Targeted screening and rational optimization of bazedoxifene analogs as pan-variant SARS-CoV-2 entry inhibitors with improved pharmacokinetics.

Through a focused screening of FDA-approved drugs using a spike RBD-ACE2 interaction assay, we identified bazedoxifene, a selective estrogen receptor modulator (SERM), as an unexpected yet potent entry inhibitor of SARS-CoV-2. Bazedoxifene disrupted spike-mediated attachment and demonstrated robust inhibition in both pseudovirus (IC50 = 1.11 μM) and live-virus (IC50 = 2.1 μM) assays. Mechanistic validation through RT-qPCR, pseudovirus entry assays, and immunofluorescence imaging confirmed entry-stage action. Notably, bazedoxifene retained efficacy across key SARS-CoV-2 variants (WT, Delta, Beta, Omicron BA.1/BA.5) and the zoonotic sarbecovirus Khosta-2, underscoring its broad-spectrum potential. A systematic SAR campaign introduced modifications at N1, C3 methyl, and the phenolic hydroxyls (C4'/C5), identifying compound 74 (C5 isosteric replacement) as a superior analog. Compound 74 exhibited pseudovirus IC50 = 1.6 μM, live-virus IC50 = 0.45 μM, and showed significantly improved PK parameters: ∼6-fold lower clearance, >10-fold longer half-life, and 7-8-fold higher AUC compared to both bazedoxifene and compound 66 (C4' modification). The metabolic stabilisation achieved through C5 modification validates it as a key hotspot driving glucuronidation and rapid clearance in bazedoxifene. Altogether, the potent antiviral activity, metabolic resilience, and enhanced drug-like properties of compound 74 position it as a promising lead for next-generation, entry-targeted antiviral development.