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Target-Based Small Molecule Drug Discovery for Colorectal Cancer: A Review of Molecular Pathways and In Silico Studies. Biomolecules 2022; 12:biom12070878. [PMID: 35883434 PMCID: PMC9312989 DOI: 10.3390/biom12070878] [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: 03/21/2022] [Revised: 06/05/2022] [Accepted: 06/17/2022] [Indexed: 01/27/2023] Open
Abstract
Colorectal cancer is one of the most prevalent cancer types. Although there have been breakthroughs in its treatments, a better understanding of the molecular mechanisms and genetic involvement in colorectal cancer will have a substantial role in producing novel and targeted treatments with better safety profiles. In this review, the main molecular pathways and driver genes that are responsible for initiating and propagating the cascade of signaling molecules reaching carcinoma and the aggressive metastatic stages of colorectal cancer were presented. Protein kinases involved in colorectal cancer, as much as other cancers, have seen much focus and committed efforts due to their crucial role in subsidizing, inhibiting, or changing the disease course. Moreover, notable improvements in colorectal cancer treatments with in silico studies and the enhanced selectivity on specific macromolecular targets were discussed. Besides, the selective multi-target agents have been made easier by employing in silico methods in molecular de novo synthesis or target identification and drug repurposing.
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Kumari S, Shivakrishna P, Sreenivasulu K. Molecular docking analysis of two bioactive molecules KLUF10 and KLUF13 isolated from the marine bacteria Micrococcus sp. OUS9 with TNF alpha. Bioinformation 2022; 17:530-535. [PMID: 35095226 PMCID: PMC8770404 DOI: 10.6026/97320630017530] [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: 03/15/2021] [Revised: 04/21/2021] [Accepted: 04/30/2021] [Indexed: 11/29/2022] Open
Abstract
Tumor necrosis factor-alpha (TNF-α) is known to be linked with tumor. Therefore, it is of interest to document the Molecular docking analysis of two bioactive molecules KLUF10 and KLUF13 isolated from the marine bacteria Micrococcus sp. OUS9 with TNF alpha.
We report the molecular interactions of KLUF10 and KLUF13 with TNF alpha.
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Affiliation(s)
- Shanthi Kumari
- Osmania University, Department of microbiology, Hyderabad, India.,KLEF University, Andhra Pradesh, India
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3
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Zhao J, Zhang T, Liang Y, Zou H, Zhang J. Inhibitory activities of 20(R, S)-protopanaxatriol against epidermal growth factor receptor tyrosine kinase. Food Chem Toxicol 2021; 155:112411. [PMID: 34271119 DOI: 10.1016/j.fct.2021.112411] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/07/2021] [Accepted: 07/12/2021] [Indexed: 12/13/2022]
Abstract
As major metabolites of protopanaxatriol-type ginsenosides, 20(R, S)-protopanaxatriol [20(R, S)-PPT] display multiple bioactivities. This work aimed to investigate the inhibitory activities of 20(R, S)-PPT against epidermal growth factor receptor tyrosine kinase and the potential mechanism. 20(R, S)-PPT inhibited the proliferation of HepG2 cells in a dose-dependent manner and blocked cell cycle progression at G1/G0 phase. Then 20(R, S)-PPT were found to influence the protein expressions involved in epidermal growth factor receptor (EGFR)-mitogen-activated protein kinase (MAPK) signaling pathway. Molecular docking suggested that 20(R, S)-PPT could bind to the active sites of all target proteins in EGFR-MAPK pathway. It is worth noting that 20(R, S)-PPT showed stronger binding capacities with EGFR, compared with other proteins. Hence, this work further investigated the binding interactions and binding stabilities between 20(R, S)-PPT and EGFR. Both hydrophobic interactions and hydrogen bonds contributed to the 20(R, S)-PPT-EGFR binding. In addition, the in vitro inhibitory activities of 20(R, S)-PPT against EGFR tyrosine kinase were observed in a homogeneous time-resolved fluorescence assay, with the IC50 values of 24.10 ± 0.17 and 33.19 ± 0.19 μM respectively. Taken together with the above results, both of 20(R)-PPT and 20(S)-PPT might serve as potential EGFR tyrosine kinase inhibitors.
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Affiliation(s)
- Jingqi Zhao
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Tiehua Zhang
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Yuan Liang
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Haoyang Zou
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Jie Zhang
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China.
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4
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Gill MSA, Saleem H, Ahemad N. Plant Extracts and their Secondary Metabolites as Modulators of Kinases. Curr Top Med Chem 2021; 20:1093-1104. [PMID: 32091334 DOI: 10.2174/1568026620666200224100219] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 01/20/2020] [Accepted: 01/24/2020] [Indexed: 12/20/2022]
Abstract
Natural Products (NP), specifically from medicinal plants or herbs, have been extensively utilized to analyze the fundamental mechanisms of ultimate natural sciences as well as therapeutics. Isolation of secondary metabolites from these sources and their respective biological properties, along with their lower toxicities and cost-effectiveness, make them a significant research focus for drug discovery. In recent times, there has been a considerable focus on isolating new chemical entities from natural flora to meet the immense demand for kinase modulators, and also to overcome major unmet medical challenges in relation to signal transduction pathways. The signal transduction systems are amongst the foremost pathways involved in the maintenance of life and protein kinases play an imperative part in these signaling pathways. It is important to find a kinase inhibitor, as it can be used not only to study cell biology but can also be used as a drug candidate for cancer and metabolic disorders. A number of plant extracts and their isolated secondary metabolites such as flavonoids, phenolics, terpenoids, and alkaloids have exhibited activities against various kinases. In the current review, we have presented a brief overview of some important classes of plant secondary metabolites as kinase modulators. Moreover, a number of phytocompounds with kinase inhibition potential, isolated from different plant species, are also discussed.
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Affiliation(s)
- Muhammad Shoaib Ali Gill
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, Petaling Jaya 47500, Selangor Darul Ehsan, Malaysia.,Institute of Pharmaceutical Sciences (IPS), University of Veterinary and Animal Sciences (UVAS), Lahore 54000, Pakistan
| | - Hammad Saleem
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, Petaling Jaya 47500, Selangor Darul Ehsan, Malaysia.,Institute of Pharmaceutical Sciences (IPS), University of Veterinary and Animal Sciences (UVAS), Lahore 54000, Pakistan
| | - Nafees Ahemad
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, Petaling Jaya 47500, Selangor Darul Ehsan, Malaysia.,Tropical Medicine and Biology Platform, Monash University Malaysia, Jalan Lagoon Selatan, Petaling Jaya 47500, Selangor Darul Ehsan, Malaysia.,Global Asia in 21st Century Platform, Monash University Malaysia, Jalan Lagoon Selatan, Petaling Jaya 47500, Selangor Darul Ehsan, Malaysia
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5
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Liang Y, Zhang T, Zhang J. Natural tyrosine kinase inhibitors acting on the epidermal growth factor receptor: Their relevance for cancer therapy. Pharmacol Res 2020; 161:105164. [PMID: 32846211 DOI: 10.1016/j.phrs.2020.105164] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/03/2020] [Accepted: 08/14/2020] [Indexed: 02/07/2023]
Abstract
Epidermal growth factor receptor (EGFR), also known as ErbB-1/HER-1, plays a key role in the regulation of the cell proliferation, migration, differentiation, and survival. Since the constitutive activation or overexpression of EGFR is nearly found in various cancers, the applications focused on EGFR are the most widely used in the clinical level, including the therapeutic drugs of targeting EGFR, monoclonal antibodies (mAbs) and tyrosine kinase inhibitors (TKIs).Over the past decades, the compounds from natural sources have been a productive source of novel drugs, especially in both discovery and development of anti-tumor drugs by targeting the EGFR pathways as the TKIs. This work presents a review of the compounds from natural sources as potential EGFR-TKIs involved in the regulation of cancer. Moreover, high-throughput drug screening of EGFR-TKIs from the natural compounds has also been summarized.
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Affiliation(s)
- Yuan Liang
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Tiehua Zhang
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Jie Zhang
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China.
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Sriwijitalai W, Wiwanitkit V. Herbs that might be effective for the management of COVID-19: A bioinformatics analysis on anti-tyrosine kinase property. JOURNAL OF RESEARCH IN MEDICAL SCIENCES 2020; 25:44. [PMID: 32582350 PMCID: PMC7306235 DOI: 10.4103/jrms.jrms_312_20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 04/04/2020] [Accepted: 04/15/2020] [Indexed: 01/22/2023]
Affiliation(s)
| | - Viroj Wiwanitkit
- Department of Community Medicine, Dr. DY Patil University, Pune, Maharashtra, India.,Department of Tropical Medicine, Hainan Medical University, Haikou, China.,Department of Biological Science, Joseph Ayobabalola University, Ikeji-Arakeji, Nigeria
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7
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Gajjar KA, Gajjar AK. Combiphore (Structure and Ligand Based Pharmacophore) - Approach for the Design of GPR40 Modulators in the Management of Diabetes. Curr Drug Discov Technol 2018; 17:233-247. [PMID: 30306872 DOI: 10.2174/1570163815666181008165822] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/05/2018] [Accepted: 10/05/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND Pharmacophore mapping and molecular docking can be synergistically integrated to improve the drug design and discovery process. A rational strategy, combiphore approach, derived from the combined study of Structure and Ligand based pharmacophore has been described to identify novel GPR40 modulators. METHODS DISCOtech module from Discovery studio was used for the generation of the Structure and Ligand based pharmacophore models which gave hydrophobic aromatic, ring aromatic and negative ionizable as essential pharmacophoric features. The generated models were validated by screening active and inactive datasets, GH scoring and ROC curve analysis. The best model was exposed as a 3D query to screen the hits from databases like GLASS (GPCR-Ligand Association), GPCR SARfari and Mini-Maybridge. Various filters were applied to retrieve the hit molecules having good drug-like properties. A known protein structure of hGPR40 (pdb: 4PHU) having TAK-875 as ligand complex was used to perform the molecular docking studies; using SYBYL-X 1.2 software. RESULTS AND CONCLUSION Clustering both the models gave RMSD of 0.89. Therefore, the present approach explored the maximum features by combining both ligand and structure based pharmacophore models. A common structural motif as identified in combiphore for GPR40 modulation consists of the para-substituted phenyl propionic acid scaffold. Therefore, the combiphore approach, whereby maximum structural information (from both ligand and biological protein) is explored, gives maximum insights into the plausible protein-ligand interactions and provides potential lead candidates as exemplified in this study.
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Affiliation(s)
- Krishna A Gajjar
- Department of Pharmaceutical Chemistry, L.M.College of Pharmacy, Ahmedabad 380009, Gujarat, India
| | - Anuradha K Gajjar
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad 382 481, Gujarat, India
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Nazarshodeh E, Gharaghani S. Toward a hierarchical virtual screening and toxicity risk analysis for identifying novel CA XII inhibitors. Biosystems 2017; 162:35-43. [PMID: 28899791 DOI: 10.1016/j.biosystems.2017.09.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Revised: 09/06/2017] [Accepted: 09/07/2017] [Indexed: 12/13/2022]
Abstract
Carbonic anhydrase isoform XII (CA XII) is a potential target for cancer treatment. In this study, pharmacophore modeling, hierarchical virtual screening, and toxicity risk analysis were performed for identifying novel CA XII inhibitors. A pharmacophore model of two classes of CA XII inhibitors was generated. The pharmacophore model indicated the important features of inhibitors for the binding with the CA XII. The model was then utilized to screen the ZINC and CoCoCo databases for retrieving potential hit compounds of CA XII. For accurate conclusions about the selectivity of inhibitors, the retrieved molecules which obey of Lipinski's rule of five (RO5) and have no toxicity risk were docked in a CA XII 3D structure by smina. Finally, on the basis of binding affinity and the binding mode of the molecules, twelve molecules were prioritized as promising hits. It should be noted that two of hits H5 and H6 were previously reported in the CHEMBL database. This hierarchical method is worthy of reducing the time and using almost all information available. The final hits may be used as a lead to discovery novel CA XII inhibitors.
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Affiliation(s)
- Elmira Nazarshodeh
- Laboratory of Bioinformatics and Drug Design (LBD), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Sajjad Gharaghani
- Laboratory of Bioinformatics and Drug Design (LBD), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
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9
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Pang X, Fu H, Yang S, Wang L, Liu AL, Wu S, Du GH. Evaluation of Novel Dual Acetyl- and Butyrylcholinesterase Inhibitors as Potential Anti-Alzheimer's Disease Agents Using Pharmacophore, 3D-QSAR, and Molecular Docking Approaches. Molecules 2017; 22:molecules22081254. [PMID: 28933746 PMCID: PMC6152156 DOI: 10.3390/molecules22081254] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 07/24/2017] [Accepted: 07/25/2017] [Indexed: 11/16/2022] Open
Abstract
DL0410, containing biphenyl and piperidine skeletons, was identified as an acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) inhibitor through high-throughput screening assays, and further studies affirmed its efficacy and safety for Alzheimer’s disease treatment. In our study, a series of novel DL0410 derivatives were evaluated for inhibitory activities towards AChE and BuChE. Among these derivatives, compounds 6-1 and 7-6 showed stronger AChE and BuChE inhibitory activities than DL0410. Then, pharmacophore modeling and three-dimensional quantitative structure activity relationship (3D-QSAR) models were performed. The R2 of AChE and BuChE 3D-QSAR models for training set were found to be 0.925 and 0.883, while that of the test set were 0.850 and 0.881, respectively. Next, molecular docking methods were utilized to explore the putative binding modes. Compounds 6-1 and 7-6 could interact with the amino acid residues in the catalytic anionic site (CAS) and peripheral anionic site (PAS) of AChE/BuChE, which was similar with DL0410. Kinetics studies also suggested that the three compounds were all mixed-types of inhibitors. In addition, compound 6-1 showed better absorption and blood brain barrier permeability. These studies provide better insight into the inhibitory behaviors of DL0410 derivatives, which is beneficial for rational design of AChE and BuChE inhibitors in the future.
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Affiliation(s)
- Xiaocong Pang
- Institute of Material Medical, Chinese Academy of Medical Sciences and Peking Union Medical College, Xian Nong Tan Street, Beijing 100050, China.
| | - Hui Fu
- Beijing Institute for Drug Control, Beijing 102206, China.
| | - Shilun Yang
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China.
| | - Lin Wang
- Institute of Material Medical, Chinese Academy of Medical Sciences and Peking Union Medical College, Xian Nong Tan Street, Beijing 100050, China.
| | - Ai-Lin Liu
- Institute of Material Medical, Chinese Academy of Medical Sciences and Peking Union Medical College, Xian Nong Tan Street, Beijing 100050, China.
- Beijing Key Laboratory of Drug Target Research and Drug Screening, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
| | - Song Wu
- Institute of Material Medical, Chinese Academy of Medical Sciences and Peking Union Medical College, Xian Nong Tan Street, Beijing 100050, China.
| | - Guan-Hua Du
- Institute of Material Medical, Chinese Academy of Medical Sciences and Peking Union Medical College, Xian Nong Tan Street, Beijing 100050, China.
- Beijing Key Laboratory of Drug Target Research and Drug Screening, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
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10
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Park K, Cho AE. Using reverse docking to identify potential targets for ginsenosides. J Ginseng Res 2016; 41:534-539. [PMID: 29021701 PMCID: PMC5628352 DOI: 10.1016/j.jgr.2016.10.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 08/30/2016] [Accepted: 10/25/2016] [Indexed: 11/25/2022] Open
Abstract
Background Ginsenosides are the main ingredients of ginseng, which, in traditional Eastern medicine, has been claimed to have therapeutic values for many diseases. In order to verify the effects of ginseng that have been empirically observed, we utilized the reverse docking method to screen for target proteins that are linked to specific diseases. Methods We constructed a target protein database including 1,078 proteins associated with various kinds of diseases, based on the Potential Drug Target Database, with an added list of kinase proteins. We screened 26 kinds of ginsenosides of this target protein database using docking. Results We found four potential target proteins for ginsenosides, based on docking scores. Implications of these “hit” targets are discussed. From this screening, we also found four targets linked to possible side effects and toxicities, based on docking scores. Conclusion Our method and results can be helpful for finding new targets and developing new drugs from natural products.
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Affiliation(s)
- Kichul Park
- Department of Bioinformatics, Korea University, Sejong, Republic of Korea
| | - Art E Cho
- Department of Bioinformatics, Korea University, Sejong, Republic of Korea
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Jaramillo S, Muriana FJ, Guillen R, Jimenez-Araujo A, Rodriguez-Arcos R, Lopez S. Saponins from edible spears of wild asparagus inhibit AKT, p70S6K, and ERK signalling, and induce apoptosis through G0/G1 cell cycle arrest in human colon cancer HCT-116 cells. J Funct Foods 2016. [DOI: 10.1016/j.jff.2016.07.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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12
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Kim OTP, Le MD, Trinh HX, Nong HV. In silico studies for the interaction of tumor necrosis factor-alpha (TNF-α) with different saponins from Vietnamese ginseng ( Panax vietnamesis). Biophys Physicobiol 2016; 13:173-180. [PMID: 27924272 PMCID: PMC5042174 DOI: 10.2142/biophysico.13.0_173] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 05/12/2016] [Indexed: 12/01/2022] Open
Abstract
Tumor necrosis factor-alpha (TNF-α) is a cytokine that plays an important role in inflammatory process and tumor development. Recent studies demonstrate that triterpene saponins from Vietnamese ginseng are efficient inhibitors of TNF-α. But the interactions between TNF-α and the saponins are still unclear. In this study, molecular docking and molecular dynamics simulations of TNF-α with three different triterpene saponins (majonoside R2, vina-ginsenoside R1 and vina-ginsenoside R2) were performed to evaluate their binding ability. Our results showed that the triterpene saponins have a good binding affinity with protein TNF-α. The saponins were docked to the pore at the top of the "bell" or "cone" shaped TNF-α trimer and the complexes were structurally stable during 100 ns molecular dynamics simulation. The predicted binding sites would help to subsequently investigate the inhibitory mechanism of triterpene saponins.
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Affiliation(s)
- Oanh T. P. Kim
- Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, 10000 Vietnam
| | - Manh D. Le
- Center for Computational Physics, Institute of Physics, Vietnam Academy of Science and Technology, Hanoi, 10000 Vietnam
| | - Hoang X. Trinh
- Center for Computational Physics, Institute of Physics, Vietnam Academy of Science and Technology, Hanoi, 10000 Vietnam
| | - Hai V. Nong
- Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, 10000 Vietnam
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13
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Atanasov AG, Waltenberger B, Pferschy-Wenzig EM, Linder T, Wawrosch C, Uhrin P, Temml V, Wang L, Schwaiger S, Heiss EH, Rollinger JM, Schuster D, Breuss JM, Bochkov V, Mihovilovic MD, Kopp B, Bauer R, Dirsch VM, Stuppner H. Discovery and resupply of pharmacologically active plant-derived natural products: A review. Biotechnol Adv 2015; 33:1582-1614. [PMID: 26281720 PMCID: PMC4748402 DOI: 10.1016/j.biotechadv.2015.08.001] [Citation(s) in RCA: 1310] [Impact Index Per Article: 145.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 07/16/2015] [Accepted: 08/07/2015] [Indexed: 01/01/2023]
Abstract
Medicinal plants have historically proven their value as a source of molecules with therapeutic potential, and nowadays still represent an important pool for the identification of novel drug leads. In the past decades, pharmaceutical industry focused mainly on libraries of synthetic compounds as drug discovery source. They are comparably easy to produce and resupply, and demonstrate good compatibility with established high throughput screening (HTS) platforms. However, at the same time there has been a declining trend in the number of new drugs reaching the market, raising renewed scientific interest in drug discovery from natural sources, despite of its known challenges. In this survey, a brief outline of historical development is provided together with a comprehensive overview of used approaches and recent developments relevant to plant-derived natural product drug discovery. Associated challenges and major strengths of natural product-based drug discovery are critically discussed. A snapshot of the advanced plant-derived natural products that are currently in actively recruiting clinical trials is also presented. Importantly, the transition of a natural compound from a "screening hit" through a "drug lead" to a "marketed drug" is associated with increasingly challenging demands for compound amount, which often cannot be met by re-isolation from the respective plant sources. In this regard, existing alternatives for resupply are also discussed, including different biotechnology approaches and total organic synthesis. While the intrinsic complexity of natural product-based drug discovery necessitates highly integrated interdisciplinary approaches, the reviewed scientific developments, recent technological advances, and research trends clearly indicate that natural products will be among the most important sources of new drugs also in the future.
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Affiliation(s)
- Atanas G. Atanasov
- Department of Pharmacognosy, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Birgit Waltenberger
- Institute of Pharmacy/Pharmacognosy and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Eva-Maria Pferschy-Wenzig
- Institute of Pharmaceutical Sciences, Department of Pharmacognosy, University of Graz, Universitätsplatz 4/I, 8010 Graz, Austria
| | - Thomas Linder
- Institute of Applied Synthetic Chemistry, Vienna University of Technology, Getreidemarkt 9/163-OC, 1060 Vienna, Austria
| | - Christoph Wawrosch
- Department of Pharmacognosy, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Pavel Uhrin
- Institute of Vascular Biology and Thrombosis Research, Center of Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - Veronika Temml
- Institute of Pharmacy/Pharmaceutical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Limei Wang
- Department of Pharmacognosy, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Stefan Schwaiger
- Institute of Pharmacy/Pharmacognosy and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Elke H. Heiss
- Department of Pharmacognosy, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Judith M. Rollinger
- Department of Pharmacognosy, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
- Institute of Pharmacy/Pharmacognosy and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Daniela Schuster
- Institute of Pharmacy/Pharmaceutical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Johannes M. Breuss
- Institute of Vascular Biology and Thrombosis Research, Center of Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - Valery Bochkov
- Institute of Pharmaceutical Sciences, Department of Pharmaceutical Chemistry, University of Graz, Humboldtstrasse 46/III, 8010 Graz, Austria
| | - Marko D. Mihovilovic
- Institute of Applied Synthetic Chemistry, Vienna University of Technology, Getreidemarkt 9/163-OC, 1060 Vienna, Austria
| | - Brigitte Kopp
- Department of Pharmacognosy, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Rudolf Bauer
- Institute of Pharmaceutical Sciences, Department of Pharmacognosy, University of Graz, Universitätsplatz 4/I, 8010 Graz, Austria
| | - Verena M. Dirsch
- Department of Pharmacognosy, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Hermann Stuppner
- Institute of Pharmacy/Pharmacognosy and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
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14
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Kwak JH, Park JY, Lee D, Kwak JY, Park EH, Kim KH, Park HJ, Kim HY, Jang HJ, Ham J, Hwang GS, Yamabe N, Kang KS. Inhibitory effects of ginseng sapogenins on the proliferation of triple negative breast cancer MDA-MB-231 cells. Bioorg Med Chem Lett 2015; 24:5409-12. [PMID: 25453798 DOI: 10.1016/j.bmcl.2014.10.041] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 10/01/2014] [Accepted: 10/14/2014] [Indexed: 11/17/2022]
Abstract
Because of poor prognosis, clinical treatment of triple-negative (TN) breast cancer remains the most challenging factor in cancer treatment. Extensive research into alternative cancer therapies includes studying the naturopathic effects of the medicinal herb ginseng. This study investigates the anti-neoplastic properties of ginseng sapogenins and the derivatives: (1) (20(S)-protopanaxadiol (PPD), (2) 20(S)-protopanaxatriol), (3) (20(S)-dihydroprotopanaxadiol, and (4) 20(S)-dihydroprotopanaxatriol). These compounds were found to prevent the proliferation of MDA-MB-231 human breast cancer cells. PPD was the most potent inhibitor, exhibiting an IC₅₀ (5.87 μM) comparable to that of the chemotherapeutic drug taxol. Furthermore, PPD induced dose-dependent cleavage of caspase-8, caspase-3, and PARP in MDA-MB-231 cells. Thus, we propose that PPD acts as anti-cancer agent by stimulating caspase-dependent apoptosis in breast cancer cells.
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Influence of Panax ginseng on Alpha-Adrenergic Receptor of Benign Prostatic Hyperplasia. Int Neurourol J 2014; 18:179-86. [PMID: 25558416 PMCID: PMC4280437 DOI: 10.5213/inj.2014.18.4.179] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 11/15/2014] [Indexed: 12/13/2022] Open
Abstract
Purpose Benign prostatic hyperplasia (BPH) is the most common prostate problem in older men. The present study aimed to investigate the inhibitory effect of Panax ginseng C.A. Meyer (P. ginseng) on a rat model of testosterone-induced BPH. Methods The rats were divided into 3 groups (each group, n=10): control, testosterone-induced BPH (20 mg/kg, subcutaneous injection), and P. ginseng (200 mg/kg, orally) groups. After 4 weeks, all animals were sacrificed to examine the blood biochemical profiles, prostate volume, weight, histopathological changes, alpha-1D adrenergic receptor (Adra1d) mRNA expression, and epidermal growth factor receptor (EGFR) and B-cell CLL/lymphoma 2 (BCL2) protein expression. Results The group treated with P. ginseng showed significantly lesser prostate size and weight than the testosterone-induced BPH group. In addition, P. ginseng decreased the mRNA expression of Adra1d as well as the expression of EGFR and BCL2 in prostate tissue. Conclusions These results suggest that P. ginseng may inhibit the alpha-1-adrenergic receptor to suppress the development of BPH.
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Siraj FM, Natarajan S, Huq MA, Kim YJ, Yang DC. Structural investigation of ginsenoside Rf with PPARγ major transcriptional factor of adipogenesis and its impact on adipocyte. J Ginseng Res 2014; 39:141-7. [PMID: 26045687 PMCID: PMC4452529 DOI: 10.1016/j.jgr.2014.10.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 10/14/2014] [Accepted: 10/16/2014] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Adipocytes, which are the main cellular component of adipose tissue, are the building blocks of obesity. The nuclear hormone receptor PPARγ is a major regulator of adipocyte differentiation and development. Obesity, which is one of the most dangerous yet silent diseases of all time, is fast becoming a critical area of research focus. METHODS In this study, we initially aimed to investigate whether the ginsenoside Rf, a compound that is only present in Panax ginseng Meyer, interacts with PPARγ by molecular docking simulations. After we performed the docking simulation the result has been analyzed with several different software programs, including Discovery Studio, Pymol, Chimera, Ligplus, and Pose View. All of the programs identified the same mechanism of interaction between PPARγ and Rf, at the same active site. To determine the drug-like and biological activities of Rf, we calculate its absorption, distribution, metabolism, excretion, and toxic (ADMET) and prediction of activity spectra for substances (PASS) properties. Considering the results obtained from the computational investigations, the focus was on the in vitro experiments. RESULTS Because the docking simulations predicted the formation of structural bonds between Rf and PPARγ, we also investigated whether any evidence for these bonds could be observed at the cellular level. These experiments revealed that Rf treatment of 3T3-L1 adipocytes downregulated the expression levels of PPARγ and perilipin, and also decreased the amount of lipid accumulated at different doses. CONCLUSION The ginsenoside Rf appears to be promising compound that could prove useful in antiobesity treatments.
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Affiliation(s)
- Fayeza Md Siraj
- Ginseng Genetic Resource Bank, Graduate School of Biotechnology, College of Life Science, Kyung Hee University, Korea
| | - Sathishkumar Natarajan
- Ginseng Genetic Resource Bank, Graduate School of Biotechnology, College of Life Science, Kyung Hee University, Korea
| | - Md Amdadul Huq
- Ginseng Genetic Resource Bank, Graduate School of Biotechnology, College of Life Science, Kyung Hee University, Korea
| | - Yeon Ju Kim
- Ginseng Genetic Resource Bank, Graduate School of Biotechnology, College of Life Science, Kyung Hee University, Korea
| | - Deok Chun Yang
- Ginseng Genetic Resource Bank, Graduate School of Biotechnology, College of Life Science, Kyung Hee University, Korea
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Siraj FM, Natarajan S, Kim YJ, Chun Yang D. In silicoscreening of ginsenoside Rh1 with PPARγ andin vitroanalysis on 3T3-L1 cell line. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.970188] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Shrestha S, Natarajan S, Park JH, Lee DY, Cho JG, Kim GS, Jeon YJ, Yeon SW, Yang DC, Baek NI. Potential neuroprotective flavonoid-based inhibitors of CDK5/p25 from Rhus parviflora. Bioorg Med Chem Lett 2013; 23:5150-4. [PMID: 23927974 DOI: 10.1016/j.bmcl.2013.07.020] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 06/24/2013] [Accepted: 07/12/2013] [Indexed: 12/18/2022]
Abstract
Rhus parviflora (Anacardiaceae) is an indigenous medicinal shrub found in South Asia with flavonoid rich edible fruit. This study examined flavonoid derivatives of R. parviflora fruit with CDK5/p25 inhibition activity. Evaluation by in vitro assay and docking simulations for CDK5/p25 revealed that the aurones, sulfuretin (1) and aureusidin (2), the aurone glycoside, aureusidin-6-O-β-D-glucopyranoside (3) and hovetrichoside C (4), the flavonoid glycoside, quercetin-3-O-β-D-galactopyranoside (5), and the biflavonoid, cupressuflavone (6), had the potential to inhibit CDK5/p25, which could be useful in the treatment of neurodegenerative disorders such as Alzheimer's disease. Compound2 showed the significant in vitro inhibition capacity (IC50 value of 4.81 μM) as well as binding affinity with docking energy of -8.73 (kcal/mol) for active sites CYS83 and GLN130 of CDK5/p25 enzyme in comparison to reference compound R-roscovitine.
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Affiliation(s)
- Sabina Shrestha
- Graduate School of Biotechnology, Institute of Life Sciences and Resources, Kyung Hee University, Yongin 446-701, Republic of Korea
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Karpagam V, Sathishkumar N, Sathiyamoorthy S, Rasappan P, Shila S, Kim YJ, Yang DC. Identification of BACE1 inhibitors from Panax ginseng saponins-An Insilco approach. Comput Biol Med 2013; 43:1037-44. [PMID: 23816176 DOI: 10.1016/j.compbiomed.2013.05.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Revised: 05/07/2013] [Accepted: 05/14/2013] [Indexed: 01/08/2023]
Abstract
BACE1, a β secretase candidate enzyme, initiates the Alzheimer's disease (AD) pathogenesis via amyloid β (Aβ) peptide production serving as a potential therapeutic target. Previous experimental evidence suggested that ginsenosides, a key component of Panax ginseng, are effective against AD. In this study, we implemented a molecular modeling method to reveal the inhibitory action of ginsenosides on BACE1 activity. We selected 12 ginsenosides and performed molecular docking studies to evaluate its interaction with the BACE1 active site, which is essential for inhibition. Further ADMET filtration was applied to find drug-like molecules with a specific ability to cross blood brain barrier (BBB), and to determine toxicity. The BACE1-ginsenosides complex was further subjected to a molecular dynamics simulation to study the stability of the complex and its hydrogen bond interactions. In summary, our findings show ginsenosides CK, F1, Rh1 and Rh2 are potential BACE1 inhibitors from Panax ginseng.
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Affiliation(s)
- Veerappan Karpagam
- Department of Biochemistry, VRR Institute of Biomedical Science, Chennai-600056, Tamilnadu, India.
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