Common Structural Features of Hydrophobic α‑Helical Hot Spots: Insights for the Design of Novel α‑Helix Mimetics

The binding conformations of α-helical hydrophobic
hot spots
are convergent into two spatial areas in protein–protein complex
structures. The physical basis for convergence was disclosed, which
allows the development of pharmacophore models for i/i + 4/i + 7 or i/i + 3/i + 4 α-helical hot
spots. Further investigation revealed that this convergence of binding
conformations is common among all hydrophobic hot spots regardless
of their α-helical positions. This observation led to a streamlined
generation of pharmacophore models for hydrophobic hot spots at any
positions along the α-helix. These successfully evaluated pharmacophore
models may be useful for designing novel α-helical hot spot
mimetics.