p53 is known as the Guardian of the Genome. The p53 protein binds to consensus DNA sequences, allowing transcription of p53-dependent genes which trigger downstream events that lead to cell cycle arrest, apoptosis or cellular senescence, thereby destroying tumour cells. The p53 protein is prone to mutation and is known to be mutated in 50 % of human tumours. There are two main routes by which mutation affects p53 function. First, mutations of the DNA binding interface directly influence DNA binding, and second, since wild-type p53 is only marginally stable at body temperature, some mutants act to destabilise its folded state. Given the critical role of p53 in cancer, there is considerable interest in designing small molecules capable of binding to mutant p53, stabilising its tertiary structure, and hence reactivating DNA binding. In this presentation we report two studies relevant to p53 restabilising drug development. First, to determine plausible binding sites for restabilising small-molecules, we have performed a pocket and druggability analysis of wild-type and mutant p53, based on molecular dynamics trajectories. This analysis was supported by a series of solvent mapping simulations using molecules known to have a stabilising effect on the Y220C mutant of p53. The solvent mapping is able to correctly identify known binding modes, but finds others in addition. We present a comprehensive picture of mutation-dependent potential binding sites on the protein surface, indicating which may be targetable in the development of future restabilising drugs. Second, the small molecule PRIMA-1 (p53 Re-activation and Induction of Massive Apoptosis) is known to restore the p53 wild-type conformation, preserve the specific DNA binding of wild-type p53, and reactivate DNA binding for many p53 mutants. PRIMA-1 is a pro-drug which performs a Michael addition to cysteine residues, but the precise molecular mechanism by which it restores p53 function is not well understood. In this study, we use classical computer simulations to explore a range of possible adducts of p53 with PRIMA-1 and other Michael acceptors. Our simulations point to the adducts stabilising critical conformations of p53 required for dimerisation, suggesting that Michael acceptors restore p53 function by stabilising the biologically active dimer. This new understanding will allow further optmisation of PRIMA-1 derivatives.

Computational investigation of the DNA binding domain of p53: A drive towards novel therapeutics

253rd National Meeting (2017)

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