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Principal Investigator: Shiqing Xu
Organization: TEXAS A&M UNIVERSITY
Fiscal Year: 2022
Award: $221,799
Funding agency: National Institute of Allergy and Infectious Diseases
PROJECT SUMMARY/ABSTRACT
The current COVID-19 pandemic caused by SARS-CoV-2 has paralyzed much of the world. Encouragingly,
a few COVID-19 vaccines have been developed and approved for human immunization. However, existing
COVID-19 vaccines target the highly mutable membrane Spike protein of SARS-CoV-2. New viral strains with
critical mutations in Spike have emerged such as alpha, beta, delta, and gamma variants that could make current
vaccines less effective. To truly overcome the threat posed by SARS-CoV-2 and its emerging variants of concern,
it is paramount to develop antiviral drugs that can combat COVID-19 and also be potentially repurposed to
combat novel coronaviruses (CoVs) in the future. To address this urgent need, this proposal aims to interface
papain-like protease (PLpro) inhibitors/binders and the emerging proteolysis targeting chimera (PROTAC)
technology for the development of broad-spectrum anti-CoV PROTACs. PLpro, one of two essential SARS-CoV-
2 proteases, plays a dual role in promoting viral transcription and replication, and antagonizing host innate
immune responses. PLpro is encoded by nonstructural protein 3 (nsp3) which is relatively conserved across
various CoVs. Thus, PLpro is an attractive target for the development of broad-spectrum anti-CoV drugs. The
proposed small-molecule PROTACs are bifunctional small molecules containing two active ligands connected
via a chemical linker. One ligand binds specifically to a viral protein target PLpro while the other ligand selectively
engages an E3 ubiquitin ligase. The recruitment of the E3 ligase to PLpro facilitates the formation of a ternary
complex, leading to ubiquitination and ultimate degradation of PLpro by the ubiquitination-proteasome pathway.
As PROTACs regulate protein function by degrading target proteins instead of inhibiting them, they offer many
advantages over traditional occupancy-based inhibitors, including (i) sub-stoichiometric activity, (ii) high barrier
to resistance, (iii) improved target selectivity, and (iv) that weak binders (no inhibition required) can become
potent degraders. On this basis, the overall goal of this application is to validate the degradation of PLpro as a
new strategy for the development of broad-spectrum antiviral therapeutics to combat CoVs. In Aim 1, to
chemically optimize non-covalent, reversible covalent, and multiple binding-mode PROTACs by linking VHL E3
ligands and PLpro inhibitors/binders, and to evaluate their degradation potency of PLpro in cell-based assays.
In Aim 2, to determine the anti-SARS-CoV-2 activity of developed PROTAC molecules. Potent PROTACs (EC50
< 500 nM) will be further tested for their antiviral activities against other CoVs. In vitro DMPK and cytotoxicity
studies of potent PROTACs will be conducted. The successful completion of the proposed study will lead to
potent anti-CoV PROTACs against COVID-19 that the mechanism of action is fundamentally different from
existing antivirals. The developed PROTAC molecules will also have the potential to be repurposed to contain
future coronavirus outbreaks.
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