Conformational analysis of a stereochemically complete set of cis-enediol peptide analogues.
A conformational analysis of a stereochemically complete set of peptide analogues based on a cis-enediol unit is presented. The cis-enediol unit, which can replace a two or a three amino acid segment of a peptide, contains two "side chains", four asymmetrical carbon atoms, and six free dihedral angles. To determine the accessible conformational space, the molecules are divided into three fragments, each containing two free dihedral angles. The energy surfaces are computed for all dihedral angle values, and the possible conformations of the cis-enediol unit analogues are built using all combinations of the surface minima. Such a "build-up" procedure, which is very fast, is able to reproduce 75% of the minima obtained from a full dihedral angle exploration of the conformational space. The cis-enediol unit minima are compared with the corresponding di- and tripeptide minima; all peptide minima can be closely matched by a cis-enediol unit minimum of low energy (less than 2.2 kcal/mol above the lowest energy conformer). However, there are low energy minima of the cis-enediol unit that have no corresponding minima in peptides. The results are shown to depend strongly on the chirality of the analogues. The ability of each of the stereoisomers to mimic natural peptides, evaluated by the present approach, is correlated with its experimental activity in a renin inhibition assay.
Michielin
Olivier
O
Contribution from the Laboratoire de Chimie Biophysique Institut Le Bel, Université Louis Pasteur, 4 rue Blaise Pascal, 67000 Strasbourg, France.
Zoete
Vincent
V
Gierasch
Tiffany Malinky
TM
Eckstein
Jens
J
Napper
Andrew
A
Verdine
Gregory
G
Karplus
Martin
M
D000438:Alcohols / Q000737:chemistry* / Q000378:metabolism / Q000494:pharmacology; D000475:Alkenes / Q000737:chemistry* / Q000378:metabolism / Q000494:pharmacology; D000595:Amino Acid Sequence; D003198:Computer Simulation; D006801:Humans; D008958:Models, Molecular; D008968:Molecular Conformation; D018716:Molecular Mimicry; D010455:Peptides / Q000737:chemistry* / Q000494:pharmacology; D012083:Renin / Q000378:metabolism; D013237:Stereoisomerism; D013499:Surface Properties; D013816:Thermodynamics; D000092502:Renin Inhibitors
D000438:Alcohols; D000475:Alkenes; D010455:Peptides; D012083:Renin; D000092502:Renin Inhibitors