Virtual Screening of Antivirals Targeting H275Y Mutation in Neuraminidase gene of Oseltamivir Drug Resistant Influenza Strains

Neuraminidase (NA) is an essential enzyme located at the outer layer of the influenza virus and plays a key role in the release of virions. This study aims to identify and analyze possible inhibitors of NA from different subtypes of influenza viruses, especially considering global outbreaks that highlight the immediate requirement for effective antiviral drugs. Initially, a thorough search was conducted in the Protein Data Bank (PDB) to gather structures of NA proteins that were attached with oseltamivir, a widely recognized inhibitor of NA. Here, 36 PDB entries were found with NA-oseltamivir complexes which were studied to evaluate the diversity and mutations present in various subtypes. Finally, N1(H1N1) protein was selected that demonstrated low IC50 value of oseltamivir with mutation H275Y. In addition, the study utilized BiMODAL generative model to generate 1000 novel molecules with comparable structures to oseltamivir. A QSAR model, based on machine learning (ML), was built utilizing the ChEMBL database to improve the selection process of candidate inhibitors. These inhibitors were subsequently analyzed by molecular docking and further the best hits compounds ( compound_375 , compound_106 and compound_597 ) were tacked to make a bigger molecule ( compound_106–375 , compound_106–597 , and compound_375–597 ) to fit into the binding pocket of protein. Further, triplicate molecular dynamics simulations lasting 100 ns to assess their effectiveness and binding stability, showed that compound_106–375 had the most stable binding with the protein. Key residues, including Asn146, Ala138, and Tyr155, form critical interactions with the ligand, contributing to its stability. The investigation was enhanced by employing principal component analysis (PCA), free energy landscape (FEL), and binding free energy calculations. The total binding free energy (G _TOTAL ) of -17.74 kcal/mol suggests that the contact between compound_106–375 and the mutant N1 (H1N1) protein is thermodynamically favorable. This approach allowed for a thorough comprehension of the binding interactions and possible effectiveness of the discovered inhibitors. Overall, these findings demonstrate that compound_106–375 exhibits favorable binding characteristics and stability, making it a promising candidate for further development as a therapeutic agent against the mutant N1 (H1N1) protein, potentially overcoming the challenges associated with drug resistance in influenza viruses.