Scutellarein (SCU), a flavone that belongs to the flavonoid family and abundantly present in
Gastric cancer was the fifth most prevalent malignancy in 2018 globally with an estimated 1 million new cases. Korea has been listed first among the global GC cases, with stomach cancer incidence rates in men of approximately 58 per 100,000 and in women of 24 per every 100,000, which is an unfortunate reality for many Koreans (
Herbal products and their components have been identified as exhibiting anticancer effects by targeting dysregulated genes that contribute to carcinogenesis in several cancer cell lines by multiple cell signaling pathways (
Human GC cell lines, AGS and SNU484, were procured from the Korea Cell Line Bank (Seoul, Korea). Antibiotics (penicillin/streptomycin), fetal bovine serum (FBS) and RPMI-1640 growth medium were purchased from Gibco, Thermo Fisher Scientific, Inc. Compound Scutellarein was procured from Chengdu Biopurify Phytochemicals Ltd. (product no. 611130). Chemicals and materials utilized for electrophoresis were procured from Bio-Rad Laboratories, Inc. 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) was purchased from Duchefa Biochemie. Antibodies for CIP2A (#148053) and PI3KCB (#3011S) were purchased from Cell Signaling Technology, Inc. OFD1 (#ab222837), VCL (#ab129002), and HIP1R (#ab226197) antibodies were purchased from Abcam. The β-actin (#MABT825) antibody was purchased from Millipore.
Mycoplasma-free AGS and SNU484 cells were cultured in RPMI-1640 medium containing 10% FBS (heat activated) and 1% antibiotics (penicillin/streptomycin) in an incubator with 5% CO2 at 37°C in a humidified condition. To confirm mycoplasma contamination, we used the e-Myco™ Mycoplasma PCR Detection kit (iNtRON Biotechnology). Cell viability assay was performed using MTT assay. The cells were at a density of 5×105 cells per well in 24-well plates and grown overnight. Subsequently treat the cells were treated with the indicated concentrations of SCU (0, 25, 50, 75, and 100 µM) for 24 h at 37°C. An amount 50 µl of MTT solution (0.5 mg/ml) was added to each well after 24 h, and incubation was carried out at 37°C for 3 h in a dark condition. DMSO (300 µl) was added to each well to solubilize the formazan contained in the cells, and the absorbance was measured at 540 nm using a microplate reader (BioTek Instruments). Cell viability was expressed as a percentage of the control and experiments were conducted in triplicates for each assay condition.
AGS and SNU484 cells were treated or untreated (control) with SCU (75 µM) for 24 h. Whole proteins were extracted from both groups of cells as previously described (
Proteins were separated using 2-DE, as reported in our previous study (
Differentially expressed protein spots from the 2-DE gel were excised manually, and digestion of protein and MS analysis were performed as previously reported (
To identify the proteins from the MS data, the peptide protein mass fingerprinting data were adopted to search against NCBI non-redundant protein database using the ProteinProspector (v 5.22.1) (
For western blotting, both cell lines were cultured in 6-well plates at 3×106 cells per well and after the cells reached optimal confluence, both the cell lines were treated with SCU (75 µM) or untreated (DMSO) for 24 h. Cells were harvested after incubation, and lysed in ice-cold RIPA buffer containing protease and phosphatase inhibitor. Total proteins were quantified using BCA protein assay and 15 µg of proteins from each group were separated by 10–12% SDS-PAGE, and the protein bands were transferred onto a polyvinylidene difluoride (PVDF) membrane. The membranes were blocked with 5% non-fat skim milk or BSA in Tris-buffered saline containing 1% Tween 20 (TBS-T, pH 7.4) at room temperature (RT) for 1 h, and incubated overnight at 4°C at a 1:1,000 dilution of the respected primary antibody. The membranes were washed five times with TBS-T for 10 min each at RT, and incubated with a 1:2,000 dilution of HRP-conjugated secondary antibody for 3 h at RT. The membranes were then rewashed five times with TBS-T. Blots were developed using the ECL detection system (GE Healthcare Life Science). The bands were quantitatively analyzed using the ImageJ software version 1.52a (National Institutes of Health) (
In the present study, the binding affinity of Scutellarein was evaluated through macromolecular docking studies using Glide of Schrödinger-Maestro v.8.5 (in silico analysis) (
SwissProt identified proteins were further submitted to Web Gestalt (
Statistical analysis was performed with the Student's t-test using SPSS version 10.0 for Windows (SPSS, Inc.) and a one-way ANOVA test was implemented followed by Tukey's test for the comparison of multiple independent variables. A fold-change ≥1.5 and statistical significance of P<0.05 were considered for the selection of differential expressed protein spots. Data were considered statistically significant at P<0.05. All the results are expressed as the mean ± standard deviation (SD) of triplicates.
In our previous study, we reported that SCU was able to inhibit the cell viability of AGS and SNU484 human GC cells via inducing apoptotic cell death (
Proteomic analysis of AGS and SNU484 cells in response to SCU treatment was conducted. To analyze the proteome changes upon treatment with SCU to induce cell death in AGS and SNU484 cells, 400 µg total proteins were separated by isoelectric focusing (IEF) on 18 cm IPG strips in the first dimension, and resolved by 2-DE, followed by silver staining for visualization. Three gels per sample were analyzed simultaneously by confirming the representative 2-DE patterns of protein spots from the control and SCU-treated (75 µM) AGS and SNU484 cells (
Oral-facial-digital syndrome 1 protein (OFD1), vinculin (VINC), voltage-dependent calcium channel subunit α-2/δ-1 (CACNA2D1), Huntingtin-interacting protein 1-related protein (HIP1R), proto-oncogene vav 1 (VAV1), phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit β isoform (PIK3CB) and synaptonemal complex protein 1 (SYCP1) were found to be the 7 proteins commonly expressed in both GC cells treated with SCU by the comparative analysis using GeneCodis (
To verify the identified proteins from 2-DE, the immunoblotting analysis was performed in the SCU-treated AGS and SNU484 cells for a few selected important proteins.
Molecular docking analysis against Scutellarein revealed that all the significant protein macromolecules chosen form a stable H-bond with Scutellarein.
The Gene Ontology bioinformatics tool was useful to facilitate the interpretation of the proteomics data. WebGestalt (
Recent developments in proteome comparative analysis are intermittently used in the identification of protein expression alterations upon drug treatment of cancer cells (
Initially, OFD1 was found to be expressed in oral-facial-digital syndrome, and is subject to ciliopathies such as retinitis pigmentosa, and Simpson-Golabi-Behmel syndrome type 2 (
BUB1B, DNMT3A, PIK3CA, PDGFRA, DNM1L, ARHGEF2, TLR2, and AKT3 are critical proteins that participate in a majority of biological processes from the GO analysis of the differentially expressed proteins from SCU-treated GC cells. The mitotic checkpoint serine/threonine-protein kinase that involves kinases (BUB1B) is responsible for chromosome segregation, and plays a key role in spindle checkpoint operation. BUB1B is bound to the kinetochore, and helps inhibition at the anaphase-promoting complex, which tends to procrastinate the initiation of anaphase and provides better chromosome segregation (
The present study consists of the preliminary data of altered proteins upon treatment of GC cells with SCU;
In conclusion, the current study highlights an innovative strategy to investigate physiologically relevant targets of SCU treatment, with an emphasis on its functional effects. The synergistic analyses of proteomics data were successful in identifying a unique set of proteins regulated by SCU to induce apoptosis in both treated GC cell lines. Proteins such as PIK3CB, OFD1, CIP2A, BUB1B, ARHGEF2, VCL, EPHB2, IF4G2, CACNA2D1, HIP1R, VAV, and TLR2 have been previously reported to be associated with apoptosis, cell cycle arrest and tumor suppressors induced by another flavonoid in GC cell lines (
Not applicable.
The present study was supported by the National Research Foundation of Korea funded by the Ministry of Science and ICT (grant nos. 2012M3A9B8019303 and 2020R1A2B5B01001807).
All data generated or analyzed during this study are included in this published article.
VVGS and GSK conceived and designed the experiments, performed the experiments, organized focus group discussion, collected, analyzed all study data and prepared the final manuscript. PV, RM and HJL carried out the bioinformatics analysis, contributed to the statistical analysis and editing of the manuscript. SMK, SEH, JDH and EHK participated in focus group discussion and revised the study design, revised the results and final revision of the manuscript for publication. All authors read and approved the manuscript for publication.
Not applicable.
Not applicable.
The authors declare that they have no competing interests.
SCU attenuates GC cell viability in a dose-dependent manner. (A) Chemical structure of Scutellarein (5,6,7,4′-tetrahydroxy flavone). (B) AGS and SNU484 GC cells were treated with different concentrations of SCU (0–100 µM) or untreated (DMSO) for 24 h followed determination of cell viability using MTT assay. The results are the representatives of three independent experiments and are expressed as mean ± standard deviation (SD). Statistical differences were analyzed with Student's t-test and a one-way ANOVA test was implemented followed by Tukey's test for the comparison of multiple independent variables. *P<0.05, significant difference vs. the control (DMSO). GC, gastric cancer; SCU, Scutellarein.
2-DE protein pattern of differentially expressed proteins identified by MALDI-TOF-MS analysis in AGS cells. (A) Control (DMSO) and (B) SCU-treated (75 µM) GC AGS cells. Cells were treated with the indicated concentrations of SCU or DMSO for 24 h. A total of 400 µg of total proteins was separated on 18-cm linear IPG strips (pH 4.0-7.0) by IEF and 12% SDS-PAGE gels were used in the second dimension of separation followed by silver staining of the gels. The arrows indicated by numbers are the protein spots identified successfully by MALDI-TOF-MS on protein database search. The experiments were performed in triplicate. 2-DE, two-dimensional gel electrophoresis; MALDI-TOF, matrix-assisted laser desorption/ ionization-time of flight; IEF, isoelectric focusing; GC, gastric cancer; SCU, Scutellarein; MW, molecular weight.
2-DE protein pattern of differentially expressed proteins identified by MALDI-TOF-MS analysis in SNU484 cells. (A) Control (DMSO) and (B) SCU (75 µM) GC SNU484 cells. The cells were treated with the indicated concentrations of SCU or DMSO for 24 h. A total of 400 µg of total proteins was separated on 18-cm linear IPG strips (pH 4–7) by IEF and 12% SDS-PAGE gels were used in the second dimension separation followed by silver staining of the gels. The arrows indicated by numbers are the protein spots identified successfully by MALDI-TOF-MS on protein database search. The experiments were performed in triplicate. 2-DE, two-dimensional gel electrophoresis; MALDI-TOF, matrix-assisted laser desorption/ ionization-time of flight; IEF, isoelectric focusing; GC, gastric cancer; SCU, Scutellarein; MW, molecular weight.
The differentially expressed proteins that overlapped between AGS and SNU484 cells are represented by a Venn diagram. All of the differentially expressed proteins from both GC cell lines treated with SCU were subjected to a comparative protein analysis for commonly expressed proteins using GENECODIS (
Western blot analysis confirmation of differentially expressed proteins. (A) AGS and (B) SNU484 GC cell lines were treated with control (DMSO) or SCU (75 µM), incubated for 24 h and protein samples were prepared and separated on 10–12% SDS-PAGE. OFD1, VCL, PIK3CB, HIP1R and CIP2A proteins were assessed using the respective antibodies. For the loading control β-actin was used and normalized to measure the expression changes. The bands are representative of three independent experiments [*P<0.05, significant difference vs. the control (DMSO)]. GC, gastric cancer; SCU, Scutellarein; OFD1, oral-facial-digital syndrome 1 protein; VCL, vinculin; PIK3CB, phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit β isoform; HIP1R, Huntingtin-interacting protein 1-related protein; CIP2A, cancerous inhibitor of protein phosphatase 2A.
Ligand-interaction and Molecular docking of the target proteins with SCU. The amino acid residues in the proteins showing stable hydrogen bonding with SCU and molecular binding models of the structural complex. (A) The LigPlot of protein PIK3CB with SCU. (B) The LigPlot of protein HIP1R with SCU. (C) The LigPlot of protein VCL with SCU. (D) The binding model of protein PIK3CB complexed with SCU. (E) The binding model of protein HIP1R complexed with SCU. (F) The binding model of protein VCL complexed with SCU. SCU, Scutellarein; PIK3CB, phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit β isoform; HIP1R, Huntingtin-interacting protein 1-related protein; VCL, vinculin.
GOSlim summary of the proteins differentially altered in the GC cell lines (A) AGS and (B) SNU484 cells treated with SCU. The GO profile of differential expressed proteins in both the cell lines grouped in terms of Biological process, Cellular component and Molecular function by using WebGestalt (
Pathway enrichment of the differentially altered proteins in GC AGS cells treated with SCU. The significantly altered proteins in AGS cells treated with SCU when compared with the untreated group of cells were grouped based on the enriched pathways using PANTHER database (
Pathway enrichment of the differentially altered proteins in GC SNU484 cells treated with SCU. The significantly altered proteins in SNU484 cells treated with SCU when compared with untreated group of cells were grouped based on the enriched pathways using PANTHER database (
List of differentially expressed proteins in AGS cells treated with SCU, as identified using MALDI-TOF/TOF-MS analysis.
Spot no. | Uniprot ID | Protein name | Accession no. | MOWSE score | Sequence coverage (%)/peptides matched | Protein MW (Da) | pI value | Fold change | Up/Down |
---|---|---|---|---|---|---|---|---|---|
1 | OGT1_HUMAN | UDP-N-acetylglucosamine-peptide N-acetylglucosaminyltransferase 110 kDa subunit | O15294 | 9.02E+06 | 24.7/20 | 116926 | 6.2 | 3.2 | ↑ |
2 | KIF11_HUMAN | Kinesin-like protein KIF11 | P52732 | 2.07E+16 | 28.6/10 | 119160 | 5.5 | 2.1 | ↓ |
3 | KI20A_HUMAN | Kinesin-like protein KIF20A | O95235 | 2.65E+08 | 11.7/11 | 100279 | 6.5 | 1.9 | ↓ |
4 | NALP7_HUMAN | NACHT, LRR and PYD domains-containing protein 7 | Q8WX94 | 1.14E+12 | 12.6/13 | 111808 | 5.9 | 2 | ↓ |
5 | CPSF2_HUMAN | Cleavage and polyadenylation specificity factor subunit 2 | Q9P2I0 | 1.94E+06 | 21.1/20 | 88488 | 5 | 1.6 | ↓ |
6 | IF4G2_HUMAN | Eukaryotic translation initiation factor 4 γ 2 | P78344 | 3.07E+09 | 16.8/11 | 102363 | 6.7 | 1.8 | ↓ |
7 | CCD57_HUMAN | Coiled-coil domain-containing protein 57 | Q2TAC2 | 5.16E+08 | 18.4/17 | 103168 | 6.1 | 2 | ↓ |
8 | GG6L6_HUMAN | Golgin subfamily A member 6-like protein 6 | A8MZA4 | 6.36E+06 | 11.5/13 | 90953 | 5.1 | 1.5 | ↑ |
9 | KTU_HUMAN | Protein kintoun | Q9NVR5 | 2.60E+06 | 19.4/27 | 91115 | 5.1 | 6.5 | ↓ |
10 | FETA_HUMAN | α-fetoprotein | P02771 | 7.09E+06 | 28.7/31 | 68678 | 5.5 | 5.1 | ↑ |
11 | AT1A2_HUMAN | Sodium/potassium-transporting ATPase subunit α-2 | P50993 | 1.05E+06 | 35.9/28 | 112266 | 5.5 | 1.6 | ↑ |
12 | GCR_HUMAN | Glucocorticoid receptor | P04150 | 1.53E+09 | 12.8/13 | 85660 | 6 | 1.6 | ↓ |
13 | VPS35_HUMAN | Vacuolar protein sorting-associated protein 35 | Q96QK1 | 2.43E+06 | 18.2/29 | 91708 | 5.3 | 1.7 | ↓ |
↓ | |||||||||
15 | DREB_HUMAN | Drebrin | Q16643 | 2.61E+07 | 22.8/22 | 71430 | 4.4 | 10.6 | ↑ |
16 | DNM3A_HUMAN | DNA (cytosine-5)-methyltransferase 3A | Q9Y6K1 | 6.32E+08 | 15.8/14 | 101859 | 6.2 | 2.1 | ↑ |
17 | UBA6_HUMAN | Ubiquitin-like modifier-activating enzyme 6 | A0AVT1 | 4.37E+07 | 38.1/48 | 117971 | 5.8 | 2.4 | ↓ |
↓ | |||||||||
19 | ITB1_HUMAN | Integrin β-1 | P05556 | 1.07E+06 | 26.3/25 | 88416 | 5.3 | 5.7 | ↑ |
20 | TAXB1_HUMAN | Tax1-binding protein 1 | Q86VP1 | 1.61E+07 | 11.9/9 | 90878 | 5.3 | 6 | ↑ |
↑ | |||||||||
22 | HSP74_HUMAN | Heat shock 70 kDa protein 4 | P34932 | 1.30E+07 | 17/27 | 94332 | 5.1 | 1.5 | ↓ |
↑ | |||||||||
24 | KIF5C_HUMAN | Kinesin heavy chain isoform 5C | O60282 | 3.50E+09 | 33.3/18 | 109496 | 5.9 | 1.9 | ↑ |
↓ | |||||||||
27 | UBP29_HUMAN | Ubiquitin carboxyl-terminal hydrolase 29 | Q9HBJ7 | 5.67E+06 | 16.3/13 | 104157 | 5.6 | 1.9 | ↑ |
28 | BUB1B_HUMAN | Mitotic checkpoint serine/threonine-protein kinase BUB1 β | O60566 | 4.19E+07 | 15.9/9 | 119546 | 5.2 | 1.9 | ↓ |
29 | PK3CA_HUMAN | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit α isoform | P42336 | 1.11E+20 | 25.1/14 | 124285 | 6.9 | 1.7 | ↓ |
30 | AKIB1_HUMAN | Ankyrin repeat and IBR domain-containing protein 1 | Q9P2G1 | 5.67E+06 | 27.9/26 | 122003 | 5 | 1.8 | ↓ |
31 | ANPRA_HUMAN | Atrial natriuretic peptide receptor 1 | P16066 | 4.88E+07 | 19/19 | 118920 | 6.2 | 1.9 | ↑ |
32 | STK31_HUMAN | Serine/threonine-protein kinase 31 | Q9BXU1 | 1.28E+07 | 47.8/53 | 115695 | 5 | 1.6 | ↓ |
33 | PGFRA_HUMAN | Platelet-derived growth factor receptor α | P16234 | 1.44E+07 | 13.3/11 | 122671 | 5.1 | 2.2 | ↓ |
34 | DNM1L_HUMAN | Dynamin-1-like protein | O00429 | 1.12E+06 | 24.2/23 | 81878 | 6.4 | 2.5 | ↑ |
35 | ARHG2_HUMAN | Rho guanine nucleotide exchange factor 2 | Q92974 | 1.05E+10 | 21.7/18 | 111544 | 6.9 | 2.2 | ↓ |
36 | DISC1_HUMAN | Disrupted in schizophrenia 1 protein | Q9NRI5 | 3.96E+08 | 26.3/30 | 93611 | 6 | 2.1 | ↑ |
37 | MMS19_HUMAN | MMS19 nucleotide excision repair protein homolog | Q96T76 | 3.32E+07 | 25/23 | 113291 | 5.9 | 2.3 | ↑ |
39 | APOBR_HUMAN | Apo lipoprotein B receptor | Q0VD83 | 1.00E+06 | 33.4/21 | 114875 | 4.4 | 6.6 | ↓ |
40 | AKT3_HUMAN | RAC-gamma serine/threonine-protein kinase | Q9Y243 | 4.93E+09 | 20.5/13 | 55775 | 5.7 | 1.6 | ↓ |
41 | ITA4_HUMAN | Integrin α-4 | P13612 | 8270000 | 26/28.5 | 114901 | 6 | 1.6 | ↓ |
Proteins indicated in bold print are commonly expressed protein among both the AGS and SNU484 cell treated with SCU. SCU, scutellarein. ↑, upregulated; ↓, downregulated.
List of differentially expressed proteins in SNU484 cells treated with SCU, as identified using MALDI-TOF/TOF-MS analysis.
Spot no. | Uniprot ID | Protein name | Accession no. | MOWSE score | Sequence coverage (%)/ peptides matched | Protein MW (Da) | pI value | Fold change | Up/Down |
---|---|---|---|---|---|---|---|---|---|
|
↓ | ||||||||
2 | RBGP1_HUMAN | Rab GTPase-activating protein 1 | Q9Y3P9 | 8.29E+09 | 26.6/33 | 121738 | 5.1 | 2.4 | ↓ |
|
↑ | ||||||||
4 | GTF2I_HUMAN | General transcription factor II–I | P78347 | 1.69E+08 | 24.1/21 | 112417 | 6.1 | 2.6 | ↑ |
5 | PKHG5_HUMAN | Pleckstrin homology domain-containing family G member 5 | O94827 | 4.29E+06 | 16.9/18 | 117452 | 5.9 | 1.6 | ↑ |
6 | GCP5_HUMAN | Gamma-tubulin complex component 5 | Q96RT8 | 6.00E+07 | 27.9/20 | 118322 | 5.6 | 1.9 | ↑ |
7 | SAFB1_HUMAN | Scaffold attachment factor B1 | Q15424 | 2.56E+10 | 35.6/41 | 102642 | 5.3 | 1.9 | ↓ |
8 | NALP2_HUMAN | NACHT, LRR and PYD domains-containing protein 2 | Q9NX02 | 1.41E+07 | 16.6/19 | 120516 | 5.7 | 1.4 | ↑ |
9 | TLR2_HUMAN | Toll-like receptor 2 | O60603 | 4.38E+07 | 25.5/14 | 89838 | 6.2 | 1.8 | ↓ |
10 | PTPRH_HUMAN | Receptor-type tyrosine-protein phosphatase H | Q9HD43 | 1.63E+07 | 12.6/10 | 122353 | 5.2 | 1.2 | ↑ |
↓ | |||||||||
12 | PARG_HUMAN | Poly(ADP-ribose) glycohydrolase | Q86W56 | 1.71E+08 | 25.4/22 | 111111 | 6 | 1.8 | ↑ |
↓ | |||||||||
14 | CIP2A_HUMAN | Protein CIP2A | Q8TCG1 | 7.22E+12 | 29..8/38 | 102186 | 5.9 | 1.5 | ↓ |
15 | RNBP6_HUMAN | Ran-binding protein 6 | O60518 | 3.58E+07 | 24.2/21 | 124715 | 4.9 | 1.2 | ↑ |
↓ | |||||||||
17 | KIF1C_HUMAN | Kinesin-like protein KIF1C | O43896 | 2.08E+08 | 27.1/30 | 122948 | 6.5 | 2.2 | ↓ |
↑ | |||||||||
19 | EPHB2_HUMAN | Ephrin type-B receptor 2 | P29323 | 7.46E+08 | 21.8/20 | 117494 | 6.1 | 1.4 | ↓ |
20 | STK10_HUMAN | Serine/threonine-protein kinase 10 | O94804 | 1.28E+10 | 25.3/36 | 112136 | 6.5 | 1.4 | ↑ |
21 | AP3B2_HUMAN | AP-3 complex subunit β-2 | Q13367 | 1.86E+09 | 37.8/29 | 119060 | 5.4 | 1.7 | ↓ |
↓ | |||||||||
23 | ZW10_HUMAN | Centromere/kinetochore protein zw10 homolog | O43264 | 2.60E+10 | 32.6/21 | 88830 | 5.9 | 2.1 | ↑ |
24 | PDE2A_HUMAN | cGMP-dependent 3′,5′-cyclic phosphodiesterase | O00408 | 5.94E+09 | 32.7/26 | 105718 | 5.2 | 1.7 | ↑ |
25 | TMF1_HUMAN | TATA element modulatory factor | P82094 | 2.56E+09 | 27.7/28 | 122843 | 4.9 | 5.4 | ↑ |
26 | KDM4A_HUMAN | Lysine-specific demethylase 4A | O75164 | 7.79E+08 | 21.1/18 | 120663 | 5.6 | 1.7 | ↓ |
27 | DDX42_HUMAN | ATP-dependent RNA helicase DDX42 | Q86XP3 | 1.87E+07 | 28.1/22 | 102976 | 6.5 | 1.5 | ↑ |
28 | UBP28_HUMAN | Ubiquitin carboxyl-terminal hydrolase 28 | Q96RU2 | 8.82E+07 | 24.8/19 | 122492 | 5.1 | 1.5 | ↑ |
29 | LIFR_HUMAN | Leukemia inhibitory factor receptor | P42702 | 6.58E+11 | 26.6/26 | 123744 | 5.5 | 1.6 | ↑ |
30 | ZEB1_HUMAN | Zinc finger E-box-binding homeobox 1 | P37275 | 3.65E+08 | 22.8/24 | 124075 | 4.9 | 1.5 | ↑ |
31 | KS6C1_HUMAN | Ribosomal protein S6 kinase δ-1 | Q96S38 | 2.13E+06 | 25.8/18 | 118683 | 4.8 | 3.3 | ↑ |
Proteins indicated in bold print are commonly expressed protein among both the AGS and SNU484 cells treated with SCU. SCU, scutellarein. ↓, downregulated; ↑, upregulated.
Number of interacting amino acid residues with the different Glide parameters of selected macromolecules with Scutellarein.
Sr. No. | Macromolecule | Interacting residues | No of H-bonds | Glide G-Score | Glide energy |
---|---|---|---|---|---|
1 | CIP2A | Glu34; Val35; Gln82; AspB6 | 5 | −2.952 | −29.625 |
2 | PIK3CB | Glu692; Ile685; Gln683; Lys636; Ser614 | 5 | −8.767 | −58.531 |
3 | VINC | Lys236; Glu240; Lys708; Arg246; Glu243; Ser656; Lys261; Lys666 | 5 | −6.049 | −54.679 |
4 | HIPR1 | ThrA:965; GluI:818; ArgI:963; SerF:955 | 4 | −4.678 | −47.516 |
5 | VAV | Tyr56; Ser129; Thr75 | 6 | −6.666 | −59.988 |
List of differentially expressed proteins involved in different biological processes in AGS cells treated with Scutellarein.
AGS cell line | |||
---|---|---|---|
Sr. No. | Protein | Description | Biological process |
1 | VCL | Vinculin | GO:0030168: platelet |
VAV1 | av guanine nucleotide exchange factor 1 | activation | |
PIK3CB | Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit β | ||
PIK3CA | Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit α | ||
PDGFRAV | Platelet derived growth factor receptor α | ||
2 | ITGB1 | Integrin subunit β 1 | GO:0051897: positive |
VAV1 | Vav guanine nucleotide exchange factor 1 | regulation of protein | |
PIK3CB | Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit β | kinase B signaling | |
PIK3CA | Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit α | ||
PDGFRA | Platelet derived growth factor receptor α | ||
3 | DBN1 | Drebrin 1 | GO:0048667: cell |
VCL | Vinculin | morphogenesis involved | |
ITGB1 | Integrin subunit β 1 | in neuron differentiation | |
KIF5C | Kinesin family member 5C | ||
PIK3CB | Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit β | ||
PIK3CA | Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit α | ||
DNM1L | Dynamin 1 like | ||
ITGA4 | Integrin subunit α 4 | ||
4 | ATP1A2 | ATPase Na+/K+ transporting subunit α 2 | GO:0098657: import |
ITGB1 | Integrin subunit β 1 | into cell | |
CACNA2D1 | Calcium voltage-gated channel auxiliary subunit α2δ1 | ||
HIP1R | Huntingtin interacting protein 1 related | ||
VAV1 | Vav guanine nucleotide exchange factor 1 | ||
PIK3CB | Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit β | ||
PIK3CA | Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit α | ||
DNM1L | Dynamin 1 like | ||
APOBR | Apolipoprotein B receptor | ||
ITGA4 | Integrin subunit α 4 | ||
5 | DNAAF2 | Dynein axonemal assembly factor 2 | GO:0120036: plasma |
VPS35 | VPS35, retromer complex component | membrane bounded cell | |
OFD1 | OFD1, centriole and centriolar satellite protein | projection organization | |
DBN1 | Drebrin 1 | ||
UBA6 | Ubiquitin like modifier activating enzyme 6 | ||
VCL | Vinculin | ||
ITGB1 | Integrin subunit β 1 | ||
KIF5C | Kinesin family member 5C | ||
PIK3CB | Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit β | ||
PIK3CA | Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit α | ||
DNM1L | Dynamin 1 like | ||
DISC1 | DISC1 scaffold protein | ||
ITGA4 | Integrin subunit α 4 | ||
6 | KIF11 | Kinesin family member 11 | GO:0006928: movement |
KIF20A | Kinesin family member 20A | of cell or subcellular | |
DNAAF2 | Dynein axonemal assembly factor 2 | component | |
ATP1A2 | ATPase Na+/K+ transporting subunit α 2 | ||
OFD1 | OFD1, centriole and centriolar satellite protein | ||
VCL | Vinculin | ||
ITGB1 | Integrin subunit β 1 | ||
CACNA2D1 | Calcium voltage-gated channel auxiliary subunit α2δ1 | ||
KIF5C | kinesin family member 5C | ||
VAV1 | Vav guanine nucleotide exchange factor 1 | ||
PIK3CB | Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit β | ||
PIK3CA | Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit α | ||
PDGFRA | Platelet derived growth factor receptor α | ||
ARHGEF2 | Rho/Rac guanine nucleotide exchange factor 2 | ||
DISC1 | DISC1 scaffold protein | ||
AKT3 | AKT serine/threonine kinase 3 | ||
ITGA4 | Integrin subunit α 4 | ||
7 | DNAAF2 | Dynein axonemal assembly factor 2 | GO:0030030: cell |
VPS35 | VPS35, retromer complex component | projection organization | |
OFD1 | OFD1, centriole and centriolar satellite protein | ||
DBN1 | Drebrin 1 | ||
UBA6 | Ubiquitin like modifier activating enzyme 6 | ||
VCL | Vinculin | ||
ITGB1 | Integrin subunit β 1 | ||
KIF5C | Kinesin family member 5C | ||
PIK3CB | Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit β | ||
PIK3CA | Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit α | ||
DNM1L | Dynamin 1 like | ||
DISC1 | DISC1 scaffold protein | ||
ITGA4 | Integrin subunit α 4 | ||
8 | DBN1 | Drebrin 1 | GO:0048699: generation |
DNMT3A | DNA methyltransferase 3 α | of neurons | |
UBA6 | Ubiquitin like modifier activating enzyme 6 | ||
VCL | Vinculin | ||
ITGB1 | Integrin subunit β 1 | ||
KIF5C | Kinesin family member 5C | ||
PIK3CB | Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit β | ||
PIK3CA | Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit α | ||
DNM1L | Dynamin 1 like | ||
ARHGEF2 | Rho/Rac guanine nucleotide exchange factor 2 | ||
DISC1 | DISC1 scaffold protein | ||
ITGA4 | Integrin subunit α 4 | ||
9 | DNAAF2 | Dynein axonemal assembly factor 2 | |
ATP1A2 | ATPase Na+/K+ transporting subunit α 2 | ||
VPS35 | VPS35, retromer complex component | ||
VCL | Vinculin | ||
ITGB1 | Integrin subunit β 1 | ||
KIF5C | Kinesin family member 5C | ||
VAV1 | Vav guanine nucleotide exchange factor 1 | ||
PIK3CB | Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit β | ||
PIK3CA | Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit α | ||
PDGFRA | Platelet derived growth factor receptor α | ||
ARHGEF2 | Rho/Rac guanine nucleotide exchange factor 2 | ||
DISC1 | DISC1 scaffold protein | ||
AKT3 | AKT serine/threonine kinase 3 | ||
ITGA4 | Integrin subunit α 4 | ||
10 | OGT | O-linked N-acetylglucosamine (GlcNAc) transferase | GO:0006915: apoptotic |
NR3C1 | Nuclear receptor subfamily 3 group C member 1 | process | |
VPS35 | VPS35, retromer complex component | ||
DNMT3A | DNA methyltransferase 3 α | ||
ITGB1 | Integrin subunit β 1 | ||
TAX1BP1 | Tax1 binding protein 1 | ||
HIP1R | Huntingtin interacting protein 1 related | ||
VAV1 | Vav guanine nucleotide exchange factor 1 | ||
PIK3CB | Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit β | ||
BUB1B | BUB1 mitotic checkpoint serine/threonine kinase B | ||
PIK3CA | Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit α | ||
PDGFRA | Platelet derived growth factor receptor α | ||
DNM1L | Dynamin 1 like | ||
ARHGEF2 | Rho/Rac guanine nucleotide exchange factor 2 | ||
ITGA4 | Integrin subunit α 4 |
List of differentially expressed proteins involved in different biological processes in SNU484 cells treated with Scutellarein.
SNU484 cell line | |||
---|---|---|---|
Sr. No. | Protein | Description | Biological process |
1 | TLR2 | Toll like receptor 2 | GO:0036005: response to |
PDE2A | Phosphodiesterase 2A | macrophage colony- | |
stimulating factor | |||
2 | TLR2 | Toll like receptor 2 | GO:0036006: cellular response to |
PDE2A | Phosphodiesterase 2A | macrophage colony-stimulating | |
factor stimulus | |||
3 | HIP1R | Huntingtin interacting protein 1 related | GO:2000369: regulation of |
PIK3CB | Phosphatidylinositol-4,5-bisphosphate 3-kinase | clathrin-dependent endocytosis | |
catalytic subunit β | |||
4 | SYCP1 | Synaptonemal complex protein 1 | GO:0007289: spermatid nucleus |
TMF1 | TATA element modulatory factor 1 | differentiation | |
5 | TUBGCP5 | Tubulin gamma complex associated protein 5 | GO:0090307: mitotic spindle |
OFD1 | OFD1, centriole and centriolar satellite protein | assembly | |
PIBF1 | Progesterone immunomodulatory binding factor 1 | ||
6 | TUBGCP5 | Tubulin γ complex associated protein 5 | GO:1902850: microtubule |
OFD1 | OFD1, centriole and centriolar satellite protein | cytoskeleton organization involved | |
ZW10 | zw10 kinetochore protein | in mitosis | |
PIBF1 | Progesterone immunomodulatory binding factor 1 | ||
7 | TUBGCP5 | Tubulin γ complex associated protein 5 | GO:0007052: mitotic spindle |
OFD1 | OFD1, centriole and centriolar satellite protein | organization | |
PIBF1 | Progesterone immunomodulatory binding factor 1 | ||
8 | TUBGCP5 | Tubulin γ complex associated protein 5 | GO:0051225: spindle assembly |
OFD1 | OFD1, centriole and centriolar satellite protein | ||
PIBF1 | Progesterone immunomodulatory binding factor 1 | ||
9 | SYCP1 | Synaptonemal complex protein 1 | GO:0000280: nuclear division |
TUBGCP5 | Tubulin γ complex associated protein 5 | ||
OFD1 | OFD1, centriole and centriolar satellite protein | ||
ZW10 | zw10 kinetochore protein | ||
PIBF1 | Progesterone immunomodulatory binding factor 1 | ||
10 | PLEKHG5 | Pleckstrin homology and RhoGEF domain containing G5 | GO:0006915: apoptotic process |
NLRP2 | NLR family pyrin domain containing 2 | ||
TLR2 | Toll like receptor 2 | ||
PTPRH | Protein tyrosine phosphatase, receptor type H | ||
HIP1R | Huntingtin interacting protein 1 related | ||
PIK3CB | Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic | ||
subunit β | |||
EPHB2 | EPH receptor B2 | ||
TMF1 | TATA element modulatory factor 1 | ||
DDX42 | DEAD-box helicase 42 | ||
USP28 | Ubiquitin specific peptidase 28 |