Structural States of Hdm2 and HdmX: X‐ray Elucidation of Adaptations and Binding Interactions for Different Chemical Compound Classes

Abstract

Hdm2 (human MDM2, human double minute 2 homologue) counteracts p53 function by direct binding to p53 and by ubiquitin‐dependent p53 protein degradation. Activation of p53 by inhibitors of the p53–Hdm2 interaction is being pursued as a therapeutic strategy in p53 wild‐type cancers. In addition, HdmX (human MDMX, human MDM4) was also identified as an important therapeutic target to efficiently reactivate p53, and it is likely that dual inhibition of Hdm2 and HdmX is beneficial. Herein we report four new X‐ray structures for Hdm2 and five new X‐ray structures for HdmX complexes, involving different classes of synthetic compounds (including the worldwide highest resolutions for Hdm2 and HdmX, at 1.13 and 1.20 Å, respectively). We also reveal the key additive 18‐crown‐ether, which we discovered to enable HdmX crystallization and show its stabilization of various Lys residues. In addition, we report the previously unpublished details of X‐ray structure determinations for eight further Hdm2 complexes, including the clinical trial compounds NVP‐CGM097 and NVP‐HDM201. An analysis of all compound binding modes reveals new and deepened insight into the possible adaptations and structural states of Hdm2 (e.g., flip of F55, flip of Y67, reorientation of H96) and HdmX (e.g., flip of H55, dimer induction), enabling key binding interactions for different compound classes. To facilitate comparisons, we used the same numbering for Hdm2 (as in Q00987) and HdmX (as in O15151, but minus 1). Taken together, these structural insights should prove useful for the design and optimization of further selective and/or dual Hdm2/HdmX inhibitors.

Discovery, X-ray structure and CPP-conjugation enabled uptake of p53/MDM2 macrocyclic peptide inhibitors

“…Interestingly, the Phe-pocket of MDM2 is less occupied by Val(7) of CMR19 than the Phe of p53 in MDM2. 28 Both biphenyls are penetrating deeply into the MDM2 protein. The almost parallel arrangement of the adjacent biphenyls is stabilized by an edge-to-face interaction between the opposite aromatic rings.…”

Focused Library Generator: case of Mdmx inhibitors

“…Its long straight chain lies across the cleft of the protein and the hydrophobic pocket shrinks significantly to fit around it. In the crystal structure of Mdmx complex with Mdmx selective inhibitor (PDB ID: 6q9y; compound 16, IC 50 of 3.7 µM), we can observe the similar binding conformation [72]. Apart from filling the Trp23 and Leu26 pockets, the remaining phenyl group nicely overlaps with Ser20 of p53.…”

Proteasomal Degradation of Zn-Dependent Hdacs: The E3-Ligases Implicated and the Designed Protacs That Enable Degradation

“…The p53 binding site is located at the N -terminal end of these ligases and is comprised of three hydrophobic pockets that interact with residues Phe19, Trp23, and Leu26 which are part of the α-helix of p53 that interacts with MDM2 and MDMX [ 131 ]. The interaction of MDM2 with p53 is stabilized by two hydrogen bonds established between F19 and W23 of p53 and Q72 and L54 in MDM2, respectively ( Figure 10 ) [ 132 ]. The p53 binding sites of MDM2 and MDMX are very similar; nevertheless, they differ slightly in the amino acid sequence of the leucine and tryptophan pockets, which is being exploited for the design of inhibitors of the MDMX-p53 interaction [ 15 , 131 ].…”