A Chemical Probe for Tudor Domain Protein Spindlin1 to Investigate Chromatin Function

Abstract

Modifications of histone tails, including lysine/arginine methylation, provide the basis of a 'chromatin or histone code'. Proteins that contain 'reader' domains can bind to these modifications and form specific effector complexes, which ultimately mediate chromatin function. The spindlin1 (SPIN1) protein contains three Tudor methyllysine/arginine reader domains and was identified as a putative oncogene and transcriptional co-activator. Here we report a SPIN1 chemical probe inhibitor with low nanomolar in vitro activity, exquisite selectivity on a panel of methyl reader and writer proteins, and with submicromolar cellular activity. X-ray crystallography showed that this Tudor domain chemical probe simultaneously engages Tudor domains 1 and 2 via a bidentate binding mode. Small molecule inhibition and siRNA knockdown of SPIN1, as well as chemoproteomic studies, identified genes which are transcriptionally regulated by SPIN1 in squamous cell carcinoma and suggest that SPIN1 may have a roll in cancer related inflammation and/or cancer metastasis. a n ≥ 2. Abbreviations; BLI (BioLayer Interferometry), ITC (Isothermal Titration Calorimetry), nd (not determined).

Structure‐Guided Discovery of a Potent and Selective Cell‐Active Inhibitor of SETDB1 Tudor Domain

“…( R , R )‐59 and its inactive enantiomer ( S , S )‐59 could serve as a pair of early‐stage tool compounds for investigating biological functions and disease associations of SETDB1‐TTD. Moreover, the current study together with recent discoveries of potent and selective small molecule inhibitors of Spindlin1 [7b, c] clearly demonstrated the feasibility of targeting tudor domains.…”

“…Nevertheless, unlike the widely studied bromodomain (BRD)‐containing proteins (acetyllysine readers), which have a large amount of inhibitors reported with several having already reached clinical trials, [6] a very limited number of small molecule inhibitors targeting tudor domain‐containing proteins have been reported [7] . And only two potent and selective inhibitors were disclosed, namely MS31 [7b] and VinSpinln, [7c] both of which are inhibitors of the Tudor domain containing protein, Spindlin1.…”

Advances and Opportunities in Epigenetic Chemical Biology

“…[199,200] Building upon these SPIN1 inhibitors, an international team has employed structure based drug design to develop a potent and selective SPIN1 probe named VinSpinIn. [201] The use of DNA-encoded chemical libraries (DELs) is a technique that has been used extensively for the identification of small-molecule probes [202] and has recently been applied to chromodomains. A DEL approach was used to improve the selectivity and affinity of a small-molecule inhibitor for chromodomain CBX8.…”

Driving Integrative Structural Modeling with Serial Capture Affinity Purification

“…We demonstrate the striking capabilities of this technology using a pair of proteins, Spindlin1 (SPIN1) and SPINDOC (c11orf84), which have previously been proposed to directly interact in biochemical 9 and computational 3 studies. SPIN1 is a well characterized histone methylation reader [9][10][11][12][13][14][15][16][17][18][19][20][21] , while SPINDOC has only been defined by its ability to bind SPIN1 9 . In this study, we first characterize the direct interaction and co-diffusion of SPIN1 and SPINDOC in live cells using imaging methods.…”