Nirmatrelvir exerts distinct antiviral potency against different human coronaviruses

Abstract

Nirmatrelvir is the main component of Paxlovid, an oral antiviral drug approved for the treatment of COVID-19 caused by SARS-COV-2 infection. Nirmatrelvir targets the main protease (M^pro), which is substantially conserved among different coronaviruses. Here, our molecular docking analysis indicates comparable affinity of nirmatrelvir binding to the M^pro enzymes of SARS-CoV-2 and three seasonal coronaviruses (OC43, 229E and NL63). However, in cell culture models, we found that nirmatrelvir potently inhibited SARS-CoV-2, OC43 and 229E, but not NL63. The insensitivity of NL63 to nirmatrelvir treatment was demonstrated at both viral replication and infectious titer levels. The antiviral activity of nirmatrelvir against OC43 and 229E was further confirmed in human airway organoids. The combination of nirmatrelvir and molnupiravir exerted differential patterns of antiviral response against OC43 and 229E. These results revealed disparities in the ability of nirmatrelvir to inhibit different coronaviruses, and caution against repurposing of nirmatrelvir as a pan-coronavirus treatment.

Keywords: Antiviral activity; Disparity; Nirmatrelvir; Pan-coronavirus.

Fig. 1

Molecular docking of the main protease of SARS-CoV-2, 229E, NL63 and OC43 with nirmatrelvir. The interacting interface of the receptor with the ligand and its corresponding 2D interaction with the M^pro of (A) SARS-CoV-2, (B) 229E, (C) NL63 and (D) OC43 along with the dock scores. Interactions of the catalytic dyad residues present on the receptor (His41 and Cys144/145) with the ligand are highlighted. Corresponding bonding patterns are shown in different color codes.

Fig. 2

Antiviral activity of nirmatrelvir against four coronaviruses in cell culture models. (A) The effects of nirmatrelvir on intracellular viral RNA levels of SARS-CoV-2 in Calu-3 cells, OC43 and 229E in Huh7 cells and NL63 in LLC-MK2 cells (n = 4–9). (B) Virus replication curves of these coronaviruses in Calu-3, Huh7 and LLC-MK2 cells treated with nirmatrelvir (n = 4–9). (C) TCID50 assay quantifying titers of secreted infectious virus particles at 48 h post-treatment of nirmatrelvir (n = 4–5). (D) The effects of nirmatrelvir on intracellular viral RNA levels of OC43 and 229E in human airway organoids (hAOs) (n = 5). (E & F) Immunofluorescence staining of OC43 and 229E viral dsRNA, cytomembrane marker EpCAM and DAPI in hAOs.

Fig. 3

Combinational effects of nirmatrelvir and molnupiravir against OC43 and 229E coronaviruses. (A) The antiviral effects of combining nirmatrelvir and molnupiravir in OC43-infected Huh7 cells based on intracellular viral RNA levels (n = 4–7). (B) Synergy distribution of pairwise combination of nirmatrelvir and molnupiravir in OC43-infected Huh7 cells (n = 4–7). (C) The antiviral effects of combining nirmatrelvir and molnupiravir in 229E-infected Huh7 cells based on intracellular viral RNA levels (n = 4–9). (D) Synergy distribution of pairwise combination of nirmatrelvir and molnupiravir in 229E-infected Huh7 cells (n = 4–9).