Design and Repurposing of Some Nucleoside Analogs Targeting Some Key Proteins of the Avian H5N1 Clade 2.3.4.4b Using Molecular Docking and Simulation

(1) Background: The highly pathogenic avian influenzas virus H5N1 clade 2.3.4.4b is an emerging threat that poses great risk to the poultry industry. Few human cases have been linked to the infection with this clade in many parts of the world, including the USA. Unfortunately, there are no specific vaccines or antiviral drugs that could help prevent and treat the infection of this virus in birds. Our major objective is to identify/repurpose some (novel/known) antiviral compounds that may inhibit viral replication by targeting some key viral proteins. (2) Methods: We used state-of-the-art machine learning tools such as molecular docking and MD-simulation methods from Bio-via Discovery Studio (v24.1.0.321712). The target proteins homology models were validated through structural assessment via DOPE scores, Ramachandran plots, and Ver-ify-3D metrics, ensuring reliable structural representations, confirming their reliability for subsequent in silico approaches, including molecular docking and molecular dynamics simulation for 50 ns highlighted the structural stability and compactness of the docked complexes. (3) Results: Molecular docking revealed strong binding affinities of both compounds, particularly the GS441524, which demonstrated superior interaction energy and hydrogen bonding with critical functional residues of (HA, NA, M2, and PB2/CBD). The MM-GBSA binding free energy calculations supported these findings, with GS441524 showing more favorable energies than several known standard inhibitors for HA (F0045S), NA (Zanamivir), M2 (Rimantadine and Amantadine) and PB2/CBD (Pb2-39), especially in its interaction with NA and PB2/CBD. Molecular dynamics simulations over 50 ns highlighted the structural stability and compactness of the GS441524 complex with PB2/CBD. Hydrogen bond analysis further confirmed persistent and specific interactions, suggesting that GS441524 may effectively disrupt PB2-mediated RNA synthesis. (4) Conclusions: Our findings are consistent with previous evidence supporting the antiviral activity of certain nucleoside analog inhibitors, including GS441524, against various coronaviruses. These results further support the potential repurposing of GS441524 as a promising therapeutic candidate against H5N1 avian influenza clade 2.3.4.4b. However, additional functional studies are necessary to validate these in silico predictions of its anti-H5N1 activity.