Journal of Structural Biology, Vol.115, No.3, 267-274, 1995
Molecular mechanics studies on conformationally restricted dipeptide models: 1-Acetylamino-N-methyl-2,5-cyclohexadiene-1-carboxamide and its derivatives
We present conformation energy calculations on the model dipeptide 1-acetylamino-N-methyl-2,5-cyclohexadiene-1 -carboxamide (1) and its two derivatives in which the C-2 and C-6 of the cyclohexadiene ring are substituted. The energy calculations have been done using molecular mechanics methods with a force field derived from MM2. The salient features are expressed in terms of conformational energy plots, drawn as a function of the backbone torsion angles phi(C-N-C-alpha-C) and psi(N-C-alpha-C-N). Two families of conformations are found to be the global minima in the (phi psi) space, one corresponding to a region with fully extended structures characterized by (phi psi) = (180 degrees +/- 20 degrees 180 degrees +/- 20 degrees) and the other characterized by (phi psi) = (180 degrees +/- 20 degrees, +/- 60 +/- 20 degrees). The low energy structures of these model compounds are qualitatively consistent with the available amount of X-ray crystal structure data on peptido-mimetics similar to 1. The salient results obtained have important implications on the design of constrained peptidomimetics with the above two conformations. (C) 1995 Academic Press, Inc.