Structure‐based design, Fourrier transformed infrared and Raman studies and structure‐activity relationships of synthetic peptides with trans/cis‐cinnamic and dihydrocinnamic acids as inhibitors for thrombin

Abstract

As a part of a research proposal aimed at studying structure activity relationship in the field of peptides inhibitors for thrombin, we performed molecular docking experiments using the software “SCULPT” (from MDL) and designed “in silico” libraries of peptides as potential inhibitors for thrombin. Our original experiments generated a candidate group of peptides (with both L- and D- amino acids) that were characterized by a predicted free energy based on Van der Waals interactions with thrombin in the range from −20 to −100 kcal/mol. New peptides containing phenylalanine (Phe) analogs such as (trans/cis)cinnamic and dihydrocinnamic acids were designed to scan the P3 position in the sequence space D-Phe (P3)–Pro(P2)–D-Arg(P1)-P1′-CONH2 which was shown to inhibit reversibly thrombin in vitro. The P1′ position contains the most conserved L-amino acids found in the natural substrates of thrombin such as Gly, Ile, Ala, Cys and Ser. The cis-cinnamoyl peptides were obtained from trans-cinnamoyl peptides by exposing the solution of trans-cinnamoyl peptide to UV-light (354 nm) for 5 minutes. Fourier transform-infrared (FTIR) and Raman microsspectroscopy of solid peptide films were used to determine the conversion of trans-cinnamoyl peptides into cis-cinnamoyl peptides. The in vitro thrombin inhibition assays showed that transcinnamoyl peptides are stronger inhibitors than cis-cinnamoyl and dihydrocinnamoyl-peptides with inhibitory constants in the range of 1-200 uM.