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Pasha MH, Gondal HY, Munir S, Alhussain SA, Zaki MEA. New enantioenriched β-indolyl ketones as aromatase inhibitors: Unraveling heme-ligand interactions by MD simulation and MMPBSA analysis. Arch Pharm (Weinheim) 2024; 357:e2400010. [PMID: 38578079 DOI: 10.1002/ardp.202400010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/09/2024] [Accepted: 03/11/2024] [Indexed: 04/06/2024]
Abstract
A series of enantioenriched β-indolyl ketones as aromatase inhibitors (AI) is synthesized through the Michael-type Friedel-Crafts alkylation of indole. A highly efficient bifunctionalized amino catalyst is developed to access structurally diverse β-indolyl ketones in high yields (up to 91%) and excellent enantioselectivity (enantiomeric ratio up to 98:2). All the synthesized compounds demonstrated promising aromatase inhibitory potential, where ortho-substituted analogs (3c and 3e) were found most active with IC50 values of 0.68 and 0.90 µM, respectively. Both of these compounds exhibited significant cytotoxicity (IC50 = 0.34 and 0.37 µM) against the MCF-7 breast cancer cell line in the (3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyl tetrazolium bromide) assay. Molecular docking studies of the synthesized compounds demonstrate favorable binding interactions with the estrogens controlling CYP19A1 (3EQM) and metabolizing CYP3A4 (5VCC) enzymes. Molecular dynamic (MD) simulation analysis revealed the essentiality of heme-ligand interactions to build a stable protein-ligand complex. An average root mean square deviation of 0.35 nm observed during a 100-ns MD simulation and binding free energy in the range of -190 to -227 kJ/mol calculated by g_mmpbsa analysis authenticated the stability of the 3c-3EQM complex. ADMET and drug-likeness parameters supported the suitability of these indole derivatives as the drug lead to develop potent inhibitors for estrogen-dependent breast cancer.
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Affiliation(s)
- Maira Hasnain Pasha
- Institute of Chemistry, Faculty of Science, University of Sargodha, Sargodha, Pakistan
| | | | - Shanza Munir
- Institute of Chemistry, Faculty of Science, University of Sargodha, Sargodha, Pakistan
| | - Sami A Alhussain
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Magdi E A Zaki
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
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2
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Hajirahimkhan A, Howell C, Bartom ET, Dong H, Lantvit DD, Xuei X, Chen SN, Pauli GF, Bolton JL, Clare SE, Khan SA, Dietz BM. Breast cancer prevention with liquiritigenin from licorice through the inhibition of aromatase and protein biosynthesis in high-risk women's breast tissue. Sci Rep 2023; 13:8734. [PMID: 37253812 PMCID: PMC10229614 DOI: 10.1038/s41598-023-34762-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 05/07/2023] [Indexed: 06/01/2023] Open
Abstract
Breast cancer risk continues to increase post menopause. Anti-estrogen therapies are available to prevent postmenopausal breast cancer in high-risk women. However, their adverse effects have reduced acceptability and overall success in cancer prevention. Natural products such as hops (Humulus lupulus) and three pharmacopeial licorice (Glycyrrhiza) species have demonstrated estrogenic and chemopreventive properties, but little is known regarding their effects on aromatase expression and activity as well as pro-proliferation pathways in human breast tissue. We show that Gycyrrhiza inflata (GI) has the highest aromatase inhibition potency among these plant extracts. Moreover, phytoestrogens such as liquiritigenin which is common in all licorice species have potent aromatase inhibitory activity, which is further supported by computational docking of their structures in the binding pocket of aromatase. In addition, GI extract and liquiritigenin suppress aromatase expression in the breast tissue of high-risk postmenopausal women. Although liquiritigenin has estrogenic effects in vitro, with preferential activity through estrogen receptor (ER)-β, it reduces estradiol-induced uterine growth in vivo. It downregulates RNA translation, protein biosynthesis, and metabolism in high-risk women's breast tissue. Finally, it reduces the rate of MCF-7 cell proliferation, with repeated dosing. Collectively, these data suggest that liquiritigenin has breast cancer prevention potential for high-risk postmenopausal women.
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Affiliation(s)
- Atieh Hajirahimkhan
- Division of Breast Surgery, Department of Surgery, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, 303 E. Superior, 4-220, Chicago, IL, 60611, USA.
| | - Caitlin Howell
- Department of Physiology and Biophysics, College of Medicine, University of Illinois Chicago, Chicago, IL, USA
| | - Elizabeth T Bartom
- Department of Biochemistry and Molecular Genetics, The Louis A. Simpson and Kimberly K. Querrey Biomedical Research Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Huali Dong
- University of Illinois Cancer Center, College of Medicine, University of Illinois Chicago, Chicago, IL, USA
| | - Daniel D Lantvit
- UIC Center for Botanical Dietary Supplements Research, Pharmacognosy Institute and Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, IL, USA
| | - Xiaoling Xuei
- Department of Medical and Molecular Genetics, College of Medicine, Indiana University, Indianapolis, IN, USA
| | - Shao-Nong Chen
- UIC Center for Botanical Dietary Supplements Research, Pharmacognosy Institute and Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, IL, USA
| | - Guido F Pauli
- UIC Center for Botanical Dietary Supplements Research, Pharmacognosy Institute and Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, IL, USA
| | - Judy L Bolton
- UIC Center for Botanical Dietary Supplements Research, Pharmacognosy Institute and Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, IL, USA
| | - Susan E Clare
- Division of Breast Surgery, Department of Surgery, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, 303 E. Superior, 4-220, Chicago, IL, 60611, USA
| | - Seema A Khan
- Division of Breast Surgery, Department of Surgery, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, 303 E. Superior, 4-220, Chicago, IL, 60611, USA
| | - Birgit M Dietz
- UIC Center for Botanical Dietary Supplements Research, Pharmacognosy Institute and Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, IL, USA
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3
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Leechaisit R, Pingaew R, Prachayasittikul V, Worachartcheewan A, Prachayasittikul S, Ruchirawat S, Prachayasittikul V. Synthesis, molecular docking, and QSAR study of bis-sulfonamide derivatives as potential aromatase inhibitors. Bioorg Med Chem 2019; 27:115040. [DOI: 10.1016/j.bmc.2019.08.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/30/2019] [Accepted: 08/01/2019] [Indexed: 01/03/2023]
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4
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Shoombuatong W, Schaduangrat N, Nantasenamat C. Towards understanding aromatase inhibitory activity via QSAR modeling. EXCLI JOURNAL 2018; 17:688-708. [PMID: 30190660 PMCID: PMC6123608 DOI: 10.17179/excli2018-1417] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 07/10/2018] [Indexed: 12/14/2022]
Abstract
Aromatase is a rate-limiting enzyme for estrogen biosynthesis that is overproduced in breast cancer tissue. To block the growth of breast tumors, aromatase inhibitors (AIs) are employed to bind and inhibit aromatase in order to lower the amount of estrogen produced in the body. Although a number of synthetic aromatase inhibitors have been released for clinical use in the treatment of hormone-receptor positive breast cancer, these inhibitors may lead to undesirable side effects (e.g. increased rash, diarrhea and vomiting; effects on the bone, brain and heart) and therefore, the search for novel AIs continues. Over the past decades, there has been an intense effort in employing medicinal chemistry and quantitative structure-activity relationship (QSAR) to shed light on the mechanistic basis of aromatase inhibition. To the best of our knowledge, this article constitutes the first comprehensive review of all QSAR studies of both steroidal and non-steroidal AIs that have been published in the field. Herein, we summarize the experimental setup of these studies as well as summarizing the key features that are pertinent for robust aromatase inhibition.
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Affiliation(s)
- Watshara Shoombuatong
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | - Nalini Schaduangrat
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | - Chanin Nantasenamat
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
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5
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Favia AD, Nicolotti O, Stefanachi A, Leonetti F, Carotti A. Computational methods for the design of potent aromatase inhibitors. Expert Opin Drug Discov 2013; 8:395-409. [DOI: 10.1517/17460441.2013.768983] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Angelo Danilo Favia
- Dipartimento di Farmacia, Università degli Studi di Bari “Aldo Moro”,
via Orabona 4, I-70125 Bari, Italy ;
- Lilly China R&D Center,
Building 8, 338 Jia Li Lue Road Zhangjiang Hi-Tech Park Pudong, 201203, Shanghai, China
| | - Orazio Nicolotti
- Dipartimento di Farmacia, Università degli Studi di Bari “Aldo Moro”,
via Orabona 4, I-70125 Bari, Italy ;
| | - Angela Stefanachi
- Dipartimento di Farmacia, Università degli Studi di Bari “Aldo Moro”,
via Orabona 4, I-70125 Bari, Italy ;
| | - Francesco Leonetti
- Dipartimento di Farmacia, Università degli Studi di Bari “Aldo Moro”,
via Orabona 4, I-70125 Bari, Italy ;
| | - Angelo Carotti
- Dipartimento di Farmacia, Università degli Studi di Bari “Aldo Moro”,
via Orabona 4, I-70125 Bari, Italy ;
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Sgrignani J, Magistrato A. Influence of the Membrane Lipophilic Environment on the Structure and on the Substrate Access/Egress Routes of the Human Aromatase Enzyme. A Computational Study. J Chem Inf Model 2012; 52:1595-606. [DOI: 10.1021/ci300151h] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Jacopo Sgrignani
- CNR-IOM-Democritos National Simulation Center c/o International Studies for Advanced Studies (SISSA/ISAS), via Bonomea 265, 34165 Trieste
(TS), Italy
| | - Alessandra Magistrato
- CNR-IOM-Democritos National Simulation Center c/o International Studies for Advanced Studies (SISSA/ISAS), via Bonomea 265, 34165 Trieste
(TS), Italy
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Abstract
Aromatase is an enzyme that plays a critical role in the development of estrogen receptor positive breast cancer. As aromatase catalyzes the aromatization of androstenedione to estrone, a naturally occurring estrogen, it is a promising drug target for therapeutic management. The undesirable effects found in aromatase inhibitors (AIs) that are in clinical use necessitate the discovery of novel AIs with higher selectivity, less toxicity and improving potency. In this study, we elucidate the binding mode of all three generations of AI drugs to the crystal structure of aromatase by means of molecular docking. It was demonstrated that the docking protocol could reliably reproduce the interaction of aromatase with its substrate with an RMSD of 1.350 Å. The docking study revealed that polar (D309, T310, S478 and M374), aromatic (F134, F221 and W224) and non-polar (A306, A307, V370, L372 and L477) residues were important for interacting with the AIs. The insights gained from the study herein have great potential for the design of novel AIs.
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Pharmacophore modeling strategies for the development of novel nonsteroidal inhibitors of human aromatase (CYP19). Bioorg Med Chem Lett 2010; 20:3050-64. [DOI: 10.1016/j.bmcl.2010.03.113] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2009] [Revised: 03/27/2010] [Accepted: 03/31/2010] [Indexed: 12/17/2022]
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9
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Neves MAC, Dinis TCP, Colombo G, Sá e Melo ML. Fast Three Dimensional Pharmacophore Virtual Screening of New Potent Non-Steroid Aromatase Inhibitors. J Med Chem 2008; 52:143-50. [DOI: 10.1021/jm800945c] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marco A. C. Neves
- Centro de Estudos Farmacêuticos, Laboratório de Química Farmacêutica, Faculdade de Farmácia, Universidade de Coimbra, 3000-295, Coimbra, Portugal, Centro de Neurociências, Laboratório de Bioquímica, Faculdade de Farmácia, Universidade de Coimbra, 3000-295, Coimbra, Portugal, and Istituto di Chimica del Riconoscimento Molecolare, CNR, 20131, Milano, Italy
| | - Teresa C. P. Dinis
- Centro de Estudos Farmacêuticos, Laboratório de Química Farmacêutica, Faculdade de Farmácia, Universidade de Coimbra, 3000-295, Coimbra, Portugal, Centro de Neurociências, Laboratório de Bioquímica, Faculdade de Farmácia, Universidade de Coimbra, 3000-295, Coimbra, Portugal, and Istituto di Chimica del Riconoscimento Molecolare, CNR, 20131, Milano, Italy
| | - Giorgio Colombo
- Centro de Estudos Farmacêuticos, Laboratório de Química Farmacêutica, Faculdade de Farmácia, Universidade de Coimbra, 3000-295, Coimbra, Portugal, Centro de Neurociências, Laboratório de Bioquímica, Faculdade de Farmácia, Universidade de Coimbra, 3000-295, Coimbra, Portugal, and Istituto di Chimica del Riconoscimento Molecolare, CNR, 20131, Milano, Italy
| | - M. Luisa Sá e Melo
- Centro de Estudos Farmacêuticos, Laboratório de Química Farmacêutica, Faculdade de Farmácia, Universidade de Coimbra, 3000-295, Coimbra, Portugal, Centro de Neurociências, Laboratório de Bioquímica, Faculdade de Farmácia, Universidade de Coimbra, 3000-295, Coimbra, Portugal, and Istituto di Chimica del Riconoscimento Molecolare, CNR, 20131, Milano, Italy
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Karkola S, Lilienkampf A, Wähälä K. A 3D QSAR model of 17beta-HSD1 inhibitors based on a thieno[2,3-d]pyrimidin-4(3H)-one core applying molecular dynamics simulations and ligand-protein docking. ChemMedChem 2008; 3:461-72. [PMID: 18224704 DOI: 10.1002/cmdc.200700271] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The 17beta-hydroxysteroid dehydrogenase type 1 (17beta-HSD1) enzyme plays a crucial role in female hormonal regulation by catalysing the NADPH-dependent reduction of the less potent estrone E1 into the biologically active estradiol E2. Because 17beta-HSD1 is a key enzyme in E2 biosynthesis, it has emerged as an attractive drug target for inhibitor development. Herein we report the plausible binding modes and a 3D QSAR model of 17beta-HSD1 inhibitors based on a (di)cycloalkenothieno[2,3-d]pyrimidin-4(3H)-one core. Two generated enzyme complexes with potent inhibitors were subjected to molecular dynamics simulation to mimic the dynamic process of inhibitor binding. A set of 17beta-HSD1 inhibitors based on the thieno[2,3-d]pyrimidin-4(3H)-one core were docked into the resulting active site, and a CoMFA model employing the most extensive training set to date was generated. The model was validated with an external test set. Active site residues involved in inhibitor binding and CoMFA fields for steric and electrostatic interactions were identified. The model will be used to guide structural modifications of 17beta-HSD1 inhibitors based on a thieno[2,3-d]pyrimidin-4(3H)-one core in order to improve the biological activity as well as in the design of novel 17beta-HSD1 inhibitors.
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Affiliation(s)
- Sampo Karkola
- Laboratory of Organic Chemistry, Department of Chemistry, University of Helsinki, PO Box 55, 00014 Helsinki, Finland
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Karkola S, Höltje HD, Wähälä K. A three-dimensional model of CYP19 aromatase for structure-based drug design. J Steroid Biochem Mol Biol 2007; 105:63-70. [PMID: 17583493 DOI: 10.1016/j.jsbmb.2006.11.023] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2006] [Accepted: 11/15/2006] [Indexed: 10/23/2022]
Abstract
Aromatase (CYP450(arom), CYP19) is an enzyme responsible for converting the aliphatic androgens androstenedione and testosterone to the aromatic estrogens estrone and estradiol, respectively. These endogenous hormones are a key factor in cancer tumor formation and proliferation through a cascade starting from estrogen binding to estrogen receptor. To interfere with the overproduction of estrogens especially in tumor tissue, it is possible to inhibit aromatase activity. This can be achieved using aromatase inhibitors. In order to design novel aromatase inhibitors, it is necessary to have an understanding of the active site of aromatase. As no crystal structure of the enzyme has yet been published, we built a homology model of aromatase using the first crystallized mammalian cytochrome enzyme, rabbit 21-progesterone hydroxylase 2C5, as a template structure. The initial model was validated with exhaustive molecular dynamics simulation with and without the natural substrate androstenedione. The resulting enzyme-substrate complex shows very good stability and only two of the residues are in disallowed regions in a Ramachandran plot.
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Affiliation(s)
- Sampo Karkola
- Laboratory of Organic Chemistry, Department of Chemistry, Faculty of Science, P.O. Box 55, University of Helsinki, FIN-00014, Finland
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Abstract
The discipline of molecular biology has become increasingly important in recent times for the process of drug discovery. We describe the impact of molecular biology across the whole process of drug discovery and development, including (i) the identification and validation of new drug targets, (ii) the development of molecular screens to find new candidate drugs, and (iii) the generation of safety data and competences leading to enhanced clinical efficacy. We also speculate on emerging developments in drug discovery where it seems likely that molecular biology will play an even more vital role in the generation of future therapies.
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