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

Abstract

p53 is a marginally stable protein that is mutated in 50 % of all human cancers [1]. The region of the protein that contains most of these mutations is the DNA binding domain (DBD). This DBD controls the transcription of p53-dependent genes through the binding of DNA, and is the main focus of the work presented in this thesis.

Three aspects of this DBD are investigated in this work. The first looks at the coordi-nated zinc ion of the DBD. Treatment of this zinc ion in molecular dynamics simulations has been performed in a variety of ways previously in the literature. Application of six of these zinc ion models to this DBD system has been done and examination of their similarities and differences of their respective molecular dynamics trajectories has been performed. It was determined that a bonded model named ZAFF [2] was the most preferable way to describe the structural zinc ion of the p53 DBD.

A second investigation looked into the differences between many of the mutations of the DBD of p53. This was done by performing pocket analysis and druggability analysis based on molecular dynamics trajectories to determine any potential binding sites on the surfaces of each of the mutants, with the motivation of looking for novel ways to restabilise the p53 protein. This analysis was supported by a series of solvent mapping simulations using molecules known to have a beneficial effect on the Y220C mutant of p53. The solvent mapping simulations added extra information as to where fragment-like molecules may like to bind on the surface of this mutant. Overall, this investigation reports a comprehensive review of potential binding sites over the surface of all of the most common ‘hotspot’ p53 mutants, and the Y220C mutant. This gave insight into the pockets that are targetable in future restabilising molecule development investigations.
The final investigation of this thesis, looked at a conformational flip of a loop at the DNA binding surface. This loop is implicated in both DNA binding and viral protein binding in different conformations. A free energy analysis between the two conformations was performed using umbrella sampling simulations. These simulations ultimately showed a difference of less than 1 kcal/mol between the two loop conformers. This means that blocking the viral protein conformer site could be a viable therapeutic option against this simian virus 40 (SV40).

Overall, this thesis has explored a variety of different methods to model the DBD of p53 computationally. The main drive of this work was towards the development of therapeutics, which has been discussed in the latter two investigations of this thesis.

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Identifiers

ORCID for Jonathan W. Essex: orcid.org/0000-0003-2639-2746

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