Simulação molecular de inibidores da subunidade da ricina, RTA

• Autor(a) principal: Chaves, Elton Jose Ferreira
• Data de Publicação: 2016
• Tipo de documento: Dissertação
• Idioma: por
• Título da fonte: Biblioteca Digital de Teses e Dissertações da UFPB
• Texto Completo: https://repositorio.ufpb.br/jspui/handle/tede/9691
• topic: Ricinus communis; Steered molecular dynamics; Força de ruptura; Ricinus communis; Ricin toxin A; Steered molecular dynamics; Rupture force; CIENCIAS BIOLOGICAS

Ricinus communis, specifically fruit, castor bean, has gained industry, media and government attention due to the derivate properties such as ricin and castor oil. The total fatty acids xtracted from castor bean, 90% comprises ricinoleic acid. Beyond the castor oil, castor bean processing generate co-products: fruit peel and the castor cake. These co-products present significant amounts of fibers and proteins, in addition to a potential use as nematicide. Since world production of castor oil is 1.5 million tons per year and the proportion of co-product production with castor oil production is approximately 1:1, so, it’s essential to find an economically viable destination for these co-products. In addition to the destinations used, a route with high commercial value would be the use as animal feed, however, this does not occur due to the presence of ricin. Ricin its a ribosome inactivating protein present in the castor bean seed, that consists of two subunits, RTA and RTB, with the RTA being the catalytic subunit. In addition this problem, ricin is used as a biological weapon by terrorists and activists. The inhibition of mechanism of ricin action has biotechnological interest, where RTA is the target for inhibitors synthesis. In this context, the method used to search for new inhibitors its Molecular Docking. This method evaluates thousands of ligands in a short time, however, presents low accuracy in the prediction of binding affinity. In this perspective, SMD simulations can be used. This method is based on the correlation of the mean force profile needed to decouple the ligand from the protein with its affinity. The scientific literature has reported promising results with the approach to discern active binders from inactive. In the present study, beyond the validation data from known RTA inhibitors, the binding affinity potential of 6 novel structures to form complexes with RTA using SMD simulations was evaluated. It was necessary to use Molecular Docking and Molecular Dynamics aproaches to obtain and refine new RTA complexes with novel ligands and next submitted to SMD simulation (k = 2 kcal/mol/Ų, v = 0.005 nm/ps). In addition to the mean force profile obtained from multiple independent SMD simulations, the rupture force and the average of pulling work were measured, these being a direct relation with the binding affinity. In summary, the results of the validation of rupture force and average of pulling work with the experimental data showed a correlation and determination coefficient with R = -0.992 and R² = 0.984 (rupture force) and R -0.958 and R² = 0.918 (average of pulling work), respectively. By means of these validations, the evaluation of novel structures using SMD simulations showed that 4 of the 6 proposed structures present in silico, binding affinity potential for RTA.