The chemical synthesis of peptides through solid-phase chemistry has been refined over the past decades to the point where virtually any sequence can be synthesized. However, even in the hands of experts, peptide synthesis is not a perfect process. The synthesis of a given sequence often produces systematic low-level byproducts due to incomplete deprotection or reaction with free protecting groups. These side products can include truncated or deleted sequences, isomers and other unwanted residues (Figure 18.1.1). Moreover, the yield of a given peptide chain is inversely proportional to its length. This is because as the peptide grows, it becomes increasingly likely that one or more of its amino acid chains will undergo an unfavorable reaction such as isomerization or degradation by microbial colonies (Figure 18.1.2).
To reduce these side reactions, a number of chemistry-based strategies are used to optimize the synthesis of long peptides. For example, different protecting groups are matched to Fmoc or Boc for optimized deprotection and coupling, and scavengers such as water, anisol or thiol derivatives are added during the synthesis to react with any free protective groups. Likewise, the cleavage step is designed to avoid acid-catalyzed side reactions by using sulfonic acids that have a pKa of
Despite these advances, the biological activity of synthetic peptides still falls short of that observed for native ECM proteins. Generally, the reduced biological activity of synthetic peptides is due to their poor ability to mimic the multiple binding sites found in continuous proteins. For example, the canonical RGD peptide only has an average of seven binding sites to the 8 integrin subtypes of the extracellular matrix (Figure 18.1.3). The lack of multiple interactions also makes it difficult for peptides to exert the synergistic and complementary binding mechanisms required to trigger cellular responses. This problem is expected to be addressed through advances in structure-based design, which will enable the generation of synthetic peptides that mimic the multifunctional properties of complex proteins.