Cassandre's Research Blog

Fall 2024


Research Topic

Development of Anti-Cancer Peptidomimetics Targeting Enhancer of Zeste Homolog 2 (EZH2) Mediated Protein-Protein Interactions in the Polycomb Repressive Complex 2 (PRC2)


Background

The polycomb repressive complex 2 (PRC2) is a chromatin regulatory complex that plays a crucial role in the repression of various developmental genes. PRC2 possess methyltransferase activity, catalyzing the monomethylation (H3K27me1), dimethylation (H3K27me2), and trimethylation (H3K27me3) of lysine 27 on histone H3. These post-translational modifications are necessary for the regulation of chromatin structure,  organizational development, cellular identity, and the maintenance of gene expression patterns through the facilitation of proper gene silencing. Dysregulation of PRC2 activity, often due to mutations, are known to contribute to the development and progression of various types of cancer, establishing PRC2 as a high-priority area of research in the field of cancer epigenetics and a promising target for therapeutic intervention1.

The PRC2 complex is comprised of four core subunits: EZH1, EZH2, EED, and SUZ12. Enhancer of zeste homolog 2 (EZH2), the paralog of EZH1, is considered to be the primary catalytic subunit of PRC2, playing a central role in embryonic development. It is known to be highly effective in the catalyzation of H3K27 methylation, a function dependent on the presence of EED and SUZ12. In the absence of these subunits, EZH2 becomes inhibited and its activity becomes significantly impaired. Additionally, SUZ12 stabilizes the PRC2 complex via its VEFS domain, making it essential for the structural integrity. All together, these subunits form a tightly regulated system essential for the catalytic activity and proper function of the PRC2 complex2

Among these subunits, EZH2 has garnered significant attention in research due to its involvement in cancer development. Studies have shown that the overexpression and mutation of EZH2 is observed in many types of cancers, including breast cancer, prostate cancer, endometrial cancer, melanoma, bladder cancer, colon cancer, liver cancer, lung cancer, and more. One of the prominent functions of EZH2 is the silencing of multiple tumor suppressor genes through its histone methyltransferase activity by targeting genes involved in cell differentiation and cell proliferation, as well as apoptosis, migration, and invasion. However, EZH2 has been shown to operate independent of its role as a repressor, behaving as a transcriptional coactivator in various tumors.This dysregulation can lead to the aberrant silencing of critical tumor suppressor genes, promoting uncontrolled cell growth, resistance to apoptosis, and enhanced metastatic potential. As a result, EZH2 has become a cancer target, that will be the focus of my research 3.


Introduction

The aim of this research is to use computational modeling to gain insights into designing peptidomimetics that effectively target protein-protein interactions involved in the methyltransferase activity of the Polycomb Repressive Complex 2 (PRC2). This involved familiarizing myself with Maestro Schrödinger software to model and analyze peptides capable of dysregulation of EZH2 and other catalytic subunits involved in the development of cancer. 


Getting Familiar with Maestro 

The starting point of my research involved getting familiar with Maestro, a molecular modeling software developed by Schrödinger. Maestro is a widely utilized platform in computational chemistry, structural biology, and drug discovery, capable of molecular visualization, structure optimization, dynamic simulations, and comprehensive data analysis. To build a foundation with this platform, I began by completing several key tutorials. The first was “A Chemist Guide to Maestro” which involved learning how to navigate the software, create and modify molecules, draw structures, and present them in both 2D and 3D forms, as well as construct protein-ligand complexes. Next, I completed the "Introduction to Structure Preparation and Visualization" tutorial , which focused on preparing protein and ligand structures for visualization, simulations and analyses. Following this, I explored the “Re-scoring Docked Ligands with MM-GBSA" and "Structure-Based Virtual Screening Using Glide,” tutorial, which introduced the molecular mechanics with generalized Born and surface area (MM-GBSA) calculation method used to approximate the free energy of binding in protein-ligand complexes. Additionally, I was provided insight into Glide, a docking tool used to predict ligand binding poses and assess binding affinities at target protein's active sites. Lastly, I completed the “Introduction to All-Atom Molecular Dynamics Simulations with Desmond" tutorial, which covered molecular model simulations used to investigate processes like protein folding and ligand interactions, offering valuable insights into drug discovery. Overall, these tutorials have provided me with a deeper understanding of effective molecular modeling and analysis, which can be applied in the discovery of anti-cancer peptidomimetics.


References

(1) Laugesen, A.; Højfeldt, J. W.; Helin, K. Molecular Mechanisms Directing PRC2 Recruitment and H3K27 Methylation. Molecular Cell 2019, 74 (1), 8–18. https://doi.org/10.1016/j.molcel.2019.03.011.

(2) van Mierlo, G.; Veenstra, G. J. C.; Vermeulen, M.; Marks, H. The Complexity of PRC2 Subcomplexes. Trends in Cell Biology 2019, 29 (8), 660–671. https://doi.org/10.1016/j.tcb.2019.05.004.

(3) Huang, J.; Gou, H.; Yao, J.; Yi, K.; Jin, Z.; Matsuoka, M.; Zhao, T. The Noncanonical Role of EZH2 in Cancer. Cancer Science 2021, 112 (4), 1376–1382. https://doi.org/10.1111/cas.14840.