Design of a novel MDM2 binding peptide based on the p53 family

Abstract

p53 is a major tumor suppressor protein, that binds to, and is negatively regulated by MDM2. In tumors overexpressing MDM2, p53 function can be rescued through the disruption of the MDM2-p53 interactions by small molecules and peptides. It is known that MDM2 also binds p73 but not p63, the two homologues of p53. We dissect the structural and energetic reasons underlying this discrimination and have identified a peptide that is intrinsically less helical than p53 and yet has a higher affinity for MDM2. The increased disorder has been introduced by localizing a cationic residue in between two anionic residues, imparting a degree of frustration to the system. In addition, the introduction of a bulkier hydrophobic group towards the centre of the peptide enables the peptide to adapt a bound conformation that on the one hand is most strained, and yet enables the peptide to straddle the largest surface of MDM2, amongst all the peptides. Computations also reveal that this peptide is a dual inhibitor, binding also to MDMX. The computed affinity of the new peptide has been validated against MDM2 using fluorescence-based thermal shift assays.

Differential binding of p53 and nutlin to MDM2 and MDMX: Computational studies

“…Several peptides, small molecules and peptidomimetics have been identified as inhibitors of this interaction between p53 and MDM2/ MDMX. 17,24,[28][29][30][31][32][33][34][35][36][37] The crystal structure of nutlin complexed to MDM2, PDB code 1RV1, 28 has been resolved at 2.3 Å. It shows (Fig.…”

“…Towards this goal, the technique of molecular dynamics (MD) simulations have been applied extensively to investigate biochemical phenomena. 41,42 Several groups have applied MD to understand the binding of p53 peptides to MDM2, [18][19][20]32,[43][44][45][46][47] and MDMX [48][49][50] providing valuable insights into this interaction. Here we examine the differential binding of p53 peptide and nutlin to MDM2 and MDMX using MD simulations.…”

p53-family proteins and their regulators: hubs and spokes in tumor suppression

“…42,50 The crucial amino acids required for MDM2 binding are conserved in p63, but molecular modeling suggests that other residues in the N-terminal domain of p63 may render this interaction significantly weaker. 51 In line with its role as primary regulator of p53, MDM2 stability, localization, and function are tightly controlled, and hence the p53-MDM2 core circuit responds to a multitude of signaling pathways, including DNA damage, oncogene activation, and nucleolar/ribosome stress (see Kruse and Gu 5 , Vousden and Prives 6 and references therein). Similarly, stress-activated kinases can regulate MDMX activity.…”

Stapled peptides in the p53 pathway: Computer simulations reveal novel interactions of the staples with the target protein

“…[26][27][28][29][30][31] The reactivation of p53 regulated apoptotic pathways through the inhibition of MDM2 and MDMX has been shown to be a viable approach to suppress tumor growth in cancer cells. 23,32 Both peptidomimetics 26,[33][34][35][36][37][38][39][40] and small molecules 25,41 have been reported to inhibit the interaction of MDM2-p53 and reactivate the transcriptional pathway; recently the mechanism underpinning the differences in the interactions of peptides and of small molecules has been described. 31,42 Clinical trials with some of these molecules are currently in progress.…”