Design of serine protease inhibitors with conformation restricted by amino acid side-chain-side-chain CH/π interaction

A novel type of conformationally restricted peptides with the structure of H–D‐Xaa–Phe–NH–CH2–C6H5 has been developed as inhibitors of serine proteinase chymotrypsin. The D‐Xaa–alkyl and Phe–phenyl groups resulted in a formation of the hydrophobic core due to the side‐chain–side‐chain CH/π interaction. Their spatial proximity was evidenced by 400 MHz 1H‐nmr measurements, observing large upfield shifts of proton signals of D‐Xaa–alkyl and nuclear Overhauser effect (NOE) enhancements between the D‐Xaa–alkyl and Phe–phenyl groups. This conformational restriction brought by CH/π interaction produced an inhibitory structure, in which the C‐terminal amide‐benzyl group fits the chymotrypsin S1 site and the hydrophobic core binds to the S2 site. The inhibitory conformation was demonstrated crystallographically for the complex between the dipeptide H‐D–Leu–Phe–NH–CH2–C6H4(p‐F) and γ‐chymotrypsin. Detailed structure–activity studies have substantiated the structure of dipeptides in the active center of the enzyme. © 1999 John Wiley & Sons, Inc. Biopoly 51: 9–17, 1999