A Computational Approach to Handling Small Molecule and Protein Interactions

A protein and small molecule technology, applied in the field of computational toxicology, can solve problems such as human damage, inability to combine functional molecules, changes in protein secondary structure content, etc., to achieve the effect of simple key principles, improved production efficiency, and wide application

Inactive Publication Date: 2015-11-25
TONGJI UNIV
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

Under normal circumstances, the presence of pollutants will affect the changes in the secondary structure content of proteins; secondly, the active sites of proteins are occupied by pollutants, and some functional molecules cannot be combined, resulting in some critical effects on human health. The substances cannot be synthesized or transformed, and the human body will eventually be damaged due to the lack of these important substances that should be synthesized

Method used

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Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0024] The present invention is divided into two functional modules of Presearch and SearchProtein. It is mainly written in ANSIC++ language and can run under Windows and Linux operating systems. There are 18 source programs and header files in the program package, the main process is: read-in of receptor and ligand molecules, mainly in mol2 file format; preprocessing of receptor and ligand molecules, mainly atom types, single axis can be rotated Key assignment, etc. The PreSearch program needs to prepare the presearch.txt file before running; then randomly initialize the small molecules, and the initial position of the small molecules is around the active center Randomly generated within the range; then use Presearch to search and docking calculations. The docking RMSD (root mean square offset), docking free energy ΔG and the coordinates of the docking site were calculated. Establish a protein database, and use the SearchProtein module to perform reverse docking experimen...

Embodiment 2

[0028] A method to find protein receptors that PFOS may interfere with. Using the reverse docking program PreSearch and reverse docking program SearchProtein, 4 proteins that may bind to PFOS were found from the self-built protein receptor library. These proteins are phosphodiesterases 4D catalytic domain, urokinase catalytic domain, type II carbonic anhydrase and type IV dipeptidyl peptidase, and briefly analyzed the situation of PFOS in the active sites of these proteins. The specific process is as follows:

[0029] The PreSearch program needs to prepare the presearch.txt file before running.

[0030] . / PreSearch-ppresearch.txt-lresult.log-oenergy.txt

[0031] Calculated 10 times in the work, so that the evaluation of energy is more average. 1a2c.mol2 and 1a2c-l.mol2 represent the mol2 file of the protein and the mol2 file of the ligand, respectively. After each calculation of a protein is completed, the program will generate a result.log file and an energy.txt file. The...

Embodiment 3

[0037] A method for studying the interaction mechanism between pollutant 2,4-d and human serum protein HAS, as mentioned in Example 1, using the docking program PreSearch to find out that 2,4-D may replace androgen and estrogen The position on HSA interferes with the transportation of these two hormones in the human body, affecting their normal functions, which may cause the imbalance of sex hormones in the body, and the possibility of 2,4-D affecting the transportation of thyroxine on serum proteins very small.

[0038] We used the docking results of Presearch to analyze the effects of three molecules with similar results, 2, 4-D, estrogen, androgen, and HSA after docking. The active center selected for docking is the IIA active site. It is worth mentioning that, When repeatedly calculating the binding free energy of 2,4-D and HSA, a special phenomenon was found when docking with other molecules. Instead of one value, the two values ​​are -34.0kJ / mol and -37.4kJ / mol. Howeve...

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Abstract

The invention relates to a computing method for processing interaction between small molecules and proteins. The method includes the following steps that (1) ligand file data of the proteins and the small molecules are read in; (2) atom types in ligands of the proteins and the small molecules are judged; (3) positions and angles of the ligands of the small molecules are randomly initialized; (4) a search protein algorithm is operated, coordinates and angles of the ligands of the small molecules are optimized, and a chemscore formula serves as an evaluation function; (5) the computing is ended after maximum iterative times are achieved; and (6) results such as root mean square deviation (RMSD), binding free energy delta G and coordinates of a binding site are analyzed and output. Compared with computing methods for processing the interaction between the small molecules and the proteins in prior art, the computing method for processing the interaction between the small molecules and the proteins has the advantages that when pollutants and biomacromolecules are interacted can be rapidly determined, and the like.

Description

technical field [0001] The present invention relates to the field of computational toxicology, and in particular to a computational method for dealing with the interaction of small molecules and proteins. Background technique [0002] With the development of human society, the environmental problems faced by human beings are becoming more and more serious. All kinds of industrial and agricultural wastewater, waste gas, and waste residues are discharged into the public environment where human beings live. These "three wastes" often contain many harmful compounds. At present, many countries and regions in the world have restricted and prohibited the discharge of "three wastes", set strict limits on the content of pollutants in the environment, and formulated relevant laws and regulations to protect the human body from harm. The process of pollutants causing damage to the human body is the process in which pollutants enter the body and combine with some important proteins in t...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G06F19/12
Inventor 管翀赵国华曹同成黄晓峰张莹莹
Owner TONGJI UNIV
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