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X-ray crystallographic, molecular modelling and docking studies of two analogues of NifurtimoxÒ
Maurício Vegaa (PG), I. Caracellia (PQ), Margot Paulinob (PQ), H. Cerecettob (PQ) and J. Zukerman-Schpectora (PQ)
aLaboratório de Cristalografia, Esterodinâmica e Modelagem Molecular, LaCrEMM, Departamento de Química, UFSCar, bFacultad de Química, Montevideo, Uruguay
Palavras-chaves: anti-chagássicos, polimorfismo, proteína-ligante
Chaga’s disease, endemic in Latin America, presents two stages: the acute one, which occurs approximately 10-15 days after infection and may be lethal in some cases, and the chronic phase. Effective drugs for the treatment of the chronic phase are not yet available and those used in the acute phase and in congenital infection as NifurtimoxÒ, present undesirable side effects associated with their high toxicity. These drawbacks led to the synthesis of a new series of NifurtimoxÒ analogues two of which, (1): 4-(2-phenylethyl)-1-(5-nitrofurylidene)semicarbazide, (2): 4-(2-phenylethyl)-1-(5-nitrothienylidene)semicarbazide, are presented here. In order to try to understand their behaviour a molecular modelling (MM) and rigid docking studies in Glutathione reductase (GR) and Trypanothione reductase (TR) which are homodimeric flavoproteins-NADP dependent, were performed. As the crystal structure is the best starting point for MM a three-dimensional X-ray diffraction study was also performed. One of the most outstanding results from the crystallographic studies was founding that compound (1) presents two different conformations and (2) only one which is different from those of (1), as can be seen in the ZORTEP figures.
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Crystal data (1): C14 H14 N4 O4 , fw = 302.29, triclinic, P -1, a = 14.274(2), b = 11.899(1), c = 8.6864(9) Å, a = 86.34(1), b = 76.93(1), g = 82.66(1)o, V = 1424.4(3) Å3, Z = 4, dx = 1.410 Mg/m3, R1 = 0.0782 for 6507 reflections and 397 refined parameters.
Crystal data (2): C14 H11 N4 O3 S. 2H2O , fw = 351.36, monoclinic, P21/n, a = 18.415(2), b = 4.7990(9), c = 18.562(2) Å, b = 93.92(1)o , V = 1636.6(4)Å3 , Z = 4,
dx = 1.426 Mg/m3, R1 = 0.0457 for 2653 reflections and 218 refined parameters
Analyses of the rotational barriers around C=C-C=N and N-C-C-CB torsion angles for (1) and (2) showed that the crystallographic conformations are in energy minima and that the energy barrier to pass from one conformation to the other in (1) is of almost 2 kcal/mol. As the crystallographic conformations were found to be excellent starting points they were used for Molecular Dynamics studies of 10 ps of heating from 0 K to 1000 K and then the temperature was maintained for 200 ps. The chosen configurations were quenched to 0 K in 2 ps of MD. These structures were minimised by MM+ followed by AM1. The final conformation of (2) is almost equal to that in the crystal, the main difference being that of the relative orientation of the phenyl ring. The extended conformation of (1) converges to itself and the other one converges to a conformation, which is almost equal to the one obtained for (2). It means that by MD only two different conformations were obtained the main is in the relative orientation of the heterocyclic ring.
The rigid docking method was used, always with the lead that the 3-D complementarity in molecular shape and molecular properties between ligand and ligand-binding site of the receptor are the most important for the specific binding to the target receptor. In the target proteins, GR and TR, three important structural regions are observed: a) the active site around the disulphide enzymatic bound. The TR' s active site has a negative charge while the GR' s is positively charged; b) a site between the monomers, the interface domain, which presents a symmetric character; c) the NADP binding site. From the docking studies, which were performed in the three regions, it can be concluded that both compounds can be inhibitors, but it may be postulated that they will not be specific for only one of the proteins.