Expanding and engineering the genetic code for biomedical applications

Abstract

Ample numbers of chemical and genetic approaches are available to modify proteins for a wide variety of applications. All these modifications were mainly focused on utilizing the functional chemistry available in the amino acids. Similar to lysine and cysteine modifications, tyrosine-based modifications have drawn considerable attractions due to better stability, selectivity, and structural integrity. However, nature evolved with limited sets of conserved amino acids to biosynthesize proteins. In recent decades, a general approach was developed to genetically encode unnatural amino acids (UNAAs) with diverse functional properties in cells and animals. Such a building block with novel chemical and physical properties allowed evolving alloproteins for the exploration of protein structure and functions. Among them, genetically encoded controlled labeling of proteins provided a potential advantage to probe cells with fluorophores. In this context, cell labeling was executed by amino acid surrogates through azide chemistry; Cu (I) catalyzed azide-alkyne cycloaddition and strain promoted cycloaddition of cyclooctynes. Further, cell labeling was accelerated by converting the catechol moiety of the protein into quinone through oxidation controlled cycloaddition. However, the above methods have considerable limitations due to toxicity, bio-incompatibility, and byproduct formation. To overcome this, in the first chapter of this thesis, enzyme-mediated Strain Promoted Oxidation Controlled Cycloaddition (SPOCQ) reactions have been developed by genetically replacing the tyrosine residue with its surrogate 3, 4- dihydroxyphenylalanine (DOPA) through the mis-aminoacylation method. Here, tyrosinase was used to convert DOPA into the DOPA quinone without the formation of an intermediate. This method was initially validated with a small molecule (DOPA). The formation of DOPA quinone from DOPA was confirmed by UV and mass spectrometric analysis. Further, the genetic incorporation of DOPA in proteins, conversion of DOPA into DOPA qui