Abstract 5070: Structure-function studies and drug design on the human histone lysine methyltransferases NSD1, NSD2 and NSD3
Authors: Luccio Eric Di , Mevius Damiaan E.H.F , Shen Yunpeng , Noh Yeon Jeong , Kim Jihyeon , Morishita Masayo 
Published: July 2017

Chromatin dynamics are plastic processes controlled by epigenetic modifications on the DNA and histone tails that play a critical role in gene expression. Interestingly, DNA and histones modifications are also under the influence of exogenous factors such as pollutants, smoking, sun exposure, daily diet, alcohol consumption and environmental stress. Departure from “normal” cellular homeostatic conditions is influenced by aberrant accumulation of specific epigenetic patterns, which may contribute to the onset of diseases ranging from diabetes to cancers and neurological disorders. Moreover, epigenetic modifications appear to be inheritable to some extend and affect gene expression in the offspring.

One of the key epigenetic modifications is histone methylation, which is catalyzed by histone methyl transferases (HMTases). The nuclear receptor binding SET domain proteins (NSDs) consist of a family of three HMTases, NSD1, NSD2 and NSD3 all of which are bona fide oncoproteins. The NSD HMTases are primarily responsible for methylation of H3K36 and H4K20 in vivo. However, the outlines of the NSDs biological roles in normal and pathological conditions remain unclear. Mutation, alteration or overexpression of the NSD HMTases results in growth defects and is linked to an increasing number of pathologies, carcinogenesis and is a maker for tumor progression and prognosis. However, inhibition of HMTases and especially NSDs by small molecules may offer therapeutic opportunities, especially in cases with poor prognoses, such as multiple myeloma. To date, few HMTase inhibitors exist and no inhibitors specific to the NSD family have been identified. Therefore, a better understanding of the structure-function relationship and the design of specific, selective and bioavailable HMTase inhibitors is essential for novel cancer therapy.

In this study, we first we focused on understanding the substrate specificity of the NSDs in vitro to get insight into the druggability of the NSDs. Next, we performed virtual ligand screening and identified the hit molecule LEM-07/14 with an IC50 value of 11.5 µM inhibition against NSD2. LEM-07/14 derivatives resulted in a 45% methylation activity reduction in vitro. Furthermore, we identified BIX-01294 as an NSD inhibitor that differentially inhibits H3K36 methylation by NSD1, NSD2, and NSD3 with IC50 values of 40~112 µM and investigated the molecular basis of inhibition using docking studies on the NSD homology models. Next, we present our X-ray crystallographic efforts on the NSDs and their applications to selective and specific drug-design.

Citation Format: Eric Di Luccio, Damiaan E.H.F Mevius, Yunpeng Shen, Yeon Jeong Noh, Jihyeon Kim, Masayo Morishita. Structure-function studies and drug design on the human histone lysine methyltransferases NSD1, NSD2 and NSD3 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5070. doi:10.1158/1538-7445.AM2017-5070