RESUMEN
Rationale The recent emergence of a novel coronavirus, SARS-CoV-2, has led to the global pandemic of the severe disease COVID-19 in humans. While efforts to quickly identify effective antiviral therapies have focused largely on repurposing existing drugs, the current standard of care, remdesivir, remains the only authorized antiviral intervention of COVID-19 and provides only modest clinical benefits. Thus, new antivirals targeting SARS-CoV-2 are urgently needed. Methods Artificial intelligence algorithm MediKanren was used to query FDA-approved and late-stage drug compounds for potential interactions with SARS-CoV-2 proteins, coronaviruses, and host cell networks for possible antiviral activity. From this, 157 compounds were further tested in an antiviral screen against live SARS-CoV-2 for reduction in viral growth. Select compounds were further assessed for synergistic activity with remdesivir. Both in vitro and cell free systems identified tocopherol succinate compounds that inhibited the RNA-dependent RNA polymerase (RdRp). Validation of antiviral and synergistic activity was performed in primary human airway epithelial cell cultures against multiple SARS-CoV-2 variants.Results Here we show that water-soluble derivatives of α-tocopherol have potent antiviral activity and synergize with remdesivir as inhibitors of the SARS-CoV-2 (RdRp). Through an artificial-intelligence-driven in silico screen and in vitro viral inhibition assay, we identified D-α-tocopherol polyethylene glycol succinate (TPGS) as an effective antiviral against SARS-CoV-2 and β-coronaviruses more broadly that also displays strong synergy with remdesivir. We subsequently determined that TPGS and other water-soluble derivatives of α- tocopherol inhibit the transcriptional activity of purified SARS-CoV-2 RdRp and identified affinity binding sites for these compounds within a conserved, hydrophobic interface between SARS-CoV- 2 nonstructural protein 7 and nonstructural protein 8 that is functionally implicated in the assembly of the SARS-CoV-2 RdRp. Conclusion In summary, solubilizing modifications to α-tocopherol allow it to interact with the SARS-CoV-2 RdRp, making it an effective antiviral molecule alone and even more so in combination with remdesivir. These findings are significant given that many tocopherol derivatives, including TPGS, are considered safe for humans, orally bioavailable, and dramatically enhance the activity of the only approved antiviral for SARS-CoV-2 infection.
RESUMEN
Rationale: SARS-CoV-2 is a novel β-coronavirus that causes a severe disease (COVID-19) in humans. Currently, approved antivirals only provide modest benefits to critically ill patients, require intravenous administration, and are in limited supply. Methods: To address the urgent need for new therapeutics, we performed a computational screen using the freely available platform, mediKanren, to identify a list of 120 FDA-approved drugs with purported activity against SARS-CoV-2. To test these compounds in vitro, we developed a mid-throughput assay based on immunohistochemistry compatible with a 96-well microplate to quantifying the antiviral activity of these compounds against virulent SARS-CoV-2 in the Vero E6 cell line. Results: Of the 120 FDA-approved compounds tested, we identified 11 candidates with potent anti-viral activity. Follow up testing showed all but one of these candidates were equally effective against the seasonal coronavirus, OC-43, and five of these candidates were effective at stopping viral propagation when given 24 hours post infection. Using this same assay to test across a range of doses, we determined the dose-response curves for our 11 best compounds. Based on the predicted efficacy of each drug, we then screened for synergy between all pair-wise combinations of our top hits. We found that the combination of remdesivir with another top candidate, DL-alpha-tocopherol polyethylene glycol succinate (TPGS), was nearly ten times more potent than either drug alone. These results were validated by performing curve-shift analysis, which identified another six drugs that combine with remdesivir in an additive fashion. Response-surface analysis revealed that an equipotent mixture of TPGS and remdesivir yielded maximum synergy, but the potency of both drugs can be significantly enhanced by combining one drug with as little as 10% of the dose of the other drug. Finally, these findings were validated in the Calu 3 cell line. Conclusions: In addition to identifying eleven FDA-approved drugs with antiviral activity against SARS-CoV-2, these results are significant given that cheap, widely available drugs can markedly improve the potency of and protect against resistance to the current standard of care for COVID-19.