title: Molecular docking between the RNA polymerase of the Moniliophthora perniciosa mitochondrial plasmid and Rifampicin produces a highly stable complex.
abstract: BACKGROUND
  Moniliophthora perniciosa (Stahel) Aime & Phillips-Mora is the causal agent of witches' broom disease (WBD) in cacao (Theobroma cacao). When the mitochondrial genome of this fungus had been completely sequenced, an integrated linear-type plasmid that encodes viral-like RNA polymerases was found. The structure of this polymerase was previously constructed using a homology modeling approach.
  
  
  METHODS
  Using a virtual screening process, accessing the Kegg, PubChem and ZINC databases, we selected the eight most probable macrocyclic polymerase inhibitors to test against M. perniciosa RNA polymerase (RPO). AutoDock Vina was used to perform docking calculations for each molecule. This software returned affinity energy values for several ligand conformations. Subsequently, we used PyMOL 1.4 and Ligand Scout 3.1 to check the stereochemistry of chiral carbons, substructure, superstructure, number of rotatable bonds, number of rings, number of donor groups, and hydrogen bond receptors.
  
  
  RESULTS
  On the basis of this evidence we selected Rifampicin, a bacterial RNA polymerase inhibitor, and then AMBER 12 was used to simulate the behavior of the RPO-Rifampicin complex after a set of 5000 ps and up to 300 K in water. This calculation returned a graph of potential energy against simulation time and showed that the ligand remained inside the active site after the simulation was complete, with an average energy of -15 x 10(2) Kcal/Mol.
  
  
  CONCLUSIONS
  The results indicate that Rifampicin could be a good inhibitor for testing in vitro and in vivo against M. perniciosa.
authors: Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia, Jequié, Brazil. bandrade@uesb.edu.br
authors: Bruno
authors: B
authors: Andrade
authors: Catiane
authors: C
authors: Souza
authors: Aristóteles
authors: A
authors: Góes-Neto
mesh_terms: D001487:Basidiomycota / Q000378:metabolism*; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D008928:Mitochondria / Q000378:metabolism*; D062105:Molecular Docking Simulation; D010957:Plasmids; D012293:Rifampin / Q000378:metabolism*
chemical_list: D012321:DNA-Directed RNA Polymerases; D012293:Rifampin