Antitumor small molecule compounds targeting st3gal1 and uses thereof
By designing a small molecule compound, N'-[1-(4-fluorophenyl)-1H-pyrazolo[3,4-d]pyrimidin-4-yl]-4-methoxybenzoylhydrazine, targeting ST3GAL1 through virtual screening, the problem of the lack of ST3GAL1 inhibitors in the prior art was solved, and a significant inhibitory effect on human pancreatic cancer cells was achieved.
Patent Information
- Authority / Receiving Office
- CN · China
- Patent Type
- Patents(China)
- Current Assignee / Owner
- Filing Date
- 2024-09-04
- Publication Date
- 2026-03-20
AI Technical Summary
Current targeted therapies for tumors suffer from challenges such as target complexity and drug resistance, particularly the lack of inhibitors targeting ST3GAL1, which limits their therapeutic efficacy.
We designed and synthesized a small molecule compound, N'-[1-(4-fluorophenyl)-1H-pyrazolo[3,4-d]pyrimidin-4-yl]-4-methoxybenzoylhydrazine, which targets ST3GAL1. We obtained its three-dimensional structure through virtual screening and performed molecular dynamics simulations to verify its binding stability with ST3GAL1.
This small molecule compound significantly inhibited the expression of ST3GAL1, showing a dose-dependent inhibitory effect on human pancreatic cancer PANC-1 and BxPC-3 cells, with IC50 values of 42.17 μM and 46.83 μM, respectively, demonstrating its potential as an anti-tumor drug.
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Figure CN119101056B_ABST
Abstract
Description
TECHNICAL FIELD
[0001] The present application relates to the field of biotechnology and medicine, in particular to an anti-tumor small molecule compound targeting ST3GAL1 and its application. BACKGROUND
[0002] Malignant tumor, as one of the major threats to global health, its complex pathogenesis and high heterogeneity bring great challenges to clinical treatment. With the in-depth study of the biological characteristics of tumors, scientists have gradually realized that a variety of molecules and signaling pathways in the tumor microenvironment play a key role in the occurrence, development and metastasis of tumors. Therefore, targeted therapy for these key molecules or pathways has become an important direction of current anti-tumor research. Computer-aided drug design greatly reduces the research and development cost of traditional drugs, shortens the cycle, and is strong in pertinence, which is a great tool for developing tumor targeted therapy drugs.
[0003] ST3GAL1 (ST3 beta-galactoside alpha-2, 3-sialyltransferase 1) is an important glycosyltransferase that plays a core role in the sialylation of cell surface glycoproteins and glycolipids. In recent years, more and more studies have shown that abnormal expression of ST3GAL1 is related to the progression and chemoresistance of a variety of malignant tumors. ST3GAL1 affects cell adhesion, signal transduction, and immune escape by catalyzing the sialylation modification of specific proteins or lipids, thereby promoting the growth, invasion and metastasis of tumor cells [1,2] .
[0004] Currently, anti-tumor targeted inhibitors are widely used in clinical tumor treatment due to their good effect, relatively small side effects and other advantages, but there are still some limitations, such as easy drug resistance, complexity and diversity of target points. To date, there are few studies on glycosylated proteins, and no studies have reported inhibitors targeting ST3GAL1. Therefore, it is of great significance to find ST3GAL1 inhibitors and develop an anti-tumor drug targeting ST3GAL1 to provide more reliable solutions for the treatment of cancer.
[0005] REFERENCES
[0006] [1] Yeo H L, Fan T C, Lin R J, et al. Sialylation of vasorin by ST3Gal1 facilitates TGF-β1-mediated tumor angiogenesis and progression [J]. Int J Cancer, 2019, 144(8): 1996-2007.
[0007] [2]Wu X, Zhao J, Ruan Y, et al. Sialyltransferase ST3GAL1 promotes cell migration, invasion, and TGF-β1-induced EMT and confers paclitaxel resistance in ovarian cancer [J]. Cell Death Dis, 2018, 9(11): 1102. SUMMARY
[0008] The technical problem solved by the present application is to provide an anti-tumor small molecule compound targeting ST3GAL1 and its application in view of the above-mentioned deficiencies in the prior art.
[0009] To solve the above technical problems, the technical solution adopted by the present application is as follows: In a first aspect, the present application provides an anti-tumor small molecule compound targeting ST3GAL1, which is N'-[1-(4-fluorophenyl)-1H-pyrazolo[3,4-d]pyrimidin-4-yl]-4-methoxybenzohydrazide, and its structure is shown in the following formula I:
[0010]
[0011] Preferably, the small molecule compound can inhibit the expression of ST3GAL1.
[0012] Preferably, the small molecule compound is obtained by virtual screening, and the virtual screening method is as follows:
[0013] The small molecule compound is obtained by obtaining the human ST3GAL1 protein sequence, using Swiss-Model for homology modeling, using Gromacs for structure optimization of the modeled protein structure, using AutoDock Vina software for virtual screening, and finally using Desmond for molecular dynamics simulation.
[0014] Preferably, the virtual screening method is as follows:
[0015] S1, protein sequence acquisition and modeling: obtain the human ST3GAL1 protein sequence from the Uniprot database, and use Swiss-Model for three-dimensional structure homology modeling;
[0016] S2, structure optimization: use Gromacs software to optimize the modeled protein structure to ensure the accuracy and reliability of the model;
[0017] S3, virtual screening: three rounds of virtual screening are performed by using AutoDock Vina software, different exhaustive indices are used in each round, and the top 10% of compounds in each round of docking are reserved to obtain candidate compounds;
[0018] S4, molecular dynamics simulation: the selected candidate compounds are subjected to molecular dynamics simulation by using Desmond software, the binding stability of the candidate compounds and ST3GAL1 is verified, and the candidate compounds with stable stability are screened to obtain the small molecule compound.
[0019] Preferably, the Gromacs software version is 2023.1, the AutoDock Vina software version is 1.2.3, and the Desmond software version is 2023.4.
[0020] In a second aspect of the present application, the application of the small molecule compound N'-[1-(4-fluorophenyl)-1H-pyrazolo[3,4-d]pyrimidin-4-yl]-4-methoxybenzohydrazide and its pharmaceutically acceptable salt as described above in the preparation of an antitumor drug is provided.
[0021] Preferably, the antitumor drug is obtained by combining the small molecule compound as an active ingredient with one or more pharmaceutically acceptable solid or liquid excipients and / or adjuvants.
[0022] Preferably, the tumor is a tumor disease related to ST3GAL1.
[0023] Preferably, the tumor includes lung cancer, breast cancer, esophageal cancer, gastric cancer, liver cancer, colorectal cancer, pancreatic cancer, and cholangiocarcinoma.
[0024] In a third aspect of the present application, the application of the small molecule compound and its pharmaceutically acceptable salt as described above in the preparation of an ST3GAL1 inhibitor is provided.
[0025] The present application has the following beneficial effects:
[0026] The present application obtains an anti-tumor small molecule compound targeting ST3GAL1 through virtual screening, which can inhibit the expression of ST3GAL1 and has the potential to be applied to tumor treatment and preparation of an antitumor drug. The experiments of the present application show that the small molecule compound provided by the present application has a significant inhibitory effect on human pancreatic cancer PANC-1 cell lines and human in situ pancreatic cancer BxPC-3 cell lines after 48 hours of action, and the effect is dose-dependent, wherein the IC50 value for PANC-1 cells is 42.17 μM, and the IC50 value for BxPC-3 cells is 46.83 μM. BRIEF DESCRIPTION OF DRAWINGS
[0027] Figure 1CCK-8 proliferation experiment results of PANC-1 cells;
[0028] Figure 2 CCK-8 proliferation experiment results of BxPC-3 cells;
[0029] Figure 3 CCK-8 results of PANC-1 cells treated with compound C312-ST01 for 48h;
[0030] Figure 4 CCK-8 results of BxPC-3 cells treated with compound C312-ST01 for 48h. DETAILED DESCRIPTION
[0031] The application will be further described in conjunction with the examples below, so that those skilled in the art can implement the application according to the description.
[0032] It should be understood that the terms such as "have", "contain" and "include" used herein do not exclude the presence or addition of one or more other elements or combinations thereof.
[0033] The test methods used in the following examples are conventional methods unless otherwise specified. The materials and reagents used in the following examples, unless otherwise specified, can be obtained commercially. The specific conditions not specified in the following examples are carried out according to the conventional conditions or the conditions recommended by the manufacturer. The reagents or instruments used, if not specified by the manufacturer, are conventional products that can be obtained by commercial purchase.
[0034] The application provides an anti-tumor small molecule compound targeting ST3GAL1, which is obtained by virtual screening. The virtual screening method is as follows: the human ST3GAL1 protein sequence is obtained, Swiss-Model is used for homology modeling, Gromacs is used for structure optimization of the modeled protein structure, then AutoDock Vina software is used for three rounds of virtual screening, the compounds with docking scores in the top 10% of each round of screening are retained, finally Desmond is used for molecular dynamics simulation to evaluate the binding stability of the compounds with ST3GAL1 protein, and finally the small molecule compound is screened.
[0035] The small molecule compound is N'-[1-(4-fluorophenyl)-1H-pyrazolo[3,4-d]pyrimidin-4-yl]-4-methoxybenzohydrazide, and the molecular formula is C 19 H 15 FN6O2, code C312-ST01, the structure of which is shown in the following formula I:
[0036]
[0037] The public information of the compound refers to the following website:
[0038] https: / / pubchem.ncbi.nlm.nih.gov / #query=K405-4012.
[0039] Among them, the small molecule compound can inhibit the expression of ST3GAL1.
[0040] In a preferred embodiment, the virtual screening method is:
[0041] S1, protein sequence acquisition and modeling: obtain the human ST3GAL1 protein sequence from the Uniprot database, and use Swiss-Model for three-dimensional structure homology modeling;
[0042] S2, structure optimization: use Gromacs software to optimize the protein structure after modeling to ensure the accuracy and reliability of the model;
[0043] S3, virtual screening: use AutoDock Vina software for three rounds of virtual screening, use different exhaustive indices in each round, and retain the top 10% of compounds in each round of docking score to obtain candidate compounds;
[0044] S4, molecular dynamics simulation: the selected candidate compounds are subjected to molecular dynamics simulation by Desmond software to verify the binding stability of the candidate compounds and ST3GAL1, and to screen stable candidate compounds to obtain small molecule compounds.
[0045] In a preferred embodiment, the version of Gromacs software is 2023.1, the version of AutoDock Vina software is 1.2.3, and the version of Desmond software is 2023.4.
[0046] The application also provides a use of the above small molecule compound N'-[1-(4-fluorophenyl)-1H-pyrazolo[3,4-d]pyrimidin-4-yl]-4-methoxybenzohydrazide and its pharmaceutical salt in the preparation of an antitumor drug.
[0047] In a preferred embodiment, the antitumor drug is obtained by combining the small molecule compound as an active ingredient with one or more pharmaceutically acceptable solid or liquid excipients and / or adjuvants.
[0048] In a preferred embodiment, the tumor is a tumor disease related to ST3GAL1.
[0049] In a preferred embodiment, the tumor includes lung cancer, breast cancer, esophageal cancer, gastric cancer, liver cancer, colorectal cancer, pancreatic cancer, and cholangiocarcinoma.
[0050] The application also provides a use of the small-molecule compound and the pharmaceutical salt thereof in the preparation of an ST3GAL1 inhibitor.
[0051] The above is the general idea of the application, and the following provides detailed examples and comparative examples based thereon to further illustrate the application.
[0052] Example 1: Virtual screening of small-molecule compound C312-ST01
[0053] S1, Protein sequence acquisition and modeling: The human ST3GAL1 protein sequence was obtained from the Uniprot database (website: https: / / www.uniprot.org), and the three-dimensional structure homology modeling was performed using Swiss-Model (website: https: / / swissmodel.expasy.org);
[0054] S2, Structure optimization: The optimized protein structure was optimized using Gromacs software (version 2023.1) to ensure the accuracy and reliability of the model;
[0055] S3, Virtual screening: AutoDock Vina software (version 1.2.3) was used for three rounds of virtual screening, each round used a different exhaustive index, and the top 10% of compounds in each round of docking were retained;
[0056] S4, Molecular dynamics simulation: The selected candidate compounds were subjected to molecular dynamics simulation by Desmond software (version 2023.4) to verify the binding stability of the compounds and ST3GAL1;
[0057] S5, Final screening of compounds: The potential inhibitor, small-molecule compound C312-ST01, i.e., N'-[1-(4-fluorophenyl)-1H-pyrazolo[3,4-d]pyrimidin-4-yl]-4-methoxybenzohydrazide, was screened by the above process, and its structural formula is shown as formula I:
[0058]
[0059] Example 2: Anti-tumor activity experiment of small-molecule compound C312-ST01
[0060] In this example, the common CCK-8 method was used to perform a tumor cell proliferation inhibition experiment on the small-molecule compound C312-ST01 obtained by virtual screening in Example 1.
[0061] The molecular formula of the small-molecule compound is C 19 H 15 FN6O2, code C312-ST01, purchased from Tao Shu Biological Co., Ltd.;
[0062] The sources of the main materials used below are as follows:
[0063] Human pancreatic cancer PANC-1 cells and human pancreatic cancer BxPC-3 cells were purchased from Beina Biological Technology Co., Ltd., with the numbers BNCC339759 and BNCC338477, respectively; DMEM basic medium and RPMI-1640 basic medium were purchased from Meilunbio, with the numbers MA0212 and MA0215, respectively; penicillin-streptomycin solution (100x) was purchased from Biosharp, with the number BL505A; serum (FBS) was purchased from CellMax, with the number SA211.02; trypsin-EDTA digestion solution was purchased from Solabio, with the number T1300; CCK-8 reagent was purchased from Yikai Biological Technology Co., Ltd., with the number ATWF06121.
[0064] The experimental method includes the following steps:
[0065] 1. Sample configuration: Compound C312-ST01 was dissolved in DMSO to form a 100 mM solution as a stock solution, which was diluted with the corresponding complete medium to different concentrations for cell treatment according to the experimental requirements in subsequent experiments;
[0066] 2. Cell strain: human pancreatic cancer PANC-1 cells and human pancreatic cancer BxPC-3 cells;
[0067] 3. Culture medium: DMEM basic medium + FBS + double antibody for human pancreatic cancer PANC-1 cells, and RPMI-1640 basic medium + FBS + double antibody for human pancreatic cancer BxPC-3 cells.
[0068] 4. Experimental method: CCK-8 method.
[0069] PANC-1 and BxPC-3 cells were inoculated in 96-well plates at 3000 cells per well, and after 24 h, they were treated with small molecule compound C312-ST01 at concentrations of 25, 50 and 100 μM, respectively. At 0, 24 and 48 h, 10 μL of CCK-8 reagent was added to each well, and after 1 h of incubation in the incubator, the OD value was measured at 450 nm on a microplate reader.
[0070] 5. Experimental results:
[0071] Reference Figure 1For the CCK-8 proliferation experiment results of PANC-1 cells, C312-ST01 compound was used to treat PANC-1 cells for 0, 24 and 48 hours, and then CCK-8 detection was performed. The experimental results show that the effect of C312-ST01 on PANC-1 cells is not obvious after 24 hours of treatment, while C312-ST01 has a significant inhibitory effect on PANC-1 cells after 48 hours of treatment, and the effect is dose-dependent.
[0072] Reference Figure 2 For the CCK-8 proliferation experiment results of BxPC-3 cells, C312-ST01 compound was used to treat BxPC-3 cells for 0, 24 and 48 hours, and then CCK-8 detection was performed. The experimental results show that C312-ST01 has a significant inhibitory effect on BxPC-3 cells after 24 and 48 hours of treatment, and the effect is dose-dependent.
[0073] Reference Figure 3 For the CCK-8 results of PANC-1 cells treated with C312-ST01 compound for 48 hours, it can be seen that when the concentration of C312-ST01 reaches 42.17 μM, half of the PANC-1 cells can be killed.
[0074] Reference Figure 4 For the CCK-8 results of BxPC-3 cells treated with C312-ST01 compound for 48 hours, it can be seen that when the concentration of C312-ST01 reaches 46.83 μM, half of the BxPC-3 cells can be killed.
[0075] In summary, the above results show that C312-ST01 compound has a significant inhibitory effect on PANC-1 and BxPC-3 cells, and the effect is dose-dependent. The IC50 value of C312-ST01 on PANC-1 cells is 42.17 μM, and the IC50 value of C312-ST01 on BxPC-3 cells is 46.83 μM.
[0076] Although the embodiments of the present application have been disclosed as above, they are not limited to the application listed in the specification and embodiments, and can be fully applied to various fields suitable for the present application. Additional modifications can be easily realized by those skilled in the art, and therefore the present application is not limited to specific details, but is within the general concept defined by the claims and their equivalents.
Claims
1. An antitumor small molecule compound targeting ST3GAL1 and its pharmaceutical salt in the preparation of antitumor drugs; The small molecule compound is: N'-[1-(4-fluorophenyl)-1H-pyrazolo[3,4-d]pyrimidin-4-yl]-4-methoxybenzoylhydrazine, and its structure is shown in Formula I below: 。 2. The application according to claim 1, characterized in that, The small molecule compound described above can inhibit the expression of ST3GAL1.
3. The application according to claim 1, characterized in that, The small molecule compounds were obtained through virtual screening. The virtual screening method is as follows: By obtaining the human ST3GAL1 protein sequence, homology modeling was performed using Swiss-Model, and the structure of the modeled protein was optimized using Gromacs. Then, virtual screening was performed using AutoDock Vina software, and finally, molecular dynamics simulation was performed using Desmond to obtain the small molecule compound.
4. The application according to claim 3, characterized in that, The virtual filtering method is as follows: S1. Protein sequence acquisition and modeling: The human ST3GAL1 protein sequence was obtained from the Uniprot database, and three-dimensional structural homology modeling was performed using Swiss-Model. S2. Structure Optimization: The modeled protein structure is optimized using Gromacs software to ensure the accuracy and reliability of the model. S3. Virtual screening: AutoDock Vina software was used to conduct three rounds of virtual screening. Each round used a different exhaustive index and retained the top 10% of the compounds in each round of docking scores to obtain candidate compounds. S4. Molecular dynamics simulation: The selected candidate compounds were subjected to molecular dynamics simulation using Desmond software to verify the binding stability of the candidate compounds with ST3GAL1. Candidate compounds with qualified stability were screened to obtain the small molecule compounds.
5. The application according to claim 4, characterized in that, The software versions are Gromacs 2023.1, AutoDockVina 1.2.3, and Desmond 2023.
4.
6. The application according to claim 1, characterized in that, The antitumor drug is obtained by combining the small molecule compound as the active ingredient with one or more pharmaceutically acceptable solid or liquid excipients and / or adjuvants.
7. The application according to claim 1, characterized in that, The tumors mentioned are tumors related to ST3GAL1.
8. The application according to claim 1, characterized in that, The tumors include lung cancer, breast cancer, esophageal cancer, stomach cancer, liver cancer, colorectal cancer, pancreatic cancer, and bile duct cancer.
9. The use of a small molecule compound as described in any one of claims 1-5 and its pharmaceutical salt in the preparation of ST3GAL1 inhibitors.