Ryan Hili

Macrocyclization of Linear Peptides Enabled by Amphoteric Molecules

There has been enormous interest in both naturally occurring and synthetic cyclic peptides as scaffolds that preorganize a given amino acid sequence into a rigid conformation. Such molecules have been employed as nanomaterials, imaging agents, and therapeutics. Unfortunately, the laboratory synthesis of cyclic peptides directly from linear precursors is afflicted by several thermodynamic and kinetic challenges, resulting in low chemical yields and poor chemo- and stereoselectivities. Here we report that amphoteric amino aldehydes can be used for efficient syntheses of cyclic peptides in high yields and selectivities starting from alpha-amino acids or linear peptides. The cyclizations effectively operate at unusually high molar concentrations (0.2 M), while side processes such as epimerization and cyclodimerization are not observed. The products are equipped with sites that allow for a highly specific, late-stage structural modification. The overall efficiency of the macrocyclization is due to the coexistence of nucleophilic and electrophilic reaction centers in amphoteric amino aldehydes.

Enzyme-free translation of DNA into sequence-defined synthetic polymers structurally unrelated to nucleic acids

The translation of DNA sequences into corresponding biopolymers enables the production, function, and evolution of the macromolecules of life. In contrast, methods to generate sequence-defined synthetic polymers with similar levels of control have remained elusive. Here we report the development of a DNA-templated translation system that enables the enzyme-free translation of DNA templates into sequence-defined synthetic polymers that have no necessary structural relationship with nucleic acids. We demonstrate the efficiency, sequence-specificity, and generality of this translation system by oligomerizing building blocks including polyethylene glycol (PEG), α-(d)-peptides, and β-peptides in a DNA-programmed manner. Sequence-defined synthetic polymers with molecular weights of 26 kDa containing 16 consecutively coupled building blocks and 90 densely functionalized β-amino acid residues were translated from DNA templates using this strategy. We integrated the DNA-templated translation system developed here into a complete cycle of translation, coding sequence replication, template regeneration, and re-translation suitable for the iterated in vitro selection of functional sequence-defined synthetic polymers unrelated in structure to nucleic acids.

Synchronized Synthesis of Peptide‐Based Macrocycles by Digital Microfluidics

made with high chemoselectivity from amino acids or linear peptides, isocyanides, and amphoteric aziridine aldehydes in a one-step process. Importantly, the resulting products possess useful structural features that allow specific modification at defined positions. In our initial work, we formed serial batches of peptides using conventional macroscale synthetic techniques. The utility of this method is limited, however, without a high-throughput approach for generating focused libraries of peptide macrocycles. Such a method would be automated and would enable multistep reactions to be handled in parallel. Herein, we present a new miniaturized technique for synchronized on-chip synthesis of peptide macrocycles and related products. The most common format for miniaturized synthesis is enclosed microchannels in planar platforms. Such systems have been used for conventional organic synthesis, polymerization reactions, formation of biomolecules, such as peptides and DNA, and generation of nanoparticles and colloids. However, there are some challenges that limit the scope of their use for parallel chemical synthesis. For example, many microchannel platforms are formed from poly(dimethylsiloxane), a material that is susceptible to degradation in common organic solvents. Furthermore, control of many reagents simultaneously (a feature required to implement parallel synthetic reactions) in microchannels requires pumps, tubing, valves, and/or threedimensional channel networks that can be difficult to fabricate and operate. This has prompted researchers to develop specialized techniques to overcome this limitation. Another disadvantage associated with the microchannel format is the challenge inherent in the removal of solvents and re-dissolution of solids that are common steps in synthesis. Solid reagents and products can clog microchannels, making targeted reagent delivery difficult to control. Finally, the small volumes of samples in microchannels makes it difficult to recover them in sufficient quantities for off-line analysis techniques, such as NMR spectroscopy. In need of a platform capable of generating a) peptide macrocycles for downstream transfer onto functionalized surfaces, and b) spatially resolved macrocyclic peptide products in the solid state, we chose an alternative format for automation of synthesis, called digital microfluidics. In digital microfluidics, discrete nL to mL sized droplets of samples and reagents are controlled in parallel by applying a series of electrical potentials to an array of electrodes coated with a hydrophobic insulator (Figure 1). Digital microfluidics has become popular for biological and chemical applications, including cell culture and assays, enzyme assays, immunoassays, protein processing, clinical sample processing and analysis, and synthesis of anisotropic Scheme 1. Synthesis of peptide-based macrocycles and their structurally modified derivatives.

Synthesis of peptide macrocycles using unprotected amino aldehydes

This protocol describes a method for synthesizing peptide macrocycles from linear peptide precursors, isocyanides and aziridine aldehydes. The effects of the reaction components on the efficiency of the process are discussed. Macrocyclization is exemplified by the preparation of a nine-membered ring peptide macrocycle. The product is further functionalized by nucleophilic opening of the aziridine ring with a fluorescent thiol. This transformation constitutes a useful late-stage functionalization of a macrocyclic peptide molecule. The experimental section describes the selection of the required starting materials, and the preparation of a representative aziridine-2-carboxaldehyde dimer. The synthesis and isolation of the peptide macrocycle can be accomplished in 6 h, and the ring-opening requires approximately 6–8 h. The aziridine-2-carboxaldehyde reagent is commercially available or can be synthesized from readily available starting materials in approximately 4 d. The strategy described is not limited to the specific peptide, isocyanide, aziridine aldehyde or nucleophile used in the representative synthesis.

Amphoteric Amino Aldehydes Reroute the Aza-Michael Reaction

Amphoteric amino aldehydes, which exist as stable dimers, participate in an aza-Michael/aldol domino reaction with alpha,beta-unsaturated aldehydes to afford stable 1,5-aminohydroxyaldehydes in high yields and diastereoselectivies. The reaction outcome hinges upon the dimeric nature of amphoteric amino aldehydes and the orthogonality between the NH aziridine and the two aldehyde functionalities during the reaction. Through the use of reaction conditions that disfavor dimer dissociation, the aza-Michael process has been directed toward a novel 8-(enolendo)-exo-trig cyclization. The results described herein further demonstrate the potential of amphoteric molecules in reaction discovery.

DNA Ligase-Mediated Translation of DNA Into Densely Functionalized Nucleic Acid Polymers

We developed a method to translate DNA sequences into densely functionalized nucleic acids by using T4 DNA ligase to mediate the DNA-templated polymerization of 5′-phosphorylated trinucleotides containing a wide variety of appended functional groups. This polymerization proceeds sequence specifically along a DNA template and can generate polymers of at least 50 building blocks (150 nucleotides) in length with remarkable efficiency. The resulting single-stranded highly modified nucleic acid is a suitable template for primer extension using deep vent (exo-) DNA polymerase, thereby enabling the regeneration of template DNA. We integrated these capabilities to perform iterated cycles of in vitro translation, selection, and template regeneration on libraries of modified nucleic acid polymers.

Enzymatic Synthesis of Sequence-Defined Synthetic Nucleic Acid Polymers with Diverse Functional Groups

The development and in-depth analysis of T4 DNA ligase-catalyzed DNA templated oligonucleotide polymerization toward the generation of diversely functionalized nucleic acid polymers is described. The NNNNT codon set enables low codon bias, high fidelity, and high efficiency for the polymerization of ANNNN libraries comprising various functional groups. The robustness of the method was highlighted in the copolymerization of a 256-membered ANNNN library comprising 16 sub-libraries modified with different functional groups. This enabled the generation of diversely functionalized synthetic nucleic acid polymer libraries with 93.8 % fidelity. This process should find ready application in DNA nanotechnology, DNA computing, and in vitro evolution of functional nucleic acid polymers.

Generation of Synthetic Copolymer Libraries by Combinatorial Assembly on Nucleic Acid Templates

Recent advances in nucleic acid-templated copolymerization have expanded the scope of sequence-controlled synthetic copolymers beyond the molecular architectures witnessed in nature. This has enabled the power of molecular evolution to be applied to synthetic copolymer libraries to evolve molecular function ranging from molecular recognition to catalysis. This Review seeks to summarize different approaches available to generate sequence-defined monodispersed synthetic copolymer libraries using nucleic acid-templated polymerization. Key concepts and principles governing nucleic acid-templated polymerization, as well as the fidelity of various copolymerization technologies, will be described. The Review will focus on methods that enable the combinatorial generation of copolymer libraries and their molecular evolution for desired function.

A High-Fidelity Codon Set for the T4 DNA Ligase-Catalyzed Polymerization of Modified Oligonucleotides

In vitro selection of nucleic acid polymers can readily deliver highly specific receptors and catalysts for a variety of applications; however, it is suspected that the functional group deficit of nucleic acids has limited their potential with respect to proteinogenic polymers. This has stimulated research toward expanding their chemical diversity to bridge the functional gap between nucleic acids and proteins to develop a superior biopolymer. In this study, we investigate the effect of codon library size and composition on the sequence specificity of T4 DNA ligase in the DNA-templated polymerization of both unmodified and modified oligonucleotides. Using high-throughput DNA sequencing of duplex pairs, we have uncovered a 256-membered codon set that yields sequence-defined modified ssDNA polymers in high yield and with high fidelity.

In Vitro Selection of Diversely Functionalized Aptamers

We describe the application of T4 DNA ligase-catalyzed DNA templated oligonucleotide polymerization toward the evolution of a diversely functionalized nucleic acid aptamer for human α-thrombin. Using a 256-membered ANNNN comonomer library comprising 16 sublibraries modified with different functional groups, a highly functionalized aptamer for thrombin was raised with a dissociation constant of 1.6 nM. The aptamer was found to be selective for thrombin and required the modifications for binding affinity. This study demonstrates the most differentially functionalized nucleic acid aptamer discovered by in vitro selection and should enable the future exploration of functional group dependence during the evolution of nucleic acid polymer activity.