A Rationally Designed Aldolase Foldamer

Abstract

Current strategies for creating enzyme-like catalysts range from rational[1] and computational design [2] to evolutionary searches of large molecular libraries.[3] Sequence-specific polymers are particularly attractive starting points for these efforts because of their ability to adopt threedimensional structures that preorganize functional groups for catalysis. Although natural enzymes are constructed from α-amino acids, many other backbone structures can give rise to well-defined secondary and tertiary structures. Such non-natural oligomers, often referred to as "foldamers", have the potential to display properties akin to those of proteins. [4][5][6][7][8] β-Peptides are interesting in this context because they adopt a variety of stable secondary structures, including helices, sheets and turns, [4,9] and quarternary helix-bundle assemblies have been generated. [10,11] Their predictable structures have been exploited to inhibit microbial growth, [12] disrupt protein-protein interactions, [13] and for other applications. [4,5] Here we show that β-peptides presenting arrays of discrete side chain functional groups can also act as effective catalysts.As a model reaction, we examined the retro-aldol cleavage of β-hydroxyketone 1 to give benzaldehyde and pyruvate. This reaction is subject to amine catalysis (Figure 1). The catalytic cycle is initiated by nucleophilic attack of an unprotonated amine on the carbonyl group of the substrate. The resulting iminium ion activates the substrate for C-C bond scission, which occurs with concomitant deprotonation of the hydroxyl group to release benzaldehyde. Tautomerization of the enamine and subsequent hydrolysis produces pyruvate and regenerates the catalyst. This mechanism is exploited by natural type I aldolases, [14] and has been mimicked by lysine-rich amphiphilic α-helical peptides, [15] This strategy, which has been successfully utilized in the design of helical α-peptide catalysts, [15,17,19] can be extended to the construction of helical β-peptide catalysts.One of the best-understood β-peptide secondary structures is the 14-helix, characterized by 14-membered hydrogen bonds between N-H of residue i and C=O of i+2. [4,9] This helix is favored by β 3 -amino acid residues, which bear a side chain on the backbone carbon adjacent to nitrogen. To stabilize such structures in aqueous solution, electrostatic interactions between the side chains [20] or conformationally restricted building blocks[21] can be employed. For example, the cyclically constrained trans-2-aminocyclohexanecarboxylic acid (ACHC), which has a very high helical propensity, has been used to construct short β-peptides that reliably adopt the 14-helical conformation in water, regardless of temperature, pH, or concentration. [21,22] A β-peptide sequence containing multiple ACHC residues along with β 3 -homolysine (β 3 -hLys) residues in an i, i+3, i+6 array should lead to alignment of the amine-containing side chains along one side of a 14-helix ( Figure 2). We anticipated that this clustering of β 3 -h...

Enhancing β3‐Peptide Bundle Stability by Design

“…[3] There is considerable interest currently in the design of higher-order, nonproteinaceous assemblies possessing defined oligomeric states, [13] as materials with these properties have potential as nanomaterials [14] and catalysts. [15] Here we show that the stability of a b-peptide bundle can be tuned by controlling the length of a solvent-exposed surface salt-bridge interaction. Combined with previous work on the roles of internal packing residues, [1a, b, d, f] these results provide another critical step in the "bottom-up" assembly of b-peptide assemblies with defined sizes, reproducible structures, and sophisticated function.…”

Origins of catalysis by computationally designed retroaldolase enzymes

“…Analogous to the strategy used by type I aldolases (10), formation of the iminium intermediate with the enzymatic lysine side chain provides an electron sink, facilitating the retroaldol cleavage. Several catalytic antibodies and peptide systems have been developed that utilize this lysine iminium strategy (11)(12)(13)(14)(15)(16).…”

Folded biomimetic oligomers for enantioselective catalysis

“…Further advancement of foldamers will benefit from design strategies that enable sophisticated functions such as catalysis (39). In this respect, peptoids represent an outstanding opportunity, inasmuch as: (i) peptoids self-organize with chain lengths as short as five residues, simplifying synthesis; (ii) peptoid folding does not rely on hydrogen bonding, enabling use in solvents that otherwise would interfere with hydrogen bonds; (iii) peptoids are chemically inert toward Kinetic resolution of 1-phenylethanol catalyzed by peptoid oligomers.…”