CN-122024846-A - Screening method of natural compound for resisting macrobrachium rosenbergii iridovirus based on MCP protein target spot

Abstract

The application relates to the field of material science and engineering, and particularly discloses a screening method of natural anti-macrobrachium rosenbergii iridovirus compounds based on MCP protein targets. The method comprises the steps of constructing a three-dimensional structure of virus main capsid protein MCP and determining an active pocket, carrying out structure pretreatment on a natural compound library, carrying out multiple rounds of virtual screening by taking the active pocket as a target point through molecular docking to obtain candidate compounds with the binding energy less than or equal to-10.0 kcal/mol, establishing a macrobrachium rosenbergii artificial infection model, measuring the virus inhibition rate and the protection rate of the candidate compounds, and screening out active compounds. The photinia phenol, amentoflavone, paris polyphylla saponin II and solamargine screened by the method show remarkable antiviral effect in vivo injection test and culture verification. The application realizes accurate screening from target prediction to in-vivo verification.

Inventors

• ZHENG XIAOCHUAN
• LIU BO
• DENG XIN
• SUN CUNXIN
• LIU BO

Assignees

• 中国水产科学研究院淡水渔业研究中心

Dates

Publication Date

20260512

Application Date

20260112

Claims (10)

1. 1. The screening method of the natural compound for resisting the macrobrachium rosenbergii iridovirus based on the MCP protein target spot is characterized by comprising the following steps of: s1, determining an active pocket of the main capsid protein MCP of the iridovirus by taking the three-dimensional structure of the main capsid protein MCP of the iridovirus as a target point; S2, carrying out three-dimensional structure modeling and energy optimization on the compounds in the natural compound library; S3, adopting molecular docking software, taking the active pocket as a docking area, and carrying out at least two rounds of step-by-step fine virtual screening on the optimized compound library, wherein the docking binding energy threshold of the last round of virtual screening is set to be less than or equal to-10.0 kcal/mol so as to screen out candidate compounds with high affinity; S4, establishing a palaemon rosenbergii iridovirus DIV1 artificial infection model, and determining the protection rate of the candidate compound screened in the step S3 on virus infection or the inhibition rate on virus replication by an injection virus attack mode; Wherein the candidate compound with the protection rate not less than 40% and/or the inhibition rate not less than 90% is determined as a natural compound with anti-macrobrachium rosenbergii iridovirus activity.
2. 2. The method for screening natural anti-macrobrachium rosenbergii iridovirus compounds based on MCP protein targets according to claim 1, wherein in step S1, the three-dimensional structure of MCP protein is predicted using AlphaFold software and the active pocket thereof is determined by analysis using AutoDockTools software.
3. 3. The method of claim 1, wherein in step S3, the at least two rounds of virtual screening comprises: In the first round of screening, setting exhaustiveness parameters of molecular docking as 1, and selecting a compound with docking binding energy of top 200; setting exhaustiveness parameters of molecular docking as 8 in the second screening, docking the compounds screened in the first screening, and selecting the compounds with docking binding energy of 40 rank; And thirdly, screening, namely setting exhaustiveness parameters of molecular docking as 16, carrying out refined docking on the compounds screened in the second round, and selecting the compounds with docking binding energy less than or equal to-10.0 kcal/mol.
4. 4. The method for screening natural anti-macrobrachium rosenbergii iridovirus compounds based on MCP protein target according to claim 3, wherein the molecular docking software used in step S3 is AutoDockVina.
5. 5. The method of claim 1, wherein in step S1, the active pocket comprises amino acid residues Trp-93, pro-190 and Lys-158.
6. 6. The method for screening natural anti-macrobrachium rosenbergii iridovirus compounds based on MCP protein targets according to claim 1, wherein in step S4, the establishment of the artificial infection model comprises the steps of preparing DIV1 virus crude extract, and determining half lethal dose LD50 of macrobrachium rosenbergii by using a Reed-Muench method, wherein the virus concentration of the injection challenge is 5 times to 10 times LD50.
7. 7. The method for screening natural anti-macrobrachium rosenbergii iridovirus compounds based on MCP protein targets according to claim 6, wherein the inhibition rate is determined by taking macrobrachium rosenbergii hepatopancreatic tissue 48 hours after virus attack, extracting DNA, and detecting viral load by real-time fluorescent quantitative PCR using primers for DIV1MCP gene.
8. 8. The method for screening natural anti-macrobrachium rosenbergii iridovirus compounds based on MCP protein targets according to claim 1, wherein in step S2, the two-dimensional structure of the compound is converted into a three-dimensional structure by OpenBabel software, and energy minimization treatment is performed, and the compound is stored in PDBQT format for molecular docking.
9. 9. The natural compound of the giant freshwater prawn iridovirus based on the MCP target point, which is characterized in that the compound is obtained by screening by adopting the screening method of the natural compound of the giant freshwater prawn iridovirus based on the MCP protein target point according to any one of claims 1 to 8.
10. 10. The natural compound of claim 9, wherein the compound is selected from one or more of the group consisting of glaucenol, amentoflavone, paris polyphylla saponin II and solamargine.

Description

Screening method of natural compound for resisting macrobrachium rosenbergii iridovirus based on MCP protein target spot Technical Field The application relates to the field of material science and engineering, in particular to a screening method of natural compounds for resisting macrobrachium rosenbergii iridovirus based on MCP protein targets. Background In recent years, market conditions of river crabs, crayfish, penaeus vannamei and other varieties are greatly fluctuated, and price and cultivation income of macrobrachium rosenbergii are relatively stable, even the counter-potential rises. So that the macrobrachium rosenbergii becomes a main-pushing culture variety in Jiangsu and other areas. In recent years, the development of the macrobrachium rosenbergii breeding industry faces the challenge of serious economic loss caused by frequent occurrence of the iridovirus. The Octopus iridovirus has strong infectivity, high mortality and wide harmful species. Viral infectivity is largely dependent on capsid formation and stability, with capsid proteins being potential targets for antiviral activity. The major capsid protein of the decapod iridovirus DIV1 plays a key role in viral particle assembly and infection of host cells. In addition, viral structural proteins are a key immunogenic protein that stimulates the host immune response. Inhibitors specifically binding to structural proteins such as MCP are designed to disrupt the life cycle of the virus. In addition, the conservation degree of MCP protein is very high, so that MCP can be used as a target for screening and developing anti-iridovirus drugs. At present, effective antiviral drugs of the Macrobrachium rosenbergii iridovirus are lacking, and the traditional chemical drugs have the problems of drug resistance and environmental toxicity. The traditional Chinese medicine and the natural compound have the advantages of multiple targets, low toxicity and environmental friendliness, and become an important direction for screening antiviral drugs. Research on vertebrate virus infection models such as largehead black bass iridovirus and grouper iridovirus proves that natural compounds such as aloe-emodin and epigallocatechin gallate have good antiviral effects. In addition, the natural compounds have the characteristics of multiple ways and multiple targets in exerting antiviral mechanisms, such as direct effects by combining virus structural proteins to destroy virus structures, interfering with virus infection of host cells, interfering with virus replication cycle and the like, and indirect antiviral functions by regulating host antiviral immune responses such as invertebrate Toll, IMD and JAK/STAT pathways. However, the screening of the antiviral traditional Chinese medicine at present has the problems of traditional method, long time consumption, large workload, limited screening amount and undefined target spot, and truly effective candidate medicines are extremely easy to miss. Disclosure of Invention In order to solve the problems that the screening method of antiviral traditional Chinese medicines in the prior art is traditional, time-consuming, large in workload, limited in screening amount, undefined in target spot and extremely easy to miss truly effective candidate medicines, the application provides a screening method of natural compounds of anti-macrobrachium rosenbergii iridovirus based on MCP protein targets. The first aspect of the invention provides a screening method of natural compounds for resisting the macrobrachium rosenbergii iridovirus based on MCP protein targets. The method constructs a screening system from target identification to activity verification by integrating computational biology and experimental biology, and comprises the following steps: S1, preparing a target structure, namely taking main capsid protein MCP of the decapod iridovirus as a target for antiviral drug design. And constructing a high-confidence three-dimensional structure model of the MCP protein by adopting protein three-dimensional structure prediction software. The three-dimensional structure is analyzed by using molecular simulation software, and a key active pocket on the surface of the three-dimensional structure is identified and determined, wherein the pocket is a functional key region in the virus assembly or infection process and is used as an accurate target area for subsequent molecular docking. And S2, constructing and preprocessing a compound library, namely collecting compound information from a plurality of natural product databases and constructing an initial natural compound library. Three-dimensional conformational transformations and generation were performed using the two-dimensional structure of all compounds using chemoinformatics software. And then, carrying out molecular mechanics optimization on each three-dimensional structure to enable the three-dimensional structure to reach a stable conformation with low energy, uniformly conv