Indomethacin-based PROTACs as pan-coronavirus antiviral agents

Abstract

Indomethacin (INM), a well-known non-steroidal anti-inflammatory drug, has recently gained attention for its antiviral activity demonstrated in drug repurposing studies against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Although the mechanism of action of INM is not yet fully understood, recent studies have indicated that it acts at an early stage of the coronaviruses (CoVs) replication cycle. In addition, a proteomic study reported that the anti-SARS-CoV-2 activity of INM could be also ascribed to its ability to inhibit human prostaglandin E synthase type 2 (PGES-2), a host protein which interacts with the SARS-CoV-2 NSP7 protein. Although INM does not potently inhibit SARS-CoV-2 replication in infected Vero E6 cells, here we have explored for the first time the application of the Proteolysis Targeting Chimeras (PROTACs) technology in order to develop more potent INM-derived PROTACs with anti-CoV activity. In this study, we report the design, synthesis, and biological evaluation of a series of INM-based PROTACs endowed with antiviral activity against a panel of human CoVs, including different SARS-CoV-2 strains. Two PROTACs showed a strong improvement in antiviral potency compared to INM. Molecular modelling studies support human PGES-2 as a potential target of INM-based antiviral PROTACs, thus paving the way toward the development of host-directed anti-CoVs strategies. To the best of our knowledge, these PROTACs represent the first-in-class INM-based PROTACs with antiviral activity and also the first example of the application of PROTACs to develop pan-coronavirus agents.

Development of a PROTAC-Based Targeting Strategy Provides a Mechanistically Unique Mode of Anti-Cytomegalovirus Activity

“…This illustrates that this prototypic CDK9-targeted PROTAC, which exerts the intended degradative mechanism as experimentally verified, presents a measurable advantage over the non-PROTAC parental inhibitor. Notable, a similarly sized five-fold increase in activity was recently described for anti-coronaviral PROTACs based on indomethacin [ 42 ], indicating that this magnitude is easily achievable by converting an inhibitor to its corresponding PROTAC, an approach that is still open for optimization as a focus of our continued studies on antiviral options against human pathogenic viruses, including HCMV.…”

“…For this reason, our prioritized approach with currently synthesized PROTACs will be directed to multiprotein complexes essential for virus replication. Despite these potential benefits, only telaprevir-based PROTACs active against the hepatitis C virus and indomethacin-derived PROTACs with anti-coronavirus activity have been reported on so far [ 42 , 55 ]. Taken together, data of this study underline that PROTACs harbor untapped, possible game-changing potential in regard to antiviral drug development, so that skillful procedures of PROTAC synthesis and a structure–activity relationship may guarantee further success in the near future.…”

PROTACs: past, present and future

“…Their PROTAC demonstrated robust viral spike protein receptor binding domain (RBD) degradation capabilities in human cells and the ability to inhibit infection-competent viral production. Recently Desantis et al revealed the first indomethacin-based small molecular PROTAC 157 as a pan-coronavirus antiviral agent that targets a host protein (prostaglandin E synthase type 2) rather than a viral one for degradation with the advantage of overcoming resistance issues. In 2020, Haniff et al have designed a ribonuclease targeting chimera (RIBOTAC) 158 that recruits a cellular ribonuclease to degrade the viral genome leading to inhibition of SARS-CoV-2 frameshifting.…”

Discovery of novel SARS-CoV-2 inhibitors targeting the main protease Mpro by virtual screenings and hit optimization

“…Plaque reduction assays (PRA) with different CoVs were performed as previously described ( Desantis et al, 2021 ). For SARS-CoV-2, Vero E6 cells were seeded at a density of 1 × 10 5 cells per well in 24-well plates and the next day, were infected with 80 Plaque Forming Unit (PFU) per well of SARS-CoV-2 (SARS-CoV-2/NL/2020 strain).…”