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Computational identification of a transiently open L1/S3 pocket for reactivation of mutant p53
Christopher D Wassman1, Roberta Baronio, Özlem Demir
1Department of Computer Science, University of California, Irvine, Irvine, California 92697, USA.
Abstract:
The tumour suppressor p53 is the most frequently mutated gene in human cancer. Reactivation of mutant p53 by small molecules is an exciting potential cancer therapy. Although several compounds restore wild-type function to mutant p53, their binding sites and mechanisms of action are elusive. Here computational methods identify a transiently open binding pocket between loop L1 and sheet S3 of the p53 core domain. Mutation of residue Cys124, located at the centre of the pocket, abolishes p53 reactivation of mutant R175H by PRIMA-1, a known reactivation compound. Ensemble-based virtual screening against this newly revealed pocket selects stictic acid as a potential p53 reactivation compound. In human osteosarcoma cells, stictic acid exhibits dose-dependent reactivation of p21 expression for mutant R175H more strongly than does PRIMA-1. These results indicate the L1/S3 pocket as a target for pharmaceutical reactivation of p53 mutants.
Insights
Researchers identified a new binding site on mutant p53 (a key cancer gene) and found stictic acid can reactivate its function, offering a promising cancer therapy approach.
Area of Science:
- Oncology
- Molecular Biology
- Drug Discovery
Background:
- The p53 tumor suppressor is frequently mutated in human cancers.
- Reactivating mutant p53 using small molecules is a potential therapeutic strategy.
- The binding sites and mechanisms of p53-reactivating compounds are not well understood.
Purpose of the Study:
- To identify novel binding sites for p53 reactivation compounds.
- To discover new compounds capable of reactivating mutant p53.
- To validate a computational approach for identifying drug targets on p53.
Main Methods:
- Computational methods were used to identify a transient binding pocket in the p53 core domain.
- Ensemble-based virtual screening was performed against the identified pocket.
- Mutational analysis of Cys124 and cellular assays were used to validate compound efficacy.
Main Results:
- A novel binding pocket between loop L1 and sheet S3 of the p53 core domain was identified.
- Mutation of Cys124 abolished p53 reactivation by PRIMA-1, confirming the pocket's importance.
- Stictic acid was identified as a potential p53 reactivation compound via virtual screening.
- Stictic acid demonstrated dose-dependent reactivation of p21 expression in osteosarcoma cells harboring mutant p53 (R175H).
Conclusions:
- The L1/S3 pocket represents a druggable target for reactivating mutant p53.
- Stictic acid shows potential as a therapeutic agent for cancers with p53 mutations.
- Computational screening can effectively identify novel binding sites and compounds for p53 reactivation.
