Enhanced Antiviral Activity of Novel Umifenovir Derivatives against SARS-CoV-2: Insights from an International Collaborative Study

Abstract

Despite the availability of vaccines and treatments for COVID-19, the emergence of new SARS-CoV-2 variants continues to challenge vaccine-induced immunity, emphasizing the need to develop antiviral therapies to combat these variants and other viruses. Umifenovir (UMF), marketed as Arbidol, is a broad-spectrum antiviral drug approved in Russia and China for influenza viruses A and B. Recent studies have suggested its potential against SARS-CoV-2, demonstrating its ability to inhibit viral replication and obstruct viral entry by targeting the spike protein, despite having low oral bioavailability and short half-life. In this work, we conducted an initial antiviral screening that identified a hit compound (a UMF analogue), followed by the rational design, synthesis, and evaluation of novel UMF derivatives against SARS-CoV-2. This process employed generative models and structure–activity relationship studies (SAR), focusing on the UMF binding site on the S2 subunit of the spike protein. The derivatives demonstrated potent antiviral activity, with EC50 values ranging from 0.05 to 1.23 μM in S-Fuse assays against the Omicron variant (BA.2.86.1 lineage) and from 1.4 to 1.53 μM in Calu-3 cells, while showing low cytotoxicity and high selectivity. The most promising compound, 11, predicted by the machine learning-based generative models, exhibited an antiviral potency (EC50) of 1.53 μM in Calu-3 cells infected with the B.1. variant, a CC50 of 93.9 μM, with a selectivity index of 61.37. Additionally, 11 displayed substantial antiviral activity against various SARS-CoV-2 variants, including against the Omicron variant (BA.2.86.1), with an EC50 of 0.73 μM in the S-Fuse assay. Furthermore, 11 demonstrated favorable mouse pharmacokinetic properties, including improved aqueous solubility at physiological pH, a prolonged terminal half-life, and increased systemic exposure. Overall, virucidal assays demonstrated that 11 lacks direct virucidal activity, and viral adsorption assays further showed that this compound does not impair viral attachment. Consistent with these findings, exploratory molecular docking results should be regarded as hypothesis-generating, suggesting a potential involvement of compound 11 in later viral entry events rather than in direct viral inactivation. These findings provide a foundation for advancing 11 as a hit compound for further optimization within antiviral strategies against SARS-CoV-2 variants.