CN108399315B - Screening method of Bcr-Abl protein kinase inhibitor - Google Patents
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Abstract
The invention provides a screening method of a Bcr-Abl protein kinase inhibitor, which comprises the steps of firstly, docking small molecules which are obtained by grain similarity search and have high similarity with the known Bcr-Abl protein kinase inhibitor and a docking target, and then, scoring the intermolecular interaction of the docking conformation of the small molecules of the protein by a scoring function SPA to obtain an affinity value E; calculating the thermodynamic specificity ISR value and the kinetic specificity RT value of each small molecule and the docking target by combining the obtained affinity value E with a thermodynamic specificity and kinetic specificity formula, and finally obtaining the Bcr-Abl protein kinase inhibitor with the structure of the formula (I); the results show that the inhibitor obtained by the screening method has good inhibition effect on CML cells, has no toxicity on normal cells in a large concentration range, and has the effect of inhibiting CML variant tumors comparable to that of ponatinib.
Description
Technical Field
The invention relates to the field of drug screening, in particular to a screening method of a Bcr-Abl protein kinase inhibitor.
Background
The Bcr-Abl tyrosine kinase is one of the protein kinases, which is expressed by the Bcr-Abl oncogene. The Bcr-Abl oncogene is formed by rearrangement of the abelson (Abl) gene on chromosome 9 and the break point cluster (Bcr) gene on chromosome 22 with each other. The sustained activity of Bcr-Abl tyrosine kinase is responsible for Chronic Myelogenous Leukemia (CML). The enhanced kinase activity entails intracellular phosphorylation and activation of various signaling molecules that accelerate cell proliferation while inhibiting apoptosis. Therefore, inhibition of Bcr-Abl tyrosine kinase activity is an effective approach to targeted therapy of CML.
Imatinib, the first FDA approved drug for the treatment of CML in 2001, was also the first kinase inhibitor. The Bcr-Abl tyrosine kinase is a typical kinase that develops resistance in CML patients. More than 100 site mutations were found to be resistant to treatment with the first generation drug imatinib (imatinib). Due to the development of drug resistance, drugs against Bcr-Abl tyrosine kinase have been developed into the post-imatinib era (post-imatinib era) to combat drug resistance. In the posterior imatinib age, two second generation drugs, nilotinib (nilotinib) and dasatinib (dasatinib), have stronger drug effects, and more importantly, the two drugs can keep inhibition on Bcr-Abl drug-resistant mutants. However, neither drug inhibited the drug-resistant T315I kinase mutant. This led to the development and production of the third generation drug ponatinib (ponatinib), and received us FDA approval for marketing in 12 months of 2012. Ponatinib was the first pan Bcr-Abl kinase inhibitor (pan-Bcr-Abl kinase inhibitor) that inhibits all known mutants of anti-imatinib, including the T315I mutant. However, studies in recent years have shown that ponatinib has serious side effects, and therefore, there is an urgent need for a drug having better drug efficacy and higher specificity than ponatinib in clinical use.
Despite the great advances in drug development for the Abl-Bcr tyrosine kinase, such as the third generation drug ponatinib, the possibility of new drug resistance site mutations still exists. This has prompted the continued necessity to develop more effective inhibitors. Meanwhile, each inhibitor can generate the drug resistance mutation spectrum of the inhibitor, and the CML patients can obtain better curative effect by simultaneously using a plurality of inhibitors. In addition, the current targeted drugs for treating CML are expensive, and there is a need for a drug alternative that has better efficacy and resistance to drug than ponatinib and is lower in price. Therefore, the development of new inhibitors to improve and enhance the existing therapeutic effects remains a major concern for the treatment of CML, especially the development of third generation pan Abl-Bcr kinase inhibitors capable of inhibiting the T315I mutant.
The discovery of lead compounds (lead compounds) capable of having potential recognition capability and interaction with target proteins is the key of the early drug development (drug discovery), and the research and understanding of the recognition and interaction mechanism of proteins and small molecules has direct application to the development and design of new drugs. Efficient and specific binding of small molecules to their target proteins depends on two aspects, namely binding affinity (affinity) and binding specificity (specificity). Affinity refers to the stability of the protein-small molecule binding complex, and specificity refers to the preference of small molecules to bind to the target protein but not to other proteins. High affinity does not guarantee high specificity, which is critical to avoid side effects of drug molecules. In screening and designing a new drug, the expected effect is that the new drug can effectively bind to the target protein while reacting with other proteins as little as possible, thereby avoiding the occurrence of side effects. Therefore, quantification of the specificity of protein binding to small molecules is crucial to the development and design of new drugs. At present, theoretical calculation and experimental determination of protein-small molecule interaction mainly quantify the magnitude of affinity, and neglect the consideration of specificity. This is because the quantification of specificity is very difficult. Specificity includes thermodynamic specificity (therynamic specificity) and kinetic specificity (kinetic specificity). Quantification of thermodynamic specificity requires comparison of binding affinities between one small molecule and all proteins, which is difficult to achieve under existing data information and experimental conditions. Kinetic specificity refers to the Residence Time (RT) of a small molecule on a protein. Although experimental techniques can measure small molecule residence times in bulk to quantify kinetic specificity, there is a limit in the capital and number of small molecule assays. It is still very challenging, theoretically, to calculate the kinetic residence time of a large number of protein-small molecule complexes using molecular dynamics simulations. Therefore, providing a more efficient method for screening Abl-Bcr kinase inhibitors in order to save costs and obtaining drugs with higher activity are problems that need to be solved at present.
Disclosure of Invention
In view of the above, the present invention provides a method for screening a Bcr-Abl protein kinase inhibitor, which has high screening efficiency and high activity of the obtained inhibitor.
The invention provides a screening method of a Bcr-Abl protein kinase inhibitor, which comprises the following steps:
1) docking small molecules which are obtained by the similarity search of the cereal samples and have high similarity with known Bcr-Abl protein kinase inhibitors with docking targets, and then performing intermolecular interaction scoring on the protein-small molecule docking conformation by adopting a scoring function SPA to obtain the total energy between the target protein and the small molecules, namely an affinity value E;
2) calculating the thermodynamic specificity ISR value and the kinetic specificity RT value of each small molecule and the docking target by utilizing the affinity value E obtained in the step 1) and combining a thermodynamic specificity formula and a kinetic specificity formula,
wherein the thermodynamic property formula is:
delta E is the difference between the lowest energy and the average energy, i.e. delta E ═ EN-<E>，
Δ E is the energy fluctuation, i.e. ()<E2>-<E>2)1/2；
The dynamic characteristic formula is as follows:
f (r) is the affinity value at the different binding positions r,
KBt and D (r) are constants;
3) normalizing the obtained affinity value E, thermodynamic specificity ISR value and kinetic specificity RT value of the small molecule to obtain P of the small moleculeE，PISR，PRTThen, the three are added to obtain a small molecule multidimensional parameter S, the obtained small molecule multidimensional parameter S is compared with the multidimensional parameter of ponatinib to obtain the Bcr-Abl protein kinase inhibitor with the structure of the formula (I),
wherein R is1Is of the formula (R)1-1), formula (R)1-2) or formula (R)1-3)，
R2 is a nitrogen-containing aromatic group of C5-C8.
Preferably, the method for obtaining the small molecules with high similarity to known Bcr-Abl protein kinase inhibitors by the grain similarity search specifically comprises the following steps:
and (3) preliminarily screening about 40,000,000 small molecules in a PubChem database by utilizing a valley similarity search, and selecting the small molecules in the database, wherein the structural similarity of the small molecules to any one of imatinib, nilotinib, dasatinib and ponatinib is greater than 90% of the valley coefficient, namely the small molecules have high similarity to the known Bcr-Abl protein kinase inhibitor.
Preferably, the docking targets are activated wild-type protein kinase, activated T315I mutant protein kinase, inactivated wild-type protein kinase and inactivated T315I mutant protein kinase.
Preferably, the software used for docking is autodock 4.2.
Preferably, said R is2Is of the formula (R)2-1), or formula (R)2-2)，
Preferably, the Bcr-Abl protein kinase inhibitor is of formula (I-1), formula (I-2) or formula (I-3),
compared with the prior art, the invention provides a screening method of a Bcr-Abl protein kinase inhibitor, which comprises the steps of docking micromolecules which are obtained by grain similarity search and have high similarity with the known Bcr-Abl protein kinase inhibitor with a docking target, and then performing intermolecular interaction scoring on protein-micromolecule docking conformation by adopting a scoring function SPA to obtain the total energy between a target protein and the micromolecules, namely an affinity value E; and combining the obtained affinity value E with thermodynamic specificity and kinetic specificity formulas to calculate thermodynamic specificity ISR value and kinetic specificity RT value of each small molecule and the docking target, and normalizing the values to obtain P of the small moleculesE，PISR，PRTThen, adding the three to obtain a small molecule multidimensional parameter S, and comparing the obtained small molecule multidimensional parameter with the multidimensional parameter of ponatinib to obtain a Bcr-Abl protein kinase inhibitor with a structure shown in a formula (I); experimental results show that the inhibitor obtained by the screening method provided by the invention has a good effect of inhibiting CML cells, has no toxicity to normal cells in a large concentration range, and has an effect of inhibiting CML variant tumors comparable to that of ponatinib.
Drawings
FIG. 1 is a schematic structural diagram of the Bcr-Abl protein in both its inactive and active conformations;
FIG. 2 shows the results of the inhibition of proliferation of three leukemia cells and two normal cells by different concentrations of PA;
FIG. 3 shows the result of different concentrations of PA induced apoptosis of three leukemia cells;
FIG. 4 is a graph of the effect of different concentrations of PA on the cell cycle of three leukemias;
FIG. 5 is a graph of the effect of PA on mitochondrial membrane potential in cells;
FIG. 6 shows the results of measuring the Reactive Oxygen Species (ROS) levels in three leukemia cells after 24h treatment with different concentrations of PA;
FIG. 7 is a graph showing the effect of different concentrations of PA on the expression levels of the fusion protein Bcr-Abl and its phosphorylated proteins in three leukemia cells;
FIG. 8 is a graph showing the effect of PA on inhibiting the growth of transplanted tumor cells in animals.
Detailed Description
The invention provides a screening method of a Bcr-Abl protein kinase inhibitor, which comprises the following steps:
1) docking small molecules which are obtained by the similarity search of the cereal samples and have high similarity with known Bcr-Abl protein kinase inhibitors with docking targets, and then performing intermolecular interaction scoring on the protein-small molecule docking conformation by adopting a scoring function SPA to obtain the total energy between the target protein and the small molecules, namely an affinity value E;
2) calculating the thermodynamic specificity ISR value and the kinetic specificity RT value of each small molecule and the docking target by utilizing the affinity value E obtained in the step 1) and combining a thermodynamic specificity and kinetic specificity formula,
wherein the thermodynamic property formula is:
delta E is the difference between the lowest energy and the average energy, i.e. delta E ═ EN-<E>，
Δ E is the energy fluctuation, i.e. ()<E2>-<E>2)1/2；
The dynamic characteristic formula is as follows:
f (r) is the affinity value at the different binding positions r,
KBt and D (r) are constants;
3) normalizing the obtained affinity value E, thermodynamic specificity ISR value and kinetic specificity RT value of the small molecule to obtain P of the small moleculeE，PISR，PRTThen adding the three to obtain small molecular multidimensionalParameter S, comparing the obtained small molecule multidimensional parameter with the multidimensional parameter of ponatinib to obtain the Bcr-Abl protein kinase inhibitor with the structure of formula (I),
wherein R is1Is of the formula (R)1-1), formula (R)1-2) or formula (R)1-3)，
R2Is a nitrogen-containing aromatic group of C5-C8.
According to the invention, the micromolecules which are obtained by the similarity search of the cereal and have high similarity with the known Bcr-Abl protein kinase inhibitor are butted with a butting target, and then a scoring function SPA is adopted to score the intermolecular interaction of the protein-micromolecule butting conformation to obtain the total energy between the target protein and the micromolecules, namely an affinity value E; wherein the docking targets are preferably activated wild-type protein kinase (PDB ID 2GQG), activated T315I mutant protein kinase (PDB ID 2V7A), non-activated wild-type protein kinase (PDB ID 1E1P) and non-activated T315I mutant protein kinase (PDB ID 3IK 3); the software adopted for the docking is preferably AutoDock 4.2; the scoring function for scoring intermolecular interactions in the protein-small molecule docking conformation is not particularly required in the present invention, and any scoring function known in the art can be used, for example, the scoring function SPA disclosed in the article "Yan, Z.and Wang, J. (2012) Specificity qualification of biomolecular registration and its evaluation for drug discovery. Sci.Rep., 2, 1-7".
In the present invention, the method for obtaining a small molecule with high similarity to an existing drug molecule by a valley similarity search is preferably:
and (3) preliminarily screening about 40,000,000 small molecules in a PubChem database by utilizing a valley similarity search, and selecting the small molecules in the database, wherein the structural similarity of the small molecules to any one of imatinib, nilotinib, dasatinib and ponatinib is greater than 90% of the valley coefficient, namely the small molecules have high similarity to the known Bcr-Abl protein kinase inhibitor.
According to the invention, the affinity value E obtained in the step 1) is combined with a thermodynamic specificity and kinetic specificity formula to calculate the thermodynamic specificity ISR value and the kinetic specificity RT value of each small molecule and the docking target,
wherein the thermodynamic property formula is:
delta E is the difference between the lowest energy and the average energy, i.e. delta E ═ EN-<E>，
Δ E is the energy fluctuation, i.e. ()<E2>-<E>2)1/2；
The dynamic characteristic formula is as follows:
f (r) is the affinity value at the different binding sites r, i.e.the binding energy value.
In the calculation, the RT formula adopts discretization calculation summation, KBT and D (r) are constants.
According to the invention, the affinity value E, the thermodynamic specificity ISR value and the kinetic specificity RT value of the obtained small molecule are normalized to obtain the P of the small moleculeE，PISR，PRTThen, adding the three to obtain a small molecule multidimensional parameter S, and comparing the obtained small molecule multidimensional parameter with the multidimensional parameter of ponatinib to obtain a Bcr-Abl protein kinase inhibitor with a structure shown in a formula (I); the method for normalization processing has no special requirements, and the method for normalization processing can be any known normalization processing method in the field; in the Bcr-Abl protein kinase inhibitor with the structure of the formula (I), R is2Preferably of the formula (R)2-1), or formula (R)2-2)，
More specifically, the Bcr-Abl protein kinase inhibitor is shown as a formula (I-1), a formula (I-2) or a formula (I-3),
the invention provides a screening method of a Bcr-Abl protein kinase inhibitor, which comprises the steps of docking micromolecules which are obtained by grain similarity search and have high similarity with the known Bcr-Abl protein kinase inhibitor with a docking target, and then adopting a scoring function SPA to score the intermolecular interaction of protein-micromolecule docking conformation to obtain the total energy between a target protein and the micromolecules, namely an affinity value E; and combining the obtained affinity value E with thermodynamic specificity and kinetic specificity formulas to calculate thermodynamic specificity ISR value and kinetic specificity RT value of each small molecule and the docking target, and normalizing the values to obtain P of the small moleculesE，PISR，PRTThen, adding the three to obtain a small molecule multidimensional parameter S, and comparing the obtained small molecule multidimensional parameter with the multidimensional parameter of ponatinib to obtain a Bcr-Abl protein kinase inhibitor with a structure shown in a formula (I); the inhibitor obtained by the invention has good inhibition effect on CML cells, has no toxicity on normal cells in a large concentration range, and has the effect of inhibiting CML variant tumors comparable to that of ponatinib.
The following will clearly and completely describe the technical solutions of the embodiments of the present invention, and it is obvious that the described embodiments are only a part of the embodiments of the present invention, and not all embodiments. 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.
Examples
1) Similarity screening
Approximately 40,000,000 small molecules in the PubChem database were initially screened by using a Valley similarity search (Tanimoto similarity search). The small molecules in the library have a structural similarity with any one of imatinib, nilotinib, dasatinib and ponatinib which is greater than 90% of the trough coefficient and are retained for the next molecular docking. By this screening, a group of small molecule compounds with relatively small numbers but very similar structures to drug molecules was obtained, and the results are shown in table 1, and in addition, a diversity set (diversity set) of the National Cancer Institute (NCI) was selected as a control group.
TABLE 1 number of small molecule compounds in the pubchem database with high similarity to existing drug molecules
2) Docking and energy calculation
The small molecules obtained above were molecularly docked with four docking targets (activated wild type (PDB ID 2GQG), activated T315I mutant (PDB ID 2V7A), non-activated wild type (PDB ID 1E1P) and non-activated T315I mutant (PDB ID 3IK3)) using docking software autodock 4.2. After the docking, the protein-small molecule docking conformation is re-scored for intermolecular interaction by using a scoring function SPA reported in Yan, Z.and Wang, J. (2012), Specificity quantification of biomolecellular recognition and its visualization for drug discovery. Sci. Rep., 2, 1-7, and the obtained energy value is used for calculation of thermodynamic Specificity and kinetic Specificity. SPA is a set of interatomic interaction energy values, and the total energy between a target protein and a small molecule, namely the affinity, can be calculated by using the value of SPA. Wherein, the structural schematic diagram of the Bcr-Abl protein in the non-activated state and the activated state is shown in figure 1, and the structural schematic diagram of the Bcr-Abl protein in the non-activated state and the activated state is shown in figure 1.
3) Calculation of specificity
And calculating the thermodynamic specificity ISR value and the kinetic specificity RT value of each small molecule and the docking target by utilizing the obtained docking molecule conformation and the affinity value E obtained by the SPA scoring and combining a thermodynamic specificity and kinetic specificity formula. The ISR calculation formula is derived from the funnel energy landform theory. The RT calculation formula is derived from a diffusion equation. The two formulas are respectively as follows:
delta E is the difference between the lowest energy and the average energy, i.e. delta E ═ EN-<E>. Δ E is the energy fluctuation, i.e. ()<E2>-<E>2)1/2. F (r) is the affinity value at the different binding sites r, i.e.the binding energy value. In the calculation, the RT formula adopts discretization calculation summation, KBT and D (r) are constants.
4) Multidimensional screening
Through the steps, the affinity value E, the thermodynamic specificity ISR value and the kinetic specificity RT value of each molecule and the docking target are obtained. Because the dimension and the represented meaning of each parameter are different, each dimension is respectively normalized to obtain PE，PISR，PRTAnd then the three are added to obtain a parameter S, namely a multidimensional parameter. All small molecules are ordered using the value of the multidimensional parameter S. By comparison, the Bcr-Abl protein kinase inhibitor having the formula (I-1), the formula (I-2) or the formula (I-3) is obtained. The three small molecular compounds can be used as lead compounds for early experimental tests and possible clinical tests. The small molecular compound (named as PA, CID 24826974) with the formula (I-3) has multidimensional parameter values obviously superior to those of the existing drug Plutinib, and the result is shown in Table 2.
Table 2 comparison of lead compound (PA) with the drug ponatinib.
5) Experimental verification
Aiming at the screened lead small-molecule compound ponatinib derivative PA with the structure shown in the formula (I-3), a scientific research group carries out biochemical tests on the small-molecule compounds through a series of in vitro and in vivo experiments, wherein the biochemical tests comprise proliferation experiments (MTS) method for determining the proliferation influence of the lead compound on cancer cell lines and normal cell lines; determining the influence of the lead compound on the apoptosis of the three CML cells by DAPI cell staining and a flow cytometry experiment; further measuring the intracellular mitochondrial membrane potential, Reactive Oxygen Species (ROS) and protein expression to determine the mechanism of leading compound PA for causing apoptosis; the inhibition effect of the lead compound on the tumor is observed through a tumor transplantation animal experiment.
Specifically, toxicity experiments of three CML cells and normal cells are performed, and all experiments are tested by an enzyme-labeling instrument of an MTS method; the results are shown in fig. 2, and fig. 2 shows the results of the proliferation inhibition effect of PA at different concentrations on three leukemia cells and two normal cells (n-3); wherein, a in the figure is the structure of the PA compound and the toxicity test on three leukemia cells; b is the toxicity of PA on mouse fibroblasts (L929) and human normal colon epithelial cells (NCM 460). As can be seen in the figure, the PA compounds have nanomolar (nM) IC on both wild type Bcr-Abl and CML cells expressed by variant T315I50The value, and the inhibition with concentration increase in concentration dependence, and compared with ponatinib PA on normal cells without toxicity;
PA with different concentrations is adopted to induce three leukemia cell apoptosis, the result is processed by DAPI staining, the result is shown in figure 3, figure 3 is the result of PA with different concentrations inducing three leukemia cell apoptosis, wherein, (a) the cell morphology changes under a fluorescence microscope after PA treatment for 24 hours (scale bar: 50 μm); (b) annexin V-FITC/PI double staining flow cytometry is used for detecting the apoptosis rate. As can be seen, the nuclei of the control cells were round and the chromatin density was uniform. The medicinal group has irregular cell nucleus edge, dense chromosome, heavy coloring and cell nucleus contraction. Therefore, it was morphologically shown that PA was able to induce apoptosis in cells.
The results are shown in fig. 4, which is the effect of different concentrations of PA on the cell cycle of three leukemias; as can be seen from the figure, the flow cytometry experiment detection structure shows that the apoptosis rate is obviously improved along with the increase of the concentration compared with the control group.
The apoptosis mechanism is probably related to mitochondrial membrane potential and active oxygen, the mitochondrial membrane potential reduction is a marker event in the early apoptosis stage of cells, and whether the cells are subjected to apoptosis is judged by detecting JC-1 monomers and JC-1 polymers and observing the conversion of JC-1 from red fluorescence to green fluorescence by using a fluorescence microscope. The results are shown in FIG. 5, FIG. 5 is the effect of PA on the mitochondrial membrane potential of cells; wherein JC-1 is a method for detecting mitochondrial membrane potential delta psimThe fluorescent probe of (1). (a) JC-1 monomer (green fluorescence); (b) JC-1 dimer (red fluorescence); (c) mixing; as can be seen from FIG. 5, with the addition of PA, the red fluorescence in the cells decreased and the green fluorescence increased, indicating that the mitochondrial membrane potential decreased and the cells underwent apoptosis.
The intracellular ROS level is quantitatively detected by measuring the change of the fluorescence intensity of the DCFH-DA fluorescent dye through a flow cytometer, the result is shown in figure 6, and figure 6 is the result of detecting the intracellular Reactive Oxygen Species (ROS) level of three types of leukemia after the treatment of PA with different concentrations for 24 hours.
The relationship between apoptosis and expression level of the fusion protein Bcr-Abl was investigated by Western blotting, and the results are shown in FIG. 7, and FIG. 7 is the effect of different concentrations of PA on the expression level of the fusion protein Bcr-Abl and its phosphorylated protein in three leukemia cells, from which it can be seen that protein expression decreases with increasing concentration of PA. Meanwhile, the tumor size of transplanted animal (mouse) tumor is obviously reduced along with the increase of the administration time, which shows that the lead compound has good treatment effect on variant tumor.
The results of H & E immunohistological staining are shown in FIG. 8, and FIG. 8 is a result of PA effectively inhibiting the growth of transplanted tumor cells in animals, wherein (a-b) the inhibition of PA on the growth of variant tumors; (c) change in tumor volume after administration; (d) change in body weight of mice after dosing; (e) h & E immunostaining of the five organ tissues and staining of antibody tumor tissues. As can be seen from the figure, PA has no toxicity to the five internal organs, but has good inhibitory effect on c-abl protein.
The above description of the embodiments is only intended to facilitate the understanding of the method of the invention and its core idea. It should be noted that, for those skilled in the art, it is possible to make various improvements and modifications to the present invention without departing from the principle of the present invention, and those improvements and modifications also fall within the scope of the claims of the present invention.
Claims (4)
1. A method of screening for a Bcr-Abl protein kinase inhibitor, comprising:
1) docking small molecules which are obtained by the similarity search of the cereal samples and have high similarity with known Bcr-Abl protein kinase inhibitors with docking targets, and then performing intermolecular interaction scoring on the protein-small molecule docking conformation by adopting a scoring function SPA to obtain the total energy between the target protein and the small molecules, namely an affinity value E;
the method for obtaining the small molecules with high similarity with the known Bcr-Abl protein kinase inhibitor by the grain similarity search specifically comprises the following steps:
preliminary screening 40,000,000 small molecules in a PubChem database by utilizing a millet similarity search, and selecting the small molecules in the PubChem database, the structural similarity of which to any one of imatinib, nilotinib, dasatinib and ponatinib is greater than 90% of a millet coefficient, namely the small molecules with high similarity to a known Bcr-Abl protein kinase inhibitor;
the docking targets are activated wild-type protein kinase, activated T315I mutant protein kinase, inactivated wild-type protein kinase and inactivated T315I mutant protein kinase;
2) calculating the thermodynamic specificity ISR value and the kinetic specificity RT value of each small molecule and the docking target by utilizing the affinity value E obtained in the step 1) and combining a thermodynamic specificity formula and a kinetic specificity formula,
wherein the thermodynamic property formula is:
delta E is the difference between the lowest energy and the average energy, i.e. delta E ═ EN-<E>，
Δ E is the energy fluctuation, i.e. ()<E2>-<E>2)1/2；
The dynamic characteristic formula is as follows:
f (r) is the affinity value at the different binding positions r,
KBt and D (r) are constants;
3) normalizing the obtained affinity value E, thermodynamic specificity ISR value and kinetic specificity RT value of the small molecule to obtain P of the small moleculeE,PISR,PRTThen, the three are added to obtain a small molecule multidimensional parameter S, the obtained small molecule multidimensional parameter S is compared with the multidimensional parameter of ponatinib to obtain the Bcr-Abl protein kinase inhibitor with the structure of the formula (I),
wherein R is1Is of the formula (R)1-1), formula (R)1-2) or formula (R)1-3)，
R2Is a nitrogen-containing aromatic group of C5-C8.
2. The screening method of claim 1, wherein the software used for docking is autodock 4.2.
3. The screening method according to claim 1, wherein R is2Is of the formula (R)2-1), or formula (R)2-2)，
4. The screening method according to claim 1, wherein the Bcr-Abl protein kinase inhibitor is of formula (I-1), formula (I-2) or formula (I-3),
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