This readme file was generated on 2024-10-01 by Victoria Lucia Alonso


GENERAL INFORMATION

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

Author/Associate or Co-investigator Information
Name: Victoria Lucia Alonso
ORCID:0000-0001-9518-8576
Institution:Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario IBR-CONICET; Argentina 
Address: Suipacha 531-2000-Rosario-Santa Fe-Argentina  
Email: alonso@ibr-conicet.gov.ar

Author/Principal Investigator Information
Name: Esteban Serra
ORCID: 0000-0001-5986-7459
Institution: Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario IBR-CONICET; Argentina  
Address: Suipacha 531-2000-Rosario-Santa Fe-Argentina
Email: serra@ibr-conicet.gov.ar

Author/Alternate Contact Information
Name: Elvio Rodriguez Araya
ORCID: 0009-0005-1373-6265
Institution:Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario IBR-CONICET; Argentina 
Address: Suipacha 531-2000-Rosario-Santa Fe-Argentina  
Email: rodriguezaraya@ibr-conicet.gov.ar

Date of data collection: 2022-01-01 to 2023-12-31

Geographic location of data collection: Rosario, Santa Fe, Argentina

Information about funding sources that supported the collection of the data: 
Agencia Nacional de Promoción de la Investigación, el Desarrollo Tecnológico y la Innovación. PICT-2020-SERIEA-01704 and PICT2019-0526.
Universidad Nacional de Rosario. 800-201903-00048UR

SHARING/ACCESS INFORMATION

Links to publications that cite or use the data: https://doi.org/10.3389/fmicb.2024.1465672

Links/relationships to ancillary data sets: 

Was data derived from another source? No

Recommended citation for this dataset: Alonso, Victoria Lucia; Escalante, Andrea Marta; Rodríguez Araya, Elvio; Frattini, Gianfranco; Tavernelli, Luis Emilio; Moreno, Diego M.; Furlan, Ricardo Luis Eugenio; Serra, Esteban Carlos, 2024, "Experimental data on the binding and activity of 1,3,4-Oxadiazoles to Bromodomain factor 3 (TcBDF3) of Trypanosoma cruzi", https://doi.org/10.57715/UNR/NWDOCK, RDA UNR

DATA & FILE OVERVIEW

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).

Additional related data collected that was not included in the current data package: No

Are there multiple versions of the dataset? No

METHODOLOGICAL INFORMATION

Description of methods used for collection/generation of data: All methods used to collect and generate the data are detailed in: Alonso, V. L., Escalante, A. M., Araya, E. R., Frattini, G., Tavernelli, L. E., Moreno, D. M., Furlan, R. L., & Serra, E. (2024). 1,3,4-Oxadiazoles as inhibitors of the atypical member of the BET family Bromodomain Factor 3 from Trypanosoma cruzi (TcBDF3). Frontiers in Microbiology, 15, 1465672. https://doi.org/10.3389/FMICB.2024.1465672 doi: 10.3389/fmicb.2024.1465672

Description of the beta-galactosidase assay used can be obtain in: Alonso VL, Manarin R, Perdomo V, Gulin E, Serra E, Cribb P. In Vitro Drug Screening Against All Life Cycle Stages of Trypanosoma cruzi Using Parasites Expressing β-galactosidase. J Vis Exp. 2021 Nov 5;(177). doi: 10.3791/63210. PMID: 34806703.

Instrument- or software-specific information needed to interpret the data: 
GrapPad Prism, Version: 9.0
AmberTools, Version: 22
Schrödinger, Version: 2023-3
Maestro, Version: Biorad
IQ-TREE2, Version: 2.3.6

Describe any quality-assurance procedures performed on the data: Controls of each experiment are detailed in: Alonso, V. L., Escalante, A. M., Araya, E. R., Frattini, G., Tavernelli, L. E., Moreno, D. M., Furlan, R. L., & Serra, E. (2024). 1,3,4-Oxadiazoles as inhibitors of the atypical member of the BET family Bromodomain Factor 3 from Trypanosoma cruzi (TcBDF3). Frontiers in Microbiology, 15, 1465672. https://doi.org/10.3389/FMICB.2024.1465672 doi: 10.3389/fmicb.2024.1465672 

People involved with sample collection, processing, analysis and/or submission: Alonso, Victoria Lucia; Escalante, Andrea Marta; Rodríguez Araya, Elvio; Frattini, Gianfranco; Tavernelli, Luis Emilio; Moreno, Diego M.

DATA-SPECIFIC INFORMATION FOR: Betagalactosidase assay

Number of variables: 2 (concentration of A1B4c and A5B4c vs. Absorbance 590 nm)

Number of cases/rows: 5 to 8 depending on the compound.

Variable List: Absorbance at 570 nm 

DATA-SPECIFIC INFORMATION FOR: MTT assay

Number of variables: 2 (concentration of A1B4c and A5B4c vs. Absorbance 540 nm)

Number of cases/rows: 4 for each compound.

Variable List: Absorbance at 540 nm 


DATA-SPECIFIC INFORMATION FOR: Differential Scanning Fluorescence assay

Number of variables: 2 (concentration of A1B4, A5B4, A1B4c and A5B4c vs. Melting temperature for TcBDF3 and TcBD3)

Number of cases/rows: 6 for each compound.

Variable List: Melting temperature 

DATA-SPECIFIC INFORMATION FOR: Fluorescence Polarization assay

Number of variables: 2 (concentration of A1B4, A1B4c and A5B4c vs. Fluorescence Polarization (mP) for TcBD3)

Number of cases/rows: 8 for each compound.

Variable List: Fluorescence polarization

DATA-SPECIFIC INFORMATION FOR: Fluorescence Quenching assay

Number of variables: 2 (concentration of A1B4 and iBET151 vs. Fluorescence for TcBD3, TcBDF3, TcBD2, TcBDF3m)

Number of cases/rows: 4 concentrations of A1B4 or iBET151.

Variable List: Fluorescence (arbritary units)