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Method and device for screening candidate drugs for COVID-19

A technology of medicine and medicinal chemistry, applied in bioinformatics, instrumentation, genomics, etc., can solve problems such as new drugs or vaccines with little practical significance, and achieve the effect of accelerating drug development speed, high precision, and reducing drug development costs

Inactive Publication Date: 2020-04-28
GENEIS TECH BEIJING CO LTD
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

Developing new drugs or vaccines from scratch has little practical significance

Method used

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  • Method and device for screening candidate drugs for COVID-19
  • Method and device for screening candidate drugs for COVID-19
  • Method and device for screening candidate drugs for COVID-19

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0076] 1. Sample information

[0077] The whole genome sequences of 12 RNA viruses from NCBI database and the chemical structures of 78 drugs from DrugBank database and PubMed database were selected as samples.

[0078] 2. Experimental steps

[0079] 1. Preprocessing:

[0080] 1.1 Mining viruses similar to 2019-nCoV from ICTV virus data, the initial statistics are 11 kinds, including influenza viruses including A-H1N1, A-H5N1 and A-H7N9, chronic hepatitis C virus (HCV), HIV-1 and HIV-2, Hendra virus, human cytomegalovirus, Middle East respiratory syndrome coronavirus (MERS virus), severe acute respiratory syndrome (SARS) virus, and respiratory syncytial virus.

[0081] 1.2 Download the associated drugs of 11 viruses from the DrugBank database.

[0082] 1.3 From the PubMed database to search for drugs associated with 11 viruses.

[0083] 1.4 Construct virus-drug association database, and build image 3 matrix shown.

[0084] Similarity calculation:

[0085] 2.1 Download ...

Embodiment 2

[0115] The other steps of Example 2 are the same as those of Example 1 unless otherwise specified. The sample information in this embodiment is to select the whole genome sequences of 11 RNA viruses from the NCBI database and the chemical structures of 63 drugs from the DrugBank database and the PubMed database as samples. Among them, the viruses are SARS virus and its similar viruses A-H1N1, A-H5N1, A-H7N9, HCV, HIV-1, HIV-2, Hendra virus, human cytomegalovirus, MERS virus and respiratory syncytial virus.

[0116] In this embodiment, after determining the performance of the model, SARS is regarded as a new virus, and the drug information associated with it is completely covered up, and the random walk algorithm with restart is used to predict the drug associated with SARS. Table 2-4 shows the 63 drugs associated with SARS and their rankings. All of these small molecule drugs are FDA-approved.

[0117] Table 2-4 Drugs and their rankings associated with SARS

[0118]

[0...

Embodiment 3

[0122] The other steps of Example 3 are the same as those of Example 1 unless otherwise specified.

[0123] The sample information in this embodiment is to select the whole genome sequences of 11 viruses from the NCBI database and the chemical structures of 69 drugs from the DrugBank database and the PubMed database as samples. The viruses are MERS virus and its similar viruses A-H1N1, A-H5N1, A-H7N9, HCV, HIV-1, HIV-2, Hendra virus, human cytomegalovirus, SARS virus and respiratory syncytial virus.

[0124] In this example, after determining the performance of the model, MERS is regarded as a new virus, and the drug information associated with it is completely covered up, and the random walk algorithm with restart is used to predict the drugs associated with MERS. Table 3-4 shows the 69 drugs associated with SARS and their rankings. All of these small molecule drugs are FDA-approved.

[0125] Table 3-4 Drugs and their rankings associated with MERS

[0126]

[0127] In t...

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Abstract

The invention discloses a method and device for screening COVID-19 drugs. On the basis of obtaining sequence similarity information between viruses and structure similarity information between pharmaceutical chemical structures, a heterogeneous network based on virus sequence similarity and drug similarity is constructed, and training is performed on the constructed data set by using a random walkalgorithm so as to obtain a COVID-19 drug screening model. Based on the drug screening model, drugs related to new coronal pneumonia can be effectively screened. According to the method, the researchand development cost of the COVID-19 drugs can be reduced, and the screening speed and accuracy of the COVID-19 drugs exceed those of representative methods applied to other bioinformatics fields.

Description

technical field [0001] The invention relates to the field of virus drug screening, in particular to a method for screening candidate drugs for COVID-19 based on the whole genome sequence of the virus and the chemical structure of the drug. Background technique [0002] Since the end of December 2019, patients with severe pneumonia have been found in Wuhan, China and many other places. On February 11, 2020, the World Health Organization announced that the pneumonia caused by the new coronavirus was named "New Coronary Pneumonia" (COVID-19). The name of the new coronavirus was officially named 2019-nCoV by the International Committee on Taxonomy of Viruses. The virus is highly transmissible, and there is evidence that there is a risk of human-to-human transmission during the incubation period, which can be as long as 24 days. COVID-19 has had a great impact on the physical and mental health of the people and the development of the national economy. The World Health Organizat...

Claims

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Application Information

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IPC IPC(8): G16B20/30G16C20/30
CPCG16B20/30G16C20/30
Inventor 彭利红杨家亮田埂董如一鹿晴晴郎继东梁乐彬
Owner GENEIS TECH BEIJING CO LTD
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