Evaluation of biologically relevant short alpha-helices stabilized by a main-chain hydrogen-bond surrogate

Minimalist and universal peptidomimetics

Many "new generation" peptidomimetics are designed to present amino acid side chains only; they do not have structural features that resemble peptide main chains. These types of molecules have frequently been presented in the literature as mimics of specific secondary structures. However, many "side-chain only" peptidomimetics do not rest in single conformational states, but exist in a limited number of freely interconverting forms. These different conformations may resemble different secondary structures, so referring to them as, for instance, turn- or helical-mimics understates the ways they could adapt to various binding situations. Sets of scaffolds that can be used to mimic aspects of nearly every secondary structure, i.e. universal peptidomimetics, can be constructed. These may assume a privileged place in library design, particularly in high throughput screening for pharmacological probes for which binding conformations, or even the target itself, is unknown at the time the library is designed (critical review, 101 references).

Universal peptidomimetics

This paper concerns peptidomimetic scaffolds that can present side chains in conformations resembling those of amino acids in secondary structures without incurring excessive entropic or enthalpic penalties. Compounds of this type are referred to here as minimalist mimics. The core hypothesis of this paper is that small sets of such scaffolds can be designed to analogue local pairs of amino acids (including noncontiguous ones) in any secondary structure; i.e., they are universal peptidomimetics. To illustrate this concept, we designed a set of four peptidomimetic scaffolds. Libraries based on them were made bearing side chains corresponding to many of the protein-derived amino acids. Modeling experiments were performed to give an indication of kinetic and thermodynamic accessibilities of conformations that can mimic secondary structures. Together, peptidomimetics based on these four scaffolds can adopt conformations that resemble almost any combination of local amino acid side chains in any secondary structure. Universal peptidomimetics of this kind are likely to be most useful in the design of libraries for high-throughput screening against diverse targets. Consequently, data arising from submission of these molecules to the NIH Molecular Libraries Small Molecule Repository (MLSMR) are outlined.

Solid-phase synthesis of short α-helices stabilized by the hydrogen bond surrogate approach

Stabilized α-helices and nonpeptidic helix mimetics have emerged as powerful molecular scaffolds for the discovery of protein-protein interaction inhibitors. Protein-protein interactions often involve large contact areas, which are often difficult for small molecules to target with high specificity. The hypothesis behind the design of stabilized helices and helix mimetics is that these medium-sized molecules may pursue their targets with higher specificity because of a larger number of contacts. This protocol describes an optimized synthetic strategy for the preparation of stabilized α-helices that feature a carbon-carbon linkage in place of the characteristic N-terminal main-chain hydrogen bond of canonical helices. Formation of the carbon-carbon bond is enabled by a microwave-assisted ring-closing metathesis reaction between two terminal olefins on the peptide chain. The outlined strategy allows the synthesis and purification of a hydrogen bond surrogate (HBS) α-helix in ∼ 1 week.

Structural and pharmacological effects of ring-closing metathesis in peptides

Applications of ring-closing alkene metathesis (RCM) in acyclic α- and β-peptides and closely related systems are reviewed, with a special emphasis on the structural and pharmacological effects of cyclization by RCM.

Inhibition of hypoxia inducible factor 1-transcription coactivator interaction by a hydrogen bond surrogate alpha-helix

Designed ligands that inhibit hypoxia-inducible gene expression could offer new tools for genomic research and, potentially, drug discovery efforts for the treatment of neovascularization in cancers. We report a stabilized alpha-helix designed to target the binding interface between the C-terminal transactivation domain (C-TAD) of hypoxia-inducible factor 1alpha (HIF-1alpha) and cysteine-histidine rich region (CH1) of transcriptional coactivator CBP/p300. The synthetic helix disrupts the structure and function of this complex, resulting in a rapid downregulation of two hypoxia-inducible genes (VEGF and GLUT1) in cell culture.

Disruption of the IS6-AID linker affects voltage-gated calcium channel inactivation and facilitation

Two processes dominate voltage-gated calcium channel (Ca_V) inactivation: voltage-dependent inactivation (VDI) and calcium-dependent inactivation (CDI). The Ca_Vβ/Ca_Vα₁-I-II loop and Ca²⁺/calmodulin (CaM)/Ca_Vα₁–C-terminal tail complexes have been shown to modulate each, respectively. Nevertheless, how each complex couples to the pore and whether each affects inactivation independently have remained unresolved. Here, we demonstrate that the IS6–α-interaction domain (AID) linker provides a rigid connection between the pore and Ca_Vβ/I-II loop complex by showing that IS6-AID linker polyglycine mutations accelerate Ca_V1.2 (L-type) and Ca_V2.1 (P/Q-type) VDI. Remarkably, mutations that either break the rigid IS6-AID linker connection or disrupt Ca_Vβ/I-II association sharply decelerate CDI and reduce a second Ca²⁺/CaM/Ca_Vα₁–C-terminal–mediated process known as calcium-dependent facilitation. Collectively, the data strongly suggest that components traditionally associated solely with VDI, Ca_Vβ and the IS6-AID linker, are essential for calcium-dependent modulation, and that both Ca_Vβ-dependent and CaM-dependent components couple to the pore by a common mechanism requiring Ca_Vβ and an intact IS6-AID linker.

Dynamical binding of hydrogen-bond surrogate derived Bak helices to antiapoptotic protein Bcl-xL

A new peptide modification strategy was recently developed to replace the i to i + 4 hydrogen bond of the main chain of an alpha-helix with a carbon-carbon covalent bond to afford highly stable constrained alpha-helices, termed hydrogen-bond surrogate (HBS) helices. HBS helices that mimic the Bak BH3 domains were experimentally demonstrated to target protein Bcl-x(L) with high affinity. In this study, molecular dynamics (MD) simulation is used to understand how the covalent modification of the natural Bak sequence affects the binding to Bcl-x(L) at molecular levels. The binding mechanism of HBS helix to Bcl-x(L) and the effect of synthesized cyclic structures are analyzed by MD and MM-PBSA calculations for comparison with the native binding of Bak-Bcl-x(L). The present MD result shows that the entropy of the HBS structure is considerably reduced, and the presence of the N-terminal HBS macrocycle impacts residues at the C-terminus of the helix, but the conformation of the corresponding binding structures is not significantly changed. Our analysis shows that substitution of an aspartic acid residue--a helix breaker--with a hydrophobic residue not only enhances the helicity of the peptide but also stabilizes the structure of the binding complex. The present computational result is consistent with the experimental observation and provides explanations for the altered binding properties of the artificial Bak alpha-helix. Our study underscores the importance of the dynamical effect in protein-peptide interaction in which entropic effect plays a major role.

A hydrogen bond surrogate approach for stabilization of short peptide sequences in alpha-helical conformation

Alpha-helices constitute the largest class of protein secondary structures and play a major role in mediating protein-protein interactions. Development of stable mimics of short alpha-helices would be invaluable for inhibition of protein-protein interactions. This Account describes our efforts in developing a general approach for constraining short peptides in alpha-helical conformations by a main-chain hydrogen bond surrogate (HBS) strategy. The HBS alpha-helices feature a carbon-carbon bond derived from a ring-closing metathesis reaction in place of an N-terminal intramolecular hydrogen bond between the peptide i and i + 4 residues. Our approach is centered on the helix-coil transition theory in peptides, which suggests that the energetically demanding organization of three consecutive amino acids into the helical orientation inherently limits the stability of short alpha-helices. The HBS method affords preorganized alpha-turns to overcome this intrinsic nucleation barrier and initiate helix formation. The HBS approach is an attractive strategy for generation of ligands for protein receptors because placement of the cross-link on the inside of the helix does not block solvent-exposed molecular recognition surfaces of the molecule. Our metathesis-based synthetic strategy utilizes standard Fmoc solid phase peptide synthesis methodology, resins, and reagents and provides HBS helices in sufficient amounts for subsequent biophysical and biological analyses. Extensive conformational analysis of HBS alpha-helices with 2D NMR, circular dichroism spectroscopies and X-ray crystallography confirms the alpha-helical structure in these compounds. The crystal structure indicates that all i and i + 4 C=O and NH hydrogen-bonding partners fall within distances and angles expected for a fully hydrogen-bonded alpha-helix. The backbone conformation of HBS alpha-helix in the crystal structure superimposes with an rms difference of 0.75 A onto the backbone conformation of a model alpha-helix. Significantly, the backbone torsion angles for the HBS helix residues fall within the range expected for a canonical alpha-helix. Thermal and chemical denaturation studies suggest that the HBS approach provides exceptionally stable alpha-helices from a variety of short sequences, which retain their helical conformation in aqueous buffers at exceptionally high temperatures. The high degree of thermal stability observed for HBS helices is consistent with the theoretical predictions for a nucleated helix. The HBS approach was devised to afford internally constrained helices so that the molecular recognition surface of the helix and its protein binding properties are not compromised by the constraining moiety. Notably, our preliminary studies illustrate that HBS helices can target their expected protein receptors with high affinity.

Contemporary strategies for the stabilization of peptides in the alpha-helical conformation

Herein we review contemporary synthetic and protein design strategies to stabilize the alpha-helical motif in short peptides and miniature proteins. Advances in organometallic catalyst design, specifically for the olefin metathesis reaction, enable the use of hydrocarbon bridges to either crosslink side chains of specific residues or mimic intramolecular hydrogen bonds with carbon-carbon bonds. The resulting hydrocarbon-stapled and hydrogen bond surrogate alpha-helices provide unique synthetic ligands for targeting biomolecules. In the protein design realm, several classes of miniature proteins that display stable helical domains have been engineered and manipulated with powerful in vitro selection technologies to yield libraries of sequences that retain their helical folds. Rational re-design of these scaffolds provide distinctive reagents for the modulation of protein-protein interactions.

Development of a series of cross-linking agents that effectively stabilize alpha-helical structures in various short peptides

A series of cross-linking agents of varying rigidity and length were designed to stabilize helical structures in short peptides and were then synthesized. The sequences of the short peptides employed in this study each include two X residues (X=Dap, Dab, Orn, and Lys) at the i/i+4, i/i+7, or i/i+11 positions to provide the sites for cross-linking. These peptides were subjected to reaction with the synthesized cross-linking agents, and the helical content of the resulting cross-linked peptides were analyzed in detail by circular dichroism. For each of the peptide classes we found combinations with the cross-linking agents suitable for the construction of stable helical structures up to >95 % helicity at 5 degrees C. Our method could also be applied to biologically related sequences seen in native proteins such as Rev.

Trapping a folding intermediate of the alpha-helix: stabilization of the pi-helix

We report the design, synthesis, and characterization of a short peptide trapped in a pi-helix configuration. This high-energy conformation was nucleated by a preorganized pi-turn, which was obtained by replacing an N-terminal intramolecular main chain i and i + 5 hydrogen bond with a carbon-carbon bond. Our studies highlight the nucleation parameter as a key factor contributing to the relative instability of the pi-helix and allow us to estimate fundamental helix-coil transition parameters for this conformation.

Design and synthesis of alpha-helical peptides and mimetics

The alpha-helix is the most abundant secondary structural element in proteins and is an important structural domain for mediating protein-protein and protein-nucleic acid interactions. Strategies for the rational design and synthesis of alpha-helix mimetics have not matured as well as other secondary structure mimetics such as strands and turns. This perspective will focus on developments in the design, synthesis and applications of alpha-helices and mimetics, particularly in the last 5 years. Examples where synthetic compounds have delivered promising biological results will be highlighted as well as opportunities for the design of mimetics of the type I alpha-helical antifreeze proteins.

Optimized synthesis of hydrogen-bond surrogate helices: surprising effects of microwave heating on the activity of Grubbs catalysts

This manuscript discusses microwave-assisted solid-phase synthesis of hydrogen-bond surrogate based alpha-helices and analogues by ring-closing metathesis (RCM). Microwave-mediated RCM allows access to a greater variety of amino acid residues in the macrocycles in shorter reaction times and higher yields compared to conventional heating. Surprisingly, we discovered that the Grubbs II catalyst is highly active under the influence of microwaves but catalytically dead under oil-bath conditions for the metathesis of these peptide bisolefins. [reaction: see text]

Nucleation and stability of hydrogen-bond surrogate-based alpha-helices

We have reported a new class of artificial alpha-helices in which a pre-organized alpha-turn nucleates the helical conformation [R. N. Chapman, G. Dimartino, and P. S. Arora, J Am. Chem. Soc., 2004, 126, 12252 and D. Wang, K. Chen, J. L. Kulp, III, and P. S. Arora, J. Am. Chem. Soc., 2006, 128, 9248]. This manuscript describes the effect of the core nucleation template on the overall helicity of the peptides and demonstrates that the macrocycle which most closely mimics the 13-membered hydrogen-bonded alpha-turn in canonical alpha-helices also affords the most stable artificial alpha-helix. We also investigate the stability of these synthetic helices through classical helix-coil parameters and find that the denaturation behavior of HBS alpha-helices agrees with the theoretical properties of a peptide with a well-defined and stable helix nucleus.