Experimental data on the binding and activity of 1,3,4-Oxadiazoles to Bromodomain factor 3 (TcBDF3) of Trypanosoma cruzi

Abstract

File List: Folder 1- Table_raw_data_antiparasitic_activity: Contains table files with the raw data used to obtain the IC50 of compounds A1B4c and A5B4c in epimastigotes, trypomastigotes and amastigotes (Betagal ETA.tab)(Absorbance 570 nm vs concentration tables) and Vero cells (MTT ciclicos.tab) (Absorbance 540 nm vs concentration tables). 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. Folder 2- Tables_raw_data_binding: Contains table files with the raw data of the Differential Scanning Fluorescence (DSF) assay (Differential_Scanning_Fluorescence.tab) to obtain temperature vs concentration plots. The fluorescnece polatization raw data (Fluorescence_Polarization.tab) to obtain the FP vs concentration plots. And the fluorescence quenching raw data (Fluorescence_Quenching_A1B4.tab) to obtain the concentration vs fluorescence plots. Data was analyzed by performing concentration vs. relative fluorescence for quenching assays. For DSF 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. Folder 3- bdf3_sequence_and_phylogenetic_analysis: Has all the files needed 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. Run the script file filtering_analysis.py. AF2 BDF3 ET model used as query in Foldseek and its output can be found in BDF3_ET_foldseek_query. HMMER output for BD detection using highly confident ET containing proteins (prob > 0.9) is in both TXT and XLSX formats, along with the commands used to run hmmsearch (hmmer_commands.sh). 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. Folder 4- Docking: Contains the .pdb files of the docking simulations of TcBDF3 with the small molecules A1B4, A1B4c and A7B4. 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).