Paramjit S. Arora

Contemporary Strategies for the Stabilization of Peptides in the α-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.

An Orthosteric Inhibitor of the RAS–SOS Interaction

Mimics of α-helices on protein surfaces have emerged as powerful reagents for antagonizing protein-protein interactions, which are difficult to target with small molecules. Herein we describe the design of a cell-permeable synthetic α-helix based on the guanine nucleotide exchange factor Sos that interferes with Ras-Sos interaction and downregulates Ras signaling in response to receptor tyrosine kinase activation.

Assessing Helical Protein Interfaces for Inhibitor Design

Structure-based design of synthetic inhibitors of protein-protein interactions (PPIs) requires adept molecular design and synthesis strategies as well as knowledge of targetable complexes. To address the significant gap between the elegant design of helix mimetics and their sporadic use in biology, we analyzed the full set of helical protein interfaces in the Protein Data Bank to obtain a snapshot of how helices that are critical for complex formation interact with the partner proteins. The results of this study are expected to guide the systematic design of synthetic inhibitors of PPIs. We have experimentally evaluated new classes of protein complexes that emerged from this data set, highlighting the significance of the results described herein.

A Hydrogen Bond Surrogate Approach for Stabilization of Short Peptide Sequences in α-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.

Cellular uptake of N-methylpyrrole/N-methylimidazole polyamide-dye conjugates.

The cellular uptake and localization properties of DNA binding N-methylpyrrole/N-methylimidazole polyamide-dye conjugates in a variety of living cells have been examined by confocal laser scanning microscopy. With the exception of certain T-cell lines, polyamide-dye conjugates localize mainly in the cytoplasm and not in the nucleus. Reagents such as methanol typically used to fix cells for microscopy significantly alter the cellular localization of these DNA-binding ligands.

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

Assessment of helical interfaces in protein–protein interactions

Herein we identify and analyze helical protein interfaces as potential targets for synthetic modulators of protein-protein interactions.

Inhibition of HIV‐1 Fusion by Hydrogen‐Bond‐Surrogate‐Based α Helices

Entry of HIV-1 into its target cells to establish an infection is mediated by viral envelope glycoprotein (Env) and cellsurface receptors (CD4 and a coreceptor, such as CXCR4 or CCR5). The mature Env complex is a trimer, with three gp120 glycoproteins associated noncovalently with three membrane-anchored gp41 subunits. Binding of gp120/gp41 to cellular receptors triggers a series of conformational changes in gp41 that ultimately leads to the formation of a postfusion trimer-of-hairpins structure and membrane fusion. The core of the postfusion trimer-of-hairpins structure is a bundle of six a helices: three N-peptide helices form an interior, parallel, coiled-coil trimer, while three C-peptide helices pack in an antiparallel manner into hydrophobic grooves on the coiled-coil surface (Figure 1). The N-peptide region features a hydrophobic pocket targeted by C-peptide residues W628, W631, and I635. Peptides and synthetic molecules that bind to the N-terminal hydrophobic pocket and inhibit the formation of the six-helix bundle have been shown to effectively inhibit gp41-mediated HIV fusion. Herein, we describe the structure–activity relationships of hydrogen-bond-surrogate-derived a helices that inhibit HIV fusion in cell culture. Our work suggests that hydrogen-bond-surrogate (HBS) helices can potentially function as in vivo inhibitors of protein–protein interactions involved in viral fusion. HBS a helices are obtained by replacing an N-terminal main-chain i and i+4 hydrogen bond with a carbon–carbon bond through a ring-closing metathesis reaction (Figure 2). The hydrogen-bond surrogate preorganizes an a turn and stabilizes the peptide sequence in an a-helical conformation. We have shown that hydrogen-bond-surrogate a helices adopt stable a-helical conformations from a variety

High Specificity in Protein Recognition by Hydrogen-Bond-Surrogate α-Helices: Selective Inhibition of the p53/MDM2 Complex

Stabilized α-helices and nonpeptidic helix mimetics have emerged as powerful molecular scaffolds for the discovery of protein-protein interaction inhibitors.[1–8] Protein-protein interactions often involve large contact areas, which are often difficult for small molecules to target with high specificity.[9–10] 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. We recently introduced a new strategy for the preparation of stabilized α-helices, termed hydrogen bond surrogate (HBS) helices, which involves replacement of one of the main chain hydrogen bonds with a covalent linkage (Figure 1A).[11] The salient feature of the HBS approach is its ability to constrain very short peptides into highly stable α-helical conformation without blocking any molecular recognition surfaces. We have extensively analyzed the conformation adopted by HBS α-helices with 2D NMR, X-ray, and circular dichroism spectroscopies.[12–14] In addition, HBS helices have been shown to target their expected protein partners with high affinity in cell-free and cell culture assays.[15–17]

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.