Protein Domain Mimics as Modulators of Protein–Protein Interactions

Abstract

CONSPECTUS 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, PP...

N‐locking stabilization of covalent helical peptides: Application to Bfl‐1 antagonists

“…More recently, introduction of covalent warheads on peptide or peptide mimetics to target Cys (de Araujo, Lim, Good, Skerlj, & Fairlie, ; Baggio et al, ; Barile et al, ; Harvey et al, ; Huhn, Guerra, Harvey, Bird, & Walensky, ; Stebbins et al, ), and more recently also Lys and Tyr residues (Baggio et al, ), is emerging strategies to increase affinity and selectivity of these agents. A large number of therapeutically viable PPIs are mediated by an alpha helix (Bullock, Jochim, & Arora, ; Sawyer, Watkins, & Arora, ), suggesting that helical peptides could in principle also be used as starting point for the design of new therapeutic agents. However, isolated alpha‐helical peptides in solution tend to be disordered, with only a small population forming the bioactive alpha‐helical conformation.…”

“…A large number of therapeutically viable PPIs are mediated by an alpha helix (Bullock, Jochim, & Arora, 2011; | 413 BAGGIO et Al. Sawyer, Watkins, & Arora, 2017), suggesting that helical peptides could in principle also be used as starting point for the design of new therapeutic agents. However, isolated alpha-helical peptides in solution tend to be disordered, with only a small population forming the bioactive alpha-helical conformation.…”

Effects of chiral center on an all‐hydrocarbon tethered peptide

“…In this regard, peptide ligands mimicing the interacting motif with the conserved key interacting residues show potentials to target these intracellular targets. Peptides constraint with suitable methods were shown to have improved biophysical properties, including enhanced protease resistance, cell‐penetration, and/or target binding affinity . Many chemical methods have been developed to constrain peptides into helical conformation by attaching different tethers to the peptide side chains, including disulfide/thioether bond formation, ring‐closing metathesis, lactam ring formation, “click” chemistry, addition of perfluoroarenes, vinyl‐sulfide formation, and so on.…”

Emerging roles of allosteric modulators in the regulation of protein‐protein interactions (PPIs): A new paradigm for PPI drug discovery

“…Despite these challenges, a small fraction of PPIs has been successfully tailored by orthosteric PPI ligands. Many excellent reviews have been written on the discovery of orthosteric PPI ligands, 6,8,[11][12][13][14][15][16][17][18][19][20][21] which have provided complete and thorough mechanistic insights into their mechanisms, so we will not describe the repertoire of orthosteric PPI ligands any further here.…”

“…Although many reviews have been published on the topic of PPI modulators, [6][7][8]13,15,18,19,21 the majority of them mainly focused on orthosteric PPI ligands. Furthermore, compared with the action modes of orthosteric PPI modulators, the mechanisms underlying the allosteric regulation towards PPIs are more complicated, and a comprehensive review on this topic is still lacking.…”