Three-dimensional substructure-based drug molecule comparison method

A three-dimensional substructure, drug molecule technology, applied in molecular design, chemical structure search, special data processing applications, etc., can solve the need for 3D substructure retrieval and comparison without considering the importance of substructure parts to biological activity and other issues to achieve the effect of improving flexibility

Active Publication Date: 2018-02-02
广州市爱菩新医药科技有限公司
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  • Claims
  • Application Information

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Problems solved by technology

[0004] The main disadvantage of using the above two methods to compare the shape of drug molecules is: the GMA algorithm can only search for two-dimensional substructures, and cannot

Method used

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  • Three-dimensional substructure-based drug molecule comparison method
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  • Three-dimensional substructure-based drug molecule comparison method

Examples

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Embodiment 1

[0040] Example 1: Comparison of comprehensive similarity between two molecules when only one query substructure is defined

[0041] Such as figure 1 Shown, method of the present invention comprises the steps:

[0042] Step (1), read the two-dimensional or three-dimensional structure information of the library molecule, define the query substructure, and obtain the substructure matching atomic sequence of the library molecule, specifically including:

[0043] The substructure defined in the query molecule is a query substructure, and the defined substructure can be one or more, and the atomic sequence of the query substructure is obtained;

[0044] Read in the structural information of the query substructure, the structure information including the type of each atom and bond in the query substructure;

[0045] reading in two-dimensional or three-dimensional structural information of library molecules, said two-dimensional or three-dimensional structural information including ...

Embodiment 2

[0064] Embodiment 2: The comparison of the comprehensive similarity between two molecules when multiple query substructures are defined, such as image 3 shown.

[0065] When multiple query substructures are defined, multiple query substructures cannot overlap when defined. After using the GMA algorithm to obtain the substructure matching atomic sequence of the library molecule, judge whether there are repeated atoms in the multiple substructure matching atomic sequences of the library molecule, discard the sequence with repeated atoms, and only keep the multiple substructure matching sequences without repeated atoms; Multiple substructure matching sequences without repeating atoms are merged into one substructure sequence, which is regarded as a substructure, and all matching substructure matching atomic sequences of the library molecules are found by the method of Example 1, and the self of each substructure of the two molecules is calculated The overlapping volume is compa...

Embodiment 3

[0066] Embodiment 3: The comparison of molecular comprehensive similarity when defining a query substructure and one or more exogenous substructures, such as Figure 4 shown.

[0067] When the defined query substructure is one, one or more exogenous substructures can be defined (exogenous substructures are substructures that are not in the query molecule but have similar functions to the query substructure), using the GMA algorithm After obtaining the matching atomic sequence of the substructure corresponding to the query substructure or the foreign substructure of the library molecule, there is no need to judge whether there are repeated atoms in all the matching atomic sequences. The exogenous substructure will be regarded as a separate substructure, continue to match the substructure of the library molecule using the method of Example 1, use the method of Example 1 to find all matching substructure matching atomic sequences of the library molecule, and calculate the respect...

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Abstract

The invention discloses a three-dimensional substructure-based drug molecule comparison method, and relates to the technical fields of drug molecule design and screening. The method comprises the following steps: reading two-dimensional or three-dimensional structure information of a library molecule, and obtaining substructure matching atom sequences of the library molecule; reading three-dimensional structure information of a query molecule and the library molecule and related information of a query substructure, and respectively calculating self-overlapping volumes of respective substructures of the query molecule and the library molecule and self-overlapping volumes of respective side chains; calculating overlapping volumes of the query molecule and the library molecule in various overlapping cases; and respectively calculating a substructure similarity degree of the query molecule and the library molecule. The method can improve flexibility of molecule shape comparison, more facilitates discovery of lead compounds, and can be applied to virtual screening of drug molecules.

Description

technical field [0001] The invention relates to the technical field of drug molecule design and screening, in particular to a method for comparing drug molecules based on three-dimensional substructures. Background technique [0002] Molecules with dissimilar two-dimensional structures may have the same or similar biological activities due to having the same or similar substructures. For the two-dimensional substructure search of molecules, the maximum common substructure algorithm GMA (Journal of chemical information and computer sciences, 1996, 36(1): 25-34.) can be realized, and the atomic sequence of the substructure identified by the atomic number in the molecule can be obtained ; [0003] The biological activity of drug molecules mainly depends on their three-dimensional structure. A molecular superposition algorithm based on weighted Gaussian function WEGA (Journal of chemical information and modeling, 2013, 53(8):1967-1978.) can realize the three-dimensional shape o...

Claims

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Application Information

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IPC IPC(8): G06F19/00
CPCG16C20/40G16C20/50
Inventor 徐峻利秀明严鑫
Owner 广州市爱菩新医药科技有限公司
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