Andrei K. Yudin

Contemporary strategies for peptide macrocyclization

Peptide macrocycles have found applications that range from drug discovery to nanomaterials. These ring-shaped molecules have shown remarkable capacity for functional fine-tuning. Such capacity is enabled by the possibility of adjusting the peptide conformation using the techniques of chemical synthesis. Cyclic peptides have been difficult, and often impossible, to prepare using traditional synthetic methods. For macrocyclization to occur, the activated peptide must adopt an entropically disfavoured pre-cyclization conformation before forming the desired product. Here, we review recent solutions to some of the major challenges in this important area of contemporary synthesis.

Small heterocycles in multicomponent reactions.

Benjamin H. Rotstein,†,‡ Serge Zaretsky,† Vishal Rai,†,§ and Andrei K. Yudin*,† †Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario Canada, M5S 3H6 ‡Division of Nuclear Medicine and Molecular Imaging, Massachusetts General Hospital, and Department of Radiology, Harvard Medical School, 55 Fruit Street, Boston, Massachusetts 02114, United States Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal, Indore By-pass Road, Bhauri, Bhopal 462 066, MP India

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.

Amphoteric α-Boryl Aldehydes

A new class of stable molecules, α-boryl aldehydes, has been prepared from oxiranyl N-methyliminodiacetyl boronates by a 1,2-boryl migration with concomitant epoxide scission. A range of boryl imines, alkenes, alcohols, acids, enol ethers, enamides, and other functionalized boronic acid derivatives that are difficult or impossible to prepare using established protocols can be accessed from α-boryl aldehydes. The chemoselective transformations of these building blocks, including the facile synthesis of functionalized unnatural amino acids from silyloxy and amido vinyl boronates, attest to the potential of α-boryl aldehydes in chemical synthesis.

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.

Boroalkyl Group Migration Provides a Versatile Entry into α-Aminoboronic Acid Derivatives

A reaction exemplifying migration of boron-substituted carbon is described. We show that α-boroalkyl groups of transient boroalkyl acyl azide intermediates readily migrate from carbon to nitrogen. This process allows access to a new class of stable molecules, α-boryl isocyanates, from α-borylcarboxylic acid precursors. The methodology facilitates synthesis of a wide range of α-aminoboronic acid derivatives, including α,α-disubstituted analogues.

A simple and efficient method for the preparation of pyridine-N-oxides II

Abstract Oxidation of pyridines with bis(trimethylsilyl)peroxide in the presence of catalytic amounts of inorganic rhenium derivatives gives high yields of their analytically pure N-oxides by simple work-ups, typically a filtration or a Kugelrohr distillation.

Unprotected vinyl aziridines: facile synthesis and cascade transformations.

Functionalized vinylaziridines, readily available from water-stable aziridine aldehydes have led to the construction of a variety of stereochemically rich heterobicycles. A cascade ring-opening/ring-contraction mechanism operates in the course of the process. These results underscore the notion that interesting and useful nitrogen-mediated relay processes can arise when elements of strain are merged with the manifolds of enamine/iminium ion reactivity.

Chemoselective peptidomimetic ligation using thioacid peptides and aziridine templates.

Chemoselective peptidomimetic ligation has been made possible using thioacid peptides and NH aziridine-terminated amino acids and peptides. In the course of this reaction, a reduced amide bond is incorporated into the backbone of a peptide. This process enables incorporation of reduced cysteine, reduced substituted cysteine, reduced phenylalanine, and reduced alanine. Our method should be adaptable to other unnatural amino acid residues at the ligation site. Experiments aimed at evaluating the chemoselectivity of this process in the presence of competing thiol nucleophiles suggest high specificity at micromolar concentrations. This holds even in the presence of glutathione, which neutralizes xenobiotic electrophiles in cells.

Air- and Moisture-Stable Amphoteric Molecules: Enabling Reagents in Synthesis

Researchers continue to develop chemoselective synthesis strategies with the goal of rapidly assembling complex molecules. As one appealing approach, chemists are searching for new building blocks that include multiple functional groups with orthogonal chemical reactivity. Amphoteric molecules that possess nucleophilic and electrophilic sites offer a versatile platform for the development of chemoselective transformations. As part of a program focused on new methods of synthesis, we have been developing this type of reagents. This Account highlights examples of amphoteric molecules developed by our lab since 2006. We have prepared and evaluated aziridine aldehydes, a class of stable unprotected α-amino aldehydes. Structurally, aziridine aldehydes include both a nucleophilic amine nitrogen and an electrophilic aldehyde carbon over the span of three atoms. Under ambient conditions, these compounds exist as homochiral dimers with an aziridine-fused five-membered cyclic hemiaminal structure. We have investigated chemoselective reactions of aziridine aldehydes that involve both the aziridine and aldehyde functionalities. These transformations have produced a variety of densely functionalized nitrogen-containing compounds, including amino aldehydes, 1,2-diamines, reduced hydantoins, C-vinyl or alkynyl aziridines, and macrocyclic peptides. We have also developed air- and moisture-stable α-boryl aldehydes, another class of molecules that are kinetically amphoteric. The α-boryl aldehydes contain a tetracoordinated N-methyliminodiacetyl (MIDA) boryl substituent, which stabilizes the α-metalloid carbonyl system and prevents isomerization to its O-bond enolate form. Primarily taking advantage of chemoselective transformations at the aldehyde functionality, these α-boryl aldehydes have allowed us to synthesize a series of new functionalized boron-containing compounds that are difficult or impossible to prepare using established protocols, such as α-borylcarboxylic acids, boryl alcohols, enol ethers, and enamides. Using α-borylcarboxylic acids as starting materials, we have also prepared several new amphoteric borylated reagents, such as α-boryl isocyanates, isocyanides, and acylboronates. These compounds are versatile building blocks in their own right, enabling the rapid synthesis of other boron-containing molecules.