Characterizing loop dynamics and ligand recognition in human- and avian-type influenza neuraminidases via generalized born molecular dynamics and end-point free energy calculations

Abstract

The comparative dynamics and inhibitor binding free energies of group-1 and group-2 pathogenic influenza A subtype neuraminidase (NA) enzymes are of fundamental biological interest and relevant to structure-based drug design studies for antiviral compounds. In this work, we present seven generalized Born molecular dynamics simulations of avian (N1)- and human (N9)-type NAs in order to probe the comparative flexibility of the two subtypes, both with and without the inhibitor oseltamivir bound. The enhanced sampling obtained through the implicit solvent treatment suggests several provocative insights into the dynamics of the two subtypes, including that the group-2 enzymes may exhibit similar motion in the 430-binding site regions but different 150-loop motion. End-point free energy calculations elucidate the contributions to inhibitor binding free energies and suggest that entropic considerations cannot be neglected when comparing across the subtypes. We anticipate the findings presented here will have broad implications for the development of novel antiviral compounds against both seasonal and pandemic influenza strains.

Figure 1

Motions of the 150- and 430-loops. Loop conformations are shown in cartoon representation for the most dominant configurations of (a) the N1-apo-closed (orange) and the N1-oseltamivir-bound-closed (red), (b) the N1-apo-open (orange) and the N1-oseltamivir-bound-open (red), and (c) the N9-apo-closed (orange) and the N9-oseltamivir-bound-closed (red) trajectories. The N1 open (blue) and N1 closed (green) crystal structures are shown for comparison.

Figure 2

Equilibrium orientations of oseltamivir in the different binding sites. Overall orientations (left panel) and active-site interactions (right panel) of oseltamivir bound to (a) the N1-closed, (b) the N1-open, and (c) the N9-closed system. The original conformations of the 150- and 430-loops are shown in blue and red, respectively, to highlight the loop motion observed in the course of the dynamics. Active-site residues within 4 Å of oseltamivir are shown explicitly. The original conformation of oseltamivir is shown in violet for comparison.

Figure 3

Open−closed loop transitions. Root-mean-square deviations of the 150-loop (comprising residues N146−R152) from the MD with respect to the open (gray) and closed (black) crystal structures are shown for the N1-apo-closed (a), the N1-oseltamivir-bound-closed (b), the N1-apo-open (c), the N1-oseltamivir-bound-open (d), the N9-apo-closed (e), and the N9-oseltamivir-bound-closed (f) structures.