Codon optimization as a design variable in biotherapeutics

Codon optimization (CO) is a key design variable in biotherapeutics that is used to enhance expression of recombinant proteins, gene therapies, and vaccines. Although synonymous codon substitutions were historically considered neutral, codon choice can influence messenger RNA (mRNA) stability, translation kinetics, cotranslational folding, and immunogenicity. Current optimization strategies integrate computational parameters including codon adaptation indices, tRNA availability, mRNA structure, cytosine-phosphate-guanine dinucleotide content, codon pair bias, and machine learning approaches to balance expression and product quality. Additionally, dynamic tRNA modifications within the epitranscriptome modulate codon-biased translation in a context-dependent manner. While CO has not been implicated in adverse clinical outcomes, its context-dependent effects on protein conformation, post-translational modifications, and immune responses necessitate rigorous characterization. This opinion article presents our viewpoint on mechanisms, applications, and regulatory considerations for CO in biologics.