Computational protocol: Inhibition of poly(ADP-ribose) Polymerase Interferes with Trypanosoma cruzi Infection and Proliferation of the Parasite

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Protocol publication

[…] IC50 values were determined for the best inhibitors based on the inhibitor screening. The IC50 value for the first generation PARP inhibitor 3-AB was determined as a reference value. The separate data points were measured in quadruplicates. The assay setup was similar to the inhibitor screening, but the incubation time was set so that the substrate conversion in the control wells was approximately 20%. The fluorescence signal was converted to inhibition percentage and fitted using sigmoidal dose-response fitting with variable slope (Graphpad Prism). The curves were extrapolated to 0% and 100% of inhibition by setting their inhibitor concentration 2 log units below or above the first and the last inhibitor concentration, respectively. [...] Sequences in the protein data bank were searched for homologues of TcPARP (Uniprot id: Q4PQV7). Homologous high quality structures of hPARP-1 (PDB code 3GJW ), human PARP-2 (hPARP-2) (PDB code 3KJD ) and human PARP-3 (hPARP-3) (PDB code 3C4H ) were selected and aligned with TcPARP using ClustalW with minor manual editing based on the superposed structures. Alignment was analyzed using Aline . TcPARP was modeled using the hPARP-1 structure and multiple sequence alignment using Modeller . Superpositions used in the text and figures were made using the SSM superposition algorithm in COOT , . Structural representations were made using Pymol . […]

Pipeline specifications

Software tools Dr Fit, Clustal W, MODELLER, Coot, PyMOL
Applications Drug design, Protein structure analysis
Organisms Trypanosoma cruzi, Homo sapiens
Diseases Infection
Chemicals Adenosine Diphosphate, Poly Adenosine Diphosphate Ribose, Ribose