Origins of Conformational Heterogeneity in Peptoid Helices Formed by Chiral N-1-Phenylethyl Sidechains

Sequence-defined peptoids via iterative exponential growth

Synthetic control over polymer sequence, composition, and stereochemistry is critical to understanding their influence on the intramolecular and intermolecular interactions of polymers. We report an iterative exponential growth (IEG) strategy for peptoids, a class of sequence-defined peptidomimetics, relying on orthogonally protected monomers. The IEG technique enables the synthesis of monodisperse peptoids with varied sequences, side chains, and stereoconfigurations on a scale that is useful for material science applications. The method allows for direct monitoring of the reaction progress without the need for cleavage from a solid-support. This IEG strategy offers higher molecular weights than other solution-phase sequence-defined synthetic strategies for peptoids and seeks to mimic the precise structural organization of sequence-defined biopolymers for a synthetic polymer system, which we anticipate will enable the rational design of functional polymer materials.

Uprising Unconventional Nanobiomaterials: Peptoid Nanosheets as a Multi-Modular Platform for Advanced Biological Studies

Peptoids are bio-inspired peptidomimetic polymers that can be designed to self-assemble into a variety of nanostructures. Among these different assemblies, peptoid nanosheets are the most studied. Peptoid nanosheets are 2D highly ordered nanostructures, able to free float in aqueous solutions while featuring versatile chemical displays that can be tuned to incorporate a plethora of functional units. In this review, the synthetic approach used to prepare sequence-defined oligomers and highlight their main characteristics is introduced. The ability of peptoids to fold into nanostructures is then reviewed with an extensive emphasis on peptoid nanosheets, and their physico-chemical characteristics, assembly mechanism, and stability. A particular focus is also placed on the variety of functionalization incorporated into the peptoid nanosheets to tune their properties toward specific applications, especially within the fields of biology and medicine. Finally, the comparison between peptoid nanosheets and other 2D nanomaterials is discussed to address the challenges in the current nanomaterials and underline the future development of peptoid nanosheets in the field of biology.

Enhancing molecular diversity of peptoid oligomers using amino acid synthons

We report the use of unprotected amino acids as submonomer reagents in the solid-phase synthesis of N-substituted glycine peptoid oligomers. Subsequent coupling of an amine, alcohol, or thiol to the free carboxylate of the incorporated amino acid provides access to peptoids bearing amides, esters, and thioesters as side chain pendant groups and permits further elongation of the peptoid backbone. The palette of readily obtained building blocks suitable for solid-phase peptoid synthesis is substantially expanded through this protocol, further enhancing the chemical diversity and potential applications of sequence-specific peptoid oligomers.

Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations

Peptoids are a class of sequence-defined biomimetic polymers with peptide-like backbones and side chains located on backbone nitrogens rather than alpha carbons. These materials demonstrate a strong ability for precise control of single-chain structure, multiunit self-assembly, and macromolecular assembly through careful tuning of sequence due to the diversity of available side chains, although the driving forces behind these assemblies are often not understood. Prior experimental work has shown that linked 15mer peptoids can mimic the protein helical hairpin structure by leveraging the chirality-inducing nature of bulky side chains and hydrophobicity, but there are still gaps in our understanding of the relationship between sequence, stability, and particular secondary or tertiary structure. We present a molecular dynamics (MD) study on the folding behavior of these polymers into hairpins, discussing the differences in structure from sequences with various characteristics in water and acetonitrile, and then compare the handedness preference of common helical motifs between solvents.

Martinoid: the peptoid martini force field

Many exciting innovations have been made in the development of assembling peptoid materials. Typically, these have utilised large oligomeric sequences, though elsewhere the study of peptide self-assembly has yielded numerous examples of assemblers below 6-8 residues in length, evidencing that minimal peptoid assemblers are not only feasible but expected. A productive means of discovering such materials is through the application of in silico screening methods, which often benefit from the use of coarse-grained molecular dynamics (CG-MD) simulations. At the current level of development, CG models for peptoids are insufficient and we have been motivated to develop a Martini forcefield compatible peptoid model. A dual bottom-up and top-down parameterisation approach has been adopted, in keeping with the Martini parameterisation methodology, targeting the reproduction of atomistic MD dynamics and trends in experimentally obtained log D7.4 partition coefficients, respectively. This work has yielded valuable insights into the practicalities of parameterising peptoid monomers. Additionally, we demonstrate that our model can reproduce the experimental observations of two very different peptoid assembly systems, namely peptoid nanosheets and minimal tripeptoid assembly. Further we can simulate the peptoid helix secondary structure relevant for antimicrobial sequences. To be of maximum usefulness to the peptoid research community, we have developed freely available code to generate all requisite simulation files for the application of this model with Gromacs MD software.

Minimal Peptoid Dynamics Inform Self-Assembly Propensity

Peptoids are structural isomers of natural peptides, with side chain attachment at the amide nitrogen, conferring this class of compounds with the ability to access both cis and trans ω torsions as well as an increased diversity of ψ/φ states with respect to peptides. Sampling within these dimensions is controlled through side chain selection, and an expansive set of viable peptoid residues exists. It has been shown recently that "minimal" di- and tripeptoids with aromatic side chains can self-assemble into highly ordered structures, with size and morphological definition varying as a function of sequence pattern (e.g., XFF and FXF, where X = a nonaromatic peptoid monomer). Aromatic groups, such as phenylalanine, are regularly used in the design of minimal peptide assemblers. In recognition of this, and to draw parallels between these compounds classes, we have developed a series of descriptors for intramolecular dynamics of aromatic side chains to discern whether these dynamics, in a preassembly condition, can be related to experimentally observed nanoscale assemblies. To do this, we have built on the atomistic peptoid force field reported by Weiser and Santiso (CGenFF-WS) through the rigorous fitting of partial charges and the collation of Charmm General Force Field (CGenFF) parameters relevant to these systems. Our study finds that the intramolecular dynamics of side chains, for a given sequence, is dependent on the specific combination of backbone ω torsions and that homogeneity of sampling across these states correlates well with the experimentally observed ability to assemble into nanomorphologies with long-range order. Sequence patterning is also shown to affect sampling, in a manner consistent for both tripeptoids and tripeptides. Additionally, sampling similarities between the nanofiber forming tripeptoid, Nf-Nke-Nf in the cc state, and the nanotube forming dipeptide FF, highlight a structural motif which may be relevant to the emergence of extended linear assemblies. To assess these properties, a variety of computational approaches have been employed.

Thermodynamic Basis for the Stabilization of Helical Peptoids by Chiral Sidechains

Peptoids are a class of highly customizable biomimetic foldamers that retain properties from both proteins and polymers. It has been shown that peptoids can adopt peptide-like secondary structures through the careful selection of sidechain chemistries, but the underlying conformational landscapes that drive these assemblies at the molecular level remain poorly understood. Given the high flexibility of the peptoid backbone, it is essential that methods applied to study peptoid secondary structure formation possess the requisite sensitivity to discriminate between structurally similar yet energetically distinct microstates. In this work, a generalizable simulation scheme is used to robustly sample the complex folding landscape of various 12mer polypeptoids, resulting in a predictive model that links sidechain chemistry with preferential assembly into one of 12 accessible backbone motifs. Using a variant of the metadynamics sampling method, four peptoid dodecamers are simulated in water: sarcosine, N-(1-phenylmethyl)glycine (Npm), (S)-N-(1-phenylethyl)glycine (Nspe), and (R)-N-(1-phenylethyl)glycine (Nrpe)─to determine the underlying entropic and energetic impacts of hydrophobic and chiral peptoid sidechains on secondary structure formation. Our results indicate that the driving forces to assemble Nrpe and Nspe sequences into polyproline type-I helices in water are found to be enthalpically driven, with small benefits from an entropic gain for isomerization and steric strain due to the presence of the chiral center. The minor entropic gains from bulky chiral sidechains in Nrpe- and Nspe-containing peptoids can be explained through increased configurational entropy in the cis state. However, overall assembly into a helix is found to be overall entropically unfavorable. These results highlight the importance of considering the many various competing interactions in the rational design of peptoid secondary structure building blocks.