» Articles » PMID: 37443295

Disruptor: Computational Identification of Oncogenic Mutants Disrupting Protein-protein and Protein-DNA Interactions

Overview
Journal Commun Biol
Specialty Biology
Date 2023 Jul 13
PMID 37443295
Authors
Affiliations
Soon will be listed here.
Abstract

We report an Osprey-based computational protocol to prospectively identify oncogenic mutations that act via disruption of molecular interactions. It is applicable to analyse both protein-protein and protein-DNA interfaces and it is validated on a dataset of clinically relevant mutations. In addition, it is used to predict previously uncharacterised patient mutations in CDK6 and p16 genes, which are experimentally confirmed to impair complex formation.

Citing Articles

Decoding the functional impact of the cancer genome through protein-protein interactions.

Fu H, Mo X, Ivanov A Nat Rev Cancer. 2025; 25(3):189-208.

PMID: 39810024 DOI: 10.1038/s41568-024-00784-6.


DexDesign: an OSPREY-based algorithm for designing de novo D-peptide inhibitors.

Guerin N, Childs H, Zhou P, Donald B Protein Eng Des Sel. 2024; 37.

PMID: 38757573 PMC: 11099876. DOI: 10.1093/protein/gzae007.

References
1.
Shi Y, Hata A, Lo R, Massague J, Pavletich N . A structural basis for mutational inactivation of the tumour suppressor Smad4. Nature. 1997; 388(6637):87-93. DOI: 10.1038/40431. View

2.
Tate J, Bamford S, Jubb H, Sondka Z, Beare D, Bindal N . COSMIC: the Catalogue Of Somatic Mutations In Cancer. Nucleic Acids Res. 2018; 47(D1):D941-D947. PMC: 6323903. DOI: 10.1093/nar/gky1015. View

3.
Al-Numair N, Martin A . The SAAP pipeline and database: tools to analyze the impact and predict the pathogenicity of mutations. BMC Genomics. 2013; 14 Suppl 3:S4. PMC: 3665582. DOI: 10.1186/1471-2164-14-S3-S4. View

4.
Li Z, Ivanov A, Su R, Gonzalez-Pecchi V, Qi Q, Liu S . The OncoPPi network of cancer-focused protein-protein interactions to inform biological insights and therapeutic strategies. Nat Commun. 2017; 8:14356. PMC: 5316855. DOI: 10.1038/ncomms14356. View

5.
Muller P, Vousden K . p53 mutations in cancer. Nat Cell Biol. 2012; 15(1):2-8. DOI: 10.1038/ncb2641. View