Novel Arbidol derivatives against SARS-CoV-2: a comprehensive approach using computer- and AI-assisted drug design

Despite the availability of vaccines and treatments for COVID-19, the emergence of new SARS-CoV-2 variants poses ongoing challenges to vaccine-induced immunity, highlighting the urgent need for additional antiviral therapies. Arbidol, a broad-spectrum antiviral drug approved in Russia and China for treating influenza A and B, has shown promise against a variety of viruses, including SARS-CoV-2, through its ability to inhibit viral replication and block viral entry by targeting the spike protein. However, its cytotoxicity limits its clinical applications. In this study, we designed, synthesized, and evaluated novel arbidol derivatives against SARS-CoV-2 using structure-activity relationship studies, machine learning (ML) models, generative design (MegaSyn), and molecular docking calculations, focusing on the arbidol binding site on the S2 subunit of the spike protein. We synthesized and characterized forty-five new compounds and assessed their antiviral activity against various SARS-CoV-2 variants in two cell lines. The new compounds exhibited promising antiviral effects, with IC₅₀ values ranging from 0.49 to 2.34 µM in the SFuse test using Vero cells infected with Wuhan, Delta, XBB15, and BA2.86.1 strains. The most effective compounds were also tested in Calu-3 cells infected with the SARS-CoV-2 B.1 lineage, yielding EC₅₀ values between 1.4 and 9.9 µM. Importantly, these compounds demonstrated low cytotoxicity and high selectivity index in Calu-3 cells. Notably, H3D-020453, the most promising compound predicted by ML models with a 94% probability of activity, exhibited an in vitro antiviral potency (EC₅₀) of 1.53 µM and cytotoxicity (CC₅₀) of 93.9 µM. Molecular docking indicated that these derivatives effectively bind at the arbidol binding site on the S2 subunit, forming hydrogen bonds with residues L947 and L776 and exhibiting hydrophobic interactions with N1023 and T1027. In conclusion, our findings underscore the significant antiviral activity of the new arbidol derivatives against various SARS-CoV-2 variants, emphasizing the need for further in vivo studies to explore their therapeutic potential in the context of evolving SARS-CoV-2 variants.