title: Analysis of cyclosporin A and a set of analogs as inhibitors of a T. cruzi cyclophilin by docking and molecular dynamics.
abstract: Cyclophilins (CyPs) are enzymes involved in protein folding. In Trypanosoma cruzi (T. cruzi), the most abundantly expressed CyP is the isoform TcCyP19. It has been shown that TcCyP19 is inhibited by the immunosuppressive drug cyclosporin A (CsA) and analogs, which also proved to have potent trypanosomicidal activity in vitro. In this work, we continue and expand a previous study on the molecular interactions of CsA, and a set of analogs modeled in complexes with TcCyP19. The modeled complexes were used to evaluate binding free energies by molecular dynamics (MD), applying the Linear Interaction Energy (LIE) method. In addition, putative binding sites were identified by molecular docking. In our analysis, the binding free energy calculations did not correlate with experimental data. The heterogeneity of the non-bonded energies and the variation in the pattern of hydrogen bonds suggest that the systems may not be suitable for the application of the LIE method. Further, the docking calculations identified two other putative binding sites with comparable scoring energies to the active site, a fact that may also explain the lack of correlation found. Kinetic experiments are needed to confirm or reject the multiple binding sites hypothesis. In the meantime, MD simulations at the alternative sites, employing other methods to compute binding free energies, might be successful at finding good correlations with the experimental data.
authors.affiliation: a Facultad de Química, Centro de Bioinformática Estructural, DETEMA , Universidad de la República , Gral. Flores 2124, C.P. 11800, C.C. 1157, Montevideo , Uruguay.
authors.forename: Roberto
authors.initials: R
authors.lastname: Carraro
authors.affiliation: a Facultad de Química, Centro de Bioinformática Estructural, DETEMA , Universidad de la República , Gral. Flores 2124, C.P. 11800, C.C. 1157, Montevideo , Uruguay.
authors.forename: Federico
authors.initials: F
authors.lastname: Iribarne
authors.affiliation: a Facultad de Química, Centro de Bioinformática Estructural, DETEMA , Universidad de la República , Gral. Flores 2124, C.P. 11800, C.C. 1157, Montevideo , Uruguay.
authors.forename: Margot
authors.initials: M
authors.lastname: Paulino
mesh_terms: D000596:Amino Acids / Q000737:chemistry; D001665:Binding Sites; D016001:Confidence Intervals; D018360:Crystallography, X-Ray; D021983:Cyclophilins / Q000037:antagonists & inhibitors*; D016572:Cyclosporine / Q000737:chemistry / Q000494:pharmacology*; D006860:Hydrogen Bonding; D008024:Ligands; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D019696:Peptidylprolyl Isomerase / Q000037:antagonists & inhibitors / Q000378:metabolism; D012997:Solvents; D055672:Static Electricity; D013816:Thermodynamics; D014349:Trypanosoma cruzi / Q000187:drug effects / Q000378:metabolism*
chemical_list: D000596:Amino Acids; D008024:Ligands; D012997:Solvents; D016572:Cyclosporine; D021983:Cyclophilins; D019696:Peptidylprolyl Isomerase
keywords: Chagas’ chemotherapy; binding energies; cyclophilins; cyclosporin; docking; molecular dynamics