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Zhao Y, Zhu S, Li Y, Niu X, Shang G, Zhou X, Yin J, Bao B, Cao Y, Cheng F, Li Z, Wang R, Yao W. Integrated component identification, network pharmacology, and experimental verification revealed mechanism of Dendrobium officinale Kimura et Migo against lung cancer. J Pharm Biomed Anal 2024; 243:116077. [PMID: 38460276 DOI: 10.1016/j.jpba.2024.116077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 03/11/2024]
Abstract
BACKGROUND Dendrobium officinale Kimura et Migo (DO), a valuable Chinese herbal medicine, has been reported to exhibit potential effects in the prevention and treatment of lung cancer. However, its material basis and mechanism of action have not been comprehensively analyzed. PURPOSE The objective of this study was to preliminarily elucidate the active components and pharmacological mechanisms of DO in treating lung cancer, according to UPLC-Q/TOF-MS, HPAEC-PAD, network pharmacology, molecular docking, and experimental verification. METHODS The chemical components of DO were identified via UPLC-Q/TOF-MS, while the monosaccharide composition of Dendrobium officinale polysaccharide (DOP) was determined by HPAEC-PAD. The prospective active constituents of DO as well as their respective targets were predicted in the combined database of Swiss ADME and Swiss Target Prediction. Relevant disease targets for lung cancer were searched in OMIM, TTD, and Genecards databases. Further, the active compounds and potential core targets of DO against lung cancer were found by the C-T-D network and the PPI network, respectively. The core targets were then subjected to enrichment analysis in the Metascape database. The main active compounds were molecularly docked to the core targets and visualized. Finally, the viability of A549 cells and the relative quantity of associated proteins within the major signaling pathway were detected. RESULTS 249 ingredients were identified from DO, including 39 flavonoids, 39 bibenzyls, 50 organic acids, 8 phenanthrenes, 27 phenylpropanoids, 17 alkaloids, 17 amino acids and their derivatives, 7 monosaccharides, and 45 others. Here, 50 main active compounds with high degree values were attained through the C-T-D network, mainly consisting of bibenzyls and monosaccharides. Based on the PPI network analysis, 10 core targets were further predicted, including HSP90AA1, SRC, ESR1, CREBBP, MAPK3, AKT1, PIK3R1, PIK3CA, HIF1A, and HDAC1. The results of the enrichment analysis and molecular docking indicated a close association between the therapeutic mechanism of DO and the PI3K-Akt signaling pathway. It was confirmed that the bibenzyl extract and erianin could inhibit the multiplication of A549 cells in vitro. Furthermore, erianin was found to down-regulate the relative expressions of p-AKT and p-PI3K proteins within the PI3K-Akt signaling pathway. CONCLUSIONS This study predicted that DO could treat lung cancer through various components, multiple targets, and diverse pathways. Bibenzyls from DO might exert anti-lung cancer activity by inhibiting cancer cell proliferation and modulating the PI3K-Akt signaling pathway. A fundamental reference for further studies and clinical therapy was given by the above data.
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Affiliation(s)
- Yan Zhao
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China.
| | - Shuaitao Zhu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China.
| | - Yuan Li
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China.
| | - Xuan Niu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China.
| | - Guanxiong Shang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China.
| | - Xiaoqi Zhou
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China.
| | - Jiu Yin
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China.
| | - Beihua Bao
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China.
| | - Yudan Cao
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China.
| | - Fangfang Cheng
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China.
| | - Zhipeng Li
- Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, Jiangsu 210009, China.
| | - Ran Wang
- China Tobacco Anhui Industrial Co., Ltd., Hefei, Anhui 210088, China.
| | - Weifeng Yao
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China.
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Annadurai Y, Easwaran M, Sundar S, Thangamani L, Meyyazhagan A, Malaisamy A, Natarajan J, Piramanayagam S. SPP1, a potential therapeutic target and biomarker for lung cancer: functional insights through computational studies. J Biomol Struct Dyn 2024; 42:1336-1351. [PMID: 37096999 DOI: 10.1080/07391102.2023.2199871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 03/30/2023] [Indexed: 04/26/2023]
Abstract
NIH reported 128 different types of cancer of which lung cancer is the leading cause of mortality. Globally, it is estimated that on average one in every seventeen hospitalized patients was deceased. There are plenty of studies that have been reported on lung cancer draggability and therapeutics, but yet a protein that plays a central specific to cure the disease remains unclear. So, this study is designed to identify the possible therapeutic targets and biomarkers that can be used for the potential treatment of lung cancers. In order to identify differentially expressed genes, 39 microarray datasets of lung cancer patients were obtained from various demographic regions of the GEO database available at NCBI. After annotating statistically, 6229 up-regulated genes and 10324 down-regulated genes were found. Out of 17 up-regulated genes and significant genes, we selected SPP1 (osteopontin) through virtual screening studies. We found functional interactions with the other cancer-associated genes such as VEGF, FGA, JUN, EGFR, and TGFB1. For the virtual screening studies,198 biological compounds were retrieved from the ACNPD database and docked with SPP1 protein (PDBID: 3DSF). In the results, two highly potential compounds secoisolariciresinol diglucoside (-12.9 kcal/mol), and Hesperidin (-12.0 kcal/mol) showed the highest binding affinity. The stability of the complex was accessed by 100 ns simulation in an SPC water model. From the functional insights obtained through these computational studies, we report that SPP1 could be a potential biomarker and successive therapeutic protein target for lung cancer treatment.
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Affiliation(s)
- Yamuna Annadurai
- Computational Biology Lab, Department of Bioinformatics, Bharathiar University, Coimbatore, Tamil Nadu, India
| | - Murugesh Easwaran
- Computational Biology Lab, Department of Bioinformatics, Bharathiar University, Coimbatore, Tamil Nadu, India
| | - Shobana Sundar
- Department of Biotechnology, PSG College of Technology, Coimbatore, Tamil Nadu, India
| | - Lokesh Thangamani
- Computational Biology Lab, Department of Bioinformatics, Bharathiar University, Coimbatore, Tamil Nadu, India
| | - Arun Meyyazhagan
- Dipartimento di Medicina e Chirurgia, Università di Perugia, Perugia, Italy
- Department of Life Sciences, CHRIST (Deemed to be University), Bengaluru, Karnataka, India
- Department of Translation Medicine and Surgery, Perugia University, Perugia, Italy
| | - Arunkumar Malaisamy
- Transcription Regulation Group, International centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Jeyakumar Natarajan
- Text Mining Lab, Department of Bioinformatics, Bharathiar University, Coimbatore, Tamil Nadu, India
| | - Shanmughavel Piramanayagam
- Computational Biology Lab, Department of Bioinformatics, Bharathiar University, Coimbatore, Tamil Nadu, India
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Nayila I, Sharif S, Lodhi MS, Rehman MFU, Aman F. Synthesis, characterization and anti-breast cancer potential of an incensole acetate nanoemulsion from Catharanthus roseus essential oil; in silico, in vitro, and in vivo study. RSC Adv 2023; 13:32335-32362. [PMID: 37928847 PMCID: PMC10621725 DOI: 10.1039/d3ra06335f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 10/18/2023] [Indexed: 11/07/2023] Open
Abstract
The characteristics of phytocompounds and essential oils have undergone extensive research in the medical and pharmaceutical sectors due to their extensive usage. In spite of the fact that these molecules are widely used, terpenes, terpenoids, and their derivatives have not yet been well characterized. This study intends to evaluate the prospective activity of incensole acetate (IA), a compound identified and isolated from Catharanthus roseus essential oil by GC/MS analysis and column chromatography, and to analyze the anticancer effect of an IA biosynthesized nanoemulsion against breast cancer. The in silico activity of IA against breast cancer targets was observed by molecular docking, ADMET assessment and molecular dynamics simulations. The IA-mediated nanoformulation exhibited cytotoxicity against breast cancer cell lines at an effective concentration when analyzed by MTT and crystal violet assay. The increased interleukin serum indicators were significantly improved as a result of nanoemulsion treatment in a DMBA-induced rat model. In addition, the anticancer properties of IA biosynthesized nanoemulsion are supported due to their potential effects on biochemical parameters, oxidative stress markers, proinflammatory cytokines, and upon tumor growth profiling in cancer-induced rats.
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Affiliation(s)
- Iffat Nayila
- Institute of Molecular Biology and Biotechnology, The University of Lahore Lahore Pakistan
| | - Sumaira Sharif
- Institute of Molecular Biology and Biotechnology, The University of Lahore Lahore Pakistan
| | - Madeeha Shahzad Lodhi
- Institute of Molecular Biology and Biotechnology, The University of Lahore Lahore Pakistan
| | | | - Farhana Aman
- Department of Chemistry, The University of Lahore Sargodha Campus Sargodha Pakistan
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Zhang Y, Pan H, Yu C, Liu R, Xing B, Jia B, He J, Jia X, Feng X, Zhang Q, Dang W, Hu Z, Deng X, Guo P, Liu Z, Pan W. Phytoestrogen-derived multifunctional ligands for targeted therapy of breast cancer. Asian J Pharm Sci 2023; 18:100827. [PMID: 37588993 PMCID: PMC10425851 DOI: 10.1016/j.ajps.2023.100827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 04/20/2023] [Accepted: 05/31/2023] [Indexed: 08/18/2023] Open
Abstract
Nano-targeted delivery systems have been widely used for breast tumor drug delivery. Estrogen receptors are considered to be significant drug delivery target receptors due to their overexpression in a variety of tumor cells. However, targeted ligands have a significant impact on the safety and effectiveness of active delivery systems, limiting the clinical transformation of nanoparticles. Phytoestrogens have shown good biosafety characteristics and some affinity with the estrogen receptor. In the present study, molecular docking was used to select tanshinone IIA (Tan IIA) among phytoestrogens as a target ligand to be used in nanodelivery systems with some modifications. Modified Tan IIA (Tan-NH2) showed a good biosafety profile and demonstrated tumor-targeting, anti-tumor and anti-tumor metastasis effects. Moreover, the ligand was utilized with the anti-tumor drug Dox-loaded mesoporous silica nanoparticles via chemical modification to generate a nanocomposite Tan-Dox-MSN. Tan-Dox-MSN had a uniform particle size, good dispersibility and high drug loading capacity. Validation experiments in vivo and in vitro showed that it also had a better targeting ability, anti-tumor effect and lower toxicity in normal organs. These results supported the idea that phytoestrogens with high affinity for the estrogen receptor could improve the therapeutic efficacy of nano-targeted delivery systems in breast tumors.
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Affiliation(s)
- Ying Zhang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Ministry of Education, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Hao Pan
- School of Pharmacy, Liaoning University, Shenyang 110036, China
| | - Changxiang Yu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Ministry of Education, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Rui Liu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Ministry of Education, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Bin Xing
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Ministry of Education, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Bei Jia
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Ministry of Education, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Jiachen He
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Ministry of Education, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Xintao Jia
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Ministry of Education, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Xiaojiao Feng
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Ministry of Education, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Qingqing Zhang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Ministry of Education, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Wenli Dang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Ministry of Education, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Zheming Hu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Ministry of Education, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Xiuping Deng
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Ministry of Education, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Pan Guo
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Ministry of Education, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Zhidong Liu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Ministry of Education, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Weisan Pan
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang 110016, China
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5
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Mueed A, Deng Z, Korma SA, Shibli S, Jahangir M. Anticancer potential of flaxseed lignans, their metabolites and synthetic counterparts in relation with molecular targets: current challenges and future perspectives. Food Funct 2023; 14:2286-2303. [PMID: 36820797 DOI: 10.1039/d2fo02208g] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Lignans are known dietary polyphenols found in cereals, plants and seeds. Flaxseed is one of the major sources of lignans mainly existing in the form of secoisolariciresinol diglucoside (SDG) which can be metabolised by the gut microbes into secoisolariciresinol (SECO) and mammalian lignan (enterodiol and enterolactone) that are easily absorbed through the intestines. Numerous studies reveal that flaxseed lignans (FLs) can be promising chemotherapeutics/chemopreventive agents. Their anticancer activity can occur through the induction of apoptosis, inhibition of cell proliferation, and the hindering of metastasis and angiogenesis. The anti-carcinogenesis of flaxseed lignans is achieved through multiple molecular mechanisms involving biochemical entities such as cellular kinases, cell cycle mediators, transcription factors, inflammatory cytokines, reactive oxygen species, and drug transporters. This review summarizes the bioavailability of FLs, their anticancer mechanisms in relevance to molecular targets, safety, and the scope of future research. Overall, FLs can be utilized in functional foods, dietary supplements, and pharmaceuticals for the management and prevention of cancers.
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Affiliation(s)
- Abdul Mueed
- State key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi 330047, China.
| | - Zeyuan Deng
- State key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi 330047, China.
| | - Sameh A Korma
- Department of Food Science, Faculty of Agriculture, Zagazig University, 44519 Zagazig, Egypt
| | - Sahar Shibli
- Food Science Research Institute, National Agriculture Research Center, Islamabad, Pakistan
| | - Muhammad Jahangir
- Department of Food Science & Technology, The University of Haripur, Khyber-Pakhtunkhwa, Pakistan
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Mueed A, Shibli S, Jahangir M, Jabbar S, Deng Z. A comprehensive review of flaxseed ( Linum usitatissimum L.): health-affecting compounds, mechanism of toxicity, detoxification, anticancer and potential risk. Crit Rev Food Sci Nutr 2022; 63:11081-11104. [PMID: 35833457 DOI: 10.1080/10408398.2022.2092718] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Flaxseed consumption (Linum usitatissimum L.) has increased due to its potential health benefits, such as protection against inflammation, diabetes, cancer, and cardiovascular diseases. However, flaxseeds also contains various anti-nutritive and toxic compounds such as cyanogenic glycosides, and phytic acids etc. In this case, the long-term consumption of flaxseed may pose health risks due to these non-nutritional substances, which may be life threatening if consumed in high doses, although if appropriately utilized these may prevent/treat various diseases by preventing/inhibiting and or reversing the toxicity induced by other compounds. Therefore, it is necessary to remove or suppress the harmful and anti-nutritive effects of flaxseeds before these are utilized for large-scale as food for human consumption. Interestingly, the toxic compounds of flaxseed also undergoes biochemical detoxification in the body, transforming into less toxic or inactive forms like α-ketoglutarate cyanohydrin etc. However, such detoxification is also a challenge for the development, scalability, and real-time quantification of these bioactive substances. This review focuses on the health affecting composition of flaxseed, along with health benefits and potential toxicity of its components, detoxification methods and mechanisms with evidence supported by animal and human studies.
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Affiliation(s)
- Abdul Mueed
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi, China
| | - Sahar Shibli
- Food Science Research Institute, National Agriculture Research Center, Islamabad, Pakistan
| | - Muhammad Jahangir
- Department of Food Science & Technology, The University of Haripur, Haripur, Khyber-Pakhtunkhwa, Pakistan
| | - Saqib Jabbar
- Food Science Research Institute, National Agriculture Research Center, Islamabad, Pakistan
| | - Zeyuan Deng
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi, China
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Elucidation of Agonist and Antagonist Dynamic Binding Patterns in ER-α by Integration of Molecular Docking, Molecular Dynamics Simulations and Quantum Mechanical Calculations. Int J Mol Sci 2021; 22:ijms22179371. [PMID: 34502280 PMCID: PMC8431471 DOI: 10.3390/ijms22179371] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/25/2021] [Accepted: 08/27/2021] [Indexed: 12/13/2022] Open
Abstract
Estrogen receptor alpha (ERα) is a ligand-dependent transcriptional factor in the nuclear receptor superfamily. Many structures of ERα bound with agonists and antagonists have been determined. However, the dynamic binding patterns of agonists and antagonists in the binding site of ERα remains unclear. Therefore, we performed molecular docking, molecular dynamics (MD) simulations, and quantum mechanical calculations to elucidate agonist and antagonist dynamic binding patterns in ERα. 17β-estradiol (E2) and 4-hydroxytamoxifen (OHT) were docked in the ligand binding pockets of the agonist and antagonist bound ERα. The best complex conformations from molecular docking were subjected to 100 nanosecond MD simulations. Hierarchical clustering was conducted to group the structures in the trajectory from MD simulations. The representative structure from each cluster was selected to calculate the binding interaction energy value for elucidation of the dynamic binding patterns of agonists and antagonists in the binding site of ERα. The binding interaction energy analysis revealed that OHT binds ERα more tightly in the antagonist conformer, while E2 prefers the agonist conformer. The results may help identify ERα antagonists as drug candidates and facilitate risk assessment of chemicals through ER-mediated responses.
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Marinho MM, Almeida-Neto FWQ, Marinho EM, da Silva LP, Menezes RR, dos Santos RP, Marinho ES, de Lima-Neto P, Martins AM. Quantum computational investigations and molecular docking studies on amentoflavone. Heliyon 2021; 7:e06079. [PMID: 33553750 PMCID: PMC7851790 DOI: 10.1016/j.heliyon.2021.e06079] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/01/2020] [Accepted: 01/20/2021] [Indexed: 01/02/2023] Open
Abstract
Chagas disease is a neglected tropical disease caused by the protozoan parasite Trypanosoma cruzi, with approximately 6-7 million people infected worldwide, becoming a public health problem in tropical countries, thus generating an increasing demand for the development of more effective drugs, due to the low efficiency of the existing drugs. Aiming at the development of a new antichagasic pharmacological tool, the density functional theory was used to calculate the reactivity descriptors of amentoflavone, a biflavonoid with proven anti-trypanosomal activity in vitro, as well as to perform a study of interactions with the enzyme cruzain, an enzyme key in the evolutionary process of T-cruzi. Structural properties (in solvents with different values of dielectric constant), the infrared spectrum, the frontier orbitals, Fukui analysis, thermodynamic properties were the parameters calculated from DFT method with the monomeric structure of the apigenin used for comparison. Furthermore, molecular docking studies were performed to assess the potential use of this biflavonoid as a pharmacological antichagasic tool. The frontier orbitals (HOMO-LUMO) study to find the band gap of compound has been extended to calculate electron affinity, ionization energy, electronegativity electrophilicity index, chemical potential, global chemical hardness and global chemical softness to study the chemical behaviour of compound. The optimized structure was subjected to molecular Docking to characterize the interaction between amentoflavone and cruzain enzyme, a classic pharmacological target for substances with anti-gas activity, where significant interactions were observed with amino acid residues from each one's catalytic sites enzyme. These results suggest that amentoflavone has the potential to interfere with the enzymatic activity of cruzain, thus being an indicative of being a promising antichagasic agent.
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Affiliation(s)
- Márcia M. Marinho
- Departamento de Análises Clínicas e Toxicológicas, Centro de Ciências da Saúde, Universidade Federal do Ceará, Campus Porangabussu, 60430-370, Fortaleza, Ceará, Brazil
| | - Francisco Wagner Q. Almeida-Neto
- Departamento de Química Analítica e Físico-Química, Centro de Ciências, Universidade Federal do Ceará, Campus do Pici, Bloco 940, 60440-900, Fortaleza, Ceará, Brazil
| | - Emanuelle M. Marinho
- Departamento de Química Analítica e Físico-Química, Centro de Ciências, Universidade Federal do Ceará, Campus do Pici, Bloco 940, 60440-900, Fortaleza, Ceará, Brazil
| | - Leonardo P. da Silva
- Departamento de Química Analítica e Físico-Química, Centro de Ciências, Universidade Federal do Ceará, Campus do Pici, Bloco 940, 60440-900, Fortaleza, Ceará, Brazil
| | - Ramon R.P.P.B. Menezes
- Departamento de Análises Clínicas e Toxicológicas, Centro de Ciências da Saúde, Universidade Federal do Ceará, Campus Porangabussu, 60430-370, Fortaleza, Ceará, Brazil
| | - Ricardo P. dos Santos
- Engenharia de Computação / Biotecnologia, Universidade Federal do Ceará, Campus de Sobral, 62010-560, Sobral Ceará, Brazil
| | - Emmanuel S. Marinho
- Faculdade de Filosofia Dom Aureliano Matos, Universidade Estadual do Ceará, 62930-000, Limoeiro do Norte, Ceará, Brazil
| | - Pedro de Lima-Neto
- Departamento de Química Analítica e Físico-Química, Centro de Ciências, Universidade Federal do Ceará, Campus do Pici, Bloco 940, 60440-900, Fortaleza, Ceará, Brazil
| | - Alice M.C. Martins
- Departamento de Análises Clínicas e Toxicológicas, Centro de Ciências da Saúde, Universidade Federal do Ceará, Campus Porangabussu, 60430-370, Fortaleza, Ceará, Brazil
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Lu JJ, Zhou FM, Hu XJ, Fang JJ, Liu CX, Zhu BQ, Ding ZS. Molecular docking simulation and in vitro studies on estrogenic activities of flavonoids from leaves of Carya cathayensis Sarg. Steroids 2020; 163:108726. [PMID: 32889051 DOI: 10.1016/j.steroids.2020.108726] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 08/18/2020] [Accepted: 08/25/2020] [Indexed: 12/11/2022]
Abstract
The main purpose of this study was to evaluate the estrogenic properties of total flavonoids (TFs) and five flavonoid monomers (cardamonin (Car), pinostrobin chalcone (PC), wogonin (Wo), chrysin (Chr) and Pinocembrin (PI)) from leaves of Carya cathayensis Sarg (LCC). TFs from LCC were isolated and determined using HPLC. The 3-[4,5-dimethylthiazole-2-yl]-2,5-diphenyltetrazolium bromide (MTT) assay and flow cytometry were performed to assess the effects of flavonoids on cell proliferation and cell cycle, respectively. The molecular docking technique was applied to investigate binding conformations of the monomers from LCC to the estrogen receptor ERα and ERβ. Gene and protein expression patterns were assessed using quantitative real-time PCR (qRT-PCR) and western blot, respectively. The results showed that TFs, Car, PC, Wo and Chr promoted proliferation of MCF-7 cells and cell transition from the G1 to S phase, and inhabitation of MCF-7 cell proliferation was observed after the treatment of PI. Molecular docking studies confirmed ERs as molecular targets for the monomers. TFs, Car, PC, Wo and Chr from LCC promoted gene expression of ERα, ERβ, progesterone receptor (PR) and pS2. Our collective results demonstrated that TFs and monomers from LCC may exert ER agonist activity through competitively bind to ER, inducing ER upregulation and active ER to estrogen response element (ERE)- independent gene regulation. As an abundant natural product, LCC may provide a novel medicinal source for treatment of diseases caused by estrogen deficiency.
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Affiliation(s)
- Jing-Jing Lu
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou 310053, Zhejiang, China
| | - Fang-Mei Zhou
- College of Medical Technology, Zhejiang Chinese Medical University, Hangzhou 310053, Zhejiang, China
| | - Xu-Jiao Hu
- Yinzhou People's Hospital, Ningbo, Zhejiang Province, China
| | - Jing-Jing Fang
- Yinzhou People's Hospital, Ningbo, Zhejiang Province, China
| | - Cai-Xia Liu
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou 310053, Zhejiang, China
| | - Bing-Qi Zhu
- College of Medical Technology, Zhejiang Chinese Medical University, Hangzhou 310053, Zhejiang, China
| | - Zhi-Shan Ding
- College of Medical Technology, Zhejiang Chinese Medical University, Hangzhou 310053, Zhejiang, China.
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10
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Cardoso WB, Mendanha SA. Molecular dynamics simulation of docking structures of SARS-CoV-2 main protease and HIV protease inhibitors. J Mol Struct 2020; 1225:129143. [PMID: 32863430 PMCID: PMC7443253 DOI: 10.1016/j.molstruc.2020.129143] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/20/2020] [Accepted: 08/22/2020] [Indexed: 12/12/2022]
Abstract
We consider possible repurposed-drugs candidates against SARS-CoV-2. 10 different HIV protease inhibitors were investigated. In silico simulations were used to study protease inhibitors for SARS-CoV-2.
In this paper we investigate 10 different HIV protease inhibitors (HPIs) as possible repurposed-drugs candidates against SARS-CoV-2. To this end, we execute molecular docking and molecular dynamics simulations. The in silico data demonstrated that, despite their molecular differences, all HPIs presented a similar behavior for the parameters analyzed, with the exception of Nelfinavir that showed better results for most of the molecular dynamics parameters in comparison with the N3 inhibitor.
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Affiliation(s)
- Wesley B Cardoso
- Instituto de Física, Universidade Federal de Goiás, 74.690-900, Goiânia, Goiás, Brazil
| | - Sebastião A Mendanha
- Instituto de Física, Universidade Federal de Goiás, 74.690-900, Goiânia, Goiás, Brazil
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11
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VEGF/CDK2 are involved in diabetic organ regeneration. Biochem Biophys Res Commun 2020; 529:1094-1100. [PMID: 32819570 DOI: 10.1016/j.bbrc.2020.07.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 07/05/2020] [Indexed: 11/21/2022]
Abstract
AIM/HYPOTHESIS Diabetes is a hyperglycaemic disease treated by a set of allopathic drugs and natural biomolecules along with many variety of stem cell. We aim to investigate the role of these drugs in targeting common protein molecule in diabetes and its associated disease. We also aim to investigate the organ degeneration mechanistic pathway in diabetes. METHOD We have generated diabetes using streptozotocin injection and treated them using bone marrow transplantation and curcumin administration. The organs were studied histopathologically and by immunofluorescence analysis while drugs were studied Pharmacogenomically. RESULT Mice injected with streptozotocin have higher glucose and lower insulin, islet number/diameter, bone marrow cell number compared to control and bone marrow transplanted and curcumin administered mice. Histopathology staining demonstrates damaged morphology of pancreas, kidney, brain and cardiac muscle. Further, upon comparison of all allopathic and ayurvedic drugs used for diabetes several protein targets have been identified by reverse pharmacophore analysis using PharmMapper. VEGF, CDK2, insulin receptor, HSp90, eNOS, Fructose1,6 bisphosphatase, neprilysin, AchE, MAPK are several common protein targets of anti-diabetic drugs. CONCLUSION This article demonstrates that VEGF and CDK2 are critical marker in organ damage in diabetes as well as organ regeneration.
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12
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Khayami R, Hashemi SR, Kerachian MA. Role of aldo-keto reductase family 1 member B1 (AKR1B1) in the cancer process and its therapeutic potential. J Cell Mol Med 2020; 24:8890-8902. [PMID: 32633024 PMCID: PMC7417692 DOI: 10.1111/jcmm.15581] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 05/21/2020] [Accepted: 05/27/2020] [Indexed: 02/06/2023] Open
Abstract
The role of aldo‐keto reductase family 1 member B1 (AKR1B1) in cancer is not totally clear but growing evidence is suggesting to have a great impact on cancer progression. AKR1B1 could participate in a complicated network of signalling pathways, proteins and miRNAs such as mir‐21 mediating mechanisms like inflammatory responses, cell cycle, epithelial to mesenchymal transition, cell survival and apoptosis. AKR1B1 has been shown to be mostly overexpressed in cancer. This overexpression has been associated with inflammatory mediators including nuclear factor kappa‐light‐chain‐enhancer of activated B cells (NFκB), cell cycle mediators such as cyclins and cyclin‐dependent kinases (CDKs), survival proteins and pathways like mammalian target of rapamycin (mTOR) and protein kinase B (PKB) or AKT, and other regulatory factors in response to reactive oxygen species (ROS) and prostaglandin synthesis. In addition, inhibition of AKR1B1 has been shown to mostly have anti‐cancer effects. Several studies have also suggested that AKR1B1 inhibition as an adjuvant therapy could render tumour cells more sensitive to anti‐cancer therapy or alleviate the adverse effects of therapy. AKR1B1 could also be considered as a potential cancer diagnostic biomarker since its promoter has shown high levels of methylation. Although pre‐clinical investigations on the role of AKR1B1 in cancer and the application of its inhibitors have shown promising results, the lack of clinical studies on AKR1B1 inhibitors has hampered the use of these drugs to treat cancer. Thus, there is a need to conduct more clinical studies on the application of AKR1B1 inhibitors as adjuvant therapy on different cancers.
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Affiliation(s)
- Reza Khayami
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyyed Reza Hashemi
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Amin Kerachian
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran
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13
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Huang JJ, Wei T, Lin JF, Guo LQ, Han WF, Han PY, Ye AQ. High-effective biosynthesis of baccatin Ⅲ by using the alternative acetyl substrate, N-acetyl-d-glucosamine. J Appl Microbiol 2020; 129:345-355. [PMID: 32091657 DOI: 10.1111/jam.14620] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 02/11/2020] [Accepted: 02/17/2020] [Indexed: 12/25/2022]
Abstract
AIMS Paclitaxel is a type of broad-spectrum anticancer drug in short supply. The price of acetyl-CoA (17 709 677·4 USD mol-1 ), which is the acetyl group donor for the enzymatic synthesis of the intermediate, baccatin Ⅲ, is still the bottleneck of the mass production of paclitaxel. This study reports a novel acetyl group donor, which could substantially reduce the cost of production. METHODS AND RESULTS In this study, a substrate spectrum with 14 kinds of representative acetyl-donor substitutes predicted by computer-aided methods was tested in a 10-deacetylbaccatin Ⅲ-10-O-acetyltransferase (DBAT) heterogeneous-expressed open-whole-cell catalytic system. The results of computer prediction and experimental analysis revealed the rule of the acetyl-donor compounds based on this substrate spectrum. N-acetyl-d-glucosamine (30·95 USD mol-1 , about 572 202-fold cheaper than acetyl-CoA) is selected as a suitable substitute under the rule. The yield when using N-acetyl-d-glucosamine as acetyl donor in open-whole-cell catalytic system was 2·13-fold of that when using acetyl-CoA. In the in vivo system, the yield increased 24·17%, which may indicate its cooperation with acetyl-CoA. CONCLUSION The success of open-whole-cell synthesis and in vivo synthesis of baccatin Ⅲ by adding N-acetyl-d-glucosamine as acetyl substrate demonstrates that it is a useful substrate to improve the yield of baccatin Ⅲ. SIGNIFICANCE AND IMPACT OF THE STUDY All these findings provided a potential acetyl-donor substitute for acetyl-CoA, as well as a low cost and efficient method of preparing paclitaxel through baccatin Ⅲ semi-synthesis.
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Affiliation(s)
- J-J Huang
- Department of Bioengineering, College of Food Science and Institute of Food Biotechnology, South China Agricultural University, Guangzhou, China.,Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou, China
| | - T Wei
- Department of Bioengineering, College of Food Science and Institute of Food Biotechnology, South China Agricultural University, Guangzhou, China.,Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou, China
| | - J-F Lin
- Department of Bioengineering, College of Food Science and Institute of Food Biotechnology, South China Agricultural University, Guangzhou, China.,Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou, China
| | - L-Q Guo
- Department of Bioengineering, College of Food Science and Institute of Food Biotechnology, South China Agricultural University, Guangzhou, China.,Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou, China
| | - W-F Han
- Department of Bioengineering, College of Food Science and Institute of Food Biotechnology, South China Agricultural University, Guangzhou, China.,Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou, China
| | - P-Y Han
- Department of Bioengineering, College of Food Science and Institute of Food Biotechnology, South China Agricultural University, Guangzhou, China.,Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou, China
| | - A-Q Ye
- Department of Bioengineering, College of Food Science and Institute of Food Biotechnology, South China Agricultural University, Guangzhou, China.,Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou, China
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14
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Rathee D, Lather V, Grewal AS, Dureja H. Enzymatic inhibitory activity of iridoid glycosides from Picrorrhiza kurroa against matrix metalloproteinases: Correlating in vitro targeted screening and docking. Comput Biol Chem 2018; 78:28-36. [PMID: 30497018 DOI: 10.1016/j.compbiolchem.2018.10.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 10/29/2018] [Accepted: 10/31/2018] [Indexed: 11/25/2022]
Abstract
One specific group of MMPs; gelatinases A (MMP-2) and B (MMP-9) are of precise interest in view of the development and progression of cancer. In the current work, an attempt was made to investigate the enzymatic inhibitory activity of Kutkin (KT), Kutkoside (KS), and Picroside I (PS) by inhibition assay and to further check the downregulation of the expression of mRNA levels of MMP-2 and -9. Further in silico docking studies were performed to investigate the interaction of KT, KS and PS with MMP-2 and MMP-9. The results revealed a dose dependent cytotoxic activity of the compounds under investigation and showed a significant inhibition of MMP-9 in comparison to the activity against MMP-2. In addition, a considerable decrease in expression of mRNA levels (MMP-9) was observed in KT, KS, and PS-treated MDA-MB-231 and MDA-MB-435 cancer cells as was detected by reverse transcriptase polymerase chain reaction (semi-quantitative RT-PCR). The molecular docking studies between KT, KS, PS with MMPs revealed that KT, KS, PS occupied the active site of MMP-9 and showed better binding interactions in comparison to MMP-2. The binding energies of the complexes were -7.4, -7.1 and -7.2 kJ/mol for KT, KS and PS with MMP-9, respectively and -8.9, -8.0 and -8.0 kJ/mol for KT, KS and PS with MMP-2, respectively. The findings from the in vitro studies revealed that KT, KS and PS exhibited significant anti-proliferative effects on both MDA-MB-231 and MDA-MB-435 breast cancer cells. In addition, the results of inhibition assay showed that MMP-9 activity was significantly inhibited by KT, KS and PS and the results were consistent with in silico assay.
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Affiliation(s)
- Dharmender Rathee
- Department of Pharmaceutical Sciences, MaharshiDayanand University, Rohtak, Haryana, 124001, India
| | - Viney Lather
- Amity Institute of Pharmacy, Amity University, Sector-125, Noida, 201313, U.P., India
| | - Ajmer Singh Grewal
- Chitkara College of Pharmacy, Chitkara University, Rajpura, Patiala, Punjab, 140401, India
| | - Harish Dureja
- Department of Pharmaceutical Sciences, MaharshiDayanand University, Rohtak, Haryana, 124001, India.
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15
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Younas M, Hano C, Giglioli-Guivarc'h N, Abbasi BH. Mechanistic evaluation of phytochemicals in breast cancer remedy: current understanding and future perspectives. RSC Adv 2018; 8:29714-29744. [PMID: 35547279 PMCID: PMC9085387 DOI: 10.1039/c8ra04879g] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 08/15/2018] [Indexed: 12/30/2022] Open
Abstract
Breast cancer is one of the most commonly diagnosed cancers around the globe and accounts for a large proportion of fatalities in women. Despite the advancement in therapeutic and diagnostic procedures, breast cancer still represents a major challenge. Current anti-breast cancer approaches include surgical removal, radiotherapy, hormonal therapy and the use of various chemotherapeutic drugs. However, drug resistance, associated serious adverse effects, metastasis and recurrence complications still need to be resolved which demand safe and alternative strategies. In this scenario, phytochemicals have recently gained huge attention due to their safety profile and cost-effectiveness. These phytochemicals modulate various genes, gene products and signalling pathways, thereby inhibiting breast cancer cell proliferation, invasion, angiogenesis and metastasis and inducing apoptosis. Moreover, they also target breast cancer stem cells and overcome drug resistance problems in breast carcinomas. Phytochemicals as adjuvants with chemotherapeutic drugs have greatly enhanced their therapeutic efficacy. This review focuses on the recently recognized molecular mechanisms underlying breast cancer chemoprevention with the use of phytochemicals such as curcumin, resveratrol, silibinin, genistein, epigallocatechin gallate, secoisolariciresinol, thymoquinone, kaempferol, quercetin, parthenolide, sulforaphane, ginsenosides, naringenin, isoliquiritigenin, luteolin, benzyl isothiocyanate, α-mangostin, 3,3'-diindolylmethane, pterostilbene, vinca alkaloids and apigenin.
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Affiliation(s)
- Muhammad Younas
- Department of Biotechnology, Quaid-i-Azam University Islamabad-45320 Pakistan +92-51-90644121 +92-51-90644121 +33-767-97-0619
| | - Christophe Hano
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), Plant Lignans Team, UPRES EA 1207, Université d'Orléans F 28000 Chartres France
| | | | - Bilal Haider Abbasi
- Department of Biotechnology, Quaid-i-Azam University Islamabad-45320 Pakistan +92-51-90644121 +92-51-90644121 +33-767-97-0619
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), Plant Lignans Team, UPRES EA 1207, Université d'Orléans F 28000 Chartres France
- EA2106 Biomolecules et Biotechnologies Vegetales, Universite Francois-Rabelais de Tours Tours France
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16
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Huang H, Zhang G, Zhou Y, Lin C, Chen S, Lin Y, Mai S, Huang Z. Reverse Screening Methods to Search for the Protein Targets of Chemopreventive Compounds. Front Chem 2018; 6:138. [PMID: 29868550 PMCID: PMC5954125 DOI: 10.3389/fchem.2018.00138] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 04/09/2018] [Indexed: 12/13/2022] Open
Abstract
This article is a systematic review of reverse screening methods used to search for the protein targets of chemopreventive compounds or drugs. Typical chemopreventive compounds include components of traditional Chinese medicine, natural compounds and Food and Drug Administration (FDA)-approved drugs. Such compounds are somewhat selective but are predisposed to bind multiple protein targets distributed throughout diverse signaling pathways in human cells. In contrast to conventional virtual screening, which identifies the ligands of a targeted protein from a compound database, reverse screening is used to identify the potential targets or unintended targets of a given compound from a large number of receptors by examining their known ligands or crystal structures. This method, also known as in silico or computational target fishing, is highly valuable for discovering the target receptors of query molecules from terrestrial or marine natural products, exploring the molecular mechanisms of chemopreventive compounds, finding alternative indications of existing drugs by drug repositioning, and detecting adverse drug reactions and drug toxicity. Reverse screening can be divided into three major groups: shape screening, pharmacophore screening and reverse docking. Several large software packages, such as Schrödinger and Discovery Studio; typical software/network services such as ChemMapper, PharmMapper, idTarget, and INVDOCK; and practical databases of known target ligands and receptor crystal structures, such as ChEMBL, BindingDB, and the Protein Data Bank (PDB), are available for use in these computational methods. Different programs, online services and databases have different applications and constraints. Here, we conducted a systematic analysis and multilevel classification of the computational programs, online services and compound libraries available for shape screening, pharmacophore screening and reverse docking to enable non-specialist users to quickly learn and grasp the types of calculations used in protein target fishing. In addition, we review the main features of these methods, programs and databases and provide a variety of examples illustrating the application of one or a combination of reverse screening methods for accurate target prediction.
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Affiliation(s)
- Hongbin Huang
- Key Laboratory for Medical Molecular Diagnostics of Guangdong Province, Dongguan Scientific Research Center, Guangdong Medical University Dongguan, China.,The Second School of Clinical Medicine, Guangdong Medical University Dongguan, China
| | - Guigui Zhang
- Key Laboratory for Medical Molecular Diagnostics of Guangdong Province, Dongguan Scientific Research Center, Guangdong Medical University Dongguan, China.,School of Pharmacy, Guangdong Medical University Dongguan, China
| | - Yuquan Zhou
- Key Laboratory for Medical Molecular Diagnostics of Guangdong Province, Dongguan Scientific Research Center, Guangdong Medical University Dongguan, China.,The Second School of Clinical Medicine, Guangdong Medical University Dongguan, China
| | - Chenru Lin
- Key Laboratory for Medical Molecular Diagnostics of Guangdong Province, Dongguan Scientific Research Center, Guangdong Medical University Dongguan, China.,School of Pharmacy, Guangdong Medical University Dongguan, China
| | - Suling Chen
- Key Laboratory for Medical Molecular Diagnostics of Guangdong Province, Dongguan Scientific Research Center, Guangdong Medical University Dongguan, China.,The Second School of Clinical Medicine, Guangdong Medical University Dongguan, China
| | - Yutong Lin
- Key Laboratory for Medical Molecular Diagnostics of Guangdong Province, Dongguan Scientific Research Center, Guangdong Medical University Dongguan, China.,School of Pharmacy, Guangdong Medical University Dongguan, China
| | - Shangkang Mai
- Key Laboratory for Medical Molecular Diagnostics of Guangdong Province, Dongguan Scientific Research Center, Guangdong Medical University Dongguan, China.,The Second School of Clinical Medicine, Guangdong Medical University Dongguan, China
| | - Zunnan Huang
- Key Laboratory for Medical Molecular Diagnostics of Guangdong Province, Dongguan Scientific Research Center, Guangdong Medical University Dongguan, China.,School of Pharmacy, Guangdong Medical University Dongguan, China
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17
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Kim BG, Kim JW, Kim SM, Go RE, Hwang KA, Choi KC. 3,3'-Diindolylmethane Suppressed Cyprodinil-Induced Epithelial-Mesenchymal Transition and Metastatic-Related Behaviors of Human Endometrial Ishikawa Cells via an Estrogen Receptor-Dependent Pathway. Int J Mol Sci 2018; 19:ijms19010189. [PMID: 29316692 PMCID: PMC5796138 DOI: 10.3390/ijms19010189] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Revised: 01/02/2018] [Accepted: 01/05/2018] [Indexed: 01/10/2023] Open
Abstract
Cyprodinil (CYP) is a pyrimidine amine fungicide that has been extensively used in agricultural areas. 3,3′-Diindolylmethane (DIM) is a derivative of the dietary phytoestrogen, indole-3-carbinol (I3C), which is derived from cruciferous vegetables and considered to be a cancer-preventive phytonutrient agent. In this study, the effects of CYP and DIM were examined on the cell viability, invasion, and metastasis of human endometrial cancer cells, Ishikawa, via epithelial mesenchymal transition (EMT). CYP increased the level of cell viability of Ishikawa cells compared to DMSO as a control, as did E2. Ishikawa cells lost cell-to-cell contact and obtained a spindle-shaped or fibroblast-like morphology in response to the application of E2 or CYP by the cell morphology assay. In the cell migration and invasion assay, CYP enhanced the ability of migration and invasion of Ishikawa cells, as did E2. E2 and CYP increased the expressions of N-cadherin and Snail proteins, while decreasing the expression of E-cadherin protein as EMT-related markers. In addition, E2 and CYP increased the protein expressions of cathepsin D and MMP-9, metastasis-related markers. Conversely, CYP-induced EMT, cell migration, and invasion were reversed by fulvestrant (ICI 182,780) as an estrogen receptor (ER) antagonist, indicating that CYP exerts estrogenic activity by mediating these processes via an ER-dependent pathway. Similar to ICI 182,780, DIM significantly suppressed E2 and CYP-induced proliferation, EMT, migration, and invasion of Ishikawa cancer cells. Overall, the present study revealed that DIM has an antiestrogenic chemopreventive effect to withdraw the cancer-enhancing effect of E2 and CYP, while CYP has the capacity to enhance the metastatic potential of estrogen-responsive endometrial cancer.
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Affiliation(s)
- Bo-Gyoung Kim
- Laboratory of Biochemistry and Immunology, College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Chungbuk, Korea.
| | - Jin-Wook Kim
- Laboratory of Biochemistry and Immunology, College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Chungbuk, Korea.
| | - Soo-Min Kim
- Laboratory of Biochemistry and Immunology, College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Chungbuk, Korea.
| | - Ryeo-Eun Go
- Laboratory of Biochemistry and Immunology, College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Chungbuk, Korea.
| | - Kyung-A Hwang
- Laboratory of Biochemistry and Immunology, College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Chungbuk, Korea.
| | - Kyung-Chul Choi
- Laboratory of Biochemistry and Immunology, College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Chungbuk, Korea.
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