Profiling the dynamic interfaces of fluorinated transcription complexes for ligand discovery and characterization

William C. Pomerantz, Ningkun Wang, Ashley K. Lipinski, Rurun Wang, Tomasz Cierpicki, Anna K. Mapp

Research output: Contribution to journalArticle

35 Citations (Scopus)

Abstract

The conformationally dynamic binding surfaces of transcription complexes present a particular challenge for ligand discovery and characterization. In the case of the KIX domain of the master coactivator CBP/p300, few small molecules have been reported that target its two allosterically regulated binding sites despite the important roles that KIX plays in processes ranging from memory formation to hematopoiesis. Taking advantage of the enrichment of aromatic amino acids at protein interfaces, here we show that the incorporation of six 19F-labeled aromatic side chains within the KIX domain enables recapitulation of the differential binding footprints of three natural activator peptides (MLL, c-Myb, and pKID) in complex with KIX and effectively reports on allosteric changes upon binding using 1D NMR spectroscopy. Additionally, the examination of both the previously described KIX protein-protein interaction inhibitor Napthol-ASE-phosphate and newly discovered ligand 1-10 rapidly revealed both the binding sites and the affinities of these small molecules. Significantly, the utility of using fluorinated transcription factors for ligand discovery was demonstrated through a fragment screen leading to a new low molecular weight fragment ligand for CBP/p300, 1G7. Aromatic amino acids are enriched at protein-biomolecule interfaces; therefore, this quantitative and facile approach will be broadly useful for studying dynamic transcription complexes and screening campaigns complementing existing biophysical methods for studying these dynamic interfaces.

Original languageEnglish (US)
Pages (from-to)1345-1350
Number of pages6
JournalACS Chemical Biology
Volume7
Issue number8
DOIs
StatePublished - Aug 17 2012

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Transcription
Ligands
Aromatic Amino Acids
p300-CBP Transcription Factors
Proteins
Binding Sites
Molecules
Hematopoiesis
Biomolecules
Nuclear magnetic resonance spectroscopy
Screening
Transcription Factors
Magnetic Resonance Spectroscopy
Molecular Weight
Molecular weight
Phosphates
Data storage equipment
Peptides

Cite this

Profiling the dynamic interfaces of fluorinated transcription complexes for ligand discovery and characterization. / Pomerantz, William C.; Wang, Ningkun; Lipinski, Ashley K.; Wang, Rurun; Cierpicki, Tomasz; Mapp, Anna K.

In: ACS Chemical Biology, Vol. 7, No. 8, 17.08.2012, p. 1345-1350.

Research output: Contribution to journalArticle

Pomerantz, William C. ; Wang, Ningkun ; Lipinski, Ashley K. ; Wang, Rurun ; Cierpicki, Tomasz ; Mapp, Anna K. / Profiling the dynamic interfaces of fluorinated transcription complexes for ligand discovery and characterization. In: ACS Chemical Biology. 2012 ; Vol. 7, No. 8. pp. 1345-1350.
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