Molecular-dynamics-simulation-based virtual screening method of nuclear receptor mediated endocrine disruption substances

A technology of molecular dynamics and endocrine disruption, applied in special data processing applications, instruments, electrical digital data processing, etc., can solve the problems of not introducing protein allosteric, not suitable for accumulating receptors, etc., and achieve low cost and easy operation Effect

Active Publication Date: 2013-09-25
NANJING UNIV
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Problems solved by technology

[0006] Zhang Aiqian et al. used molecular dynamics techniques to identify organic compounds with ER agonist and antagonism (Zhang Aiqian, Lin Yuan, Peng Sufen, Liu Lei, Gao Changan, Han Shuokui. Identification of an organic compound estrogen receptor agonist and antagonism Method [P]. Jiangsu: CN101381894, 2009-03-11), but this method is only for ER, and does not introduce the concept of protein allosteric, not suitable for accumulating receptors

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  • Molecular-dynamics-simulation-based virtual screening method of nuclear receptor mediated endocrine disruption substances
  • Molecular-dynamics-simulation-based virtual screening method of nuclear receptor mediated endocrine disruption substances

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Embodiment Construction

[0029] A method for virtual screening of nuclear receptor-mediated endocrine disrupting substances based on molecular dynamics simulation, the steps of which are:

[0030](1) Construct the molecular structure of the test compound in the Chemdraw software of Cambridge (this software is the most commonly used compound structural building software), and use the density functional method b3lyp / 6-311G* basis set in the Gaussian software to optimize the energy , and then use Sybyl7.3 software (classic analysis and simulation software) to endow Gasteiger-Huckel charges; the free state structure of ER is directly obtained from the protein database-PDB, and its PDB number is 1A52; then use 1A52 as a template, use Swiss-Model The network server constructs the initial structure of AR and TR; then uses the Surflex-dock module of Sybyl7.3 software to find the active mouth of the receptor macromolecule, and docks the test compounds into the pockets; select the compound conformation with the ...

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Abstract

The invention discloses a molecular-dynamics-simulation-based virtual screening method of nuclear receptor mediated endocrine disruption substances, and belongs to the field of virtual screening and activity prediction of environmental suspicious endocrine disruption substances. The molecular-dynamics-simulation-based virtual screening method includes the steps of carrying out butt joint on a receptor file obtained by the fact that optimization and testing or homology modeling are/is carried out on tested small molecules to form a compound, and then using a GROMACS software package to carry out molecular dynamics simulation. Motion trail analysis is carried out on a twelfth helix of a receptor, pollutants with the activity of the receptor are identified through a changing curve of root-mean-square deviation analysis of a space position along with time changes, within the required time, a corresponding helix is regarded to be located to a determined position when the curve tends to be stable, and the receptor has the biological activity. In addition, the located position is inspected to judge whether the activity is fitting or resistance.

Description

technical field [0001] The present invention relates to the field of virtual screening and activity prediction of environmentally suspicious endocrine disruptors, specifically, a method for virtual screening of nuclear receptor-mediated endocrine disrupting substances based on molecular dynamics simulation, more specifically, through molecular Kinetic simulation investigates three types of nuclear receptors closely related to endocrine disrupting effects——Estrogen receptor (Estrogen receptor, ER), Androgen receptor (Androgen receptor, AR) and Thyroid hormone receptor (Thyroid hormone receptor, TR ) to judge the potential endocrine disrupting effect of the test compound. Background technique [0002] Endocrine disruptors refer to substances that can simulate human hormones and disrupt the human endocrine disrupting system. Endocrine disruptors not only affect the reproductive system of organisms, induce cancer, and even harm the second and third generations. Estrogen recepto...

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F19/00
Inventor 于红霞史薇王小享
Owner NANJING UNIV
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