Method for screening anti-androgen activity of flavonoid compounds based on molecular dynamics simulation

Abstract

The invention discloses a method for screening anti-androgen activity of flavonoid compounds based on molecular dynamics simulation. The method comprises the following steps: performing butt joint on an optimized tested flavonoid compound structure and a receptor file acquired by homology modeling, then performing molecular dynamics simulation for 20 nanoseconds by using a GROMACS software package, calculating a mean square root deviation of No.12 helix 8-20ns of a flavonoid compound receptor, importing data into a R language package, establishing a distinguishing model for the calculated standard deviation and residues, and removing inactive compounds from the compounds in a fuzzy area by inspecting the movement trajectories of the compounds in the receptor and the calculated mean square root deviation. According to the method disclosed by the invention, quantitative judgment is imported for the first time, the pre-judgment accuracy is improved by the combination of quantitativeness and qualitativeness, the distinction rate of inactive flavonoid and active flavonoid reaches 87.5%, the screening rate of the inactive flavonoid reaches 90%, the laboratory workload can be greatly reduced, the consumption of test products is reduced, resources are saved, and the prediction accuracy of QSAR can also be greatly improved, so QSAR can be really applied.

Description

technical field [0001] The invention belongs to the field of biology, and particularly relates to a method for screening the antiandrogen activity of flavonoids by investigating the configuration changes between flavonoids and androgen receptors by means of molecular dynamics simulation. Background technique [0002] Endocrine disruptors refer to substances that can simulate human hormones and disrupt the human endocrine disrupting system. They not only affect the reproductive system of organisms, induce cancer, and even harm the second and third generations. Estrogen receptors, androgen receptors and thyroid receptors, as important components of the nuclear receptor superfamily, are important targets for mediating endocrine disrupting effects. Some endocrine disruptors can mimic natural hormones to activate these targets, an effect known as the pseudo-estrogen / androgenic / thyroid hormone effect, and other endocrine disruptors can inhibit the action of natural hormones, an ef...

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Problems solved by technology

[0006] Zhang Aiqian and others used molecular dynamics technology to identify organic substances with ER agonist and antagonism (Zhang Aiqian, Lin Yuan, Peng Sufen, Liu Lei, Gao Changan, Han Shuokui. Identification of an organic substance 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

[0007] Yu Hongxia and others used molecular dynamics technology to screen nuclear receptor-mediated endocrine disruptors (Yu Hongxia, Shi Wei, Wang Xiaoxiang. A virtual screening method for nuclear receptor-mediated endocrine disruptors based on molecular dynamics simulation[ P].Jiangsu: CN201310288617.3, 213-9-25), but this method can only be roughly judged by comparing waveforms, and cannot perform quantitative predictions, with low prediction accuracy and poor practicability

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