Vishal Rai

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.

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.

Bending Rigid Molecular Rods: Formation of Oligoproline Macrocycles

Bent but not broken: cyclic oligoprolines are accessed in a reaction that effectively bends rigid oligoproline peptides (see scheme; TBDMS=tert-butyldimethylsilyl). The stitching is accomplished during macrocyclization enabled by aziridine aldehydes and isocyanides. Molecular modeling studies suggest that electrostatic attraction between the termini of the linear peptide is pivotal for macrocyclization. The macrocycles were studied by circular dichroism with a polyproline II structure being observed in larger macrocycles.

Site-Selective Labeling of Native Proteins by a Multicomponent Approach

Chemical functionalization of proteins is an indispensable tool. Yet, selective labeling of native proteins has been an arduous task. The limited success of chemical methods allows N-terminus protein labeling, but the examples with side-chain residues are rare. Herein, we surpass this challenge through a multicomponent transformation that operates under physiological conditions in the presence of a protein, aldehyde, acetylene, and Cu-ligand complex. The methodology results in the labeling of a single lysine residue in nine distinct proteins.

Protein self-assembly induces promiscuous nucleophilic biocatalysis in Morita–Baylis–Hillman (MBH) reaction

Self-assembled states of proteins render efficient promiscuous nucleophilic biocatalysis in MBH reaction in a green process. The His and Arg based catalophores in proteins operate in aqueous buffer at neutral pH and ambient temperature. Steady-state fluorimetric approaches reveal that lower order aggregates play a seminal role in the biocatalytic process.