Evolving Spindlin1 Small Molecule Inhibitors Using Protein Microarrays
Narkhyun Bae1§, Monica Viviano2§, Xiaonan Su3§, Cari Sagum1,
Sabrina Castellano2,4, Claire Johnson1, Mahmoud Ibrahim Khalil1,5,
Haitao Li3*, Gianluca Sbardella2* and Mark T. Bedford1*
1Department
of Epigenetics and Molecular Carcinogenesis, The University of Texas MD
Anderson Cancer Center, Smithville, TX 78957, USA.
2Dipartimento
di Farmacia, Epigenetic Med Chem Lab, Università degli Studi di Salerno, Via
Giovanni Paolo II 132, I-84084 Fisciano (SA), Italy.
3Center
for Structural Biology, Department of Basic Medical Sciences, School of Medicine,
Tsinghua University, Beijing 100084, China.
4Dipartimento
di Medicina e Chirurgia, Università degli Studi di Salerno, Via Salvador Allende, I-
84081 Baronissi (SA), Italy.
5Molecular
Biology Unit, Department of Zoology, Faculty of Science, Alexandria University, Egypt.
Abstract
The discovery of inhibitors of methyl- and acetyl-binding domains has provided evidence
for the “druggability” of epigenetic effector molecules. The small molecule probe,
UNC1215, prevents methyl-dependent protein-protein interactions by engaging the
aromatic cage of MBT domains, and with lower affinity, Tudor domains. Using a library of
tagged UNC1215 analogs we screened a protein domain microarray of methyl-lysine
effector molecules to rapidly detect compounds with novel binding profiles - either
improved or loosened specificity. Using this approach, we identified a compound
(EML405) that acquired a novel interaction with the Tudor domain-containing protein
Spindlin1 (SPIN1). Structural studies revealed that the symmetric nature of EML405
allows it to simultaneously engage two of SPIN1’s Tudor domains, and also facilitated
the rational synthesis of more selective SPIN1 inhibitors (EML631-633). The EML631633 compounds engage SPIN1 in cells, block its ability to “read” H3K4me3 marks, and
inhibit its transcriptional coactivator activity. Protein microarrays can thus be used as a
platform to “target hop” and identify small molecules that bind and compete with
domain–motif interactions.