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Singh J, Khanduja KL, Dahiya D, Avti PK. Mechanistic Regulation of Epidermal Growth Factor and Hormonal Receptors by Kinase Inhibitors and Organofluorines in Breast Cancer Therapy. Cell Biochem Biophys 2024:10.1007/s12013-024-01546-9. [PMID: 39316263 DOI: 10.1007/s12013-024-01546-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/11/2024] [Indexed: 09/25/2024]
Abstract
Differential expression patterns of growth factor (EGFR, HER-2) and hormonal (ER, PR) receptors in breast cancer (BC) remain crucial for evaluating and tailoring therapeutic interventions. This study investigates differential expression profiles of hormonal and growth factor receptors in BC patients and across age groups, major subclasses, disease stages and tumor histology and survival rates, the efficacy of emerging clinical trial drugs (Dabrafenib and Palbociclib) and elucidating their molecular interaction mechanisms for efficient therapeutic strategies. Gene and protein expression analysis in the normal vs BC and across age groups and major subclasses reveals divergent patterns as EGFR and HER-2 levels are reduced in tumors versus normal tissue, while ER and PR levels are higher, particularly in luminal subtypes. However, there was no significant difference in survival rates among high and low/medium expression levels of EGFR and PR receptors. Conversely, patients with high HER-2 and ER expression exhibited poorer survival rates compared to low or medium expression levels. The in vitro findings indicate that Dabrafenib exhibits greater effectiveness than Palbociclib in suppressing various BC cells such as MCF-7 (Luminal), MDA-MB-231 (Triple-Negative), SKBR-3 (HER-2 + ) proliferation, promoting cell death, (IC50 of Dab < Pal) at 24 and 48 h, ROS production, and reduced ER and PR, elevated HER-2 with no change in EGFR expression. Molecular simulation studies revealed Dabrafenib's thermodynamically stable interactions (ΔG), tighter binding, and less structural deviation in the order EGFR > HER-2 > ER > PR as compared to Palbociclib (HER-2 > ER > PR = EGFR). These results indicate that Dabrafenib, compared to Palbociclib, more effectively regulates breast cancer cell proliferation through specific interactions with hormonal and growth factor receptors towards a repurposing approach.
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Affiliation(s)
- Jitender Singh
- Department of Biophysics, Postgraduate Institute of Medical Education and Research, (PGIMER), Chandigarh, India
| | - Krishan Lal Khanduja
- Department of Biophysics, Postgraduate Institute of Medical Education and Research, (PGIMER), Chandigarh, India
| | - Divya Dahiya
- Department of Surgery, Postgraduate Institute of Medical Education and Research, (PGIMER), Chandigarh, India
| | - Pramod K Avti
- Department of Biophysics, Postgraduate Institute of Medical Education and Research, (PGIMER), Chandigarh, India.
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Avti PK, Singh J, Dahiya D, Khanduja KL. Dual functionality of pyrimidine and flavone in targeting genomic variants of EGFR and ER receptors to influence the differential survival rates in breast cancer patients. Integr Biol (Camb) 2023; 15:zyad014. [PMID: 38084900 DOI: 10.1093/intbio/zyad014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 10/01/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023]
Abstract
Breast cancer ranks as one of the most prevalent forms of cancer and stands as the primary global cause of mortality among women. Overexpression of EGFR and ER receptors or their genomic alterations leads to malignant transformation, disease aggression and is linked to poor patient survival outcomes. The clinical breast cancer patient's genomic expression, survival analysis, and computational drug-targeting approaches were used to identify best-hit phytochemicals for therapeutic purposes. Breast cancer patients have genomic alterations in EGFR (4%, n = 5699) and ER (9%, n = 8461), with the highest proportion being missense mutations. No statistically significant difference was observed in the patient survival rates between the altered and unaltered ER groups, unlike EGFR, with the lowest survival rates in the altered group. Computational screening of natural compound libraries (7711) against each EGFR (3POZ) and ER (3ERT) receptor shortlists the best-hit 3 compounds with minimum docking score (ΔG = -7.9 to -10.8), MMGBSA (-40.16 to -51.91 kcal/mol), strong intermolecular H-bonding, drug-like properties with least kd, and ki. MD simulation studies display stable RMSD, RMSF, and good residual correlation of best-hit common compounds (PubChem ID: 5281672 and 5280863) targeting both EGFR and ER receptors. In vitro, studies revealed that these common drugs exhibited a high anti-proliferative effect on MCF-7 and MDA-MB-231 breast cancer cells, with effective IC50 values (15-40 μM) and lower free energy, kd, and ki (5281672 > 5280863 > 5330286) much affecting HEK-293 non-cancerous cells, indicating the safety profile. The experimental and computational correlation studies suggest that the highly expressed EGFR and ER receptors in breast cancer patients having poor survival rates can be effectively targeted with best-hit common potent drugs with a multi-target therapeutic approach. Insight Box: The findings of this study provide valuable insights into the genomic/proteomic data, breast cancer patient's survival analysis, and EGFR and ER receptor variants structural analysis. The genetic alterations analysis of EGFR and ER/ESR1 in breast cancer patients reveals the high frequency of mutation types, which affect patient's survival rate and targeted therapies. The common best-hit compounds affect the cell survival patterns with effective IC50, drug-like properties having lower equilibrium and dissociation constants demonstrating the anti-proliferative effects. This work integrates altered receptor structural analysis, molecular interaction-based simulations, and ADMET properties to illuminate the identified best hits phytochemicals potential efficacy targeting both EGFR and ER receptors, demonstrating a multi-target therapeutic approach.
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Affiliation(s)
- Pramod K Avti
- Department of Biophysics, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Jitender Singh
- Department of Biophysics, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Divya Dahiya
- Department of General Surgery, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Krishan L Khanduja
- Department of Biophysics, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
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Singh J, Sangwan N, Chauhan A, Sarma P, Prakash A, Medhi B, Avti PK. Screening and identification of phytochemical drug molecules against mutant BRCA1 receptor of breast cancer using computational approaches. Mol Cell Biochem 2022; 477:885-896. [PMID: 35067782 DOI: 10.1007/s11010-021-04338-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 12/15/2021] [Indexed: 10/19/2022]
Abstract
The American Cancer Society claims that breast cancer is the second most significant cause of cancer-related death, with over one million women diagnosed each year. Breast cancer linked to the BRCA1 gene has a significant risk of mortality and recurrence and is susceptible to alteration or over-expression, which can lead to hereditary breast cancer. Given the shortage of effective and possibly curative treatments for breast cancer, the present study combined molecular and computational analysis to find prospective phytochemical substances that can suppress the mutant gene (BRCA1) that causes the disease. Virtual screening and Molecular docking approaches are utilized to find probable phytochemicals from the ZINC database. The 3D structure of mutant BRCA1 protein with the id 3PXB was extracted from the NCBI-PDB. Top 10 phytochemical compounds shortlisted based on molecular docking score between - 11.6 and - 13.0. Following the ADMET properties, only three (ZINC000085490903 = - 12.50, ZINC000085490832 = - 12.44, and ZINC000070454071 = - 11.681) of the 10 selected compounds have drug-like properties. The molecular dynamic simulation study of the top three potential phytochemicals showed stabilized RMSD and RMSF values as compared to the APO form of the BRCA1 receptor. Further, trajectory analysis revealed that approximately similar radius of gyration score tends to the compactness of complex structure, and principal component and cross-correlation analysis suggest that the residues move in a strong correlation. Thermostability of the target complex (B-factor) provides information on the stable energy minimized structure. The findings suggest that the top three ligands show potential as breast cancer inhibitors.
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Affiliation(s)
- Jitender Singh
- Department of Biophysics, Postgraduate Institute of Medical Education and Research (PGIMER), Sector -12, Chandigarh, 160012, India
| | - Namrata Sangwan
- Department of Biophysics, Postgraduate Institute of Medical Education and Research (PGIMER), Sector -12, Chandigarh, 160012, India
| | - Arushi Chauhan
- Department of Biophysics, Postgraduate Institute of Medical Education and Research (PGIMER), Sector -12, Chandigarh, 160012, India
| | - Phulen Sarma
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research (PGIMER), Sector-12, Chandigarh, 160012, India
| | - Ajay Prakash
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research (PGIMER), Sector-12, Chandigarh, 160012, India
| | - Bikash Medhi
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research (PGIMER), Sector-12, Chandigarh, 160012, India
| | - Pramod K Avti
- Department of Biophysics, Postgraduate Institute of Medical Education and Research (PGIMER), Sector -12, Chandigarh, 160012, India.
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Engin KN, Erdem-Kuruca S, Akgün-Dar K, Çetin B, Karadenizli S, Gürel E, Yemisci B, Bilgiç S, Arslan M. The Evaluation of Human Tenon’s Fibroblasts and Endothelial Cell Responses to Antifibrotics Alone and in Combination with α-Tocopherol. Curr Eye Res 2014; 40:19-29. [DOI: 10.3109/02713683.2014.909496] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Inhibition of NF-κB nuclear translocation via HO-1 activation underlies α-tocopheryl succinate toxicity. J Nutr Biochem 2012; 23:1583-91. [DOI: 10.1016/j.jnutbio.2011.10.012] [Citation(s) in RCA: 124] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 10/26/2011] [Accepted: 10/27/2011] [Indexed: 02/07/2023]
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Li CJ, Li RW, Kahl S, Elsasser TH. Alpha-Tocopherol Alters Transcription Activities that Modulates Tumor Necrosis Factor Alpha (TNF-α) Induced Inflammatory Response in Bovine Cells. GENE REGULATION AND SYSTEMS BIOLOGY 2011; 6:1-14. [PMID: 22267916 PMCID: PMC3256998 DOI: 10.4137/grsb.s8303] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
To further investigate the potential role of α-tocopherol in maintaining immuno-homeostasis in bovine cells (Madin-Darby bovine kidney epithelial cell line), we undertook in vitro experiments using recombinant TNF-α as an immuno-stimulant to simulate inflammation response in cells with or without α-tocopherol pre-treatment. Using microarray global-profiling and IPA (Ingenuity Pathways Analysis, Ingenuity® Systems, http://www.ingenuity.com) data analysis on TNF-α-induced gene perturbation in those cells, we focused on determining whether α-tocopherol treatment of normal bovine cells in a standard cell culture condition can modify cell’s immune response induced by TNF-α challenge. When three datasets were filtered and compared using IPA, there were a total of 1750 genes in all three datasets for comparison, 97 genes were common in all three sets; 615 genes were common in at least two datasets; there were 261 genes unique in TNF-α challenge, 399 genes were unique in α-tocopherol treatment, and 378 genes were unique in the α-tocopherol plus TNF-α treatment. TNF-α challenge induced significant change in gene expression. Many of those genes induced by TNF-α are related to the cells immune and inflammatory responses. The results of IPA data analysis showed that α-tocopherol-pretreatment of cells modulated cell’s response to TNF-α challenge. In most of the canonical pathways, α-tocopherol pretreatment showed the antagonistic effect against the TNF-α-induced pro-inflammatory responses. We concluded that α-tocopherol pre-treatment has a significant antagonistic effect that modulates the cell’s response to the TNF-α challenge by altering the gene expression activities of some important signaling molecules.
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Affiliation(s)
- Cong-Jun Li
- Bovine Functional Genomics Laboratory, Animal and Natural Resources Institute, ARS, USDA, 10300 Baltimore Ave, Beltsville, MD 20705
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Li CJ, Li RW, Elsasser TH. Alpha-Tocopherol Modulates Transcriptional Activities that Affect Essential Biological Processes in Bovine Cells. GENE REGULATION AND SYSTEMS BIOLOGY 2010; 4:109-24. [PMID: 21157515 PMCID: PMC3001320 DOI: 10.4137/grsb.s6007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Using global expression profiling and pathway analysis on α-tocopherol-induced gene perturbation in bovine cells, this study has generated comprehensive information on the physiological functions of α-tocopherol. The data confirmed α-tocopherol is a potent regulator of gene expression and α-tocopherol possesses novel transcriptional activities that affect essential biological processes. The genes identified fall within a broad range of functional categories and provide the molecular basis for its distinctive effects. Enrichment analyses of gene regulatory networks indicate α-tocopherol alter the canonical pathway of lipid metabolism and transcription factors SREBP1 and SREBP2, (Sterol regulatory element binding proteins), which mediate the regulatory functions of lipid metabolism. Transcription factors HNF4-α (Hepatocyte nuclear factor 4), c-Myc, SP1 (Sp1 transcription factor), ESR1 (estrogen receptor 1, nuclear), and androgen receptor, along with several others, were centered as the hubs of transcription regulation networks. The data also provided direct evidence that α-tocopherol is involved in maintaining immuno-homeostasis through targeting the C3 (Complement Component 3) gene.
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Affiliation(s)
- Cong-Jun Li
- Bovine Functional Genomics Laboratory, Animal and Natural Resources Institute, ARS, USDA, 10300 Baltimore Ave, Beltsville, MD, 20705, USA
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Singh VK, Parekh VI, Brown DS, Kao TC, Mog SR. Tocopherol succinate: modulation of antioxidant enzymes and oncogene expression, and hematopoietic recovery. Int J Radiat Oncol Biol Phys 2010; 79:571-8. [PMID: 20950962 DOI: 10.1016/j.ijrobp.2010.08.019] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2010] [Revised: 07/15/2010] [Accepted: 08/17/2010] [Indexed: 12/13/2022]
Abstract
PURPOSE A class of naturally occurring isoforms of tocopherol (tocols) was shown to have varying degrees of protection when administered before radiation exposure. We recently demonstrated that α-tocopherol succinate (TS) is a potential radiation prophylactic agent. Our objective in this study was to further investigate the mechanism of action of TS in mice exposed to (60)Co γ-radiation. METHODS AND MATERIALS We evaluated the effects of TS on expression of antioxidant enzymes and oncogenes by quantitative RT-PCR in bone marrow cells of (60)Co γ-irradiated mice. Further, we tested the ability of TS to rescue and repopulate hematopoietic stem cells by analyzing bone marrow cellularity and spleen colony forming unit in spleen of TS-injected and irradiated mice. RESULTS Our results demonstrate that TS modulated the expression of antioxidant enzymes and inhibited expression of oncogenes in irradiated mice at different time points. TS also increased colony forming unit-spleen numbers and bone marrow cellularity in irradiated mice. CONCLUSIONS Results provide additional support for the observed radioprotective efficacy of TS and insight into mechanisms.
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Affiliation(s)
- Vijay K Singh
- Radiation Countermeasures Program, Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences, Bethesda, MD 20889, USA.
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Tang XH, Albert M, Scognamiglio T, Gudas LJ. A DNA methyltransferase inhibitor and all-trans retinoic acid reduce oral cavity carcinogenesis induced by the carcinogen 4-nitroquinoline 1-oxide. Cancer Prev Res (Phila) 2009; 2:1100-10. [PMID: 19952362 DOI: 10.1158/1940-6207.capr-09-0136] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The transcriptional silencing of some cell cycle inhibitors and tumor suppressors, such as p16 and retinoic acid receptor beta(2), by DNA hypermethylation at CpG islands is commonly found in human oral squamous carcinoma cells. We examined the effects of the DNA methyltransferase inhibitor 5-Aza-2'-deoxycytidine (5-Aza; 0.25 mg/kg body weight), all-trans retinoic acid (RA; given at 100 microg/kg body weight and 1 mg/kg body weight), and the combination of 5-Aza and the low-dose RA on murine oral cavity carcinogenesis induced by the carcinogen 4-nitroquinoline 1-oxide (4-NQO) in a mouse model. All the drug treatments were done for 15 weeks after a 10-week 4-NQO treatment. Mice in all drug treatment groups showed decreases in the average numbers of neoplastic tongue lesions. The combination of 5-Aza and RA effectively attenuated tongue lesion severity. Although all drug treatments limited the increase in the percentage of proliferating cell nuclear antigen-positive cells and the decrease in the percentage of p16-positive cells caused by the 4-NQO treatment in mouse tongue epithelial regions without visible lesions and in the neoplastic tongue lesions, the combination of 5-Aza and RA was the most effective. Collectively, our results show that the combination of a DNA demethylating drug and RA has potential as a strategy to reduce oral cavity cancer in this 4-NQO model.
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Affiliation(s)
- Xiao-Han Tang
- Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065, USA
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Lockshin RA. An attempt to understand the multiparametric control of the initiation of apoptosis. Apoptosis 2008; 13:1195-7. [DOI: 10.1007/s10495-008-0251-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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