Structural Basis of Inhibition of the Pioneer Transcription Factor NF-Y by Suramin.

Valentina Nardone,Cristina Airoldi,Diletta Dolfini,Nerina Gnesutta,Carlo Camilloni,Andrea Bernardini,Antonio Chaves-Sanjuan,Sebastiano Pasqualato,Andrea Saponaro,Roberto Mantovani,Marco Nardini,Michela Lapi

doi:10.3390/cells9112370

Valentina Nardone, Cristina Airoldi + Show 10 more

Open Access

https://doi.org/10.3390/cells9112370

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Abstract

NF-Y is a transcription factor (TF) comprising three subunits (NF-YA, NF-YB, NF-YC) that binds with high specificity to the CCAAT sequence, a widespread regulatory element in gene promoters of prosurvival, cell-cycle-promoting, and metabolic genes. Tumor cells undergo “metabolic rewiring” through overexpression of genes involved in such pathways, many of which are under NF-Y control. In addition, NF-YA appears to be overexpressed in many tumor types. Thus, limiting NF-Y activity may represent a desirable anti-cancer strategy, which is an ongoing field of research. With virtual-screening docking simulations on a library of pharmacologically active compounds, we identified suramin as a potential NF-Y inhibitor. We focused on suramin given its high water-solubility that is an important factor for in vitro testing, since NF-Y is sensitive to DMSO. By electrophoretic mobility shift assays (EMSA), isothermal titration calorimetry (ITC), STD NMR, X-ray crystallography, and molecular dynamics (MD) simulations, we showed that suramin binds to the histone fold domains (HFDs) of NF-Y, preventing DNA-binding. Our analyses, provide atomic-level detail on the interaction between suramin and NF-Y and reveal a region of the protein, nearby the suramin-binding site and poorly conserved in other HFD-containing TFs, that may represent a promising starting point for rational design of more specific and potent inhibitors with potential therapeutic applications.

Highlights

The transcription factor (TF) NF-Y is a nuclear protein that binds the CCAAT sequence in promoters with a very high specificity [1]
Identifying Suramin as a Compound Binding to NF-Y
Docking simulations were carried out using the NF-YB/NF-YC histone fold domains (HFDs) dimer (NF-Yd: derived from the 4AWL PDB structure) as a receptor

Summary

Introduction

The transcription factor (TF) NF-Y is a nuclear protein that binds the CCAAT sequence in promoters with a very high specificity [1]. The CCAAT box is an important regulatory element, typically located at a conserved distance of −60/−100 bp from the Transcriptional Start Site (TSS) and it is present in 25%. Of eukaryotic promoters [2]. This occurrence is similar to that of the TATA box, and the CCAAT box is mostly found in TATA-less promoters [2,3]. Genome-wide assays and in vitro experiments have demonstrated that NF-Y is the primary CCAAT-binding protein [4]. NF-Y is a heterotrimer formed by evolutionarily conserved subunits: NF-YA, NF-YB, and NF-YC.

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