Simeprevir Potently Suppresses SARS-CoV-2 Replication and Synergizes with Remdesivir

Abstract

The outbreak of coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a global threat to human health. Using a multidisciplinary approach, we identified and validated the hepatitis C virus (HCV) protease inhibitor simeprevir as an especially promising repurposable drug for treating COVID-19. Simeprevir potently reduces SARS-CoV-2 viral load by multiple orders of magnitude and synergizes with remdesivir in vitro . Mechanistically, we showed that simeprevir not only inhibits the main protease (M pro ) and unexpectedly the RNA-dependent RNA polymerase (RdRp) but also modulates host immune responses. Our results thus reveal the possible anti-SARS-CoV-2 mechanism of simeprevir and highlight the translational potential of optimizing simeprevir as a therapeutic agent for managing COVID-19 and future outbreaks of CoV.

Hepatitis C Virus Protease Inhibitors Show Differential Efficacy and Interactions with Remdesivir for Treatment of SARS-CoV-2 In Vitro

“…EC 50 s against SARS-CoV-2 were in the micromolar range, with the lowest EC 50 s (9 and 15 μM for simeprevir in A549-hACE2 and Vero E6 cells, respectively) approaching the EC 50 of remdesivir (0.1 and 2.5 μM in A549-hACE2 and Vero E6 cells, respectively); EC 50 s of remdesivir were in line with previously reported results ( 30 – 32 , 35 , 36 ). However, EC 50 s of PIs against SARS-CoV-2 were higher than the EC 50 s against HCV.…”

“…Thus, combination of remdesivir with the linear PIs boceprevir and narlaprevir showed mostly antagonism, while combination with macrocyclic PIs showed mostly synergism. In contrast to the previous studies ( 35 , 36 ), we confirmed these PI structure-dependent interactions with remdesivir in longer-term treatment assays in Vero E6 and A549-hACE2 cells, where the combination of remdesivir with simeprevir or grazoprevir, but not with boceprevir, resulted in added efficacy. This structure dependence might be explained by differences in viral targets.…”

“…Inhibitor efficacy can be improved by combination treatments with synergistic and thus drug-saving effects as reported here for the combination of remdesivir with the macrocyclic PIs simeprevir, paritaprevir, or grazoprevir in Vero E6 cells and with simeprevir or grazoprevir in A549-hACE2 cells. Synergism was recently suggested for the combination of remdesivir with simeprevir ( 35 , 36 ) or grazoprevir ( 36 ) in short-term assays in Vero E6 cells ( 35 , 36 ) and human embryonic kidney (HEK293T) cells ( 36 ). Our extensive results in Vero E6 and A549-hACE2 cells using short-term drug interaction assays demonstrated that the mode of interaction between PI and remdesivir depended on the PI structure.…”

“…This structure dependence might be explained by differences in viral targets. While the investigated HCV PIs were suggested to target M pro ( 30 , 33 – 36 , 57 – 77 ), simeprevir was suggested to also target the SARS-CoV-2 polymerase ( 35 ), and simeprevir, grazoprevir, and paritaprevir were suggested to also target PL pro ( 36 , 62 ). It should be noted that additional alternative viral targets, including nsp13 (helicase), nsp14 (exonuclease and methyltransferase), nsp15 (endoribonuclease), nsp16 (2′- O -ribose methyltransferase), as well as structural proteins N (capsid) and spike, were suggested for paritaprevir, grazoprevir, and simeprevir by modeling studies ( 62 , 74 , 78 – 82 ).…”

“…Most EC 50 s reported in these studies were in the same range as those reported here; the slightly higher EC 50 values observed in our study are most likely caused by differences in experimental assay conditions. EC 50 s in human lung cells were only reported for simeprevir (EC 50 , 1 μM) ( 35 ) and voxilaprevir (>10 μM), also using the A549-hACE2 cell line ( 30 ). The similar PI EC 50 values in monkey Vero E6 cells, human Huh7.5 cells, and human A549-hACE2 cells reported in our study validate Vero E6 cells for the study of HCV PI efficacy against SARS-CoV-2.…”