Accurate calculation of affinity changes to the close state of influenza A M2 transmembrane domain in response to subtle structural changes of adamantyl amines using free energy perturbation methods in different lipid bilayers

Experimental binding free energies of 27 adamantyl amines against the influenza M2(22-46) WT tetramer, in its closed form at pH 8, were measured by ITC in DPC micelles. The measured Kd's range is ~44 while the antiviral potencies (IC50) range is ~750 with a good correlation between binding free energies computed with Kd and IC50 values (r = 0.76). We explored with MD simulations (ff19sb, CHARMM36m) the binding profile of complexes with strong, moderate and weak binders embedded in DMPC, DPPC, POPC or a viral mimetic membrane and using different experimental starting structures of M2. To predict accurately differences in binding free energy in response to subtle changes in the structure of the ligands, we performed 18 alchemical perturbative single topology FEP/MD NPT simulations (OPLS2005) using the BAR estimator (Desmond software) and 20 dual topology calculations TI/MD NVT simulations (ff19sb) using the MBAR estimator (Amber software) for adamantyl amines in complex with M2(22-46) WT in DMPC, DPPC, POPC. We observed that both methods with all lipids show a very good correlation between the experimental and calculated relative binding free energies (r = 0.77–0.87, mue = 0.36–0.92 kcal mol-1) with the highest performance achieved with TI/MBAR and lowest performance with FEP/BAR in DMPC bilayers. When antiviral potencies are used instead of the Kd values for computing the experimental binding free energies we obtained also good performance with both FEP/BAR (r = 0.83, mue = 0.75 kcal mol-1) and TI/MBAR (r = 0.69, mue = 0.77 kcal mol-1). [Display omitted] •We measured Kd values for 27 adamantyl amines to influenza A M2TM WT measured with ITC in DPC micelles pH 8, differing by a factor of ~44.•The compounds antiviral potencies (IC50s) range was ~750 and there is a good correlation (r = 0.76) between ΔGbs computed with Kds and IC50s.•We investigated with MD simulations and ff19sb, CHARMM36m force fields the binding profile of the adamantyl amines.•In MD simulations were tested DMPC, DPPC, POPC or viral mimetic membranes and different experimental starting structures.•FEP/BAR and TI/MBAR binding free energy calculations based on Kd values in the tested lipid systems show r = 0.77–0.87, mue = 0.36–0.92 kcal mol−1.•The highest performance was achieved with TI/MBAR and lowest performance with FEP/BAR for M2TM WT complexes in DMPC bilayers.•FEP/BAR or TI/MBAR showed good performance based on IC50 values, r = 0.69, mue = 0.77 kcal mol−1 or r = 0.83, mue = 0.75 kcal