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Coumarins as Tool Compounds to Aid the Discovery of Selective Function Modulators of Steroid Hormone Binding Proteins. MOLECULES (BASEL, SWITZERLAND) 2021; 26:molecules26175142. [PMID: 34500576 PMCID: PMC8433903 DOI: 10.3390/molecules26175142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/17/2021] [Accepted: 08/23/2021] [Indexed: 11/20/2022]
Abstract
Steroid hormones play an essential role in a wide variety of actions in the body, such as in metabolism, inflammation, initiating and maintaining sexual differentiation and reproduction, immune functions, and stress response. Androgen, aromatase, and sulfatase pathway enzymes and nuclear receptors are responsible for steroid biosynthesis and sensing steroid hormones. Changes in steroid homeostasis are associated with many endocrine diseases. Thus, the discovery and development of novel drug candidates require a detailed understanding of the small molecule structure–activity relationship with enzymes and receptors participating in steroid hormone synthesis, signaling, and metabolism. Here, we show that simple coumarin derivatives can be employed to build cost-efficiently a set of molecules that derive essential features that enable easy discovery of selective and high-affinity molecules to target proteins. In addition, these compounds are also potent tool molecules to study the metabolism of any small molecule.
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Niinivehmas S, Postila PA, Rauhamäki S, Manivannan E, Kortet S, Ahinko M, Huuskonen P, Nyberg N, Koskimies P, Lätti S, Multamäki E, Juvonen RO, Raunio H, Pasanen M, Huuskonen J, Pentikäinen OT. Blocking oestradiol synthesis pathways with potent and selective coumarin derivatives. J Enzyme Inhib Med Chem 2018; 33:743-754. [PMID: 29620427 PMCID: PMC6010071 DOI: 10.1080/14756366.2018.1452919] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A comprehensive set of 3-phenylcoumarin analogues with polar substituents was synthesised for blocking oestradiol synthesis by 17-β-hydroxysteroid dehydrogenase 1 (HSD1) in the latter part of the sulphatase pathway. Five analogues produced ≥62% HSD1 inhibition at 5 µM and, furthermore, three of them produced ≥68% inhibition at 1 µM. A docking-based structure-activity relationship analysis was done to determine the molecular basis of the inhibition and the cross-reactivity of the analogues was tested against oestrogen receptor, aromatase, cytochrome P450 1A2, and monoamine oxidases. Most of the analogues are only modestly active with 17-β-hydroxysteroid dehydrogenase 2 – a requirement for lowering effective oestradiol levels in vivo. Moreover, the analysis led to the synthesis and discovery of 3-imidazolecoumarin as a potent aromatase inhibitor. In short, coumarin core can be tailored with specific ring and polar moiety substitutions to block either the sulphatase pathway or the aromatase pathway for treating breast cancer and endometriosis.
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Affiliation(s)
- Sanna Niinivehmas
- a Department of Biological and Environmental Science and Nanoscience Center , University of Jyvaskyla , Jyvaskyla , Finland
| | - Pekka A Postila
- a Department of Biological and Environmental Science and Nanoscience Center , University of Jyvaskyla , Jyvaskyla , Finland
| | - Sanna Rauhamäki
- a Department of Biological and Environmental Science and Nanoscience Center , University of Jyvaskyla , Jyvaskyla , Finland
| | - Elangovan Manivannan
- a Department of Biological and Environmental Science and Nanoscience Center , University of Jyvaskyla , Jyvaskyla , Finland.,b School of Pharmacy , Devi Ahilya University , Indore , India
| | - Sami Kortet
- a Department of Biological and Environmental Science and Nanoscience Center , University of Jyvaskyla , Jyvaskyla , Finland.,c Department of Chemistry and Nanoscience Center , University of Jyvaskyla , Jyvaskyla , Finland
| | - Mira Ahinko
- a Department of Biological and Environmental Science and Nanoscience Center , University of Jyvaskyla , Jyvaskyla , Finland
| | - Pasi Huuskonen
- d School of Pharmacy , University of Eastern Finland , Kuopio , Finland
| | - Niina Nyberg
- d School of Pharmacy , University of Eastern Finland , Kuopio , Finland
| | | | - Sakari Lätti
- a Department of Biological and Environmental Science and Nanoscience Center , University of Jyvaskyla , Jyvaskyla , Finland
| | - Elina Multamäki
- a Department of Biological and Environmental Science and Nanoscience Center , University of Jyvaskyla , Jyvaskyla , Finland
| | - Risto O Juvonen
- d School of Pharmacy , University of Eastern Finland , Kuopio , Finland
| | - Hannu Raunio
- d School of Pharmacy , University of Eastern Finland , Kuopio , Finland
| | - Markku Pasanen
- d School of Pharmacy , University of Eastern Finland , Kuopio , Finland
| | - Juhani Huuskonen
- c Department of Chemistry and Nanoscience Center , University of Jyvaskyla , Jyvaskyla , Finland
| | - Olli T Pentikäinen
- a Department of Biological and Environmental Science and Nanoscience Center , University of Jyvaskyla , Jyvaskyla , Finland.,f Institute of Biomedicine, University of Turku , Turku , Finland
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Bruno S, Uliassi E, Zaffagnini M, Prati F, Bergamini C, Amorati R, Paredi G, Margiotta M, Conti P, Costi MP, Kaiser M, Cavalli A, Fato R, Bolognesi ML. Molecular basis for covalent inhibition of glyceraldehyde-3-phosphate dehydrogenase by a 2-phenoxy-1,4-naphthoquinone small molecule. Chem Biol Drug Des 2017; 90:225-235. [DOI: 10.1111/cbdd.12941] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 01/05/2017] [Accepted: 01/05/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Stefano Bruno
- Department of Pharmacy; University of Parma; Parma Italy
| | - Elisa Uliassi
- Department of Pharmacy and Biotechnology; Alma Mater Studiorum - University of Bologna; Bologna Italy
| | - Mirko Zaffagnini
- Department of Pharmacy and Biotechnology; Alma Mater Studiorum - University of Bologna; Bologna Italy
| | - Federica Prati
- Department of Pharmacy and Biotechnology; Alma Mater Studiorum - University of Bologna; Bologna Italy
| | - Christian Bergamini
- Department of Pharmacy and Biotechnology; Alma Mater Studiorum - University of Bologna; Bologna Italy
| | - Riccardo Amorati
- Department of Chemistry “G. Ciamician”; Alma Mater Studiorum - University of Bologna; Bologna Italy
| | | | | | - Paola Conti
- Department of Pharmaceutical Sciences; University of Milan; Milan Italy
| | - Maria Paola Costi
- Department of Life Sciences; University of Modena and Reggio Emilia; Modena Italy
| | - Marcel Kaiser
- Swiss Tropical & Public Health Institute; Basel Switzerland
- University of Basel; Basel Switzerland
| | - Andrea Cavalli
- Department of Pharmacy and Biotechnology; Alma Mater Studiorum - University of Bologna; Bologna Italy
- CompuNet; Istituto Italiano di Tecnologia; Genova Italy
| | - Romana Fato
- Department of Pharmacy and Biotechnology; Alma Mater Studiorum - University of Bologna; Bologna Italy
| | - Maria Laura Bolognesi
- Department of Pharmacy and Biotechnology; Alma Mater Studiorum - University of Bologna; Bologna Italy
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Santoro AL, Carrilho E, Lanças FM, Montanari CA. Quantitative structure–retention relationships of flavonoids unraveled by immobilized artificial membrane chromatography. Eur J Pharm Sci 2016; 88:147-57. [DOI: 10.1016/j.ejps.2015.12.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 11/09/2015] [Accepted: 12/06/2015] [Indexed: 01/27/2023]
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In silico target fishing and pharmacological profiling for the isoquinoline alkaloids of Macleaya cordata (Bo Luo Hui). Chin Med 2015; 10:37. [PMID: 26691584 PMCID: PMC4683977 DOI: 10.1186/s13020-015-0067-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 11/10/2015] [Indexed: 01/01/2023] Open
Abstract
Background Some isoquinoline alkaloids from Macleaya cordata (Willd). R. Br. (Bo Luo Hui) exhibited antibacterial, antiparasitic, antitumor, and analgesic effects. The targets of these isoquinoline alkaloids are undefined. This study aims to investigate the compound–target interaction network and potential pharmacological actions of isoquinoline alkaloids of M. cordata by reverse pharmacophore database screening. Methods The targets of 26 isoquinoline alkaloids identified from M. cordata were predicted by a pharmacophore-based target fishing approach. Discovery Studio 3.5 and two pharmacophore databases (PharmaDB and HypoDB) were employed for the target profiling. A compound–target interaction network of M. cordata was constructed and analyzed by Cytoscape 3.0. Results Thirteen of the 65 predicted targets identified by PharmaDB were confirmed as targets by HypoDB screening. The targets in the interaction network of M. cordata were involved in cancer (31 targets), microorganisms (12 targets), neurodegeneration (10 targets), inflammation and autoimmunity (8 targets), parasitosis (5 targets), injury (4 targets), and pain (3 targets). Dihydrochelerythrine (C6) was found to hit 23 fitting targets. Macrophage migration inhibitory factor (MIF) hits 15 alkaloids (C1–2, C11–16, C19–25) was the most promising target related to cancer. Conclusion Through in silico target fishing, the anticancer, anti-inflammatory, and analgesic effects of M. cordata were the most significant among many possible activities. The possible anticancer effects were mainly contributed by the isoquinoline alkaloids as active components.
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A pharmacophore-based virtual screening approach for the discovery of Trypanosoma cruzi GAPDH inhibitors. Future Med Chem 2014; 5:2019-35. [PMID: 24215344 DOI: 10.4155/fmc.13.166] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Chagas disease is a major cause of morbidity and death for millions of people in Latin America. The drugs currently available exhibit poor efficacy and severe side effects. Therefore, there is an urgent need for new, safe and effective drugs against Chagas disease. The vital dependence on glycolysis as energy source makes the glycolytic enzymes of Trypanosoma cruzi, the causative agent of Chagas disease, attractive targets for drug design. In this work, glyceraldehyde-3-phosphate dehydrogenase from T. cruzi (TcGAPDH) was employed as molecular target for the discovery of new inhibitors as hits. RESULTS Integrated protein-based pharmacophore and structure-based virtual screening approaches resulted in the identification of three hits from three chemical classes with moderate inhibitory activity against TcGAPDH. The inhibitors showed IC50 values in the high micromolar range. CONCLUSION The new chemotypes are attractive molecules for future medicinal chemistry efforts aimed at developing new lead compounds for Chagas disease.
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Synthesis and evaluation of antioxidant and trypanocidal properties of a selected series of coumarin derivatives. Future Med Chem 2014; 5:1911-22. [PMID: 24175743 DOI: 10.4155/fmc.13.147] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
This article describes the preparation and characterization of a selected series of coumarin derivatives with the aim of evaluating their antioxidant properties and their activity against Trypanosoma cruzi, the parasite responsible for Chagas disease. All the derivatives demonstrated moderate trypanocidal activity in the epimastigote and trypomastigote stages (clone Dm28c), with Compound 3 presenting the highest trypanocidal activity of the entire series, displaying higher activity than nifurtimox, which was used as a reference compound. In addition to the trypanocidal activity, this compound proved to have a very interesting antioxidant profile, as well as no cytotoxicity. These preliminary findings encouraged the authors to study the future structural optimization of this scaffold.
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Soares FA, Sesti-Costa R, da Silva JS, de Souza MCB, Ferreira VF, da C. Santos F, Monteiro PA, Leitão A, Montanari CA. Molecular design, synthesis and biological evaluation of 1,4-dihydro-4-oxoquinoline ribonucleosides as TcGAPDH inhibitors with trypanocidal activity. Bioorg Med Chem Lett 2013; 23:4597-601. [DOI: 10.1016/j.bmcl.2013.06.029] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 06/05/2013] [Accepted: 06/11/2013] [Indexed: 10/26/2022]
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de Oliveira OV, dos Santos JD, Freitas LC. Molecular dynamics simulation of the gGAPDH–NAD+complex fromTrypanosoma cruzi. MOLECULAR SIMULATION 2012. [DOI: 10.1080/08927022.2012.696112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Sahoo GC, Dikhit MR, Rani M, Ansari MY, Jha C, Rana S, Das P. Analysis of sequence, structure of GAPDH of Leishmania donovani and its interactions. J Biomol Struct Dyn 2012; 31:258-75. [PMID: 22830998 DOI: 10.1080/07391102.2012.698189] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Drug resistance acquired by Leishmania donovani (Ldv) is a major problem in the treatment and control of visceral leishmaniasis (VL). Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), a major glycolytic enzyme has been targeted as is found in other protozoan which cause diseases like sleeping sickness. GAPDH gene of Ldv (AG83 strain) was amplified, sequenced, and modeled on the basis of crystal structure of Leishmania mexicana. The model of the Ldv GAPDH exhibited NAD-binding domain with Rossmann folding. Virtual screening of different experimentally proved compounds with the crystal and the modeled structures of GAPDH of Leishmania strains revealed diverse binding affinities of different compounds. Comparison of binding affinities (based on different programs) of compounds revealed that discovery studio v2.5 (Ligandfit) was able to predict the most hit compounds, the best hit compounds against GAPDH of Leishmania strains are hydrazine, vetrazine, and benzyl carbazate. It is predicted that patients suffering from both VL and cardiac disorders (atrial fibrillation) may benefit if they are treated with warfarin in conjunction with first-line antileishmanial therapies such as miltefosine and AmBisome.
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Affiliation(s)
- Ganesh Chandra Sahoo
- BioMedical Informatics Center, Rajendra Memorial Research Institute of Medical Sciences, Agam Kuan, 800007 Patna, India.
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Dixit SS, Upadhayaya RS, Chattopadhyaya J. New parasite inhibitors encompassing novel conformationally-locked 5′-acyl sulfamoyl adenosines. Org Biomol Chem 2012; 10:6121-9. [DOI: 10.1039/c2ob25879j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Freitas RF, Prokopczyk IM, Zottis A, Oliva G, Andricopulo AD, Trevisan MTS, Vilegas W, Silva MGV, Montanari CA. Discovery of novel Trypanosoma cruzi glyceraldehyde-3-phosphate dehydrogenase inhibitors. Bioorg Med Chem 2009; 17:2476-82. [DOI: 10.1016/j.bmc.2009.01.079] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Revised: 01/28/2009] [Accepted: 01/30/2009] [Indexed: 11/16/2022]
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Guido R, Castilho M, Mota S, Oliva G, Andricopulo A. Classical and Hologram QSAR Studies on a Series of Inhibitors of Trypanosomatid Glyceraldehyde‐3‐Phosphate Dehydrogenase. ACTA ACUST UNITED AC 2008. [DOI: 10.1002/qsar.200710139] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Moda TL, Montanari CA, Andricopulo AD. Hologram QSAR model for the prediction of human oral bioavailability. Bioorg Med Chem 2007; 15:7738-45. [PMID: 17870541 DOI: 10.1016/j.bmc.2007.08.060] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2007] [Revised: 08/22/2007] [Accepted: 08/28/2007] [Indexed: 11/20/2022]
Abstract
A drug intended for use in humans should have an ideal balance of pharmacokinetics and safety, as well as potency and selectivity. Unfavorable pharmacokinetics can negatively affect the clinical development of many otherwise promising drug candidates. A variety of in silico ADME (absorption, distribution, metabolism, and excretion) models are receiving increased attention due to a better appreciation that pharmacokinetic properties should be considered in early phases of the drug discovery process. Human oral bioavailability is an important pharmacokinetic property, which is directly related to the amount of drug available in the systemic circulation to exert pharmacological and therapeutic effects. In the present work, hologram quantitative structure-activity relationships (HQSAR) were performed on a training set of 250 structurally diverse molecules with known human oral bioavailability. The most significant HQSAR model (q(2)=0.70, r(2)=0.93) was obtained using atoms, bond, connection, and chirality as fragment distinction. The predictive ability of the model was evaluated by an external test set containing 52 molecules not included in the training set, and the predicted values were in good agreement with the experimental values. The HQSAR model should be useful for the design of new drug candidates having increased bioavailability as well as in the process of chemical library design, virtual screening, and high-throughput screening.
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Affiliation(s)
- Tiago L Moda
- Laboratório de Química Medicinal e Computacional, Centro de Biotecnologia Molecular Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, 13566-970 São Carlos, SP, Brazil
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Biava M, Porretta GC, Poce G, Deidda D, Pompei R, Tafi A, Manetti F. Antimycobacterial compounds. Optimization of the BM 212 structure, the lead compound for a new pyrrole derivative class. Bioorg Med Chem 2005; 13:1221-30. [PMID: 15670931 DOI: 10.1016/j.bmc.2004.11.018] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2004] [Accepted: 11/09/2004] [Indexed: 11/23/2022]
Abstract
Our work on antitubercular agents led to the identification of BM 212 as a lead compound among a series of pyrrole derivatives with good in vitro activity against mycobacteria and candidae. Further studies led us to synthesize additional pyrroles bearing the thiomorpholinomethyl moiety and different aryl substituents at N1 and C5. Some of them revealed very active, prompting us to design the new pyrrole derivatives 5-20 in the hope of increasing the activity and better understanding the influence of ortho halogens on the antimycobacterial activity. Microbiological data showed interesting in vitro activity toward Mycobacterium tuberculosis and atypical mycobacteria.
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Affiliation(s)
- Mariangela Biava
- Dipartimento di Studi di Chimica e Tecnologia delle Sostanze Biologicamente Attive, Università La Sapienza, P.le A. Moro 5, 00185 Rome, Italy.
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