DOI: 10.57715/unr/nwdock
title: Experimental data on the binding and activity of 1,3,4-Oxadiazoles to Bromodomain factor 3 (TcBDF3) of Trypanosoma cruzi

description: Introduction Targeting lysine acetylation, particularly bromodomain-containing proteins (acetyl-lysine binders), shows promise as a novel antiparasitic target. Our research focuses on TcBDF3, a cytoplasmic bromodomain-containing protein crucial for Trypanosoma cruzi (the causative agent of Chagas Disease) differentiation that recognizes acetylated alpha-tubulin. In previous work, A1B4 was identified as a high-affinity binder of TcBDF3, showing significant trypanocidal activity with low host toxicity in vitro. Dataset content and file organization In this dataset, we included experimental data to support the trypanocidal activity of novel 1,3,4-Oxadiazoles: 1- Experimental raw data to support the trypanocidal activity of novel 1,3,4-Oxadiazoles: growth values using a beta-galactosidase expressing Trypanosoma cruzi line and MTT assays in the Vero cell line to calculate selectivity indexes. Data was analyzed by generating dose-response curves, fitting to a non-linear regression, and obtaining the half inhibitory concentrations (IC50) in a statistical analysis program. Files are included in Folder 1- Tables_raw_data_antiparasitic_activity. 2- Experimental raw data to support the binding of the novel 1,3,4-Oxadiazoles to bromodomain factor 3 of Trypanosoma cruzi (TcBDF3): Intrinsic fluorescence quenching assay, Differential Scanning Fluorescence (DSF) assay, Fluorescence polarization (FP) assay. Data was analyzed by performing concentration vs. relative fluorescence for quenching assays. For thermal shift assays, the melting temperatures obtained were plotted vs. concentration and fitted using the differential scanning fluorescence single binding site equation to get the dissociation constants (Kd). For Fluorescence polarization assays the percentage of inhibition was derived from the equation % inhibition =100[1 − (mP − mPf )/(mPb − mPf )], in which mPf is the free probe control and mPb is the bound probe control. Based on the percentage of inhibition, the half inhibitory concentration (IC50), or the inhibitor concentration at which 50% of the bound probe is displaced, was obtained by fitting the inhibition data. Files are included in Folder 2- Tables_raw_data_binding. 3- Raw data and specifications to support the phylogenetic analysis of TcBDF3 that allowed us to include it in the Bromodomain Extra Terminal (BET) family. Files are included in Folder 3- bdf3_sequence_and_phylogenetic_analysis. To reproduce the data produced for the paper "1,3,4-Oxadiazoles as inhibitors of the atypical member of the BET family Bromodomain Factor 3 from Trypanosoma cruzi (TcBDF3)", https://doi.org/10.3389/fmicb.2024.1465672, you can run the script filtering_analysis.py. AF2 BDF3 extra-terminal (ET) model used as a query in Foldseek and its output can be found in BDF3_ET_foldseek_query. HMMER output for bromodomain (BD) detection using highly confident ET-containing proteins (prob &gt; 0.9) is in both TXT and XLSX formats, along with the commands used to run hmmsearch (hmmer_commands.sh) Multiple Sequence Alignments (MSAs) generated using Jalview can be found in MSAs using the output FASTA sequences generated with the script (Fasta_files_for_tree). The phylogenetic analysis and trees generated with IQtree2 are located in final_BD-ET_tree.zip. 4- Docking simulation files to validate the binding of 1,3,4-Oxadiazoles to TcBDF3. These are the output files in pdb format of the best docking pose of a simulation performed with Glide in extra precision (XP) mode. The structure of the protein TcBDF3 was obtained from a representative snapshot of a molecular dynamics simulation. Ligand docking was performed using Schrodinger software (version 2023-3). The Protein Preparation Wizard within the Schrodinger software was used for protein preparation. LigPrep was used for ligand preparation. The 20x grid box was centered on the binding site. The ligands A1B4, A1B4c, and A5B4c are named UNK in their corresponding file (files A1B4_DOCK.pdb, A1B4c_DOCK.pdb y A5B4c_DOCK.pdb). Files are included in Folder 4- Docking. Value of the data: Chagas disease, caused by the protozoan parasite Trypanosoma cruzi, affects millions globally with increasing urban cases outside Latin America. Treatment is based on two drugs: benznidazole and nifurtimox, but chronic cases pose several challenges. These results make TcBDF3 a unique target due to its localization and known functions not shared with higher eukaryotes, which holds promise for Chagas disease treatment.