Characterization of Hydrophilic α‑Helical Hot Spots on the Protein–Protein Interaction Interfaces for the Design of α‑Helix Mimetics

The cooperativity index, Kc, was developed to examine the binding synergy between hot spots of the ligand–protein. For the first time, the convergence of the side-chain spatial arrangements of hydrophilic α-helical hot spots Thr, Tyr, Asp, Asn, Ser, Cys, and His in protein–protein interaction (PPI) complex structures was disclosed and quantified by developing novel clustering models. In-depth analyses revealed the driving force for the protein–protein binding conformation convergence of hydrophilic α-helical hot spots. This observation allows deriving pharmacophore models to design new mimetics for hydrophilic α-helical hot spots. A computational protocol was developed to search amino acid analogues and small-molecule mimetics for each hydrophilic α-helical hot spot. As a pilot study, diverse building blocks of commercially available nonstandard L-type α-amino acids and the phenyl ring-containing small-molecule fragments were obtained, which serve as a fragment collection to mimic hydrophilic α-helical hot spots for the improvement of binding affinity, selectivity, physicochemical properties, and synthesis accessibility of α-helix mimetics.