Prophylactic pyronaridine reduces SARS-CoV-2 infection and inflammation in mice. Eight- to 10-week-old wild-type Balb/c mice (n = 5 per group) were challenged with 1 × 105 PFU of SARS-CoV-2 Beta variant (B.1.351). And treated with either nothing, molnupiravir, or pyronaridine orally beginning 12 h before infection. (A) Mouse weights were measured each day and lungs were harvested at 2 dpi for (B) viral titer quantification, (D) lung histology staining with red arrows indicating reduced lung inflammatory infiltrates and bronchovascular cuffing and (F) scoring analysis, and (C) nucleocapsid staining with hematoxylin and eosin and (E) scoring quantification for interstitial inflammation. Lungs were harvested at 2 dpi and 4 dpi for RNA extraction and RNA-sequencing analysis including (G) heatmap showing fold changes of genes relative to uninfected mice. Only genes differentially expressed at any time point (at least twofold expression change in either direction, adjusted P-value <0.01). (H) Venn diagrams showing sets of significantly upregulated (top, blue) or downregulated (bottom, red) genes, relative to mock, across the time points and treatments tested. Unt. = untreated. (I) Fold change of interferon-stimulated genes (ISGs) with pyronaridine treatment (treated vs untreated, all infected). Day 2 mean ISG levels are lower with pyronaridine treatment (P = 9.3e−15). (J) Heatmap showing the most different cytokines with pyronaridine treatment, relative to mock. Heatmap tiles outlined in black are significantly increased or decreased (adjusted P-value <0.01). n = 5 mice per group, mean ± SD is shown. *P < 0.05, **P < 0.01, and ***P < 0.001, using one-way analysis of variance with Dunnett’s multiple comparison test. The red asterisks are compared to virus-only group, whereas the green and purple asterisks are compared to molnupiravir and pyronaridine groups, respectively.