Protein-Loop Mimetics: A Diketopiperazine-Based Template to Stabilize Loop Conformations in Cyclic Peptides Containing the NPNA and RGD Motifs

We explore here an approach to mimic the structures and biological functions of protein loops in small synthetic molecules, by grafting the loop of interest onto an organic template comprising a bicyclic diketopiperazine, prepared by the formal coupling of (2S,4S)-4-aminoproline (Pro(NH2)) and aspartic acid (Asp). The Fmoc-protected template 4 is used to prepare cyclo(-Ala1-Asn2-Pro3-Asn4-Ala5- Ala6-Temp-) (5) and cyclo(-Ala1-Arg2-Gly3-Asp4-Temp-) (6) (where Temp = template derived from 4), containing the Asn-Pro-Asn-Ala (NPNA) and Arg-Gly-Asp (RGD) motifs. The conformational properties of these molecules are studied in aqueous solution by NMR and simulated-annealing methods. The NPNA motif, an immunodominant epitope on the circumsporozoite surface protein of the malaria parasite Plasmodium falciparum, is shown to adopt a stable type-I β-turn in 5. The template in 5 adopts a preferred conformation with Pro(NH2)χ1 ≈ −35° and the Asp moiety χ1 ≈ 70°. A different template conformation is inferred for 6, with Pro(NH2)χ1 ≈ 0°, but the ARGD loop appears by NMR to undergo rapid conformational averaging. Solid-phase binding assays reveal that 6 displays modest antagonist activity towards both the integrin αIIbβ3 and αvβ3 receptors.