Sequence specific peptidomimetic molecules inhibitors of a protein–protein interaction at the helix 1 level of c‐Myc

ABSTRACT Our work is focused in the broad area of strategies and efforts to inhibit protein–protein interactions. The possible strategies in this field are definitely much more varied than in the case of ATP‐pocket inhibitors. In our previous work (10), we reported that a retro‐inverso (RI) form of Helix1 (H1) of c‐Myc, linked to an RI‐internalization sequence arising from the third α‐helix of Antennapedia (Int) was endowed with an antiproliferative and proapoptotic activity toward the cancer cell lines MCF‐7 and HCT‐116. The activity apparently was dependent upon the presence of the Myc motif. In this work, by ala‐scan mapping of the H1 portion of our molecules with D‐aa, we found two amino acids necessary for antiproliferative activity: D‐Lys in 4 and D‐Arg in 5 (numbers refer to L‐forms). In the natural hetero‐dimer, these two side chains project to the outside of the four α‐helix bundle. Moreover, we were able to obtain three peptides more active than the original lead. They strongly reduced cell proliferation and survival (RI‐Int‐VV‐H1‐E2A,S6A,F8A; RI‐Int‐VV‐H1‐S6A,F8A,R11A; RI‐Int‐VV‐H1‐S6A,F8A,Q13A): after 8 days at 10 µM total cell number was ∼1% of the number of cells initially seeded. In these more potent molecules, the ablated side chains project to the inside in the corresponding natural four α‐helix bundle. In the present work, we also investigated the behavior of our molecules at the biochemical level. Using both a circular dichroism (CD) and a fluorescence anisotropy approach, we noted that side chains projecting at the interior of the four α‐helix bundle are needed for inducing the partial unfolding of Myc‐H2, without an opening of the leucine zipper. Side chains projecting at the outside are not required for this biochemical effect. However, antiproliferative activity had the opposite requirements: side chains projecting at the outside of the bundle were essential, and, on the contrary, ablation of one side chain at a time projecting at the inside increased rather than decreased biological activity. We conclude that our active molecules probably interfere at the level of a protein–protein interaction between Myc‐Max and a third protein of the transcription complex. Finally, CD and nuclear magnetic resonance (NMR) data, plus dynamic simulations, suggest a prevalent random coil conformation of the H1 portion of our molecules, at least in diluted solutions. The introduction of a kink (substitution with proline in positions 5 or 7) led to an i