Hydrogen Bond Surrogate Research Articles

Macrocyclic β‐Sheets Stabilized by Hydrogen Bond Surrogates

AbstractMimics of protein secondary and tertiary structure offer rationally‐designed inhibitors of biomolecular interactions. β‐Sheet mimics have a storied history in bioorganic chemistry and are typically designed with synthetic or natural turn segments. We hypothesized that replacement of terminal inter‐β‐strand hydrogen bonds with hydrogen bond surrogates (HBS) may lead to conformationally‐defined macrocyclic β‐sheets without the requirement for natural or synthetic β‐turns, thereby providing a minimal mimic of a protein β‐sheet. To access turn‐less antiparallel β‐sheet mimics, we developed a facile solid phase synthesis protocol. We surveyed a dataset of protein β‐sheets for naturally observed interstrand side chain interactions. This bioinformatics survey highlighted an over‐abundance of aromatic–aromatic, cation‐π and ionic interactions in β‐sheets. In correspondence with natural β‐sheets, we find that minimal HBS mimics show robust β‐sheet formation when specific amino acid residue pairings are incorporated. In isolated β‐sheets, aromatic interactions endow superior conformational stability over ionic or cation‐π interactions. Circular dichroism and NMR spectroscopies, along with high‐resolution X‐ray crystallography, support our design principles.

Macrocyclic β-Sheets Stabilized by Hydrogen Bond Surrogates.

Mimics of protein secondary and tertiary structure offer rationally-designed inhibitors of biomolecular interactions. β-Sheet mimics have a storied history in bioorganic chemistry and are typically designed with synthetic or natural turn segments. We hypothesized that replacement of terminal inter-β-strand hydrogen bonds with hydrogen bond surrogates (HBS) may lead to conformationally-defined macrocyclic β-sheets without the requirement for natural or synthetic β-turns, thereby providing a minimal mimic of a protein β-sheet. To access turn-less antiparallel β-sheet mimics, we developed a facile solid phase synthesis protocol. We surveyed a dataset of protein β-sheets for naturally observed interstrand side chain interactions. This bioinformatics survey highlighted an over-abundance of aromatic-aromatic, cation-π and ionic interactions in β-sheets. In correspondence with natural β-sheets, we find that minimal HBS mimics show robust β-sheet formation when specific amino acid residue pairings are incorporated. In isolated β-sheets, aromatic interactions endow superior conformational stability over ionic or cation-π interactions. Circular dichroism and NMR spectroscopies, along with high-resolution X-ray crystallography, support our design principles.

Impact of Hydrogen‐Bond Surrogate Model on Helix Stabilization and Development of Protein‐Protein Interaction Inhibitors

AbstractProtein‐protein interactions (PPIs) involved in several diseases are predominantly mediated through short helical peptides. Unlike small molecules, due to the extended surface, the chemically constrained peptides with proper helical conformation can modulate the PPIs and thus contribute to the future drug developments. Several model systems have been introduced in the past to induce the helical structure in short peptides. Incorporating the unnatural constraints by various protocols has been excellent in biasing helical conformation and improving the proteolytic stability and the cell permeability of peptides. Hydrogen‐bond surrogate (HBS) is one of such well‐known protocols to mimic helical surfaces in numerous peptide sequences. Unlike ‘Stapled’ peptides, HBS‐model replaces the main‐chain i+4→i hydrogen bonding interaction with a covalent surrogate and retains the side‐chain functionality intact, which is beneficial for targeting multi‐faced PPIs. This review focuses on the chemistry behind the development of the HBS‐stabilized peptides, its biophysical characterizations, and numerous biological applications. Furthermore, this review will provide a broad overview of the HBS‐model to attract chemical biologists to target multifaced ‘difficult’ PPIs.

A Rational Design of α-Helix-Shaped Peptides Employing the Hydrogen-Bond Surrogate Approach: A Modulation Strategy for Ras-RasGRF1 Interaction in Neuropsychiatric Disorders.

In the last two decades, abnormal Ras (rat sarcoma protein)–ERK (extracellular signal-regulated kinase) signalling in the brain has been involved in a variety of neuropsychiatric disorders, including drug addiction, certain forms of intellectual disability, and autism spectrum disorder. Modulation of membrane-receptor-mediated Ras activation has been proposed as a potential target mechanism to attenuate ERK signalling in the brain. Previously, we showed that a cell penetrating peptide, RB3, was able to inhibit downstream signalling by preventing RasGRF1 (Ras guanine nucleotide-releasing factor 1), a neuronal specific GDP/GTP exchange factor, to bind Ras proteins, both in brain slices and in vivo, with an IC50 value in the micromolar range. The aim of this work was to mutate and improve this peptide through computer-aided techniques to increase its inhibitory activity against RasGRF1. The designed peptides were built based on the RB3 peptide structure corresponding to the α-helix of RasGRF1 responsible for Ras binding. For this purpose, the hydrogen-bond surrogate (HBS) approach was exploited to maintain the helical conformation of the designed peptides. Finally, residue scanning, MD simulations, and MM-GBSA calculations were used to identify 18 most promising α-helix-shaped peptides that will be assayed to check their potential activity against Ras-RasGRF1 and prevent downstream molecular events implicated in brain disorders.

Trimodular Solution‐Phase Protocol for Rapid Large‐Scale Synthesis of Hydrogen Bond Surrogate‐Constrained α‐Helicomimics

AbstractScalability, optimal reagent usage, high yields, easy isolation, and cost‐effectiveness, are key for the applicability of synthetic methodologies in the production of potential therapeutics. Hydrogen bond surrogate (HBS) constrained α‐helical peptides (α‐helicomimics) have shown promise as therapeutics based on their efficiency to interfere with protein‐biomolecular interactions. The propyl HBS‐constrained α‐helicomimics have shown the highest helicities in both single turn and extended, α‐helices (STαH, EαH). Here we present a solution‐phase synthetic (SPS) method, for the rapid, large‐scale, low‐cost synthesis of libraries of STαH and EαH in high yields. The key to efficiency is our trimodular (M1, M2, M3) synthetic protocol where M1 is a library of HBS‐linked peptidomimetic synthons of both STαH and EαH; M2 and M3 are desired oligopeptide libraries. Advantages of the trimodular method over conventional unimodular methods are demonstrated through the synthesis of large‐scale libraries of M1, STαH, and EαH.

Hydrogen bond surrogate helices as minimal mimics of protein α-helices.

Examination of complexes of proteins with biomolecular ligands reveals that proteins tend to interact with partners via folded sub-domains, in which the backbone possesses secondary structure. α-Helices comprising the largest class of protein secondary structures, play fundamental roles in a multitude of highly specific protein-protein and protein-nucleic acid interactions. We have demonstrated a unique strategy for stabilization of the α-helical conformation that involves replacement of one of the main chain i and i+4 hydrogen bonds in the target α-helix with a covalent bond. We termed this synthetic strategy a hydrogen bond surrogate (HBS) approach. Two salient features of this approach are: (1) the internal placement of the crosslink allows development of helices such that none of the solvent-exposed surfaces are blocked by the constraining element, i.e., all side chains of the constrained helices remain available for molecular recognition. (2) This approach can be deployed to constrain very short peptides (<10 amino acid residues) into highly stable α-helices. This chapter presents the biophysical basis for the development of the hydrogen bond surrogate approach, as well as methods for the synthesis and conformational analysis of the artificial helices.

Macrocyclic Control in Helix Mimetics.

The α-helix is the most commonly found natural secondary structure in proteins and is intrinsic to many protein-protein interactions involved in important biological functions. Novel peptides designed to mimic helices found in nature employ a variety of methods to control their structure. These approaches are significant due to potential applications in developing new therapeutic agents and materials. Over the years, many strategies have emerged to influence, initiate, and propagate helical content in short, synthetic peptides. Early innovations used the natural macrocycle tether of disulfide bond formation, metal-mediated or lactam group addition as a means to prompt helical formation. These examples have been applied to a host of peptides as inhibitors toward relevant diseases including cancer, viral and bacterial infection. In the most recent decades, hydrocarbon bridges to "staple" peptides across side chains or hydrogen bond surrogates in the backbone of peptides have been effective in producing biologically functional, helical peptidomimetics with non-natural elements, increased protease resistance and potency in vitro and in vivo. Modern methods expand and elaborate these, with applications of functional peptides from both synthetic and recombinant origins. Overall, efforts persist using these strategies to create peptides with great biological potential and a better understanding of the control of helical structure in protein folding.

Hydrogen Bond Surrogate Stabilization of β-Hairpins.

Peptide secondary and tertiary structure motifs frequently serve as inspiration for the development of protein-protein interaction (PPI) inhibitors. While a wide variety of strategies have been used to stabilize or imitate α-helices, similar strategies for β-sheet stabilization are more limited. Synthetic scaffolds that stabilize reverse turns and cross-strand interactions have provided important insights into β-sheet stability and folding. However, these templates occupy regions of the β-sheet that might impact the β-sheet's ability to bind at a PPI interface. Here, we present the hydrogen bond surrogate (HBS) approach for stabilization of β-hairpin peptides. The HBS linkage replaces a cross-strand hydrogen bond with a covalent linkage, conferring significant conformational and proteolytic resistance. Importantly, this approach introduces the stabilizing linkage in the buried β-sheet interior, retains all side chains for further functionalization, and allows efficient solid-phase macrocyclization. We anticipate that HBS stabilization of PPI β-sheets will enhance the development of β-sheet PPI inhibitors and expand the repertoire of druggable PPIs.

Hydrogen Bond Surrogate Beta-Hairpins to Inhibit Protein-Protein Interactions

Hydrogen Bond Surrogate Beta-Hairpins to Inhibit Protein-Protein Interactions

Protein Domain Mimics as Modulators of Protein-Protein Interactions.

Protein-protein interactions (PPIs) are ubiquitous in biological systems and often misregulated in disease. As such, specific PPI modulators are desirable to unravel complex PPI pathways and expand the number of druggable targets available for therapeutic intervention. However, the large size and relative flatness of PPI interfaces make them challenging molecular targets. This Account describes our systematic approach using secondary and tertiary protein domain mimics (PDMs) to specifically modulate PPIs. Our strategy focuses on mimicry of regular secondary and tertiary structure elements from one of the PPI partners to inspire rational PDM design. We have compiled three databases (HIPPDB, SIPPDB, and DIPPDB) of secondary and tertiary structures at PPI interfaces to guide our designs and better understand the energetics of PPI secondary and tertiary structures. Our efforts have focused on three of the most common secondary and tertiary structures: α-helices, β-strands, and helix dimers (e.g., coiled coils). To mimic α-helices, we designed the hydrogen bond surrogate (HBS) as an isosteric PDM and the oligooxopiperazine helix mimetic (OHM) as a topographical PDM. The nucleus of the HBS approach is a peptide macrocycle in which the N-terminal i, i + 4 main-chain hydrogen bond is replaced with a covalent carbon-carbon bond. In mimicking a main-chain hydrogen bond, the HBS approach stabilizes the α-helical conformation while leaving all helical faces available for functionalization to tune binding affinity and specificity. The OHM approach, in contrast, envisions a tetrapeptide to mimic one face of a two-turn helix. We anticipated that placement of ethylene bridges between adjacent amides constrains the tetrapeptide backbone to mimic the i, i + 4, and i + 7 side chains on one face of an α-helix. For β-strands, we developed triazolamers, a topographical PDM where the peptide bonds are replaced by triazoles. The triazoles simultaneously stabilize the extended, zigzag conformation of β-strands and transform an otherwise ideal protease substrate into a stable molecule by replacement of the peptide bonds. We turned to a salt bridge surrogate (SBS) approach as a means for stabilizing very short helix dimers. As with the HBS approach, the SBS strategy replaces a noncovalent interaction with a covalent bond. Specifically, we used a bis-triazole linkage that mimics a salt bridge interaction to drive helix association and folding. Using this approach, we were able to stabilize helix dimers that are less than half of the length required to form a coiled coil from two independent strands. In addition to demonstrating the stabilization of desired structures, we have also shown that our designed PDMs specifically modulate target PPIs in vitro and in vivo. Examples of PPIs successfully targeted include HIF1α/p300, p53/MDM2, Bcl-xL/Bak, Ras/Sos, and HIV gp41. The PPI databases and designed PDMs created in these studies will aid development of a versatile set of molecules to probe complex PPI functions and, potentially, PPI-based therapeutics.

Dynamic Phenylalanine Clamp Interactions Define Single-Channel Polypeptide Translocation through the Anthrax Toxin Protective Antigen Channel

Anthrax toxin is an intracellularly acting toxin where sufficient detail is known about the structure of its channel, allowing for molecular investigations of translocation. The toxin is composed of three proteins, protective antigen (PA), lethal factor (LF), and edema factor (EF). The toxin's translocon, PA, translocates the large enzymes, LF and EF, across the endosomal membrane into the host cell's cytosol. Polypeptide clamps located throughout the PA channel catalyze the translocation of LF and EF. Here, we show that the central peptide clamp, the ϕ clamp, is a dynamic site that governs the overall peptide translocation pathway. Single-channel translocations of a 10-residue, guest–host peptide revealed that there were four states when peptide interacted with the channel. Two of the states had intermediate conductances of 10% and 50% of full conductance. With aromatic guest–host peptides, the 50% conducting intermediate oscillated with the fully blocked state. A Trp guest–host peptide was studied by manipulating its stereochemistry and prenucleating helix formation with a covalent linkage in the place of a hydrogen bond or hydrogen-bond surrogate (HBS). The Trp peptide synthesized with ʟ-amino acids translocated more efficiently than peptides synthesized with D- or alternating D,ʟ-amino acids. HBS stapled Trp peptide exhibited signs of steric hindrance and difficulty translocating. However, when mutant ϕ clamp (F427A) channels were tested, the HBS peptide translocated normally. Overall, peptide translocation is defined by dynamic interactions between the peptide and ϕ clamp. These dynamics require conformational flexibility, such that the peptide productively forms both extended-chain and helical states during translocation.

Using Hydrogen Bond Surrogate Technology to Stabilize Beta-Hairpins

Beta-hairpins are comprised of two β-strands connected by a short hairpin loop. The β-hairpin motif is critical in many protein folds and diverse protein-protein interactions (PPIs). Extensive studies on the forces governing β-hairpin folding and stability have led to the development of many strategies for β-hairpin stabilization, including side-chain cross-linking, rigid loop mimics, and macrocyclization. While these strategies have provided valuable insight into β-hairpin behavior, sacrifice of side chains may limit their application in the design and evaluation of β-hairpin PPI inhibitors. To overcome these challenges, we investigated the hydrogen bond surrogate (HBS) strategy as a method for β-hairpin stabilization. Previous studies have demonstrated the effectiveness of the HBS strategy in nucleation and stabilization of peptides in the α-helical conformation. Alpha-helix nucleation is accomplished by replacing the N-terminal backbone hydrogen bond with a covalent bond using ring-closing olefin metathesis on alkene substrates positioned at the i and i+4 peptide positions. Importantly, mimicry of a backbone hydrogen bond yields peptides with a full complement of side-chain functional groups. Our model system is a well-characterized β-hairpin derived from the B1 domain of protein G (GB1). The HBS macrocycle was formed on solid support by joining alkenes that mimic a hydrogen bond between the peptide's N- and C-termini. Conformational stabilities of unconstrained and HBS peptides were evaluated by circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy. Consistent with previous results, we find that the unconstrained peptides show weak propensity for the β-hairpin conformation while HBS macrocyclization significantly increases β-hairpin propensity. We envision that the HBS strategy will be generally effective in stabilizing diverse β-hairpin sequences.

An optimal hydrogen-bond surrogate for α-helices.

Substitution of a main chain i → i + 4 hydrogen bond with a covalent bond can nucleate and stabilize the α-helical conformation in peptides. Herein we describe the potential of different alkene isosteres to mimic intramolecular hydrogen bonds and stabilize α-helices in diverse peptide sequences.

Solid phase synthesis of constrained 13-membered peptide macrocycles employing Fukuyama–Mitsunobu alkylations

Efficient strategies for the solid phase synthesis of constrained macrocyclic peptides are valuable tools for the generation of potentially biologically active compound libraries. In particular, the use of covalent linkers as hydrogen bond surrogates for the initiation and stabilization of α-helical secondary structures, resulting in the formation of a 13-membered macrocycle, is a validated approach. For these purposes, a straightforward synthetic pathway was developed, employing natural amino acids bearing usual protecting groups and mediated through two Fukuyama–Mitsunobu alkylation reactions on unprotected 1,3-propanediol on solid phase. The linear precursors were obtained in good purity and moderate yields, and the final cyclization step was carried out in solution.

Peptide therapeutics: Targeting the undruggable space

Rapid advancements in genomics have brought a better understanding of molecular mechanisms for various pathologies and identified a number of highly attractive target classes. Some of these targets include intracellular protein–protein interactions (PPIs), which control many essential biological pathways. Their surfaces are part of a diverse and unexplored biological space, where traditional small molecule scaffolds are not always successful. While large biologics can effectively modulate PPIs in the extracellular region, their limitation in crossing the cellular membrane leaves intracellular protein targets outside of their reach. There is a growing need in the pharmaceutical field to push the boundaries of traditional drug design and discover innovative molecules that are able to modulate key biological pathways by inhibiting intracellular PPIs. Peptides are one of the most promising classes of molecules that could deliver such therapeutics in the near future. In this review, we describe technological advancements and emerging chemical approaches for stabilizing active peptide conformations, including stapling, hydrogen bond surrogates, beta-hairpin mimetics, grafting on stable scaffolds, and macrocyclization. These design strategies carry the promise of opening the doors for peptide therapeutics to reach the currently “undruggable” space.

Synthesis of Hydrogen‐Bond Surrogate α‐Helices as Inhibitors of Protein‐Protein Interactions

The α-helix is a prevalent secondary structure in proteins and is critical in mediating protein-protein interactions (PPIs). Peptide mimetics that adopt stable helices have become powerful tools for the modulation of PPIs in vitro and in vivo. Hydrogen-bond surrogate (HBS) α-helices utilize a covalent bond in place of an N-terminal i to i+4 hydrogen bond and have been used to target and disrupt PPIs that become dysregulated in disease states. These compounds have improved conformational stability and cellular uptake as compared to their linear peptide counterparts. The protocol presented here describes current methodology for the synthesis of HBS α-helical mimetics. The solid-phase synthesis of HBS helices involves solid-phase peptide synthesis with three key steps involving incorporation of N-allyl functionality within the backbone of the peptide, coupling of a secondary amine, and a ring-closing metathesis step.

Pharmaceutical Implications of Helix Length Control in Helix-Mediated Protein–Protein Interactions

The most abundant protein secondary structure in nature - the α-helix - is frequently found at protein interfaces, making it an important lead structure for the design of small-molecule modulators of protein-protein interactions (PPIs). Nature's ability to precisely control the length of α-helices, especially in the context of helix-mediated PPIs, is key to ensuring the optimal interaction of protein partners. By extension, precise control over the length of α-helix mimetics is necessary to ensure optimal disruption of α-helix-mediated PPIs. This article will highlight the emerging importance of helix length control in the context of helix-mediated PPIs through a discussion of the contemporary chemical approaches to identifying novel helix mimetic inhibitors, including all-hydrocarbon stapling, hydrogen bond surrogates and optimized peptides emerging from in vitro screening methods. A current update on the therapeutic status of the different approaches is provided, as well as indications as to their long-term potential.

Correction to Inhibition of Hypoxia Inducible Factor 1–Transcription Coactivator Interaction by a Hydrogen Bond Surrogate α-Helix

Correction to Inhibition of Hypoxia Inducible Factor 1–Transcription Coactivator Interaction by a Hydrogen Bond Surrogate α-Helix

Abstract 289: Hydrogen bond surrogate (HBS) helices as orthosteric regulator of hypoxia inducible transcription

Abstract Hypoxia-Inducible Factor (HIF-1) is a heterodimeric transcriptional activator which plays a critical role in tumorigenesis and therefore is an important therapeutic target. Transcriptional activation of HIF-1 is known to involve the interaction between cysteine-histidine rich region1 (CH1) of a coactivator protein p300 or Creb Binding Protein (CBP) and C-terminal activation domain (C-TAD) of its α-subunit (HIF-1α C-TAD). Based on the hydrogen bond surrogate (HBS) approach, we have rationally designed stabilized alpha helix that can disrupt the binding interface between C-TAD domain of HIF-1α and CH1 domain of p300/CBP. We have shown by fluorescence polarization that such stabilized alpha helix mimetics can directly bind to the CH1 domain of p300 and also can disrupt the HIF-1α/p300 complex. HBS helix mimetics are also shown to selectively downregulate the hypoxia inducible genes in cell culture. Thus, orthosteric inhibition of the HIF-1 transcriptional complex by rationally designed helix mimetics offers a novel approach to downregulate the expression of key hypoxia inducible genes responsible for tumor progression. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 289. doi:1538-7445.AM2012-289

Reversible α-helix formation controlled by a hydrogen bond surrogate

Strategically placed covalent linkages have been shown to stabilize helical conformations in short peptide sequences. Here we report the synthesis of a stabilized α-helix that utilizes an internal disulfide linkage. Structural analysis indicates that the dynamic nature of the disulfide bridge allows for the reversible formation of an α-helix through oxidation and reduction reactions.