Influenza viruses are a major public health threat worldwide. The influenza hemagglutinin (HA) plays an essential role in the virus life cycle. Due to the high conservation of the HA stem region, it has become an especially attractive target for inhibitors for therapeutics. In this study, molecular simulation was applied to study the mechanism of a small molecule inhibitor (MBX2329) of influenza HA. Behaviors of the small molecule under neutral and acidic conditions were investigated, and an interesting dynamic binding mechanism was found. The results suggested that the binding of the inhibitor with HA under neutral conditions facilitates only its intake, while it interacts with HA under acidic conditions using a different mechanism at a new binding site. After a series of experiments, we believe that binding of the inhibitor can prevent the release of HA1 from HA2, further maintaining the rigidity of the HA2 loop and stabilizing the distance between the long helix and short helices. The investigated residues in the new binding site show high conservation, implying that the new binding pocket has the potential to be an effective drug target. The results of this study will provide a theoretical basis for the mechanism of new influenza virus inhibitors.Influenza virus is the causative agent of influenza, an infectious disease which usually leads to symptoms such as high fever, cough, headache, muscle and joint pain, sore throat, nasal discharge, and even a fatal illness similar to pneumonia 1-4 . Influenza viruses are divided into three types, type A, type B and type C, with influenza A virus presenting serious threats to public health worldwide due to its high mutation rate [5][6][7] . At present, two classes of drugs are approved by the Food and Drug Administration for treatment or chemoprophylaxis of influenza: matrix protein 2 (M2) inhibitors amantadine and rimantadine and the neuraminidase (NA) inhibitors (NAIs) oseltamivir and zanamivir 8,9 . However, with the wide use of these drugs, drug-resistant strains have appeared in succession 10 . Therefore, new antiviral targets with novel inhibition mechanism need to be developed.Hemagglutinin (HA), a viral receptor-binding and membrane-fusion glycoprotein involved in the invasion of influenza into host cells, plays an essential role in the life cycle of influenza A virus 3,11 . HA is a trimer of identical subunits, each of which consists of a variable membrane-distal receptor-binding globular domain (HA1) and a more conserved membrane-proximal helix-rich stem structure (HA2) 12 . Under acidic conditions, the residues on the outer surface of HA1 can be protonated easily, which leads to the large gathering of positive charges on the surface of HA 13,14 . With gradually increased charges, disaggregation of HA first occurs as the positive charges repel each other, followed by the entry of water into the interior of the protein causing further structural changes of HA2 13 . In the HA2 subunit, one short and one long α-helical segment are connected by a loop (helix-loo...
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