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Small-molecule binding sites to explore protein-protein interactions in the cancer proteome.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Xu, David Jalal, Shadia I. Sledge, George W. Meroueh, Samy O.
Description	Country affiliation: United States Author Affiliation: Xu D ( Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA.)
Abstract	The Cancer Genome Atlas (TCGA) offers an unprecedented opportunity to identify small-molecule binding sites on proteins with overexpressed mRNA levels that correlate with poor survival. Here, we analyze RNA-seq and clinical data for 10 tumor types to identify genes that are both overexpressed and correlate with patient survival. Protein products of these genes were scanned for binding sites that possess shape and physicochemical properties that can accommodate small-molecule probes or therapeutic agents (druggable). These binding sites were classified as enzyme active sites (ENZ), protein-protein interaction sites (PPI), or other sites whose function is unknown (OTH). Interestingly, the overwhelming majority of binding sites were classified as OTH. We find that ENZ, PPI, and OTH binding sites often occurred on the same structure suggesting that many of these OTH cavities can be used for allosteric modulation of enzyme activity or protein-protein interactions with small molecules. We discovered several ENZ (PYCR1, QPRT, and HSPA6) and PPI (CASC5, ZBTB32, and CSAD) binding sites on proteins that have been seldom explored in cancer. We also found proteins that have been extensively studied in cancer that have not been previously explored with small molecules that harbor ENZ (PKMYT1, STEAP3, and NNMT) and PPI (HNF4A, MEF2B, and CBX2) binding sites. All binding sites were classified by the signaling pathways to which the protein that harbors them belongs using KEGG. In addition, binding sites were mapped onto structural protein-protein interaction networks to identify promising sites for drug discovery. Finally, we identify pockets that harbor missense mutations previously identified from analysis of TCGA data. The occurrence of mutations in these binding sites provides new opportunities to develop small-molecule probes to explore their function in cancer.
File Format	HTM / HTML
ISSN	1742206X
Issue Number	10
Journal	Molecular BioSystems
Volume Number	12
e-ISSN	17422051
Language	English
Publisher	Royal Society of Chemistry
Publisher Date	2016-10-20
Publisher Place	Great Britain (UK)
Access Restriction	Subscribed
Content Type	Text
Resource Type	Article
Subject	Molecular Biology Biotechnology

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