Conserved proteins of influenza virus and coronavirus as potential novel therapeutic targets

Abstract

Direct-acting antivirals for tackling influenza infections present widely known limitations; or have still not been approved for any betacoronavirus. In this paradigm, it is essential to identify/characterize novel targets for the development of drugs that overcome classic antiviral limitations. The NS1 protein of influenza A virus emerges as a potential novel target based on its structure; key molecular interactions; and global role in influenza replication and pathogenesis. Regarding betacoronaviruses, the S protein represents the main structural protein with a vital role in the pathogenesis, transmission, and virulence of the virus. We performed an in silico analysis of the conservation and druggability of influenza A virus NS1 and betacoronavirus Spike as a result of an exhaustive large-scale sequence analysis and structural characterization. In NS1 studies, we have found 3 consensus druggable pockets; and 24 top-ranked hot spots for drug targeting. In Spike protein studies, we have found 28 consensus druggable pockets; new hot spots for SARS-related coronaviruses (n=181) and betacoronaviruses (n=72); and have additionally prioritized the S1-RBD, S1-SD1, S2-CR, S2-HR1 and S2-CH as the most promising druggable S regions. As best we know, this represents the most comprehensive work regarding the conservationdruggability of NS1 and Spike performed to date. We have further evaluated the impact of amino acid substitutions at ten NS1 hot spots (NS1-R100A, NS1-W102A, NS1-K110A, NS1-R118A, NS1-Q121A, NS1-E142A, NS1-Y171A, NS1-K175A, NS1-V180A, NS1-G184P) on influenza viral replication. NS1 mutations Y171A, K175A (CDP1), W102A (CDP3), Q121A and G184P (Multi-CDPs) impaired A(H1N1)pdm09 virus replication, in vitro. We established proof of concept regarding our structure-based map-and-mutate rationale for the discovery of antiviral targets. These NS1 and Spike hot spots exhibit advantageous structural features for pharmacological modulation and can accelerate the discovery of hit drug candidates. Such strategies are extremely relevant for improving seasonal and outbreak preparedness in the field of antiviral research.