Journal of the American Chemical Society, Vol.116, No.12, 5069-5076, 1994
From Peptide to Nonpeptide .1. The Elucidation of a Bioactive Conformation of the Arginine-Glycine-Aspartic Acid Recognition Sequence
An ensemble molecular dynamics method is used to map consensus conformations of the arginine-glycine-aspartic acid (RGD) sequence which are accessible to a set of potent, structurally diverse inhibitors of fibrinogen-glycoprotein IIbIIIa association. This procedure identifies a dominant low-energy RGD conformation that is consistent with the previously determined solution structure of a highly potent RGD-containing peptide. Enforcing an alternate, higher energy conformation is shown to eliminate activity. These observations strongly suggest that the consensus conformation identified is responsible for inhibiting fibrinogen-glycoprotein IIbIIIa binding, thus providing a structural rationale for the de novo design of potent non-peptidal inhibitors of platelet aggregation.
Keywords:MONTE-CARLO METHOD;DISTANCE GEOMETRY;ROTATING-FRAME;NUCLEIC-ACIDS;FORCE-FIELD;PROTEINS;NMR;RGD;SPECTROSCOPY;SIMULATION