Quantifying amino acid conformational preferences and side-chain-side-chain interactions in beta-hairpins

Peptide-Based Supramolecular Hydrogels as Drug Delivery Agents: Recent Advances

Supramolecular peptide hydrogels have many important applications in biomedicine, including drug delivery applications for the sustained release of therapeutic molecules. Targeted and selective drug administration is often preferential to systemic drug delivery, as it can allow reduced doses and can avoid the toxicity and side-effects caused by off-target binding. New discoveries are continually being reported in this rapidly developing field. In this review, we report the latest developments in supramolecular peptide-based hydrogels for drug delivery, focusing primarily on discoveries that have been reported in the last four years (2018-present). We address clinical points, such as peptide self-assembly and drug release, mechanical properties in drug delivery, peptide functionalization, bioadhesive properties and drug delivery enhancement strategies, drug release profiles, and different hydrogel matrices for anticancer drug loading and release.

Position-coded multivalent peptide-peptide interactions revealed by tryptophan-scanning mutagenesis

We demonstrate in this contribution the evidence that significant cooperative binding effect can be identified for the amino acid sites that are determinant to the binding characteristics in peptide-peptide interactions. The analysis of tryptophan-scanning mutagenesis of the 14-mer peptide consisting only of glycine provides a mapping of position-dependent contributions to the binding energy. The pronounced tryptophan-associated peptide-peptide interactions are originated from the indole moieties with the main chains of 14-mer glycines containing N-H and CO moieties. Specifically, with the presence of two tryptophans as determinant amino acids, cooperative binding can be observed, which are dependent on relative positions of the two tryptophans with a "volcano"-like characteristics. An optimal separation of 6-10 amino acids between two adjacent binding sites can be identified to achieve maximal binding interactions.

A general-purpose protein design framework based on mining sequence-structure relationships in known protein structures

Current state-of-the-art approaches to computational protein design (CPD) aim to capture the determinants of structure from physical principles. While this has led to many successful designs, it does have strong limitations associated with inaccuracies in physical modeling, such that a reliable general solution to CPD has yet to be found. Here, we propose a design framework-one based on identifying and applying patterns of sequence-structure compatibility found in known proteins, rather than approximating them from models of interatomic interactions. We carry out extensive computational analyses and an experimental validation for our method. Our results strongly argue that the Protein Data Bank is now sufficiently large to enable proteins to be designed by using only examples of structural motifs from unrelated proteins. Because our method is likely to have orthogonal strengths relative to existing techniques, it could represent an important step toward removing remaining barriers to robust CPD.

Bent Into Shape: Folded Peptides to Mimic Protein Structure and Modulate Protein Function

Protein secondary and tertiary structure mimics have served as model systems to probe biophysical parameters that guide protein folding and as attractive reagents to modulate protein interactions. Here we review contemporary methods to reproduce loop, helix, sheet and coiled-coil conformations in short peptides.

The relative stability of trpzip1 and its mutants determined by computation and experiment

The single-point mutations of tprzip1 are indicated at left, and their relative energetics are compared at right.

Design, characterization and evaluation of β-hairpin peptide hydrogels as a support for osteoblast cell growth and bovine lactoferrin delivery

The use of peptide hydrogels is of growing interest in bone regeneration. Self-assembling peptides form hydrogels and can be used as injectable drug delivery matrices. Injected into the defect site, they can gel in situ, and release factors that aid bone growth. We report on the design, synthesis and characterization of three β-hairpin peptide hydrogels, and on their osteoblast cytocompatibility as well as delivery of the lactoferrin glycoprotein, a bone anabolic factor. Osteoblasts cultured in hydrogels of the peptide with sequence NH₂-Leu-His-Leu-His-Leu-Lys-Leu-Lys-Val-dPro-Pro-Thr-Lys-Leu-Lys-Leu-His-Leu-His-Leu-Arg-Gly-Asp-Ser-CONH₂ (H4LMAX-RGDS) increased the osteoblast cell number and the cells appeared healthy after seven days. Furthermore, we showed that H4LMAX-RGDS was capable of releasing up to 60% of lactoferrin (pre-encapsulated in the gel) over five days while retaining the rest of the glycoprotein. Thus, H4LMAX-RGDS hydrogels are cytocompatible with primary osteoblasts and capable of delivering bio-active lactoferrin that increases osteoblast cell number.

Self-assembling peptide H4LMAX-RGDS hydrogels, designed to enhance bone regeneration, are cytocompatible and capable of delivering the bone anabolic factor lactoferrin to increase osteoblast cell number.

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.

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.

Structure and stability of clusters of β-alanine in the gas phase: importance of the nature of intermolecular interactions

We present a theoretical study of neutral clusters of β-alanine molecules in the gas phase, (β-ala)_nn ≤ 5.

Structure–mechanical property correlations of hydrogel forming β-sheet peptides

This review discusses about β-sheet peptide structure at the molecular level and the bulk mechanical properties of the corresponding hydrogels.

Nature of aryl-tyrosine interactions contribute to β-hairpin scaffold stability: NMR evidence for alternate ring geometry

The specific contribution of the acidic-aromatic β-sheet favouring amino acid tyrosine to the stability of short octapeptide β-hairpin structures is presented here. Solution NMR analysis in near-apolar environments suggests the energetically favourable mode of interaction to be T-shaped face-to-edge (FtE) and that a Trp-Tyr interacting pair is the most stabilizing. Alternate aryl geometries also exist in solution, which readily equilibrate between a preferred π···π conformation to an aromatic-amide conformation, without any change in the backbone structure. While the phenolic ring is readily accommodated at the "edge" of FtE aryl interactions, it exhibits an overall lowered contribution to scaffold stability in the "face" orientation. Such differential tyrosine interactions are key to its dual nature in proteins.

Synthetic turn mimetics and hairpin nucleators: Quo Vadimus?

Structural mimicry of peptides has witnessed perceptible progress in the last three decades. Reverse turn and β-hairpin units are the smallest secondary structural motifs that are some of the most scrutinized functional cores of peptides and proteins. The practice of mimicking, without altering the function of the bioactive core, ranges from conformational locking of the basic skeleton to total replacement of structural architecture using synthetic analogues. Development of heterogeneous backbones--using unnatural residues in place of natural ones--has broadened further opportunities for efficient structural rigidification. This feature article endeavours to trail the path of progress achieved hitherto and envisage the possibilities that lie ahead in the development of synthetic turn mimetics and hairpin nucleators.

Design of monomeric water-soluble β-hairpin and β-sheet peptides

Since the first report in 1993 (JACS 115, 5887-5888) of a peptide able to form a monomeric β-hairpin structure in aqueous solution, the design of peptides forming either β-hairpins (two-stranded antiparallel β-sheets) or three-stranded antiparallel β-sheets has become a field of growing interest and activity. These studies have yielded great insights into the principles governing the stability and folding of β-hairpins and antiparallel β-sheets. This chapter provides an overview of the reported β-hairpin/β-sheet peptides focussed on the applied design criteria, reviews briefly the factors contributing to β-hairpin/β-sheet stability, and describes a protocol for the de novo design of β-sheet-forming peptides based on them. Guidelines to select appropriate turn and strand residues and to avoid self-association are provided. The methods employed to check the success of new designed peptides are also summarized. Since NMR is the best technique to that end, NOEs and chemical shifts characteristic of β-hairpins and three-stranded antiparallel β-sheets are given.

A model for the controlled assembly of semiconductor peptides

The self-assembly of small molecules provides a potentially powerful method to create functional nanomaterials for many applications ranging from optoelectronics to oncology. However, the design of well-defined nanostructures via molecular assembly is a highly empirical process, which severely hampers efforts to create functional nanostructures using this method. In this review, we describe a simple strategy to control the assembly of functionalized peptides by balancing attractive hydrophobic effects that drive assembly with opposing electrostatic repulsions. Extended π-π contacts are created in the nanostructures when assembly is driven by π-stacking interactions among chromophores that are appended to the peptide. The formation of insoluble β-sheet aggregates are mitigated by incorporating charged side-chains capable of attenuating the assembly process. Although the application of this approach to the assembly of organic semiconductors is described, we expect this strategy to be effective for many other functional organic materials.

Cross-strand interactions of fluorinated amino acids in β-hairpin constructs

We describe herein the design, synthesis, and thermodynamic characterization of fluorinated β-hairpin constructs. Introduction of hexafluoroleucine (Hfl) did not perturb β-hairpin formation, as judged by (1)H NMR structures of four peptides determined to <1 Å backbone RMSDs, allowing direct comparison of thermodynamic stabilities of fluorinated peptides to their hydrocarbon counterparts. Judicious fluorination of peptides often results in increased thermal and chemical stability of the resultant folded structures. However, we found that when cross-strand residue partners were varied, the side-chain interaction energies followed the order Leu-Leu > Hfl-Leu > Hfl-Hfl. All peptides were more structured in 90% MeOH than in aqueous buffers. The peptides with Hfl-Leu or Hfl-Hfl cross-strand partners showed increased interaction energies in this solvent compared to those in water, in contrast to the insignificant effect on Leu-Leu. Our results inform the binding and assembly of peptides containing Hfl in the context of β-sheet structures and may be useful in interpreting binding of fluorinated ligands and peptides to biological targets.

Exploring beta-sheet structure and interactions with chemical model systems

Beta-sheets consist of extended polypeptide strands (beta-strands) connected by a network of hydrogen bonds and occur widely in proteins. Although the importance of beta-sheets in the folded structures of proteins has long been recognized, there is a growing recognition of the importance of intermolecular interactions among beta-sheets. Intermolecular interactions between the hydrogen-bonding edges of beta-sheets constitute a fundamental form of biomolecular recognition (like DNA base pairing) and are involved protein quaternary structure, protein-protein interactions, and peptide and protein aggregation. The importance of beta-sheet interactions in biological processes makes them potential targets for intervention in diseases such as AIDS, cancer, and Alzheimer's disease. This Account describes my research group's use of chemical model systems to study the structure and interactions of beta-sheets. Chemical model systems provide an excellent vehicle with which to explore beta-sheets, because they are smaller, simpler, and easier to manipulate than proteins. Synthetic chemical models also provide the opportunity to control or modulate natural systems or to develop other useful applications and may eventually lead to new drugs with which to treat diseases. In our "artificial beta-sheets", molecular template and turn units are combined with peptides to mimic the structures of parallel and antiparallel beta-sheets. The templates and turn units form folded, hydrogen-bonded structures with the peptide groups and help prevent the formation of complex, ill-defined aggregates. Templates that duplicate the hydrogen-bonding pattern of one edge of a peptide beta-strand while blocking the other edge have proven particularly valuable in preventing aggregate formation and in promoting the formation of simple monomeric and dimeric structures. Artificial beta-sheets that present exposed hydrogen-bonding edges can form well-defined hydrogen-bonded dimers. Dimerization occurs readily in chloroform solutions but requires additional hydrophobic interactions to occur in aqueous solution. Interactions among the side chains, as well as hydrogen bonding among the main chains, are important in dimer formation. NMR studies of artificial beta-sheets have elucidated the importance of hydrogen-bonding complementarity, size complementarity, and chiral complementarity in these interactions. These pairing preferences demonstrate sequence selectivity in the molecular recognition between beta-sheets. These studies help illustrate the importance of intermolecular edge-to-edge interactions between beta-sheets in peptides and proteins. Ultimately, these model systems may lead to new ways of controlling beta-sheet interactions and treating diseases in which they are involved.

Minimization and optimization of designed beta-hairpin folds

Minimized beta hairpins have provided additional data on the geometric preferences of Trp interactions in TW-loop-WT motifs. This motif imparts significant fold stability to peptides as short as 8 residues. High-resolution NMR structures of a 16- (KKWTWNPATGKWTWQE, DeltaG(U)(298) >or= +7 kJ/mol) and 12-residue (KTWNPATGKWTE, DeltaG(U)(298) = +5.05 kJ/mol) hairpin reveal a common turn geometry and edge-to-face (EtF) packing motif and a cation-pi interaction between Lys(1) and the Trp residue nearest the C-terminus. The magnitude of a CD exciton couplet (due to the two Trp residues) and the chemical shifts of a Trp Hepsilon3 site (shifted upfield by 2.4 ppm due to the EtF stacking geometry) provided near-identical measures of folding. CD melts of representative peptides with the -TW-loop-WT- motif provided the thermodynamic parameters for folding, which reflect enthalpically driven folding at laboratory temperatures with a small DeltaC(p) for unfolding (+420 J K(-)(1)/mol). In the case of Asx-Pro-Xaa-Thr-Gly-Xaa loops, mutations established that the two most important residues in this class of direction-reversing loops are Asx and Gly: mutation to alanine is destabilizing by about 6 and 2 kJ/mol, respectively. All indicators of structuring are retained in a minimized 8-residue construct (Ac-WNPATGKW-NH(2)) with the fold stability reduced to DeltaG(U)(278) = -0.7 kJ/mol. NMR and CD comparisons indicate that -TWXNGKWT- (X = S, I) sequences also form the same hairpin-stabilizing W/W interaction.

Probing the Formation of Stable Tertiary Structure in a Model Miniprotein at Atomic Resolution: Determinants of Stability of a Helical Hairpin

The minimal model system to study the basic principles of protein folding is the hairpin. The formation of beta-hairpins, which are the basic components of antiparallel beta-sheets, has been studied extensively in the past decade, but much less is known about helical hairpins. Here, we probe hairpin formation between a polyproline type-II helix and an alpha-helix as present in the natural miniprotein peptide YY (PYY). Both turn sequence and interactions of aromatic side chains from the C-terminal alpha-helix with the pockets formed by N-terminal Pro residues are shown by site-directed mutagenesis and solution NMR spectroscopy in different solvent systems to be important determinants of backbone dynamics and hairpin stability, suggesting a close analogy with some beta-hairpin structures. It is shown that multiple relatively weak contacts between the helices are necessary for the formation of the helical hairpin studied here, whereas the type-I beta-turn acts like a hinge, which through certain single amino acid substitutions is destabilized such that hairpin formation is completely abolished. Denaturation and renaturation of tertiary structure by temperature or cosolvents were probed by measuring changes of chemical shifts. Folding of PYY is both reversible and cooperative as inferred from the sigmoidal denaturation curves displayed by residues at the interface of the helical hairpin. Such miniproteins thus feature an important hallmark of globular proteins and should provide a convenient system to study basic aspects of helical hairpin folding that are complementary to those derived from studies of beta-hairpins.

Energetics of protein folding

The energetics of protein folding determine the 3D structure of a folded protein. Knowledge of the energetics is needed to predict the 3D structure from the amino acid sequence or to modify the structure by protein engineering. Recent developments are discussed: major factors are reviewed and auxiliary factors are discussed briefly. Major factors include the hydrophobic factor (burial of non-polar surface area) and van der Waals interactions together with peptide hydrogen bonds and peptide solvation. The long-standing model for the hydrophobic factor (free energy change proportional to buried non-polar surface area) is contrasted with the packing-desolvation model and the approximate nature of the proportionality between free energy and apolar surface area is discussed. Recent energetic studies of forming peptide hydrogen bonds (gas phase) are reviewed together with studies of peptide solvation in solution. Closer agreement is achieved between the 1995 values for protein unfolding enthalpies in vacuum given by Lazaridis-Archontis-Karplus and Makhatadze-Privalov when the solvation enthalpy of the peptide group is taken from electrostatic calculations. Auxiliary factors in folding energetics include salt bridges and side-chain hydrogen bonds, disulfide bridges, and propensities to form alpha-helices and beta-structure. Backbone conformational entropy is a major energetic factor which is discussed only briefly for lack of knowledge.

Synthesis of amino acid-derived cyclic acyl amidines for use in beta-strand peptidomimetics

The acyl amidine represented by the 4,5-dihydro-2(3H)-pyrazinone ring system 2 is isosteric to the vinylogous amide of the 1,2-dihydro-3(6H)-pyridinone 1, but its assembly from separate amine and amide components enables ready incorporation of an amino acid side chain with correct regio- and stereochemistry. beta-Strand peptidomimetics incorporating amino acid analogues based on 2 have recently been shown to be potent, protease-resistant ligands to a PDZ protein-interaction domain. Two routes to the protected dipeptide analogue 3 are described.

Model systems for β-hairpins and β-sheets

beta-Sheets and alpha-helices are the two principal secondary structures in proteins. However, our understanding of beta-sheet structure lags behind that of alpha-helices, largely because, until recently, there was no model system to study the beta-sheet secondary structure in isolation. With the development of well-folded beta-hairpins, this is changing rapidly. Recent advances include: increased understanding of the relative contributions of turn, strand and sidechain interactions to beta-hairpin and beta-sheet stability, with the role of aromatic residues as a common subtheme; experimental and theoretical kinetic and thermodynamic studies of beta-hairpin and beta-sheet folding; de novo protein design, including all-beta structures, mixed alpha/beta motifs and switchable systems; and the creation of functional beta-hairpins.