Α-helix Mimetics Research Articles

Microwave assisted solid phase synthesis of highly functionalized N-alkylated oligobenzamide α-helix mimetics

Protein–protein interactions (PPIs) mediate cellular pathways and are implicated in numerous aberrant conditions. α-Helix mimetics—small molecules that reproduce the spatial projection of key residues from an α-helix involved in a PPI—are attractive generic templates for development of screening libraries, however library syntheses of α-helix mimetics with diverse functionality are less established. This manuscript describes the automated, microwave assisted solid phase synthesis based on one such scaffold; an N-alkylated oligobenzamide.

Modeling of arylamide helix mimetics in the p53 peptide binding site of hDM2 suggests parallel and anti-parallel conformations are both stable.

The design of novel α-helix mimetic inhibitors of protein-protein interactions is of interest to pharmaceuticals and chemical genetics researchers as these inhibitors provide a chemical scaffold presenting side chains in the same geometry as an α-helix. This conformational arrangement allows the design of high affinity inhibitors mimicking known peptide sequences binding specific protein substrates. We show that GAFF and AutoDock potentials do not properly capture the conformational preferences of α-helix mimetics based on arylamide oligomers and identify alternate parameters matching solution NMR data and suitable for molecular dynamics simulation of arylamide compounds. Results from both docking and molecular dynamics simulations are consistent with the arylamides binding in the p53 peptide binding pocket. Simulations of arylamides in the p53 binding pocket of hDM2 are consistent with binding, exhibiting similar structural dynamics in the pocket as simulations of known hDM2 binders Nutlin-2 and a benzodiazepinedione compound. Arylamide conformations converge towards the same region of the binding pocket on the 20 ns time scale, and most, though not all dihedrals in the binding pocket are well sampled on this timescale. We show that there are two putative classes of binding modes for arylamide compounds supported equally by the modeling evidence. In the first, the arylamide compound lies parallel to the observed p53 helix. In the second class, not previously identified or proposed, the arylamide compound lies anti-parallel to the p53 helix.

Comprehensive Peptidomimetic Libraries Targeting Protein–Protein Interactions

Transient protein-protein interactions (PPIs) are essential components in cellular signaling pathways as well as in important processes such as viral infection, replication, and immune suppression. The unknown or uncharacterized PPIs involved in such interaction networks often represent compelling therapeutic targets for drug discovery. To date, however, the main strategies for discovery of small molecule modulators of PPIs are typically limited to structurally characterized targets. Recent developments in molecular scaffolds that mimic the side chain display of peptide secondary structures have yielded effective designs, but few screening libraries of such mimetics are available to interrogate PPI targets. We initiated a program to prepare a comprehensive small molecule library designed to mimic the three major recognition motifs that mediate PPIs (α-helix, β-turn, and β-strand). Three libraries would be built around templates designed to mimic each such secondary structure and substituted with all triplet combinations of groups representing the 20 natural amino acid side chains. When combined, the three libraries would contain a member capable of mimicking the key interaction and recognition residues of most targetable PPIs. In this Account, we summarize the results of the design, synthesis, and validation of an 8000 member α-helix mimetic library and a 4200 member β-turn mimetic library. We expect that the screening of these libraries will not only provide lead structures against α-helix- or β-turn-mediated protein-protein or peptide-receptor interactions, even if the nature of the interaction is unknown, but also yield key insights into the recognition motif (α-helix or β-turn) and identify the key residues mediating the interaction. Consistent with this expectation, the screening of the libraries against p53/MDM2 and HIV-1 gp41 (α-helix mimetic library) or the opioid receptors (β-turn mimetic library) led to the discovery of library members expected to mimic the known endogenous ligands. These efforts led to the discovery of high-affinity α-helix mimetics (K(i) = 0.7 μM) against HIV-1 gp41 as well as high-affinity and selective β-turn mimetics (K(i) = 80 nM) against the κ-opioid receptor. The results suggest that the use of such comprehensive libraries of peptide secondary structure mimetics, built around effective molecular scaffolds, constitutes a powerful method of interrogating PPIs. These structures provide small molecule modulators of PPI networks for therapeutic target validation, lead compound discovery, and the identification of modulators of biological processes for further study.

Therapeutic development in targeting protein–protein interactions with synthetic topological mimetics

Protein-protein interactions lie at the heart of cellular signaling pathways and the deregulation of which has frequently led to diseases. In contrast to inhibitors that bind to distinctive enzyme active sites, molecules targeting protein surface topologies have been underexploited in drug development. The challenges in developing protein surface antagonists or agonists originate from the relatively large and flat surface areas that lack well-defined cavities required for sufficient binding affinity. In the past decade, our understanding of protein recognition has served as solid basis for the design of synthetic mimetics to modulate these protein-protein interactions. Herein, we summarize recent successes in the development of synthetic α-helix mimetics, proteomimetics, and biologics with the therapeutic potentials of inhibiting tumorgenesis or cancer-related viral infections.

Amphiphilic α-helix mimetics based on a benzoylurea scaffold

The design and synthesis of amphiphilic benzoylurea α-helix mimetics is described. These conformationally constrained molecules allow for the correct angular and spatial projection of hydrophobic and hydrophilic groups and thus the reproduction of side-chains on both faces of an α-helix.

Relaxation of the rigid backbone of an oligoamide-foldamer-based α-helix mimetic: identification of potent Bcl-xL inhibitors

By conducting a structure-activity relationship study of the backbone of a series of oligoamide-foldamer-based α-helix mimetics of the Bak BH3 helix, we have identified especially potent inhibitors of Bcl-x(L). The most potent compound has a K(i) value of 94 nM in vitro, and single-digit micromolar IC(50) values against the proliferation of several Bcl-x(L)-overexpressing cancer cell lines.

Absolute Binding Free Energy Calculations to Improve the Accuracy of Near-Native Ligand Pose Predictions

When the high-resolution structure of a protein target is available, molecular docking experiments are commonly used for computer-aided drug discovery. Molecular docking experiments are advantageous since they can provide the binding mode of a molecule in a given target protein as well as the binding affinity. However, despite considerable efforts, accurate prediction of ligand poses bound to a target is still challenging due to the protein's structural flexibility. Recent free energy perturbation molecular dynamics simulation (FEP/MD) calculations have shown that the calculated binding free energies are in good agreement with experimental data for co-crystal benchmark targets. Here, we present an integrated methodology in which initial candidate selection from pose decoys obtained by docking is followed by FEP/MD calculations to improve the accuracy of near-native ligand pose prediction. Our approach is evaluated for the small molecule α-helix mimetics inhibiting protein-protein interactions such as p53-MDMX/MDM2 and BAK-MCL-1. The results demonstrate that using the centroid models of the most populated clusters of docking decoys is an efficient approach to select a small set of ligand conformations in which a near-native pose may be included and applying the FEP/MD method enhances ability in discriminating the near-native ligand conformation from the candidates.

Double-sided α-helix mimetics

The design and synthesis of substituted bis- and tris-benzamides is reported in which the projection of side-chain residues on both sides of an α-helix is reproduced. The scaffold is conformationally constrained by a series of intramolecular hydrogen bonds, allowing for spatial and angular mimicry of the i, i+2, i+4 and i+6 side-chains in the case of the bis-benzamide, and may be extended to higher-order oligomers.

Oligophenylenaminones as Scaffolds for α-Helix Mimicry

The design and synthesis of small molecule α-helix mimetics has been a productive field over the past decade. These compounds have performed well in a variety of biological systems as functional disruptors of α-helix-mediated protein-protein interactions. In our studies we have continued to develop novel, more biologically compatible scaffolds, which are often easier to assemble and capable of mimicking longer and/or more diverse helices. To this end, we have constructed a new series of i, i+4, i+7 α-helix mimics based on the enaminone scaffold. These molecules represent a step forward in the pursuit of idealized monofacial α-helix mimetics.

ChemInform Abstract: Synthesis of New Phenylpyridyl Scaffolds Using the Garlanding Approach.

One-pot reaction for the synthesis of novel phenylpyridyl derivatives and mixed quater phenylpyridyl compounds is described by using the Garlanding approach. The reactions proceed with moderate to good yields in mild conditions and good reaction times. This work represents a second application of the simplicity and versatility of Garlanding concept for the construction of new phenylpyridyl scaffolds, which can be considered as non-peptidic foldamer α-helix mimetics.

Novel Pyrrolopyrimidine-Based α-Helix Mimetics: Cell-Permeable Inhibitors of Protein−Protein Interactions

There is considerable interest in developing non-peptidic, small-molecule α-helix mimetics to disrupt α-helix-mediated protein−protein interactions. Herein, we report the design of a novel pyrrolopyrimidine-based scaffold for such α-helix mimetics with increased conformational rigidity. We also developed a facile solid-phase synthetic route that is amenable to divergent synthesis of a large library. Using a fluorescence polarization-based assay, we identified cell-permeable, dual MDMX/MDM2 inhibitors, demonstrating that the designed molecules can act as α-helix mimetics.

Solid-Phase Synthesis of Tris-Benzamides as α-Helix Mimetics

Small molecules mimicking α-helices are of great interest since numerous protein-protein interactions use helical structures at the interface. With a goal of generating libraries of α-helix mimetics, an efficient solid-phase synthetic method was developed to produce tris-benzamides. The tris-benzamide scaffold was designed to place three side-chain functional groups found at the i, i + 4, and i + 7 positions of an α-helix, emulating one helical face. The synthetic strategy involves simple and iterative reactions of removal of an allyl ester, formation of an amide bond via an O → N acyl migration, and an O-alkylation. A small library of twenty tris-benzamides containing a variety of functional groups was prepared in high purity (83-99%) to demonstrate the versatility of the synthetic approach. This methodology allowed the facile and rapid construction of α-helix mimetics that would facilitate the identification of small molecules for target proteins.

Synthesis of new phenylpyridyl scaffolds using the Garlanding approach

One-pot reaction for the synthesis of novel phenylpyridyl derivatives and mixed quater phenylpyridyl compounds is described by using the Garlanding approach. The reactions proceed with moderate to good yields in mild conditions and good reaction times. This work represents a second application of the simplicity and versatility of Garlanding concept for the construction of new phenylpyridyl scaffolds, which can be considered as non-peptidic foldamer α-helix mimetics.

Disrupting protein–protein interactions with non-peptidic, small molecule α-helix mimetics

Many biological processes are regulated by protein-protein interactions (PPIs) and as such their misregulation can cause a multitude of diseases. Often the interactions between large proteins are mediated by small protein secondary structural domains, which project a minimum number of specifically arranged residues into the complementary surface of an interacting protein. Nature has the advantage of time, and over time has optimized those secondary structures, such as alpha-helices, beta-sheets and beta-strands, found at the interfaces of PPIs. Inspired by Nature's extensive optimization, chemists have used these secondary structures as templates in the design of small molecules that may act as structural and functional mimics of large rhenylogically organized protein secondary structures. Herein recent applications of the indane, terphenyl, terphenyl-inspired templates, polycyclic ether and benzodiazepinedione scaffolds, as non-peptidic, small molecule alpha-helix mimetics, to disrupt PPIs are detailed.

Oligooxopiperazines as Nonpeptidic α-Helix Mimetics

A new class of nonpeptidic alpha-helix mimetics derived from alpha-amino acids and featuring chiral backbones is described. NMR and circular dichroism spectroscopies, in combination with molecular modeling studies, provide compelling evidence that oligooxopiperazine dimers adopt stable conformations that reproduce the arrangement of i, i+4, and i+7 residues on an alpha-helix.

A Single α‐Helical Turn Stabilized by Replacement of an Internal Hydrogen Bond with a Covalent Ethylene Bridge

Walking the carbon bridge to helix stabilization: α-Helix mimetics have been synthesized that contain an ethylene linkage in place of an (i,i+4) hydrogen bond (see structure). The smallest unit possible, a modified pentapeptide, shows the characteristic features of a helix (see CD spectrum). Incorporation of this carbon bridge into a peptide represents the first example of replacement of an internal backbone hydrogen bond.

Controlling Curvature in a Family of Oligoamide α‐Helix Mimetics

Controlling Curvature in a Family of Oligoamide α‐Helix Mimetics

Controlling Curvature in a Family of Oligoamide α‐Helix Mimetics

Controlling Curvature in a Family of Oligoamide α‐Helix Mimetics

α-Helix mimetics as inhibitors of protein–protein interactions

The inhibition of protein-protein interactions using small molecules is a viable approach for the treatment of a range of pathological conditions that result from a malfunctioning of these interactions. Our strategy for the design of such agents involves the mimicry of side-chain residues on one face of the alpha-helix; these residues frequently play a key role in mediating protein-protein interactions. The first-generation terphenyl scaffold, with a 3,2',2''-substitution pattern, is able to successfully mimic key helix residues and disrupt therapeutically relevant interactions, including the Bcl-X(L)-Bak and the p53-hDM2 (human double minute 2) interactions that are implicated in cancer. The second- and third-generation scaffolds have resulted in greater synthetic accessibility and more drug-like character in these molecules.

Synthesis of α-helix mimetics with four side-chains

The synthesis of a heterocyclic piperazine-based scaffold that mimics the i, i + 4, i + 8, i + 11 side-chain projections of an α-helix is described. The synthesis is designed to be modular to allow the targeting of a range of protein–protein interactions involving α-helices.