150-Cavity Synchronization by Extended Loop in Neuraminidase of 2009 H1N1 Influenza Type A Virus: A Simulation Study

Neuraminidase (NA) is a novel drug target for antiviral inhibitors. In this druggable target, a cavity adjacent to the active site exists and is known as the 150-cavity. NA is divided into two groups: Group 1 and Group 2. The 150-cavity is present in Group 1 and absent in Group 2. Its behaviour is largely dependent on the nature of the 150-loop. H1N1 pandemic virus is believed to be an exception to this norm because it lies in Group 1 but doesn't contain the 150-cavity. Recent studies have shown that H1N1, also known as 2009N1, is capable of showing transition states that are characterized by different conformations of 150-loop. This 100-ns simulation study and subsequent analysis focused on identifying different conformations and develop an insight into the 150-loop which is directly responsible for transition states as well as 150-cavity formation. The study indicates direct regulating participation and involvement of a modified, extended 150-loop (144–156) in the formation of 150-cavity.