Abstract
One of the most important tumor suppressor proteins in eukaryotic cells is the transcription factor called p53. The importance of this protein in cells comes from the fact that it regulates a wide variety of cellular processes including the cell cycle, metabolism, DNA repair, senescence and apoptosis. In cancer cells, p53 is a major target as the most mutated protein, which has led to the search for potential activators of the mutant protein. Currently, the only mutated-p53 activator in clinical trials is a small molecule called APR-246. There is evidence that the active metabolite of APR-246 binds covalently to mutant p53 and restores its wild-type (wt) activity. In this work, we created atomistic in silico models of the wt, mutant and drugged mutant p53 proteins each in complex with DNA. Using molecular dynamics simulations we generated equilibrated models of the complexes. Detailed analysis revealed that the binding of the APR-246 active metabolite to the mutant proteins alters their interaction with DNA. In particular, the binding of the molecule at loop L1 of the protein allows the loop to anchor the protein to DNA similarly to wt p53. Several important p53-DNA interactions lost due to mutation were also restored in the drugged mutants. These findings, not only provide a possible mechanism of action of this drug, but also criteria to use in virtual screening campaigns for other p53 activators.
Highlights
P53 is the master tumor suppressor protein [1,2,3]
As a result of this research, we have found that the reactive double bonds of the alkylating molecules methylene quinuclidinone (MQ), NB, MIRA–1, STIMA–1 and CP-31398, are all directed towards the C124 thiol group in their best binding poses
Our calculations showed that both mutants, R175H-mp53 and R273Hmp53, had lower affinities to DNA with estimated binding energy (EBE) of −39 and −49 kcal・mol–1, respectively
Summary
P53 is the master tumor suppressor protein [1,2,3]. It regulates diverse cellular processes including cell proliferation, apoptosis, senescence, metabolism and DNA repair [1,2,3]. A few compounds have been identified to restore the wt activity to mp including PRIMA–1 (short for ‘p53 reactivation and induction of massive apoptosis’) [9], MIRA–1 [10], CP-31398 [11], 3-Methylene-2-norbornanone [12], STIMA–1 [13] and stictic acid [14]. A study by Lambert et al [9] showed that PRIMA–1 and APR-246 are both prodrugs whose active product is methylene quinuclidinone (MQ) While it has been well-established that MQ restores the wt activity to mp, additional mechanisms of MQ action, reviewed in [17], have been proposed. MQ was primarily found to restore the transcriptional activity of mp53 This is supported by the fact that PRIMA–1-treated-mp, transferred to p53 null cells, led to the activation of p53 target genes transcription and the induction of apoptosis [9]. Ellipticine, 9-hydroxy-ellipticine, WR–1065 and WR-2721, which are non-alkylating p53 activators, were predicted to interact directly with C124
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