Douglas D. Young

Evolution of cyclic peptide protease inhibitors

We report a bacterial system for the evolution of cyclic peptides that makes use of an expanded set of amino acid building blocks. Orthogonal aminoacyl-tRNA synthetase/tRNACUA pairs, together with a split intein system were used to biosynthesize a library of ribosomal peptides containing amino acids with unique structures and reactivities. This peptide library was subsequently used to evolve an inhibitor of HIV protease using a selection based on cellular viability. Two of three cyclic peptides isolated after two rounds of selection contained the keto amino acid p-benzoylphenylalanine (pBzF). The most potent peptide (G12: GIXVSL; X = pBzF) inhibited HIV protease through the formation of a covalent Schiff base adduct of the pBzF residue with the ϵ-amino group of Lys 14 on the protease. This result suggests that an expanded genetic code can confer an evolutionary advantage in response to selective pressure. Moreover, the combination of natural evolutionary processes with chemically biased building blocks provides another strategy for the generation of biologically active peptides using microbial systems.

Optochemical control of RNA interference in mammalian cells

Short interfering RNAs (siRNAs) and microRNAs (miRNAs) have been widely used in mammalian tissue culture and model organisms to selectively silence genes of interest. One limitation of this technology is the lack of precise external control over the gene-silencing event. The use of photocleavable protecting groups installed on nucleobases is a promising strategy to circumvent this limitation, providing high spatial and temporal control over siRNA or miRNA activation. Here, we have designed, synthesized and site-specifically incorporated new photocaged guanosine and uridine RNA phosphoramidites into short RNA duplexes. We demonstrated the applicability of these photocaged siRNAs in the light-regulation of the expression of an exogenous green fluorescent protein reporter gene and an endogenous target gene, the mitosis motor protein, Eg5. Two different approaches were investigated with the caged RNA molecules: the light-regulation of catalytic RNA cleavage by RISC and the light-regulation of seed region recognition. The ability to regulate both functions with light enables the application of this optochemical methodology to a wide range of small regulatory RNA molecules.

Synthetase polyspecificity as a tool to modulate protein function

The site-specific incorporation of unnatural amino acids (UAAs) into proteins in bacteria is made possible by the evolution of aminoacyl-tRNA synthetases that selectively recognize and aminoacylate the amino acid of interest. Recently we have discovered that some of the previously evolved aaRSs display a degree of polyspecificity and are capable of recognizing multiple UAAs. Herein we report the polyspecificity of an aaRS evolved to encode a comarin containing amino acid. This polyspecificity was then exploited to introduce several UAAs into the fluorophore of GFP, altering its photophysical properties.

Site-specific protein immobilization using unnatural amino acids.

Protein immobilization confers the advantages of biological systems to a more chemical setting and has applications in catalysis, sensors, and materials development. While numerous immobilization techniques exist, it is optimal to develop a well-defined and chemically stable methodology to allow for full protein function. This paper describes the utilization of unnatural amino acid technologies to introduce bioorthogonal handles in a site-specific fashion for protein immobilization. To develop this approach a range of solid-supports, organic linkers, and protein immobilization sites have been investigated using a GFP reporter system. Overall, a sepharose resin derivatized with propargyl alcohol has afforded the highest yields of immobilized protein. Moreover, an unnatural amino acid residue protein context has been demonstrated, signifying a necessity to consider the protein site of immobilization. Finally, a resin-conferred stabilization was demonstrated in several organic solvents.

Development and Optimization of Glaser–Hay Bioconjugations

The prevalence of bioconjugates in the biomedical sciences necessitates the development of novel mechanisms to facilitate their preparation. Towards this end, the translation of the Glaser-Hay coupling to an aqueous environment is examined, and its potential as a bioorthogonal conjugation reaction is demonstrated. This optimized, novel, and aqueous Glaser-Hay reaction is applied towards the development of bioconjugates utilizing protein expressed with an alkynyl unnatural amino acid. Unnatural amino acid technology provides a degree of bioorthognality and specificity not feasible with other methods. Moreover, the scope of the reaction is demonstrated through protein-small molecule couplings, small-molecule-solid-support couplings, and protein-solid-support immobilizations.

Synthesis and Incorporation of Unnatural Amino Acids To Probe and Optimize Protein Bioconjugations

The utilization of unnatural amino acids (UAAs) in bioconjugations is ideal due to their ability to confer a degree of bioorthogonality and specificity. In order to elucidate optimal conditions for the preparation of bioconjugates with UAAs, we synthesized 9 UAAs with variable methylene tethers (2-4) and either an azide, alkyne, or halide functional group. All 9 UAAs were then incorporated into green fluorescent protein (GFP) using a promiscuous aminoacyl-tRNA synthetase. The different bioconjugations were then analyzed for optimal tether length via reaction with either a fluorophore or a derivatized resin. Interestingly, the optimal tether length was found to be dependent on the type of reaction. Overall, these findings provide a better understanding of various parameters that can be optimized for the efficient preparation of bioconjugates.

Development of solid-supported Glaser-Hay couplings.

While the Glaser-Hay coupling of terminal alkynes is a useful reaction, several issues associated with chemoselectivity preclude its widespread application in synthetic chemistry. To address these issues, a solid-supported Glaser-Hay methodology was developed to afford only asymmetric diyne products. This methodology was then applied to a series of immobilized alkynes with a diverse set of soluble alkynes to generate an array of heterocoupled products in high yields and purities.

Discovery of Small Molecule Modifiers of microRNAs for the Treatment of HCV Infection

While RNA has traditionally been viewed as a mechanism to transfer genetic information, its importance and functionality has only truly been demonstrated in the past 20 years. One prime example of this significance can be found within microRNAs (miRNAs), which are involved in the regulation of a substantial number of human genes. Consequently, these miRNAs represent a novel target for therapeutic agents towards the treatment of a variety of diseases and disorders. Specifically, misregulation of miR-122 has been demonstrated to be relevant in the cellular propagation of Hepatitis C (HCV), and thus modulators of miR-122 can have a substantial effect on viral loads. This protocol describes the development of an assay for the discovery of small molecule regulators of miR-122, and ultimately HCV therapeutics. Due to the excellent pharmacokinetic properties of small molecule libraries, these regulators represent a substantial advantage over traditional antisense agents.

Site-specific incorporation of a fluorescent terphenyl unnatural amino acid

The site-specific incorporation of unnatural amino acids into proteins has a wide range of biological implications. Of particular interest is the incorporation of fluorescent probes as a mechanism to track protein function, transport, and folding. Thus, the development of a novel system for the incorporation of new fluorescent unnatural amino acids has significant utility. Specifically, we have elucidated an aminoacyl-tRNA synthetase capable of recognizing a terphenyl UAA derivative, and charging a cognate tRNA with this amino acid for protein incorporation. Moreover, we have successfully incorporated this fluorescent UAA into GFP at several key residues, demonstrating a novel means to modulate fluorescence within the protein.

Photosensitive GFP mutants containing an azobenzene unnatural amino acid

The incorporation of unnatural amino acids represents a unique mechanism for the modulation of protein function. This approach has been utilized to generate photoswitchable GFP mutants, capable of demonstrating modulated fluorescence upon exposure to UV irradiation. Overall these photosensitive GFP mutants can be employed in various biosensing and diagnostic techniques to better understand protein function and processing.