPxY-containing variants that may emerge in the future. In support of our hypothesis, we present strong preliminary data showing that the PPxY motif within the S protein of SARS-CoV-2 virus can interact with host WW-domain containing proteins that are known to promote egress and spread of EBOV, MARV, and LAFV. Moreover, our current lead candidate PPxY budding inhibitors show activity in blocking egress of live SARS-CoV-2 virus infection in human lung epithelial cells. In this Phase I proposal, we will identify and evaluate host-oriented inhibitors as potential therapeutics for SARS-CoV-2 and related coronaviruses by combining the pharmaceutical and medicinal chemistry expertise of the scientists at the Fox Chase Chemical Diversity Center, Inc. (FCCDC) with the expertise and experience of the Harty Lab at the University of Pennsylvania in the experimental aspects of virus-host interactions and antiviral therapy, and the lab of Olena Shtanko at Texas Biomedical Research Institute for evaluating compounds against live viruses under BSL-3 conditions. The three aims are (1) lead finding and optimization medicinal chemistry including ADME profiling, (2) evaluation for the ability to specifically inhibit egress of SARS-CoV-2 VLPs and PPxY- mediated S-host protein interactions, and (3) in vitro and in vivo analyses against authentic SARS-CoV-2 virus.