The Journal of Physical Chemistry B ARTICLE Figure 7. Comparison of the resulting partial charge on atoms using the RESP69 method (A) Glutamate in 1FTJ structure. (B) AMPA in the 1FTM structure. (C) Glutamate in the 1FTM structure. (D) AMPA in the 1FTJ structure. Instead a water molecule occupies the position of one of the carboxylate oxygen atoms (WA in Figure 2B). Similarly, the position of the ring nitrogen in the GluA2-glutamate complex (1FTJ) is also occupied by a water molecule (WG in Figure 2A). In this sense we can consider this water molecule as part of the ligand in each case. However it is not clear why this water molecule should preferentially occupy diﬀerent sites with respect to these ligands and hence why the resulting binding pose for AMPA diﬀers from glutamate. Previous docking studies have shown that con- sideration of this water molecule is essential to retrieve the correct binding pose for AMPA and that omission of this water molecule leads to a docking pose that overlays with the glutamate-GluA2 complex.49 In the context of drug-design, there has been a lot of work aimed at determining whether water molecules in a binding site can be displaced by modiﬁcations to existing ligands. Indeed (RS)-2-amino-3-(3-carboxy-5-methyl-4-isoxazolyl) propoionic acid (ACPA), an analogue of AMPA where the 3-oxyanion moiety is replaced by a carboxylic acid, interacts directly with the side-chain OH of Thr 655.31 ACPA has both a lower IC50 (IC50 = 20 nM compared to 79 nM for AMPA)71 and lower EC50 (EC50 = 0.74 μM31 compared to 3.5 μM for AMPA72). The improvement may be more modest than expected as ACPA loses an additional water interaction that AMPA makes, the overlay is not quite perfect and there are small diﬀerences in the binding pose and the conformation of binding pocket residues. In this study we wanted to examine to what extent the observed diﬀerences in binding orientation between AMPA and glutamate could be attributed to stabilization eﬀects of water molecules and how the water molecules interact with the protein and/or ligand. Because polarization eﬀects may be critical to this analysis, we used ab initio calculations to calculate the interaction energies between the various components of the binding site. Our calculations show that a simple interaction energy calcu- lation between the ligand and the rest of the system is suﬃcient to be able to predict the correct mode of binding for glutamate, but not for AMPA. Clearly, entropic eﬀects, which are neglected in these calculations, must play a more dominant role in the case of AMPA. Table 2 shows that the “pharmacophoric water” (WG/WA) has no energetic preference for the ligand (glutamate or AMPA) 7093 dx.doi.org/10.1021/jp200776t |J. Phys. Chem. B 2011, 115, 7085–7096