Mimicking the Nucleosomal Context in Peptide-Based Binders of a H3K36me Reader Increases Binding Affinity While Altering the Binding Mode.

Velten Horn,Seino A K Jongkees,Hugo Van Ingen

doi:10.3390/molecules25214951

Velten Horn, Seino A K Jongkees + Show 1 more

Open Access

https://doi.org/10.3390/molecules25214951

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Abstract

Targeting of proteins in the histone modification machinery has emerged as a promising new direction to fight disease. The search for compounds that inhibit proteins that readout histone modification has led to several new epigenetic drugs, mostly for proteins involved in recognition of acetylated lysines. However, this approach proved to be a challenging task for methyllysine readers, which typically feature shallow binding pockets. Moreover, reader proteins of trimethyllysine K36 on the histone H3 (H3K36me3) not only bind the methyllysine but also the nucleosomal DNA. Here, we sought to find peptide-based binders of H3K36me3 reader PSIP1, which relies on DNA interactions to tightly bind H3K36me3 modified nucleosomes. We designed several peptides that mimic the nucleosomal context of H3K36me3 recognition by including negatively charged Glu-rich regions. Using a detailed NMR analysis, we find that addition of negative charges boosts binding affinity up to 50-fold while decreasing binding to the trimethyllysine binding pocket. Since screening and selection of compounds for reader domains is typically based solely on affinity measurements due to their lack of enzymatic activity, our case highlights the need to carefully control for the binding mode, in particular for the challenging case of H3K36me3 readers.

Highlights

Post-translational modifications of histone proteins, loosely referred to as epigenetic modifications, play a key role in regulating nuclear processes such as gene expression and DNA repair, replication, or transcription [1,2]
We designed two H3 tail peptide models that incorporate negatively charged residues to mimic the additional attractive electrostatic forces generated by the DNA in the nucleosomal context
We explored the potential for peptide-based binders of the PSIP1PWWP domain, a reader of the H3K36me3 modification and involved in HIV integration and cancer

Summary

Introduction

Post-translational modifications of histone proteins, loosely referred to as epigenetic modifications, play a key role in regulating nuclear processes such as gene expression and DNA repair, replication, or transcription [1,2]. Deregulation of the installation, recognition or removal of these modifications, such as phosphorylation and lysine ubiquitination, methylation or acetylation, are intimately associated with a wide range of pathologies As such the proteins that write, read or remove histone modifications have emerged as promising therapeutic targets, resulting in a growing number of small-molecule and peptide-based epigenetic drugs [3,4,5,6]. Methyllysine recognition is driven by methylation reader havebetween been developed but in general, forming the number promisingcage inhibitors cation–π interactions several[11,12,13,14], aromatic residues anofaromatic and for the this class of reader is significantly lower [15,16]. We designed two H3 tail peptide models that incorporate negatively charged residues to mimic the additional attractive electrostatic forces generated by the DNA in the nucleosomal context. NMR titration experiments with both H3 and H3E7 impact of a step-wise increase in negative charge can be monitored

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