Figure 1.
Alchemical thermodynamic paths using SRMM (A) and SRSM (B) in the bound state between wild type (wt) and a mutant (mut1).
The paths (arrows) between end states (squares) going through nonphysical reference states (ovals) are shown. The SRMM uses a common reference state ‘hub’ for all mutations and ligands (RS1*2*3* L*); SRSM uses a mutation and ligand-specific reference state (RS1* LX). Decoupled residues and ligands are noted by an ‘*’. Thermodynamic paths in the unbound state have a similar form but without the ligand.
Table 1.
Comparison of experimental ΔΔG in oseltamivir and zanamivir for three NA mutations with estimates obtained using different computational approaches.
Figure 2.
Representative structures for zanamivir (A, B and C) and oseltamivir (D, E and F) bound to WT and mutant NAs from the SRSM/HREX simulations.
Salt-bridges and hydrogen bonds are depicted as magenta and orange dashed lines, respectively. Positively charged, negatively charged, and uncharged polar groups are noted as blue, red, and purple circles, respectively, and residues of interest are labeled. Mutated residues are underlined.
Figure 3.
Comparison of WT and mutant dynamics.
For WT and H274Y, N294S, and Y252H, distance distributions between the atoms Cδ of E276 and Nε of R292 and between the atoms Cδ of E277 and Nε of R292 are shown for oseltamivir (A, C) and zanamivir (B, D), respectively.
Figure 4.
Differences in hydrogen bonding with the zanamivir tail in the H274Y mutant.
Distribution of the average distance between the atoms Oε of E276 and E277 with O21 and O23 in the trihydroxypropyl group of zanamivir in wild type (A) and in the H274Y mutant (B).
Figure 5.
Comparison of WT and N294S mutant dynamics.
(A) Distance distributions between the R292 Nε atom and N294 Oδ1 and Y347 carbonyl O atoms computed from SRSM/HREX simulations of the WT enzyme in complex with oseltamivir and zanamivir. (B) Distance distributions between the Nε atom of R292 and S294 Oγ and Y347 carbonyl O atoms computed from simulations of the complexes of the N294S mutant with the two drugs. (C) Distributions of distances between the Y347 Oη atom and Nη1 atoms from R292 and R371 computed from SRSM simulations of the WT enzyme in complexes with the two drugs and (D) for the complexes of the N294S mutant with oseltamivir and zanamivir.