Deciphering the conformational landscape of few selected aromatic noncoded amino acids (NCAAs) for applications in rational design of peptide therapeutics

Amino acids are the essential building blocks of both synthetic and natural peptides, which are crucial for biological functions and also important as biological probes for mapping the complex protein-protein interactions (PPIs) in both prokaryotic and eukaryotic systems. Mapping the PPIs through the chemical biology approach provides pharmacologically relevant peptides, which can have agonistic or antagonistic effects on the targeted biological systems. It is evidenced that >= 60 peptide-based drugs have been approved by the US-FDA so far, and the number will improve further in the foreseeable future, as >= 140 peptides are currently in clinical trials. However, natural peptides often require fine-tuning of their pharmacological properties by strategically replacing the alpha(L)-amino acids of the peptides with non-coded amino acids (NCAA), for which codons are absent in the genetic code for biosynthesis of proteins, prior to their applications as therapeutics. Considering the diverse repertoire of the NCAAs, the conformational space of many NCAAs is yet to be explored systematically in the context of the rational design of therapeutic peptides. The current study deciphers the conformational landscape of a few such C alpha-substituted aromatic NCAAs (Ing: 2-indanyl-l-Glycine; Bpa: 4-benzoyl-l-phenylalanine; Aic: 2-aminoindane-2-carboxylic acid) both in the context of tripeptides and model synthetic peptide sequences, using alanine (Ala) and proline (Pro) as the reference. The combined data obtained from the computational and biophysical studies indicate the general success of this approach, which can be exploited further to rationally design optimized peptide sequences of unusual architecture with potent antimicrobial, antiviral, gluco-regulatory, immunomodulatory, and anti-inflammatory activities.

Automated summary

Amino acids play important roles in the synthesis of both synthetic and natural peptides, and mapping protein-protein interactions using chemical biology approaches provides pharmacologically relevant peptides. Over 60 peptide-based drugs have been approved, and more peptides are currently in clinical trials. However, the pharmacological properties of natural peptides often need to be fine-tuned by replacing amino acids with non-coded amino acids. This study explores the conformational landscape of several C alpha-substituted aromatic non-coded amino acids and provides insights for the rational design of optimized peptide sequences with potent biological activities.