From concept to chemistry: integrating protection group strategy and reaction feasibility into non-natural amino acid synthesis planning

Journal article, 2025

Incorporating non-natural amino acids (NNAAs) into peptides enhances therapeutic properties, including binding affinity, metabolic stability, and in vivo half-life time. The pursuit of novel NNAAs for improved peptide designs faces the challenge of effective synthesis of these building blocks as well as the entire peptide itself. Solid-Phase Peptide Synthesis (SPPS) is an essential technology for the automated assembly of peptides with NNAAs, necessitating careful protection for effective coupling of amino acids in the peptide chain. This process requires orthogonal protection of the reactive groups in individual amino acids after synthesizing them, presenting a challenge in bridging in silico peptide design with chemical synthesis. To address this, we have developed a first-of-its-kind synthesis assistance tool, NNAA-Synth, that plans and evaluates the synthesis of individual SPPS-compatible NNAAs. Our tool unifies (i) introducing orthogonal protecting groups to NNAAs, (ii) retrosynthetic prediction to propose synthesis routes, and (iii) scoring the synthetic feasibility of these routes. We demonstrate how the tool facilitates optimal protection strategy selection for individual NNAAs. Additionally, it enables synthesizability-aware NNAA ranking and prioritization during computational screening, enhancing the quality of the in silico design by assessing the accessibility of individual building blocks.