Figure 1. Shielded hydrogen bonds confer longer residence time. (a) Schematic of a drug (yellow) bound to a receptor (green), forming, among other interactions, a hydrogen bond (red dashed line). (b) Compared with (a) the greater curvature of the binding site shields the hydrogen bond from water access, creating a larger barrier to drug dissociation. (c) For a less-curved binding site, as in (a), increasing the ligand size (blue) also shields the hydrogen bond. The difficulty with which water diffuses into and away from a shielded hydrogen bond directly impacts drug residence time, by creating a kinetic barrier to ligand binding and unbinding [111]

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Docking and Ligand Binding Affinity: Uses and Pitfalls

María J. R. Yunta

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