The Promise of Peptoids

Peptoids are not only more stable and easier to synthesize than peptides, their chemical diversity is large. As such, they have attracted significant attention as peptide and protein mimics and are being explored for a vast array of biomedical applications. Kent Kirshenbaum, associate professor in the Department of Chemistry at New York University (NYU), and his graduate student Timothy Craven spoke with Cynthia Challener, editor of the Pharmaceutical Sciences, Manufacturing & Marketplace Report, about the advantages of peptoids, their potential as therapeutic agents, and recent developments in the field.

Important side-chain connectionPharmaceutical Sciences, Manufacturing and Marketplace Report: What are peptoids and how are they different from peptides/peptidomimetics and other related biologic compounds?

Kirshenbaum and Craven (NYU)

: Peptoids are oligomers composed of N-substituted glycine monomer units that are sequence-specific heteropolymers, as are many biopolymers, including peptides and nucleic acids. Peptoids are particularly similar to peptides and proteins, in that peptoids are polyamide oligomers with backbone spacing identical to peptides.
The major difference is the location of the side-chain variable group. In peptides, the variable group is positioned at the backbone a-carbon. In peptoids, the variable group is positioned at the amide nitrogen. This substitution leads to oligomers linked through tertiary amides, which allow the peptoids to be completely resistant to proteolytic degradation.

Peptides and protein mimicryPharmaceutical Sciences, Manufacturing and Marketplace Report: Why are peptoids of interest to the pharmaceutical industry?

Kirshenbaum and Craven (NYU)

: Many peptoid oligomer sequences have been shown to fold into structures that mimic some of the secondary structure types in proteins, such as polyproline helices. These types of helices are present in many critical signaling, structural, and regulatory events in cell biology. For example, they are the ligands for SH3 and WW domains, and they make up the structural core of collagen fibers. Peptoid oligomers up to 40 monomer units long have been synthesized, potentially allowing the mimicry of more complex protein tertiary structures.

Simple synthesisPharmaceutical Sciences, Manufacturing and Marketplace Report: How are peptoids synthesized?

Kirshenbaum and Craven (NYU): Peptoids are typically synthesized using solid-phase protocols following one of two common methods.

A “submonomer” synthesis technique couples bromoacetic acid onto the amino functional end of a nascent resin-bound oligomer, followed by bromide displacement with a primary amine. These steps are repeated iteratively to construct the desired primary sequence. In addition, a “monomer” synthesis has also been demonstrated, which entails coupling of an Fmoc protected N-substituted glycine followed by deprotection with base.

The second method is analogous to standard solid-phase peptide synthesis; however, it is limited by the types of Fmoc protected N-substituted monomers that are commercially available.
Thus, “submonomer” synthesis with its ease of incorporation of side-chain functionalities, as well as the lack of the need for complex protecting group strategies, makes this method very popular and powerful. More than 200 different peptoid monomers bearing distinct side chains have been reported in the literature.

Many advantagesPharmaceutical Sciences, Manufacturing and Marketplace Report: What are the advantages of peptoids compared to conventional peptides and other large-molecule analogs (in terms of their synthesis and applications?

Kirshenbaum and Craven (NYU): The main advantage of peptoids is that diverse side chain groups can be readily incorporated into the peptoid backbone without the need for complex protection strategies. Additionally, for applications such as multivalent ligand display, peptoids offer a facile platform for controlling the sequence and fine-tuning the spacing of displayed chemical functionalities. The chemical structure of the oligomeric tertiary amides in the peptoid backbone engenders proteolytic stability to the oligomer. Thus, the peptoid structure has several advantages over peptide-based structures, including sequence diversity, facile synthesis, and proteolytic stability.

Real therapeutic potentialPharmaceutical Sciences, Manufacturing and Marketplace Report: How are peptoids used in biologic formulations?

Kirshenbaum and Craven (NYU)

: Peptoids are useful in a variety of biological applications, including as the API in drug formulations, as diagnostic tools, as sources of combinatorial libraries for discovery of hit compounds, for drug-delivery applications, and as transfection agents for nucleic acid-based therapeutics. In fact, there are multiple ways in which they may find clinical relevance.

• The folded oligomers themselves may function like peptides as ligands for biomolecular disease targets, such as large surface areas on proteins, to allow modulation of protein-protein interactions and other currently “undruggable” targets. 

• Peptoids are also highly effective scaffolds for creating multivalent displays of ligands for enhanced binding interactions to proteins and nucleic acids.

• Peptoids are proving useful as drug-delivery agents. For example, cationic peptoids have been shown to complex with nucleic acids, such as RNA oligonucleotides. This complexation can protect the RNA from degradation and permit efficient intracellular uptake, potentially enabling the development of RNA-interference therapies.

• Specific positions in bioactive peptides can be replaced with peptoid units. These peptoid-peptide hybrid architectures may provide access to new binding modes or display enhanced pharmacological attributes.

Exciting developmentsPharmaceutical Sciences, Manufacturing and Marketplace Report: What are the most recent advances in peptoid technology and what impact will they have?

Kirshenbaum and Craven (NYU)

: There are numerous recent advances in peptoid technology. We believe that some of the most exciting developments include the following:

• Demonstration of potent, broad-ranging, and selective antimicrobial activity by peptoids.

• Extraordinary work by the group of Thomas Kodadek involving the screening of huge libraries of peptoids on-resin in order to identify peptoid sequences that function as protein capture agents.

• Identification of peptoid-based multivalent displays for modulation of steroid hormone receptor activity, leading to potential new therapeutic modalities for prostate cancer.

• A broad series of advances by the Zuckermann group at the Lawrence Berkeley Laboratory to create nano-structured peptoid sheets and other peptoids for materials applications.

• The demonstration of rudimentary mimics of protein tertiary structures formed by cross-linked peptoid macrocycles.

• Development of improved computational tools for predicting peptoid structures, enabling the in silico identification of peptoid ligands for protein targets.

These developments will turbo-charge the discovery of peptoids for use as APIs and speed the identification of peptoids for use in diverse biomedical applications.