Targeting Unoccupied Surfaces on Protein–Protein Interfaces

Abstract

The use of peptidomimetic scaffolds to target protein–protein interfaces is a promising strategy for inhibitor design. The strategy relies on mimicry of protein motifs that exhibit a concentration of native hot spot residues. To address this constraint, we present a pocket-centric computational design strategy guided by AlphaSpace to identify high-quality pockets near the peptidomimetic motif that are both targetable and unoccupied. Alpha-clusters serve as a spatial representation of pocket space and are used to guide the selection of natural and non-natural amino acid mutations to design inhibitors that optimize pocket occupation across the interface. We tested the strategy against a challenging protein–protein interaction target, KIX/MLL, by optimizing a single helical motif within MLL to compete against the full-length wild-type MLL sequence. Molecular dynamics simulation and experimental fluorescence polarization assays are used to verify the efficacy of the optimized peptide sequence.

Modulation of virus-induced NF-κB signaling by NEMO coiled coil mimics

“…The failure of the CHDs bearing wild-type residues to provide potent inhibition prompted us to optimize the NEMO coiled coil with noncanonical residues to overcome the loss of the two tyrosine hot spot residues. We utilized AlphaSpace to obtain fragmentcentric topographical mapping of protein surfaces to identify underutilized pockets in PPIs 40 and enhance target engagement 41 by introducing non-canonical residues. We discovered several key pockets on the vFLIP surface that could be targeted using natural and non-natural amino acids displayed from the coiled-coil scaffold.…”

“…Pockets are represented as geometric "alpha clusters", which serve as 3-dimensional representations of the pocket and can be utilized to guide the selection or design of natural or non-natural residues to enhance pocket occupancy. This approach has been demonstrated previously in the optimization of a peptide inhibitor against a challenging protein-protein interaction target 41 .…”

Defining the hydrophobic interactions that drive competence stimulating peptide (CSP)-ComD binding in Streptococcus pneumoniae

“…2 ). To do so, one can either use computational models, when structural information of the protein/receptor is available [ 30 ], or utilize conservative point mutations within the ligand peptide to assess the occupancy level and degree of specificity. Since no structural information is available for the ComD receptors, we chose to assess the ComD1 binding pocket by synthesizing a set of CSP1 analogs bearing highly conservative point mutation in key hydrophobic positions (4, 7, 8, 11, 12 and 13).…”

Exploiting Ret Isoforms in Managing Medullary and Papillary Thyroid Cancer

“…Several antibodies that specifically target the RET51 C-terminal tail have been generated and may be effective steric inhibitors to block RET dimerization, autophosphorylation and/or interactions with signaling and adaptor molecules [31]. Peptidomimetics, small peptides that mimic natural substrates, also have the potential for development into potent and selective inhibitors against signaling molecules that bind unique protein domains and motifs [32]. For example, peptides mimicking the sequence and/or structure of the RET C-terminal tails may be useful as 'molecular sponges' to bind RET isoform-specific interactors, such as RET51-binding adaptor GRB2 [4,16,18], thereby inhibiting RET51-specific downstream signals.…”