The Chikungunya virus (CHIKV) continues to pose a significant global health challenge due to the absence of effective antiviral treatments and limited vaccine availability. This study employed a comprehensive in silico workflow, incorporating high-throughput virtual screening, binding free-energy calculations, ADMET (absorption, distribution, metabolism, excretion, and toxicity) analysis, and 200 ns molecular dynamics (MD) simulations, to identify new inhibitors targeting the E1–E2 glycoprotein complex, crucial for CHIKV entry and membrane fusion. Four promising candidates were identified from a library of 20,000 compounds, with CID 136801451 showing the most potent binding (docking score: −10.227; ΔG_bind: −51.53 kcal/mol). The top four compounds exhibited favorable ADMET profiles, meeting nearly all criteria. MD simulations confirmed stable binding and strong interactions between CID 136801451 and the E1–E2 complex, evidenced by consistently low RMSD values. These findings highlight CID 136801451 as a promising CHIKV entry inhibitor, warranting further in vitro and in vivo evaluation to advance the development of effective anti-CHIKV therapeutics.

Nipah virus (NiV) is a zoonotic virus that causes severe encephalitis and respiratory disease with a mortality rate often exceeding 70%. Currently, there are no licensed vaccines or therapeutics for NiV disease. This study aimed to identify and experimentally evaluate small-molecule inhibitors targeting the NiV-G (attachment) glycoprotein using integrated in silico and in vitro approaches. A high-throughput virtual screening of >215,000 compounds was conducted against the NiV-G glycoprotein, using docking and molecular dynamics (MD) simulations. The next potential candidates were evaluated using an established, BSL-2-compatible recombinant Cedar virus (rCedV)-based green fluorescent protein (GFP) reporter virus expressing the NiV-F (fusion) and G glycoproteins (rCedV-NiV-B-GFP). During MD simulations, quercetin demonstrated the most stable binding, maintaining a consistent RMSD (3.25 ± 0.3 Å). In vitro testing showed dose-dependent inhibition of rCedV-NiV-B-GFP infection. Although quercetin alone was less potent (IC₅₀ = 24 µM; 95% CI: 7.6–93.6 µM) than a reference NiV-neutralizing monoclonal antibody mAb-7B7 (IC₅₀ = 0.027 μg/mL; approximately 0.00018 μM; 95% CI: 0.0108 to 0.0735), combination with ascorbic acid enhanced neutralization (IC₅₀ = 4.4 µM; 95% CI: 2.9–6.8 µM). Quercetin demonstrated a high Selectivity Index of >20.8. The study identifies quercetin as a promising small-molecule inhibitor of NiV cellular infection, potentially through a stable interaction with NiV-G at the ephrin-B2/B3 binding interface identified computationally. These findings highlight the importance of combining computational screening with BSL-2 cell-based bioassays to accelerate NiV countermeasure discovery.