Differential binding of p53 and nutlin to MDM2 and MDMX: computational studies.
Half of human tumours have mutated p53 while in the other half, defective signalling pathways block its function. One such defect is the overexpression of the MDM2 and MDMX proteins. This has led to an intense effort to develop inhibitors of p53-MDM2/MDMX interactions. Nutlin is the first such compound described to block p53-MDM2 interactions. Molecular dynamics simulations have been used to explore the differences in binding of p53 and nutlin to MDM2/MDMX. Simulations reveal that p53 has a higher affinity for MDM2 than MDMX, driven by stronger electrostatic interactions. p53 is displaced from MDM2 by nutlin because it is more flexible, thus paying a larger entropic penalty upon sequestration by MDM2. The inherent plasticity of MDM2 is higher than that of MDMX, enabling it to bind both p53 and nutlin. The less flexible MDMX interacts with the more mobile p53 because the peptide can adapt conformationally to dock into MDMX, albeit with a reduced affinity; nutlin, however is rigid and hence can only interact with MDMX with low affinity. Evolutionarily, the higher affinity of MDM2 for p53 may enable MDM2 to bind p53 for longer periods as it shuttles it out of the nucleus; in contrast, MDMX only needs to mask the p53 TA domain. This study enables us to hypothesize gain of function mutations or those that have decreased affinity for nutlin. These conclusions provide insight into future drug design for dual inhibitors of MDM2 and MDMX, both of which are oncoproteins found overexpressed in many cancers.
Joseph
Thomas Leonard
TL
Bioinformatics Institute (A-STAR), Matrix, Singapore.
Madhumalar
Arumugam
A
Brown
Christopher J
CJ
Lane
David P
DP
Verma
Chandra S
CS
D000595:Amino Acid Sequence; D000596:Amino Acids / Q000378:metabolism; D001665:Binding Sites; D019295:Computational Biology; D006801:Humans; D006860:Hydrogen Bonding; D007093:Imidazoles / Q000737:chemistry / Q000378:metabolism*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009038:Motion; D050505:Mutant Proteins / Q000737:chemistry / Q000378:metabolism; D010455:Peptides; D010879:Piperazines / Q000737:chemistry / Q000378:metabolism*; D025341:Principal Component Analysis; D011485:Protein Binding; D051736:Proto-Oncogene Proteins c-mdm2 / Q000737:chemistry / Q000378:metabolism*; D016415:Sequence Alignment; D013816:Thermodynamics; D016159:Tumor Suppressor Protein p53 / Q000378:metabolism*
D000596:Amino Acids; D007093:Imidazoles; D050505:Mutant Proteins; D010455:Peptides; D010879:Piperazines; D016159:Tumor Suppressor Protein p53; C482204:nutlin 2; C497206:MDM2 protein, human; D051736:Proto-Oncogene Proteins c-mdm2