Summary for 9GUB
| Entry DOI | 10.2210/pdb9gub/pdb |
| Descriptor | Papain-like protease nsp3, (2~{S})-3-(1~{H}-indol-3-yl)-2-(7~{H}-pyrrolo[2,3-d]pyrimidin-4-ylamino)propanoic acid (3 entities in total) |
| Functional Keywords | inhibitor, sars-cov-2 mac1, macrodomain, mcd-628, viral protein |
| Biological source | Severe acute respiratory syndrome coronavirus 2 |
| Total number of polymer chains | 2 |
| Total formula weight | 37516.65 |
| Authors | |
| Primary citation | Pfannenstiel, J.J.,Duong, M.T.H.,Cluff, D.,Sherrill, L.M.,Colquhoun, I.,Cadoux, G.,Thorne, D.,Paakkonen, J.,Schemmel, N.F.,O'Connor, J.,Saenjamsai, P.,Feng, M.,Parthasarathy, S.,Hageman, M.J.,Johnson, D.K.,Roy, A.,Lehtio, L.,Ferraris, D.V.,Fehr, A.R. Identification of a series of pyrrolo-pyrimidine-based SARS-CoV-2 Mac1 inhibitors that repress coronavirus replication. Mbio, :e0386524-e0386524, 2025 Cited by PubMed Abstract: Coronaviruses (CoVs) can emerge from zoonotic sources and cause severe diseases in humans and animals. 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, although 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 compound (a.k.a. MCD-628), a pyrrolo-pyrimidine that inhibited Mac1 activity at low micromolar levels. Here, we determined the binding mode of by crystallography, further defining its interaction with Mac1. However, did 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 of . We identified four compounds that both inhibited Mac1 and inhibited murine hepatitis virus (MHV) replication: , , , and . Furthermore, and inhibited SARS-CoV-2 replication only in the presence of IFNγ, similar to a Mac1 deletion virus. To confirm their specificity, we passed MHV in the presence of to 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 with the WT virus when treated with , demonstrating the specificity of these compounds during infection. However, this virus is highly attenuated , indicating that drug resistance emerged at the expense of viral fitness.IMPORTANCECoronaviruses (CoVs) present significant threats to human and animal health, as evidenced by recent outbreaks of MERS-CoV and SARS-CoV-2. 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, although 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 CoV infections. PubMed: 40407321DOI: 10.1128/mbio.03865-24 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.1 Å) |
Structure validation
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