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Antiviral drug virtual screening method using tobacco mosaic virus RNA helicase as target

A technology of tobacco mosaic virus and RNA helicase, which is applied in special data processing applications, instruments, electronic digital data processing, etc., can solve the problem of no TMV helicase, and achieve the effect of improving the screening speed

Inactive Publication Date: 2015-04-08
GUIZHOU UNIV
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

Up to now, there is no drug molecular design or drug action mechanism research using TMV helicase as the drug target.

Method used

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  • Antiviral drug virtual screening method using tobacco mosaic virus RNA helicase as target
  • Antiviral drug virtual screening method using tobacco mosaic virus RNA helicase as target
  • Antiviral drug virtual screening method using tobacco mosaic virus RNA helicase as target

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0037] Example 1: Homology modeling of the three-dimensional structure of TMV RNA helicase

[0038] Taking the 183 kDa replica protein amino acid sequence of TMV (GenBank: AAF80604.1) as the query sequence, using the Protein BLAST program in the NCBI BLAST basic sequence alignment search tool, and using the blastp algorithm to search for known proteins in the Protein Data Bank proteins (pdb) database. Three-dimensional structures of homologous proteins. According to the degree of homology and the nature of the protein, tomato mosaic virus superfamily 1 helicase (PDB: 3VKW) was selected as the template for structural modeling. The template protein sequence length is 446, the fragment coverage rate is 27%, and the coverage corresponds to the 183 kDa protein S666-V1111, which completely contains the viral helicase domain (V829-T1085), and the sequence identity is 90%. The sequence comparison results of the two are as follows: picture 1 shown.

[0039] Using the SWISS-MODEL o...

Embodiment 2

[0041] Example 2: Molecular dynamics optimization of modeled proteins

[0042] The structure of TMV-HEL obtained in Example 1 was modified in Amber12 software. Under the FF12SB force field, the explicit water model was first optimized for the entire system until the RMS value of the energy gradient was less than 0.5 kcal / mol / L, and then the model was optimized by molecular dynamics simulation to test whether it had a stable conformation. Runs totaled 30 ns with a time step of 2 fs at a constant temperature of 300K. The relationship between the RMSD value of the TMV-HEL skeleton structure and time in the 30 ns time is shown in the figure 4As shown, the results show that the protein backbone structure changes less after 23 ns than before, so the average structure at 30 ns is taken as the initial structure for subsequent studies.

Embodiment 3

[0043] Example 3: The initial conformation of the RNA helicase of TMV bound to ATP

[0044] After the dynamic optimization structure obtained in embodiment 2, compare this structure with the three-dimensional structure in the PDB database by Dali online server (http: / / ekhidna.biocenter.helsinki.fi / dali_server), find that it is consistent with The hUpf1 protein (PDB: 2GJK) has a similar three-dimensional structure, and the corresponding relationship between the key residues of the ATP hydrolysis site is shown in the table 1 shown.

[0045] Table 1 Alignment of key residues at ATP hydrolysis sites

[0046]

[0047] Through the Fit Monomers function in the Biopolymer module of the SYBYL-X software, TMV-HEL and hUpf1 were superimposed through key residues to obtain the initial structure of the TMV helicase and ATP complex. The local enlarged map of the ATP hydrolysis site after superimposition is shown in the figure 4 shown.

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Abstract

The invention discloses an antiviral drug virtual screening method using tobacco mosaic virus RNA helicase as a target. The method is that the molecular modeling software is utilized for determining a virtual screening three-dimensional structure of virtual screened active conformation under the condition that helicase binds with ATP (Adenosine Triphosphate). The method can be used for quickly screening a compound with activity for preventing and controlling tobacco mosaic virus.

Description

technical field [0001] The invention relates to a drug screening method, in particular to a virtual screening method for novel anti-tobacco mosaic virus drugs by using molecular docking with the RNA helicase of tobacco mosaic virus as a target. Background technique [0002] Tobacco mosaic virus ( Tobacco mosaic virus , TMV) is a typical tobacco mosaic virus ( tobamovirus ) virus, which can infect a series of Solanaceae plants represented by tobacco. Symptoms include atrophy, necrosis, leaf curling, and characteristic mottled patterns of dark and light green mixed on leaf tissue. [0003] The existing comprehensive prevention and control measures for tobacco mosaic disease include selection of resistant varieties, rational fertilization, health management during the growth and development of tobacco, and chemical control. Among them, chemical control methods can be roughly divided into two categories: natural source antiviral agents and chemically synthesized antiviral age...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F19/16
CPCG16C20/64
Inventor 杨松周青郑玉涛叶意强赵远超陈玉婷胡德禹薛伟吴志兵
Owner GUIZHOU UNIV
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