Abstract

Aberrant Ras signaling drives numerous cancers, and drugs to inhibit this are urgently required. This compelling clinical need combined with recent innovations in drug discovery including the advent of biologic therapeutic agents, has propelled Ras back to the forefront of targeting efforts. Activated Ras has proved extremely difficult to target directly, and the focus has moved to the main downstream Ras-signaling pathways. In particular, the Ras-Raf and Ras-PI3K pathways have provided conspicuous enzyme therapeutic targets that were more accessible to conventional drug-discovery strategies. The Ras-RalGEF-Ral pathway is a more difficult challenge for traditional medicinal development, and there have, therefore, been few inhibitors reported that disrupt this axis. We have used our structure of a Ral-effector complex as a basis for the design and characterization of α-helical-stapled peptides that bind selectively to active, GTP-bound Ral proteins and that compete with downstream effector proteins. The peptides have been thoroughly characterized biophysically. Crucially, the lead peptide enters cells and is biologically active, inhibiting isoform-specific RalB-driven cellular processes. This, therefore, provides a starting point for therapeutic inhibition of the Ras-RalGEF-Ral pathway.

Highlights

  • Summary of binding parameters obtained from ITC for RLIP76 and peptides titrated into Ral proteins

  • The value obtained from an orthogonal assay, fluorescence polarization (FP), is included for the tightest binding peptide

  • Ϫ17.5 Ϯ 1.8 Ϫ1.6 Ϯ 0.6 Ϫ1.8 Ϯ 0.9 Ϫ0.7 Ϯ 0.4 Ϫ0.8 Ϯ 0.0 Ϫ0.7 Ϯ 0.3 Ϫ0.4 Not fitted a Stoichiometry. b Number of experiments. c S.D. of value obtained from multiple experiments. d Value obtained from FP. e Peptide behaved poorly in assays and showed low heat changes: data from a single experiment only

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Summary

Methods

Design and Synthesis ofRLIP76-based Stapled Peptides— Having established that an RLIP76 RBD-based ␣2 peptide could selectively bind to Ral in an analogous manner to the RLIP76 RBD, we sought to improve its binding affinity. Examination of the RalB1⁄7GMPPNP-RLIP76 RBD structure [33] together with computational and experimental alanine scanning mutagenesis data [17] revealed those RLIP76 RBD residues that were the most important for Ral binding (Fig. 1A) These included three residues in helix ␣1 (Leu-409, His-413, and Leu-416) and five residues in helix ␣2 (Leu-429, Trp-430, Arg-434, Thr-437, and Lys-440). Individual mutation of any of these residues to Ala reduced the binding affinity of RLIP76 RBD for RalA or RalB Ͼ5-fold [17] These vital binding residues were retained in the peptide sequences, and the chemical staples were positioned on the opposite face of the ␣-helix to allow these key residues to drive complex formation (Fig. 1, A and C).

Results
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