Identification of a series of pyrrolo-pyrimidine based SARS-CoV-2 Mac1 inhibitors that repress coronavirus replication
Authors: Pfannenstiel Jessica J. , Duong Men Thi Hoai , Cluff Daniel , Sherrill Lavania M. , Colquhoun Iain , Cadoux Gabrielle , Thorne Devyn , Pääkkönen Johan , Schemmel Nathaniel F. , O’Connor Joseph , Saenjamsai Pradtahna , Feng Mei , Hageman Michael J. , Johnson David K. , Roy Anuradha , Lehtiö Lari , Ferraris Dana V. , Fehr Anthony R. 
Published: October 2024

Coronaviruses (CoVs) can emerge from zoonotic sources and cause severe diseases in humans and animals. All CoVs encode for a macrodomain (Mac1) that binds to and removes ADP-ribose from target proteins. SARS-CoV-2 Mac1 promotes virus replication in the presence of interferon (IFN) and blocks the production of IFN, though the mechanisms by which it mediates these functions remain unknown. Mac1 inhibitors could help elucidate these mechanisms and serve as therapeutic agents against CoV-induced diseases. We previously identified compound4a(a.k.a. MCD-628), a pyrrolo-pyrimidine that inhibited Mac1 activityin vitroat low micromolar levels. Here, we determined the binding mode of4aby crystallography, further defining its interaction with Mac1. However,4adid not reduce CoV replication, which we hypothesized was due to its acidic side chain limiting permeability. To test this hypothesis, we developed several hydrophobic derivatives of4a. We identified four compounds that both inhibited Mac1in vitroand inhibited murine hepatitis virus (MHV) replication:5a,5c,6d, and6e. Furthermore,5cand6einhibited SARS-CoV-2 replication only in the presence of IFNγ, similar to a Mac1 deletion virus. To confirm their specificity, we passaged MHV in the presence of5ato identify drug-resistant mutations and identified an alanine-to-threonine and glycine-to-valine double mutation in Mac1. Recombinant virus with these mutations had enhanced replication compared to WT virus when treated with5a, demonstrating the specificity of these compounds during infection. However, this virus is highly attenuatedin vivo, indicating that drug-resistance emerged at the expense of viral fitness.

IMPORTANCE

Coronaviruses (CoVs) present significant threats to human and animal health, as evidenced by recent outbreaks of MERS-CoV and SARS-CoV-2. All CoVs encode for a highly conserved macrodomain protein (Mac1) that binds to and removes ADP-ribose from proteins, which promotes virus replication and blocks IFN production, though the exact mechanisms remain unclear. Inhibiting Mac1 could provide valuable insights into these mechanisms and offer new therapeutic avenues for CoV-induced diseases. We have identified several unique pyrrolo-pyrimidine-based compounds as Mac1 inhibitors. Notably, at least two of these compounds inhibited both murine hepatitis virus (MHV) and SARS-CoV-2 replication. Furthermore, we identified a drug-resistant mutation in Mac1, confirming target specificity during infection. However, this mutant is highly attenuated in mice, indicating that drug-resistance appears to come at a fitness cost. These results emphasize the potential of Mac1 as a drug target and the promise of structure-based inhibitor design in combating coronavirus infections.