Molecular docking method based on polarizable bond model

A molecular docking and modeling technology, which is used in the analysis of two-dimensional or three-dimensional molecular structure, molecular design, computational theoretical chemistry, etc. It can solve the problem of not considering the polarization effect, and achieve the effect of improving the accuracy of molecular docking.

Active Publication Date: 2020-05-26
EAST CHINA NORMAL UNIV
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  • Abstract
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Problems solved by technology

[0006] At present, there are no reports on the application of EPB method to molecular docking technology at home and abroad, or public literature on the app...

Method used

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  • Molecular docking method based on polarizable bond model
  • Molecular docking method based on polarizable bond model
  • Molecular docking method based on polarizable bond model

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Embodiment 1

[0052] See attached Figure 1 ~ Figure 2 , define the type of polarizable bond in the compound and calculate the polarization parameter of the polarizable bond according to the following steps:

[0053] 1) Collect the types of polarizable bonds from Drugbank, ChemBL and other databases, then construct a simplified molecular model, and obtain the polarizability and equilibrium bond length of small molecule polarizable bonds by combining molecular simulation and quantum chemistry;

[0054] 2) Download the complex and define the binding pocket;

[0055] 3) Molecular docking was performed using the Schrödinger molecular docking software Glide;

[0056] 4) Based on the small molecule EPB polarized charge model, each molecule after docking recalculates the charge in its protein environment, and then re-docks the molecule, and the updated charge is forced to be used during the docking process;

[0057] 5) Repeat step 4 to repeatedly carry out the molecular docking of the EPB model ...

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Abstract

The invention discloses a molecular docking method based on a polarizable bond model. The method is characterized in that on the basis of traditional molecular docking, polarizable bonds contained inthe ligands are recognized according to a protein environment where ligands are located and charges are updated; then molecular docking is conducted again (the updated charges are forcibly used); andthe operation is repeated till energy is converged, and the optimal binding mode is obtained. Compared with the prior art, the method has the advantages that the polarization effect of EPB charges isenhanced, the intermolecular hydrogen bond interaction is enhanced, the molecular docking precision is effectively improved; and the method is more efficient than a QM/MM equivalent molecular dockingmethod.

Description

technical field [0001] The invention relates to the technical field of drug molecular docking, in particular to a molecular docking method based on an effective polarizable bond model (EPB). Background technique [0002] Virtual screening, also known as in silico screening, is a method widely used to screen small molecule databases for putatively active compounds of a specific target. Compared with experimental screening methods, virtual screening has the advantages of fast screening, low cost and high benefit. Virtual screening has two methods: ligand-based virtual screening and structure-based screening. Ligand-based virtual screening methods, typically using 2D or 3D chemical similarity analysis to scan compound libraries for known active compounds; structure-based virtual screening methods, typically using molecular docking and scoring to assess whether a compound works well with The binding site of the target matches. [0003] Since structure-based virtual screening m...

Claims

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Application Information

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IPC IPC(8): G16B15/30G16C20/50G16C10/00
CPCG16B15/30G16C20/50G16C10/00
Inventor 季长鸽段观福张增辉
Owner EAST CHINA NORMAL UNIV
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