Unveiling the “Three‐Finger Pharmacophore” Required for p53–MDM2 Inhibition by Saturation‐Transfer Difference (STD) NMR Initial Growth‐Rates Approach

Abstract

Inhibitors of the p53-MDM2 protein-protein interaction are emerging as a new and validated approach to treating cancer. Herein, we describe the synthesis and inhibitory evaluation of a series of isoquinolin-1-one analogues, and highlight the utility of an initial growth-rates saturation-transfer difference (STD) NMR approach supported by protein-ligand docking to investigate p53-MDM2 inhibition. The approach is illustrated by the study of compound 1, providing key insights into the binding mode of this kind of MDM2 ligands and, more importantly, readily unveiling the previously proposed three-finger pharmacophore requirement for p53-MDM2 inhibition.

Identification of selective protein–protein interaction inhibitors using efficient in silico peptide-directed ligand design

“…To provide structural details of the binding of these compounds in the p53 binding site, we employed an STD NMR initial growth-rates approach to identify the binding mode and the interactions with the binding grooves of h DM2 and h DMX 27–29. Compound 4 was chosen for analysis by STD NMR because of its solubility in aqueous buffer and its relatively weak binding to both h DM2 and h DMX, allowing the binding kinetics to fall within the fast-exchange conditions necessary for STD NMR.…”

Synthesis, Biological and In Silico Evaluation of Pure Nucleobase-Containing Spiro (Indane-Isoxazolidine) Derivatives as Potential Inhibitors of MDM2–p53 Interaction

“…Previous docking studies with different compounds capable to inhibit the MDM2–p53 interaction showed that those compounds are able to mimic the key p53-residues when binding to MDM2 [58,59].…”

Evaluation of ligand-based NMR screening methods to characterize small molecule binding to HIV-1 glycoprotein-41

“…Artefacts can result with measurement of STD at a single saturation time because the accumulated saturation varies with T 1 relaxation rates across the ligand. The problem can be overcome by obtaining initial rates of magnetization transfer derived from saturation buildup curves, 28–30 or by CORCEMA-ST calculation of the buildup curves. 31 Collection of multiple saturation time points was precluded here by the rather low stability of the complexes.…”