Effect of Nutlin-3a on stability of p53-MDM2 complex
Authors: Zhou Han , Geng Yi-Zhao , Yan Shi-Wei ,   Department of Physics, Beijing Normal University, Beijing 100875, China,   School of Science, Hebei University of Technology, Tianjin 300131, China
Published: February 2023

<sec>P53 is well recognized to be a tumor suppressor protein. In response to the external stress or environmental perturbation, p53 can promote the transcription of various target genes downstream, thus regulating the cell cycle, apoptosis, DNA repair, and angiogenesis. However, the activation of p53 is further activated by another protein, MDM2, which negatively regulates the level of p53 inverse and thus reduces the activation of p53. This phenomenon is a novel potential and promising strategy for cancer therapy, i.e. restoring the activity of p53 pathway through the competitive inhibitors that can occupy the p53-binding site of MDM2 and thus inhibit the interaction between p53 and MDM2.</sec><sec>Recently, various kinds of the inhibitors have been designed for this purpose. The Nutlin family is a group of well investigated inhibitors, which shows high efficiency for tumor suppression. Nutlin-3a mimics the MDM2-binding site of p53 essentially, and blocks the binding of MDM2 to p53. Once getting free from MDM2, p53 rapidly accumulates in the nuclei of cancer cells, the p53 target genes and the p53 pathway are activated, thereby resulting in cell-cycle arrest and apoptosis. In our previous papers, we investigated the competition mechanism between Nutlin3 and p53 <i>in vitro</i> by using molecular dynamics simulations. We found that Nutlin3 can bind faster than p53 to prevent p53 from binding to MDM2 when Nutlin-3a and p53 have equal distance from MDM2. Nutlin-3a can also bind to the p53-MDM2 complex to disturb and weaken the interactions between p53 and MDM2. However, the underlying mechanisms of p53-MDM2 complex instability <i>in vivo</i> are still unclear. And these inhibitors also have a variety of specificities and biological toxicities <i>in vivo</i> environment.</sec><sec>In this study, we go a further step to investigate the effect of Nutlin-3a on the stability of p53-MDM2 complex in physiological environment with the aid of the molecular mechanics/generalized borne surface area (MM/GBSA) method. In our simulations, a group of Nutlin-3a molecules are randomly put around the p53 binding pocket of MDM2 in the initial stages to examine the dynamics among p53, MDM2 and the group of Nutlin-3a molecules and to analyze the underlying competition mechanism between Nutlin3 and p53 binding to pocket of MDM2.</sec><sec>We find that Nutlin-3a can induce the centroid distance between p53 and MDM2 to increase. Importantly, we show that Nutlin-3a weakens the binding affinity of p53-MDM2 complex. Consistently, Nutlin-3a breaks a hydrogen bond between Phe19-Gln72 and a salt bridge between Glu17-Lys94, which weakens the interactions between p53 and MDM2. From the systematic biology point of view, the regulation of p53 by MDM2 is extremely sensitive to the strength of the p53-MDM2 interaction. The avianization of the interactions between p53 and MDM2 by Nutlin-3a can promote p53 to restore its suppression functions on tumor development.</sec><sec>This study may be helpful in understanding the molecular mechanisms of p53-MDM2 complex instability mediated by Nutlin-3a and also in searching for the effective inhibitors of p53-MDM2 interaction.</sec>