Design, synthesis, and analysis of macrobicyclic peptides for targeting the Gi protein

Bicyclic peptides are important chemical tools that can function, for example, as bioactive ligands switching on/off signaling pathways mediated by guanine nucleotide-binding proteins as bicycles are more broadly applicable. Despite their relevance in medicinal chemistry, the synthesis of such peptides is challenging, and the final yield is highly dependent on the chemical composition and physicochemical properties of the scaffold. We recently discovered novel, state-specific peptide modulators targeting the G alpha i protein, namely, GPM-2/GPM-3, by screening a one-bead-two-compound combinatorial library. A more detailed analysis, including sequence alignments and computer-assisted conformational studies based on the hit compounds, revealed the new peptide 10 as a potential macrobicyclic G alpha i ligand sharing high sequence similarity to the known G alpha i modulators. The G alpha s protein was included in this study for comparison and to unravel the criteria for the specificity of modulator binding to G alpha i versus G alpha s. This work provides in-depth computer-assisted experimental studies for the analysis of novel macrobicyclic, library-derived G alpha i protein ligands. The sequence and structural comparison of 10 with the lead compounds GPM-2 and GPM-3 reveals the importance of the size and amino acid composition of one ring of the bicyclic system and suggests features enhancing the binding affinity of the peptides to the G alpha i protein.