CN111261224A

CN111261224A - Virtual screening method of targeting IKK β medicine

Info

Publication number: CN111261224A
Application number: CN202010163412.2A
Authority: CN
Inventors: 郭伟强; 孙敏轩; 马志俊
Original assignee: Suzhou University of Science and Technology
Current assignee: Suzhou University of Science and Technology
Priority date: 2020-03-10
Filing date: 2020-03-10
Publication date: 2020-06-09

Abstract

The embodiment of the invention discloses a virtual screening method of a targeted IKK β drug, which belongs to the technical field of pharmaceutical chemistry and comprises the following steps of taking ursolic acid as a ligand, taking IKK β (PDB ID: 4KIK) as a receptor protein, adopting molecular docking software to analyze a binding site, binding energy and a binding side chain group of the ursolic acid with IKK β, adopting the molecular docking software to analyze the modified binding site and binding energy of the ursolic acid with IKK β, preliminarily screening the side chain group with a better binding effect, carrying out molecular modification on the ursolic acid to obtain an ursolic acid derivative, and preliminarily determining the targeted IKK β drug by adopting the molecular docking software.

Description

Virtual screening method of targeting IKK β medicine

Technical Field

The embodiment of the invention relates to the technical field of pharmaceutical chemistry, in particular to a virtual screening method of a targeted IKK β drug.

Background

IKK β is one of the main members of IKK family, IKK (IkappaB kinase) is a key regulatory factor of an IKK/NF-kB pathway, and consists of three subunits, namely IKK α, IKK β, IKK gamma, IKK α and IKK β which have kinase domains and can play a role in phosphorylation, wherein the IKK gamma is a regulatory subunit, wherein the IKK β phosphorylates Ser32 and Ser36 in an IKK B α (inhibitor of NF-kB) molecule and induces the degradation thereof, so that the NF-kB is transported to a cell nucleus after being dissociated from a complex to start the transcription of downstream genes, therefore, the IKK β is a key subunit for activating the NF-kB pathway, the activity of the IKK β is regulated by upstream kinase, and is also involved in the regulation of target genes related to various diseases, particularly plays an important role in the development process of tumors and inflammations, and a bridge is built between the tumors.

IKK β is a potential target for preventing and treating tumors, and compared with the traditional treatment method which only takes tumor cells as targets, the therapeutic effect is obviously improved, and drug resistance is not easy to form, therefore, an IKK β inhibitor is considered as a candidate drug for treating tumors more effectively, and becomes one of the hot spots and the important points of research of people in recent years.

Ursolic acid (also known as ursolic acid) is a pentacyclic triterpene compound widely found in plants such as Nerium indicum, loquat, etc. Modern pharmacological research finds that the traditional Chinese medicine composition has the effects of resisting tumors and viruses, inhibiting bacteria, diminishing inflammation, reducing blood fat and the like. A large number of researches prove that the ursolic acid has stronger inhibitory activity in various solid tumors, small side effect and low toxicity, and shows that the ursolic acid has larger application potential in the development of antitumor drugs. However, the ursolic acid has the problems of poor solubility, difficult absorption by the body and the like, and the clinical application of the ursolic acid is limited.

Therefore, the ursolic acid is taken as a lead compound, and a target IKK β medicament is expected to be developed to meet the requirement of research on anti-tumor medicaments.

Disclosure of Invention

Therefore, the embodiment of the invention provides a virtual screening method of a targeting IKK β drug, so as to meet the requirement of research on anti-tumor drugs.

In order to achieve the above object, the embodiments of the present invention provide the following technical solutions:

according to a first aspect of embodiments of the present invention, there is provided a virtual screening method for a drug targeting IKK β, the method comprising the steps of:

1) using ursolic acid as a ligand, IKK β (PDB ID: 4KIK) as a receptor protein, and adopting molecular docking software to analyze the binding site, binding energy and a binding side chain group of the ursolic acid and the IKK β according to the binding conformation after the docking of the ursolic acid and the IKK β;

2) modifying the binding side chain group of the ursolic acid, analyzing the binding site and binding energy of the modified ursolic acid and IKK β by adopting molecular docking software, and preliminarily screening the side chain group with better binding effect;

3) molecular modification is carried out on ursolic acid by adopting the preliminarily screened side chain groups to obtain ursolic acid derivatives, and the binding sites and binding energy of the ursolic acid derivatives and IKK β are analyzed by adopting molecular docking software to preliminarily determine the targeted IKK β drugs.

Further, by adopting iGEMDOCK molecular docking software, docking parameters are set as follows: the population size (population size) is set to 200, the Number of children (Generations) is set to 70, and the Number of solutions (numbers of solutions) is set to 2.

Further, a more negative value of the binding energy indicates a stronger binding ability to IKK β.

Further, in step 3, molecular modification is performed on ursolic acid by adopting molecular superposition.

Further, the structural formula of the IKK β targeting drug is shown as the formula (I):

according to a second aspect of the embodiments of the present invention, the embodiments of the present invention provide a use of the targeted IKK β drug selected by the above method in preparing an anti-tumor drug.

The embodiment of the invention has the following advantages:

the invention is based on the principle and the method of molecular docking, the side chain group transformation is carried out on the ursolic acid, and the ursolic acid derivative with better docking capability is screened out, and has good application value and prospect in the field of development of anti-tumor drugs taking the ursolic acid as a guide drug.

Drawings

In order to more clearly illustrate the embodiments of the present invention or the technical solutions in the prior art, the drawings used in the description of the embodiments or the prior art will be briefly described below. It should be apparent that the drawings in the following description are merely exemplary, and that other embodiments can be derived from the drawings provided by those of ordinary skill in the art without inventive effort.

FIG. 1 is a structural formula of ursolic acid;

FIG. 2 is the protein crystal structure of IKK β;

FIG. 3 is a schematic diagram of molecular docking analysis of ursolic acid with IKK β;

FIG. 4 is a schematic diagram of side chain group modification of the hydroxyl group at C3 position of ursolic acid;

FIG. 5 is a schematic diagram of molecular docking analysis of ursolic acid and IKK β with hydroxyl group at C3 modified with R2;

FIG. 6 is a schematic diagram of molecular docking analysis of ursolic acid and IKK β with hydroxyl group at C3 modified with R6;

FIG. 7 is a schematic diagram of molecular docking analysis of ursolic acid and IKK β with hydroxyl group at C3 modified with R9;

FIG. 8 is a schematic diagram of side chain group modification of the carboxyl group at C28 position of ursolic acid;

FIG. 9 is a schematic diagram of molecular docking analysis of ursolic acid with IKK β after modification of carboxyl group at C28 with R1';

FIG. 10 is a schematic diagram of molecular docking analysis of ursolic acid with IKK β after modification of carboxyl group at C28 with R2';

FIG. 11 is a schematic diagram of molecular docking analysis of ursolic acid with IKK β after modification of carboxyl group at C28 with R14';

FIG. 12 is a schematic diagram of molecular docking analysis of ursolic acid derivatives with IKK β.

Detailed Description

The present invention is described in terms of particular embodiments, other advantages and features of the invention will become apparent to those skilled in the art from the following disclosure, and it is to be understood that the described embodiments are merely exemplary of the invention and that it is not intended to limit the invention to the particular embodiments disclosed. All other embodiments, which can be derived by a person skilled in the art from the embodiments given herein without making any creative effort, shall fall within the protection scope of the present invention.

Experimental example 1

Analysis of binding action of ursolic acid and IKK β by iGEMDOCK molecular docking software

IKK β is a receptor, a three-dimensional crystal structure of the receptor is derived from a PDB protein database (ID: 4KIK), ursolic acid is a ligand, IGEMDOCK molecular docking software directly introduces the receptor and the ligand, docking parameters are set, the Population Size (Population Size) is set to be 200, the Number of filial Generations (Generations) is set to be 70, the Number of solutions (Number of solutions) is set to be 2 (the same below), and the binding energy of the ursolic acid and IKK β is-98.9 kcaj/mol, which indicates that the ursolic acid and the IKK β have certain binding capacity.

Fig. 3 is a schematic diagram of molecular docking analysis of ursolic acid and IKK β, wherein the binding sites of ursolic acid and IKK β are Leu21, Thr23, Glu97 and Cys99, and are located in the active pocket of IKK β, wherein the hydroxyl group at the C3 position of ursolic acid is hydrogen-bonded with the Glu97 and Cys99 positions of IKK β, and the carboxyl group at the C28 position of ursolic acid is hydrogen-bonded with the Leu21 and Thr23 positions of IKK β, indicating that the binding side chain groups of ursolic acid are the hydroxyl group at the C3 position and the carboxyl group at the C28 position, respectively.

Example 2

Analysis of binding effect of different side chain groups on C3 position of ursolic acid and IKK β by iGEMDOCK molecular docking software

According to the result of the example 1, the hydroxyl group at the C3 position of ursolic acid is modified by a side chain group, the selected side chain groups R1-11 are shown in figure 4 (hydrogen in the side chain group is saved, the same below), and the combination effect of the modified ursolic acid and IKK β is respectively analyzed by IGEMDOCK molecular docking software.

By taking side chain groups R2, R6 and R9 as examples, and FIGS. 5-7 are respectively a schematic diagram of molecular docking analysis of the modified ursolic acid and IKK β, it can be known from the diagram that R2, R6 and R9 can generate hydrogen bond combination with Glu97 and Cys99, wherein an amino hydrogen atom of R2 penetrates deep into an ATP combination region to form hydrogen bond with Glu97 and Cys99, a carboxyl hydrogen atom of R6 and Cys99 form hydrogen bond, and a carbonyl oxygen atom and an amino hydrogen atom of R9 form hydrogen bond with Glu97 and Cys 99.

The results of the binding energy of ursolic acid with different side chain groups at position C3 to IKK β are shown in table 1.

TABLE 1

Side chain groups	Binding energy (kcaj/mol)
		R1	-82.3
R2	-100.5
		R3	-89.6
R4	-96.9
		R5	-88
R6	-98.3
		R7	-94.5
R8	-79.1
		R9	-102.61
R10	-96.18
		R11	-91.58

The result shows that the ursolic acid obtained by modifying hydroxyl on the C3 position with R9 has lower binding energy with IKK β, -102.61kcaj/mol, which indicates that R9 has better binding effect compared with other side chain groups.

Example 3

Analysis of binding effect of different side chain groups on C28 position of ursolic acid and IKK β by iGEMDOCK molecular docking software

According to the result of example 1, the carboxyl group at C28 position of ursolic acid is modified with side chain group, the selected side chain group R1 '-14' is shown in figure 8, and the binding effect of the modified ursolic acid and IKK β is analyzed by IGEMDOCK molecular docking software.

By taking side chain groups R1 ', R2' and R14 'as examples, FIGS. 9-11 are schematic diagrams of molecular docking analysis of the modified ursolic acid and IKK β, respectively, it can be known from the diagrams that both the ether oxygen of R1' and the ester oxygen of R2 'form hydrogen bonds with Thr23, which indicates that the side chain group at C28 can penetrate into Gly ring and does not interact with ATP binding region, and the carbonyl oxygen atom and amino hydrogen atom in the side chain group at R14' form hydrogen bonds with Thr23 and Leu21, respectively, which indicates that the side chain group at C28 penetrates into Gly ring.

The results of the binding energy of ursolic acid with different side chain groups at position C28 to IKK β are shown in table 2.

TABLE 2

The result shows that the ursolic acid obtained by modifying hydroxyl on the C28 position with R14 'has lower binding energy with IKK β, -106.27kcaj/mol, which indicates that R14' has better binding effect compared with other side chain groups.

Example 4

In the examples 2 and 3, the preliminarily screened side chain groups R9 and R14' are modified by molecular superposition to obtain ursolic acid derivatives, the structural formula is shown as the formula (I):

analysis of binding action of ursolic acid derivative and IKK β by iGEMDOCK molecular docking software

FIG. 12 is a schematic diagram of molecular docking analysis of ursolic acid derivatives and IKK β. As can be seen from the figure, the carbonyl oxygen atom and the amino hydrogen atom in the side chain group at the C3 position can form hydrogen bonds with Glu97 and Cys99, respectively, and the carbonyl oxygen atom and the amino hydrogen atom in the side chain group at the C28 position can form hydrogen bonds with Thr23 and Leu21, respectively, indicating that the side chain group at the C28 position extends deep into the Gly ring.

IKK 16 (a selective IKK B kinase inhibitor), IMD 0354 (an IKK β inhibitor) and ursolic acid were selected for control and analyzed using molecular docking software, respectively, and the results of the binding capacity of the different compounds to IKK β are shown in table 3.

TABLE 3

Name (R)	Binding energy (kcaj/mol)
		IKK16	-119.44
IMD 0354	-101.03
		Ursolic acid	-100.07
Ursolic acid derivatives	-123.23

The result shows that the ursolic acid derivative has lower binding energy of-123.23 kcaj/mol, which indicates that the ursolic acid derivative has better binding effect with IKK β compared with other compounds, and the ursolic acid derivative is preliminarily determined to be the target IKK β medicine.

Although the invention has been described in detail above with reference to a general description and specific examples, it will be apparent to one skilled in the art that modifications or improvements may be made thereto based on the invention. Accordingly, such modifications and improvements are intended to be within the scope of the invention as claimed.

Claims

1. A virtual screening method for a drug targeting IKK β, comprising the steps of:

1) using ursolic acid as a ligand, IKK β (PDB ID: 4KIK) as a receptor protein, and adopting molecular docking software to analyze the binding site, binding energy and a binding side chain group of the ursolic acid and the IKK β according to the binding conformation of the ursolic acid and the IKK β after docking;

2. The virtual screening method of the targeted IKK β drug according to claim 1, wherein docking parameters comprise a group size of 200, a progeny number of 70, and a solution number of 2, by using IGEMDOCK molecular docking software.

3. The virtual screening method for IKK β -targeted drugs according to claim 1, wherein a more negative value of binding energy indicates a stronger binding ability to IKK β.

4. The virtual screening method for the IKK β -targeted drugs according to claim 1, wherein in step 3, ursolic acid is subjected to molecular modification by molecular superimposition.

5. The virtual screening method of the targeted IKK β drug according to claim 1, wherein the structural formula of the targeted IKK β drug is shown as formula (I):

6. the application of the targeted IKK β drug screened by the method of any one of claims 1 to 5 in preparation of antitumor drugs.