Pentachlorophenol molecule design with lower bioconcentration through 3D-QSAR associated with molecule docking

Abstract

A three-dimensional quantitative structure activity relationship (3D-QSAR) model is built by using a comparative molecular similarity indices analysis (CoMSIA) technique with an experimentally determined logarithm of bioconcentration factors (logBCFs) for 36 phenols in fish. Meanwhile, with the pentachlorophenol (PCP) molecule as target molecules, contributions of the molecular fields indicate that the electrostatic fields are the main influences on the bioconcentration of the PCP molecule. Based on the analytical results of CoMSIA contour map of PCP and PCP molecular docking with SOD protease (PDB ID: 4A7T), the R₆ substituent positions of PCP were modified to give seven new modified PCP molecules with low bioconcentration in this paper. The energy barrier calculation of the new modified PCP molecular reaction pathways can infer the order of the substitution reactions as –SCl > –CH₂Cl > –COCl > –CCl₃ > –CH=CH₂ > –NO₂ > –SH. These calculations, combined with anaerobic biodegradation, ecotoxic effect, and mobility of new modified PCP molecules, enable a new environmentally friendly compound when the Cl at the R₆ position of PCP was replaced with –COCl substituent with low bioconcentration (reduced by 32.89%), ecotoxic effect basically unchanged (increased by 1.37%), anaerobic biodegradation increased (increased by 24.81%), and mobility basically unchanged (reduced by 0.94%) to be designed.

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