Ordering of the N-Terminus of Human MDM2 by Small Molecule Inhibitors

Abstract

Restoration of p53 function through the disruption of the MDM2-p53 protein complex is a promising strategy for the treatment of various types of cancer. Here, we present kinetic, thermodynamic, and structural rationale for the remarkable potency of a new class of MDM2 inhibitors, the piperidinones. While these compounds bind to the same site as previously reported for small molecule inhibitors, such as the Nutlins, data presented here demonstrate that the piperidinones also engage the N-terminal region (residues 10-16) of human MDM2, in particular, Val14 and Thr16. This portion of MDM2 is unstructured in both the apo form of the protein and in MDM2 complexes with p53 or Nutlin, but adopts a novel β-strand structure when complexed with the piperidinones. The ordering of the N-terminus upon binding of the piperidinones extends the current model of MDM2-p53 interaction and provides a new route to rational design of superior inhibitors.

The NMR2 Method to Determine Rapidly the Structure of the Binding Pocket of a Protein–Ligand Complex with High Accuracy

“…All complex structures so far solved by NMR 2 . They consist of four high-affinity ligands (a-d) and two low-affinity ones (e,f), all of which are consistent with previously published structures (a) 3fea [34] with an RMSD of 1.1 Å, (b) 5c5a [32] with an RMSD of 0.9 Å, (c) 2lzg [35] with an RMSD of 1.5 Å, (d) 2gqg [36] with an RMSD of 1.1 Å (in silico data), and (e) 2n0w [37] with an RMSD of 1.35; (f) represents a complex with a ligand having a new scaffold, where no other structural data were known, and therefore it is compared to the complex structure with nutlin (5c5a). In orange are the NMR 2 -derived structures and in green the reference structures.…”

Small Molecule Inhibitors of MDM2-p53 and MDMX-p53 Interactions as New Cancer Therapeutics

“…The 14−24 residues of MDM2 adopted α-helix (21-24), β-turn (17)(18)(19)(20), and β-sheet (14)(15)(16) structures upon binding to the piperidinones, whereas these N-terminal residues were un-structured in apo-MDM2. The back-folding of the β-sheet gained additional van der Waals interaction between meta-Cl phenyl moiety of piperidinones and Val14 and Thr16 [60]. Compound 7 indeed binds to MDM2 with a very high affinity with IC 50 = 2.2 nM.…”

Targeting disordered proteins with small molecules using entropy

“…Upon binding some classes of p53/MDM2 antagonists the base of the lid region becomes ordered via contacts with the ligand, with an accompanying increase in flexibility of the remainder of the disordered region compared to the unbound disordered state [46,47]. In current attempts to curtail the toxic behaviour of disordered proteins, likely milestones may include the fine-tuning of flexible disordered regions, such as the flexible lid of MDM2.…”