Conformational analysis of dipeptide mimetics

A compendium of compounds designed as dipeptide mimetics was collected from the literature. Conformational space available to these molecules was evaluated to obtain distance and torsion angle parameters to aid in selection of mimetics for specific target peptides or to explore diversity strategies. Conformations were searched using the RandomSearch algorithm in SYBYL. Data were collected for conformations of each molecule falling within 5 kcal/mol of the minimum. The distance between capping groups on the N- and C-termini of the molecules was measured as well as the pseudotorsion angle about a virtual bond between these two points. Molecules are classified based on the torsion angle space occupied and range of distances spanned by the resulting conformations. A large percentage of the dipeptide mimetics studies here have redundant conformational properties. The distribution of distances for all molecules covers an overall range of 3-15 Angstrom, the majority falling between 5-8 Angstrom. The angles for the majority of the molecules cover a wide range of torsional space with essentially no gaps in the values they can occupy, although these molecules can be subdivided by the average distance spanned by the allowed conformations. A smaller group of molecules have torsion angles that are restricted to a range of +/-60 degrees about the cis position (0 degrees). Representative examples of each group are shown. We conclude that despite the significant effort to devise unique molecular structures as dipeptide mimetics, there is a need for more conformationally restricted compounds to mimic specific peptide conformations, and to complement molecular diversity strategies. (C) 1997 John Wiley & Sons, Inc.