1
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Schneider M, Pons JL, Labesse G. Exploring the conformational space of a receptor for drug design: An ERα case study. J Mol Graph Model 2021; 108:107974. [PMID: 34274728 DOI: 10.1016/j.jmgm.2021.107974] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 06/16/2021] [Accepted: 06/17/2021] [Indexed: 10/21/2022]
Abstract
Protein flexibility is challenging for both experimentalists and modellers, especially in the field of drug design. Estrogen Receptor alpha (ERα) is an extensively studied Nuclear Receptor (NR) and a well-known therapeutic target with an important role in development and physiology. It is also a frequent off-target in standard toxicity tests for endocrine disruption. Here, we aim to evaluate the degree to which the conformational space and macromolecular flexibility of this well-characterized drug target can be described. Our approach exploits hundreds of crystallographic structures by means of molecular dynamics simulations and of virtual screening. The analysis of hundreds of crystal structures confirms the presence of two main conformational states, known as 'agonist' and 'antagonist', that mainly differ by the orientation of the C-terminal helix H12 which serves to close the binding pocket. ERα also shows some loop flexibility, as well as variable side-chain orientations in its active site. We scrutinized the extent to which standard molecular dynamics simulations or crystallographic refinement as ensemble recapitulate most of the variability features seen by the array of available crystal structures. In parallel, we investigated on the kind and extent of flexibility that are required to achieve convincing docking for all high-affinity ERα ligands present in BindingDB. Using either only one conformation with a few side-chains set flexible, or static structure ensembles in parallel during docking led to good quality and similar pose predictions. These results suggest that the several hundreds of crystal structures already known can properly describe the whole conformational universe of ERα's ligand binding domain. This opens the road for better drug design and affinity computation.
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Affiliation(s)
- Melanie Schneider
- Centre de Biochimie Structurale (CBS), CNRS, INSERM, Univ Montpellier, 34090, Montpellier, France.
| | - Jean-Luc Pons
- Centre de Biochimie Structurale (CBS), CNRS, INSERM, Univ Montpellier, 34090, Montpellier, France.
| | - Gilles Labesse
- Centre de Biochimie Structurale (CBS), CNRS, INSERM, Univ Montpellier, 34090, Montpellier, France.
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2
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Shaw R, Althagafi I, Elagamy A, Rai R, Shah C, Nemaysh V, Singh H, Pratap R. Transition metal-free synthesis of sterically hindered allylarenes from 5-hexene-2-one. Org Biomol Chem 2020; 18:6276-6286. [PMID: 32734988 DOI: 10.1039/d0ob01318h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A simple, efficient and transition metal-free strategy was established for the synthesis of highly functionalized, sterically hindered allylarenes (6, 7 & 8) by base-mediated ring transformation of 2-oxo-6-aryl-4-(methylthio/sec-amino)-2H-pyran-3-carbonitriles (3/4) with 5-hexene-2-one (5). This provides a method for the synthesis of allylarenes functionalized with different electron donating and withdrawing groups in one pot. The structures of isolated products 6c and 7a were ascertained by spectroscopic and single crystal X-ray diffraction analyses. In addition, we have performed a molecular docking study to predict the biological activity of the synthesized molecules for binding to estrogen receptor alpha (ERα) and estrogen receptor beta (ERβ).
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Affiliation(s)
- Ranjay Shaw
- Department of Chemistry, University of Delhi, North Campus, Delhi-110007, India.
| | - Ismail Althagafi
- Department of Chemistry, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Amr Elagamy
- Department of Chemistry, University of Delhi, North Campus, Delhi-110007, India.
| | - Reeta Rai
- Department of Biochemistry, All India Institute of Medical Sciences, Ansari Nagar, New Delhi-110029, India
| | - Chandan Shah
- Department of Chemistry, University of Delhi, North Campus, Delhi-110007, India.
| | - Vishal Nemaysh
- Department of Chemistry, University of Delhi, North Campus, Delhi-110007, India.
| | - Harpreet Singh
- Indian Council of Medical Research, Ansari Nagar, New Delhi-110029, India
| | - Ramendra Pratap
- Department of Chemistry, University of Delhi, North Campus, Delhi-110007, India.
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3
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Hanson AM, Perera KLIS, Kim J, Pandey RK, Sweeney N, Lu X, Imhoff A, Mackinnon AC, Wargolet AJ, Van Hart RM, Frick KM, Donaldson WA, Sem DS. A-C Estrogens as Potent and Selective Estrogen Receptor-Beta Agonists (SERBAs) to Enhance Memory Consolidation under Low-Estrogen Conditions. J Med Chem 2018; 61:4720-4738. [PMID: 29741891 DOI: 10.1021/acs.jmedchem.7b01601] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Estrogen receptor-beta (ERβ) is a drug target for memory consolidation in postmenopausal women. Herein is reported a series of potent and selective ERβ agonists (SERBAs) with in vivo efficacy that are A-C estrogens, lacking the B and D estrogen rings. The most potent and selective A-C estrogen is selective for activating ER relative to seven other nuclear hormone receptors, with a surprising 750-fold selectivity for the β over α isoform and with EC50s of 20-30 nM in cell-based and direct binding assays. Comparison of potency in different assays suggests that the ER isoform selectivity is related to the compound's ability to drive the productive conformational change needed to activate transcription. The compound also shows in vivo efficacy after microinfusion into the dorsal hippocampus and after intraperitoneal injection (0.5 mg/kg) or oral gavage (0.5 mg/kg). This simple yet novel A-C estrogen is selective, brain penetrant, and facilitates memory consolidation.
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Affiliation(s)
- Alicia M Hanson
- Department of Pharmaceutical Sciences, Center for Structure-Based Drug Design and Development , Concordia University Wisconsin , Mequon , Wisconsin 53097 , United States
| | - K L Iresha Sampathi Perera
- Department of Chemistry , Marquette University , P.O. Box 1881, Milwaukee , Wisconsin 53201-1881 , United States
| | - Jaekyoon Kim
- Department of Psychology , University of Wisconsin-Milwaukee , 2441 East Hartford Avenue , Milwaukee , Wisconsin 53211 , United States
| | - Rajesh K Pandey
- Department of Chemistry , Marquette University , P.O. Box 1881, Milwaukee , Wisconsin 53201-1881 , United States
| | - Noreena Sweeney
- Department of Pharmaceutical Sciences, Center for Structure-Based Drug Design and Development , Concordia University Wisconsin , Mequon , Wisconsin 53097 , United States
| | - Xingyun Lu
- Department of Pharmaceutical Sciences, Center for Structure-Based Drug Design and Development , Concordia University Wisconsin , Mequon , Wisconsin 53097 , United States
| | - Andrea Imhoff
- Department of Pharmaceutical Sciences, Center for Structure-Based Drug Design and Development , Concordia University Wisconsin , Mequon , Wisconsin 53097 , United States
| | - Alexander Craig Mackinnon
- Department of Pathology , Medical College of Wisconsin , 9200 West Wisconsin Avenue , Milwaukee , Wisconsin 53226 , United States
| | - Adam J Wargolet
- Department of Natural Science , Concordia University Wisconsin , Mequon , Wisconsin 53097 , United States
| | - Rochelle M Van Hart
- Department of Natural Science , Concordia University Wisconsin , Mequon , Wisconsin 53097 , United States
| | - Karyn M Frick
- Department of Psychology , University of Wisconsin-Milwaukee , 2441 East Hartford Avenue , Milwaukee , Wisconsin 53211 , United States
| | - William A Donaldson
- Department of Chemistry , Marquette University , P.O. Box 1881, Milwaukee , Wisconsin 53201-1881 , United States
| | - Daniel S Sem
- Department of Pharmaceutical Sciences, Center for Structure-Based Drug Design and Development , Concordia University Wisconsin , Mequon , Wisconsin 53097 , United States
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4
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Kayık G, Tüzün NŞ, Durdagi S. Structural investigation of vesnarinone at the pore domains of open and open-inactivated states of hERG1 K + channel. J Mol Graph Model 2017; 77:399-412. [DOI: 10.1016/j.jmgm.2017.08.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 08/17/2017] [Accepted: 08/18/2017] [Indexed: 12/22/2022]
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5
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Hassam M, Taher A, Arnott GE, Green IR, van Otterlo WAL. Isomerization of Allylbenzenes. Chem Rev 2015; 115:5462-569. [DOI: 10.1021/acs.chemrev.5b00052] [Citation(s) in RCA: 175] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Mohammad Hassam
- Department
of Chemistry and Polymer Science, Stellenbosch University, Private Bag
X1, Matieland 7602, South Africa
| | - Abu Taher
- Department
of Chemistry and Polymer Science, Stellenbosch University, Private Bag
X1, Matieland 7602, South Africa
| | - Gareth E. Arnott
- Department
of Chemistry and Polymer Science, Stellenbosch University, Private Bag
X1, Matieland 7602, South Africa
| | - Ivan R. Green
- Department
of Chemistry and Polymer Science, Stellenbosch University, Private Bag
X1, Matieland 7602, South Africa
| | - Willem A. L. van Otterlo
- Department
of Chemistry and Polymer Science, Stellenbosch University, Private Bag
X1, Matieland 7602, South Africa
- School
of Chemistry, University of the Witwatersrand, Braamfontein, Johannesburg 2000, South Africa
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6
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Study of the binding interaction between fluorinated matrix metalloproteinase inhibitors and Human Serum Albumin. Eur J Med Chem 2014; 79:13-23. [DOI: 10.1016/j.ejmech.2014.03.064] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 02/18/2014] [Accepted: 03/21/2014] [Indexed: 11/18/2022]
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7
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Liao ZQ, Dong C, Carlson KE, Srinivasan S, Nwachukwu JC, Chesnut RW, Sharma A, Nettles KW, Katzenellenbogen JA, Zhou HB. Triaryl-substituted Schiff bases are high-affinity subtype-selective ligands for the estrogen receptor. J Med Chem 2014; 57:3532-45. [PMID: 24708493 PMCID: PMC4002130 DOI: 10.1021/jm500268j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
![]()
We have explored the isoelectronic
replacement of the C=C
double bond found at the core of many nonsteroidal estrogen ligands
with a simple Schiff base (C=N). Di- and triaryl-substituted
imine derivatives were conveniently prepared by the condensation of
benzophenones with various anilines without the need for phenolic
hydroxy protection. Most of these imines demonstrated high affinity
for the estrogen receptors, which, in some cases exceeded that of
estradiol. In cell-based assays, these imines profiled as ERα
agonists but as ERβ antagonists, showing preferential reliance
on the N-terminal activation function (AF1), which is more active
in ERα. X-ray analysis revealed that the triaryl-imines distort
the ligand-binding pocket in a new way: by controlling the separation
of helices 3 and 11, which appears to alter the C-terminal AF2 surface
that binds transcriptional coactivators. This work suggests that C=N
for C=C substitution might be more widely considered as a general
strategy for preparing drug analogues.
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Affiliation(s)
- Zong-Quan Liao
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, State Key Laboratory of Virology, Wuhan University School of Pharmaceutical Sciences , Wuhan 430071, China
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8
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Dömötör O, Tuccinardi T, Karcz D, Walsh M, Creaven BS, Enyedy ÉA. Interaction of anticancer reduced Schiff base coumarin derivatives with human serum albumin investigated by fluorescence quenching and molecular modeling. Bioorg Chem 2014; 52:16-23. [DOI: 10.1016/j.bioorg.2013.10.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Revised: 10/31/2013] [Accepted: 10/31/2013] [Indexed: 12/20/2022]
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9
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McCullough C, Neumann TS, Gone JR, He Z, Herrild C, Wondergem Nee Lukesh J, Pandey RK, Donaldson WA, Sem DS. Probing the human estrogen receptor-α binding requirements for phenolic mono- and di-hydroxyl compounds: a combined synthesis, binding and docking study. Bioorg Med Chem 2014; 22:303-10. [PMID: 24315190 PMCID: PMC4013293 DOI: 10.1016/j.bmc.2013.11.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 11/05/2013] [Accepted: 11/13/2013] [Indexed: 12/23/2022]
Abstract
Various estrogen analogs were synthesized and tested for binding to human ERα using a fluorescence polarization displacement assay. Binding affinity and orientation were also predicted using docking calculations. Docking was able to accurately predict relative binding affinity and orientation for estradiol, but only if a tightly bound water molecule bridging Arg394/Glu353 is present. Di-hydroxyl compounds sometimes bind in two orientations, which are flipped in terms of relative positioning of their hydroxyl groups. Di-hydroxyl compounds were predicted to bind with their aliphatic hydroxyl group interacting with His524 in ERα. One nonsteroid-based dihdroxyl compound was 1000-fold specific for ERβ over ERα, and was also 25-fold specific for agonist ERβ versus antagonist activity. Docking predictions suggest this specificity may be due to interaction of the aliphatic hydroxyl with His475 in the agonist form of ERβ, versus with Thr299 in the antagonist form. But, the presence of this aliphatic hydroxyl is not required in all compounds, since mono-hydroxyl (phenolic) compounds bind ERα with high affinity, via hydroxyl hydrogen bonding interactions with the ERα Arg394/Glu353/water triad, and van der Waals interactions with the rest of the molecule.
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Affiliation(s)
- Christopher McCullough
- Department of Chemistry, Marquette University, PO Box 1881, Milwaukee, WI 53201-1881, United States; Department of Cancer Systems Imaging, University of Texas-M.D. Anderson Cancer Center, Houston, TX 77030, United States
| | - Terrence S Neumann
- Department of Chemistry, Marquette University, PO Box 1881, Milwaukee, WI 53201-1881, United States; School of Pharmacy, Center for Structure-based Drug Design and Development, Concordia University Wisconsin, Mequon, WI 53097, United States
| | - Jayapal Reddy Gone
- Department of Chemistry, Marquette University, PO Box 1881, Milwaukee, WI 53201-1881, United States; Toronto Research Chemicals Inc., 2 Brisbane Rd., North York, Toronto M3J 2J8, Canada
| | - Zhengjie He
- Department of Chemistry, Marquette University, PO Box 1881, Milwaukee, WI 53201-1881, United States; The State Key Laboratory of Elemento-Organic Chemistry and Department of Chemistry, Nankai University, Tianjin, China
| | - Christian Herrild
- Department of Chemistry, Marquette University, PO Box 1881, Milwaukee, WI 53201-1881, United States
| | - Julie Wondergem Nee Lukesh
- Department of Chemistry, Marquette University, PO Box 1881, Milwaukee, WI 53201-1881, United States; Division of Natural & Applied Sciences, University of Wisconsin-Green Bay, 2420 Nicolet Drive, Green Bay, WI 54311, United States
| | - Rajesh K Pandey
- Department of Chemistry, Marquette University, PO Box 1881, Milwaukee, WI 53201-1881, United States; AllExcel Inc., 135 Wood Street, West Haven, CT 06516, United States
| | - William A Donaldson
- Department of Chemistry, Marquette University, PO Box 1881, Milwaukee, WI 53201-1881, United States
| | - Daniel S Sem
- Department of Chemistry, Marquette University, PO Box 1881, Milwaukee, WI 53201-1881, United States; School of Pharmacy, Center for Structure-based Drug Design and Development, Concordia University Wisconsin, Mequon, WI 53097, United States.
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10
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Tuccinardi T, Granchi C, Iegre J, Paterni I, Bertini S, Macchia M, Martinelli A, Qian Y, Chen X, Minutolo F. Oxime-based inhibitors of glucose transporter 1 displaying antiproliferative effects in cancer cells. Bioorg Med Chem Lett 2013; 23:6923-7. [PMID: 24200808 DOI: 10.1016/j.bmcl.2013.09.037] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 09/09/2013] [Accepted: 09/11/2013] [Indexed: 01/04/2023]
Abstract
An analysis of the main pharmacophoric features present in the still limited number of inhibitors of glucose transporter GLUT1 led to the identification of new oxime-based inhibitors, which proved to be able to efficiently hinder glucose uptake and cell growth in H1299 lung cancer cells. The most important interactions of a representative inhibitor were indicated by a novel computational model of GLUT1, which was purposely developed to explain these results and to provide useful indications for the design and the development of new and more efficient GLUT1 inhibitors.
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Affiliation(s)
- Tiziano Tuccinardi
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
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11
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Paterni I, Bertini S, Granchi C, Macchia M, Minutolo F. Estrogen receptor ligands: a patent review update. Expert Opin Ther Pat 2013; 23:1247-71. [PMID: 23713677 DOI: 10.1517/13543776.2013.805206] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION The role of estrogens is mostly mediated by two nuclear receptors (ERα and ERβ) and a membrane-associated G-protein (GPR30 or GPER), and it is not limited to reproduction, but it extends to the skeletal, cardiovascular and central nervous systems. Various pathologies such as cancer, inflammatory, neurodegenerative and metabolic diseases are often associated with dysfunctions of the estrogenic system. Therapeutic interventions by agents that affect the estrogenic signaling pathway might be useful in the treatment of many dissimilar diseases. AREAS COVERED The massive chemodiversity of ER ligands, limited to patented small molecules, is herein reviewed. The reported compounds are classified on the basis of their chemical structures. Non-steroidal derivatives, which mostly consist of diphenolic compounds, are further segregated into chemical classes based on their central scaffold. EXPERT OPINION Estrogens have been used for almost a century and their earlier applications have concerned interventions in the female reproductive functions, as well as the treatment of some estrogen-dependent cancers and osteoporosis. Since the discovery of ERβ in 1996, the patent literature has started to pay a progressively increasing attention to this newer receptor subtype, which holds promise as a target for new indications, most of which still need to be clinically validated.
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Affiliation(s)
- Ilaria Paterni
- Dipartimento di Farmacia, Università di Pisa , Via Bonanno 6, 56126 Pisa , Italy +39 050 2219557 ; +39 050 2219605 ;
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12
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Hu G, Wang J. Ligand selectivity of estrogen receptors by a molecular dynamics study. Eur J Med Chem 2013; 74:726-35. [PMID: 23694906 DOI: 10.1016/j.ejmech.2013.04.049] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 03/09/2013] [Accepted: 04/22/2013] [Indexed: 02/07/2023]
Abstract
Estrogen receptors α (ERα) and β (ERβ) have different physiological functions and expression levels in different tissues. ERα and ERβ are highly homologous and have only two residue substitutions in the binding pocket. This high similarity at the active site stimulates the interests for discovering subtype selective ligands. In this study, molecular dynamics (MD) simulations combined with molecular mechanics generalized Born surface area (MM-GBSA) method have been carried out to analyze the basis of selectivity of three ligands (659, 818 and 041). The calculated binding free energies show that all the ligands bind more tightly to ERβ than to ERα. The dominant free energy components of selectivity for 659 are similar to that for 041, but different from that for 818. The decompositions of free energy contributions and structural analysis imply that there are eight residues primarily contributing to the selectivity for 659, five residues for 041, as well as two residues for 818. The structural analysis implies that two residue substitutions in binding packet cause the position of 659 in ERβ-659 complex to shift relative to that in ERα-659 complex and also cause the conformational changes of other residues in the binding pocket. The higher selectivity for 041 is mainly caused by three residues, Ile373 (Met421), His475 (His524) and Leu476 (Leu525).
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Affiliation(s)
- Guodong Hu
- Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics, Dezhou University, Dezhou, Shandong 253023, China; Department of Physics, Dezhou University, Dezhou, Shandong 253023, China.
| | - Jihua Wang
- Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics, Dezhou University, Dezhou, Shandong 253023, China; Department of Physics, Dezhou University, Dezhou, Shandong 253023, China.
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13
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Tuccinardi T, Bertini S, Granchi C, Ortore G, Macchia M, Minutolo F, Martinelli A, Supuran CT. Salicylaldoxime derivatives as new leads for the development of carbonic anhydrase inhibitors. Bioorg Med Chem 2012; 21:1511-5. [PMID: 23018095 DOI: 10.1016/j.bmc.2012.08.057] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Revised: 08/24/2012] [Accepted: 08/29/2012] [Indexed: 11/25/2022]
Abstract
New compounds containing a novel zinc binding group (salicylaldoxime system) were identified as effective inhibitors of carbonic anhydrases (CAs). This structural motif seems to bind the catalytic zinc ion of CAs, revealing itself as a new valid alternative to the sulfonamide group. Computational procedures were used to investigate the binding mode of this class of compounds, within the active site of CAII. This study suggests that the salicylaldoxime moiety binds the zinc ion through the oxime oxygen atom that also forms an H-bond with T199. The results herein obtained will allow the development of new CA-inhibitors bearing the salicylaldoxime moiety.
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Affiliation(s)
- Tiziano Tuccinardi
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Pisa, Via Bonanno 6, 56126 Pisa, Italy.
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14
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Balaji B, Ramanathan M. Prediction of estrogen receptor β ligands potency and selectivity by docking and MM-GBSA scoring methods using three different scaffolds. J Enzyme Inhib Med Chem 2011; 27:832-44. [DOI: 10.3109/14756366.2011.618990] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- B. Balaji
- Department of Pharmacology, PSG College of Pharmacy,
Coimbatore, India
| | - M. Ramanathan
- Department of Pharmacology, PSG College of Pharmacy,
Coimbatore, India
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15
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Bertini S, De Cupertinis A, Granchi C, Bargagli B, Tuccinardi T, Martinelli A, Macchia M, Gunther JR, Carlson KE, Katzenellenbogen JA, Minutolo F. Selective and potent agonists for estrogen receptor beta derived from molecular refinements of salicylaldoximes. Eur J Med Chem 2011; 46:2453-62. [PMID: 21481497 PMCID: PMC3088081 DOI: 10.1016/j.ejmech.2011.03.030] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Revised: 03/10/2011] [Accepted: 03/15/2011] [Indexed: 02/07/2023]
Abstract
In a continuing effort to improve the subtype selectivity and agonist potency of estrogen receptor β (ERβ) ligands, we have designed and developed a thus far unexplored structural series obtained by molecular refinements of monoaryl-substituted salicylaldoximes (Salaldox B). The most interesting compounds in this series (2c, d) show remarkably high ERβ-binding affinities, with Ki values reaching the sub-nanomolar range (Ki=0.38 nM for 2c and 0.57 nM for 2d), and have very high levels of ERβ-subtype selectivity. Both compounds show a potent full agonist character on ERβ (EC50=0.23 nM for 2c and 1.3 nM for 2d). Furthermore, 2d shows a remarkable functional subtype selectivity, with a β/α transcription potency ratio 50-fold higher than that of estradiol.
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Affiliation(s)
- Simone Bertini
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Andrea De Cupertinis
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Carlotta Granchi
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Barbara Bargagli
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Tiziano Tuccinardi
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Adriano Martinelli
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Marco Macchia
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Jillian R. Gunther
- Department of Chemistry, University of Illinois, 600 S. Mathews Avenue, Urbana, IL 61801, USA
| | - Kathryn E. Carlson
- Department of Chemistry, University of Illinois, 600 S. Mathews Avenue, Urbana, IL 61801, USA
| | | | - Filippo Minutolo
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
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16
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Fang J, Shen J, Cheng F, Xu Z, Liu G, Tang Y. Computational Insights into Ligand Selectivity of Estrogen Receptors from Pharmacophore Modeling. Mol Inform 2011; 30:539-49. [DOI: 10.1002/minf.201000170] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Accepted: 03/31/2011] [Indexed: 11/11/2022]
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17
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Guilarte V, Castroviejo MP, García-García P, Fernández-Rodríguez MA, Sanz R. Approaches to the Synthesis of 2,3-Dihaloanilines. Useful Precursors of 4-Functionalized-1H-indoles. J Org Chem 2011; 76:3416-37. [DOI: 10.1021/jo200406f] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Verónica Guilarte
- Departamento de Química, Área de Química Orgánica, Facultad de Ciencias, Universidad de Burgos, Pza. Misael Bañuelos s/n, 09001-Burgos, Spain
| | - M. Pilar Castroviejo
- Departamento de Química, Área de Química Orgánica, Facultad de Ciencias, Universidad de Burgos, Pza. Misael Bañuelos s/n, 09001-Burgos, Spain
| | - Patricia García-García
- Departamento de Química, Área de Química Orgánica, Facultad de Ciencias, Universidad de Burgos, Pza. Misael Bañuelos s/n, 09001-Burgos, Spain
| | - Manuel A. Fernández-Rodríguez
- Departamento de Química, Área de Química Orgánica, Facultad de Ciencias, Universidad de Burgos, Pza. Misael Bañuelos s/n, 09001-Burgos, Spain
| | - Roberto Sanz
- Departamento de Química, Área de Química Orgánica, Facultad de Ciencias, Universidad de Burgos, Pza. Misael Bañuelos s/n, 09001-Burgos, Spain
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18
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Tuccinardi T, Zizzari AT, Brullo C, Daniele S, Musumeci F, Schenone S, Trincavelli ML, Martini C, Martinelli A, Giorgi G, Botta M. Substituted pyrazolo[3,4-b]pyridines as human A1 adenosine antagonists: Developments in understanding the receptor stereoselectivity. Org Biomol Chem 2011; 9:4448-55. [DOI: 10.1039/c0ob01064b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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19
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Li L, Siebrands CC, Yang Z, Zhang L, Guse AH, Zhang L. Novel nucleobase-simplified cyclic ADP-ribose analogue: A concise synthesis and Ca(2+)-mobilizing activity in T-lymphocytes. Org Biomol Chem 2010; 8:1843-8. [PMID: 20449488 DOI: 10.1039/b925295a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A purine nucleobase-simplified cyclic ADP ribose (cADPR) analogue was synthesized, in which a 1,2,3-triazole-4-amide was constructed, instead of a purine moiety, and the northern ribose was replaced by an ether strand. Compound exhibits calcium release activity in intact T-lymphocytes and indicates that it is a membrane-permeable cADPR mimic. Thus, the cADPR analogue containing 1,2,3-triazole-4-amide provides a novel template for further designing cADPR analogues and elucidating their structure-activity relationships.
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Affiliation(s)
- Lingjun Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100083, PR China
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20
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Shen J, Li W, Liu G, Tang Y, Jiang H. Computational insights into the mechanism of ligand unbinding and selectivity of estrogen receptors. J Phys Chem B 2009; 113:10436-44. [PMID: 19583238 DOI: 10.1021/jp903785h] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Estrogen receptors (ER) belong to the nuclear receptor superfamily, and two subtypes, ERalpha and ERbeta, have been identified to date. The differentiated functions and receptor expressions of ERalpha and ERbeta made it attracted to discover subtype-specified ligands with high selectivity. However, these two subtypes are highly homologous and only two residues differ in the ligand binding pocket. Therefore, the mechanism of ligand selectivity has become an important issue in searching selective ligands of ER subtypes. In this study, steered molecular dynamics simulations were carried out to investigate the unbinding pathways of two selective ERbeta ligands from the binding pocket of both ERalpha and ERbeta, which demonstrated that the pathway between the H11 helix and the H7 approximately H8 loop was the most probable for ligand escaping. Then potentials of mean force for ligands unbinding along this pathway were calculated in order to gain insights into the molecular basis for energetics of ligand unbinding and find clues of ligand selectivity. The results indicated that His524/475 in ERalpha/ERbeta acted as a "gatekeeper" during the ligand unbinding. Especially, the H7 approximately H8 loop of ERbeta acted as a polar "transmitter" that controlled the ligand unbinding from the binding site and contributed to the ligand selectivity. Finally, the mechanism of ligand selectivity of ER subtypes was discussed from a kinetic perspective and suggestions for improving the ligand selectivity of ERbeta were also presented. These findings could be helpful for rational design of highly selective ERbeta ligands.
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Affiliation(s)
- Jie Shen
- School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
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21
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Minutolo F, Macchia M, Katzenellenbogen BS, Katzenellenbogen JA. Estrogen receptor β ligands: Recent advances and biomedical applications. Med Res Rev 2009; 31:364-442. [DOI: 10.1002/med.20186] [Citation(s) in RCA: 126] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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22
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Minutolo F, Bertini S, Granchi C, Marchitiello T, Prota G, Rapposelli S, Tuccinardi T, Martinelli A, Gunther JR, Carlson KE, Katzenellenbogen JA, Macchia M. Structural Evolutions of Salicylaldoximes as Selective Agonists for Estrogen Receptor β. J Med Chem 2009; 52:858-67. [DOI: 10.1021/jm801458t] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Filippo Minutolo
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy, Department of Chemistry, University of Illinois, 600 South Mathews Avenue, Urbana, Illinois 61801
| | - Simone Bertini
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy, Department of Chemistry, University of Illinois, 600 South Mathews Avenue, Urbana, Illinois 61801
| | - Carlotta Granchi
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy, Department of Chemistry, University of Illinois, 600 South Mathews Avenue, Urbana, Illinois 61801
| | - Teresa Marchitiello
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy, Department of Chemistry, University of Illinois, 600 South Mathews Avenue, Urbana, Illinois 61801
| | - Giovanni Prota
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy, Department of Chemistry, University of Illinois, 600 South Mathews Avenue, Urbana, Illinois 61801
| | - Simona Rapposelli
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy, Department of Chemistry, University of Illinois, 600 South Mathews Avenue, Urbana, Illinois 61801
| | - Tiziano Tuccinardi
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy, Department of Chemistry, University of Illinois, 600 South Mathews Avenue, Urbana, Illinois 61801
| | - Adriano Martinelli
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy, Department of Chemistry, University of Illinois, 600 South Mathews Avenue, Urbana, Illinois 61801
| | - Jillian R. Gunther
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy, Department of Chemistry, University of Illinois, 600 South Mathews Avenue, Urbana, Illinois 61801
| | - Kathryn E. Carlson
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy, Department of Chemistry, University of Illinois, 600 South Mathews Avenue, Urbana, Illinois 61801
| | - John A. Katzenellenbogen
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy, Department of Chemistry, University of Illinois, 600 South Mathews Avenue, Urbana, Illinois 61801
| | - Marco Macchia
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy, Department of Chemistry, University of Illinois, 600 South Mathews Avenue, Urbana, Illinois 61801
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23
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24
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Minutolo F, Bellini R, Bertini S, Carboni I, Lapucci A, Pistolesi L, Prota G, Rapposelli S, Solati F, Tuccinardi T, Martinelli A, Stossi F, Carlson KE, Katzenellenbogen BS, Katzenellenbogen JA, Macchia M. Monoaryl-Substituted Salicylaldoximes as Ligands for Estrogen Receptor β. J Med Chem 2008; 51:1344-51. [DOI: 10.1021/jm701396g] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Filippo Minutolo
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy, and Department of Molecular and Integrative Physiology and Department of Chemistry, University of Illinois, 600 S. Goodwin Avenue, Urbana, Illinois 61801
| | - Rosalba Bellini
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy, and Department of Molecular and Integrative Physiology and Department of Chemistry, University of Illinois, 600 S. Goodwin Avenue, Urbana, Illinois 61801
| | - Simone Bertini
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy, and Department of Molecular and Integrative Physiology and Department of Chemistry, University of Illinois, 600 S. Goodwin Avenue, Urbana, Illinois 61801
| | - Isabella Carboni
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy, and Department of Molecular and Integrative Physiology and Department of Chemistry, University of Illinois, 600 S. Goodwin Avenue, Urbana, Illinois 61801
| | - Annalina Lapucci
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy, and Department of Molecular and Integrative Physiology and Department of Chemistry, University of Illinois, 600 S. Goodwin Avenue, Urbana, Illinois 61801
| | - Letizia Pistolesi
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy, and Department of Molecular and Integrative Physiology and Department of Chemistry, University of Illinois, 600 S. Goodwin Avenue, Urbana, Illinois 61801
| | - Giovanni Prota
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy, and Department of Molecular and Integrative Physiology and Department of Chemistry, University of Illinois, 600 S. Goodwin Avenue, Urbana, Illinois 61801
| | - Simona Rapposelli
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy, and Department of Molecular and Integrative Physiology and Department of Chemistry, University of Illinois, 600 S. Goodwin Avenue, Urbana, Illinois 61801
| | - Francesca Solati
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy, and Department of Molecular and Integrative Physiology and Department of Chemistry, University of Illinois, 600 S. Goodwin Avenue, Urbana, Illinois 61801
| | - Tiziano Tuccinardi
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy, and Department of Molecular and Integrative Physiology and Department of Chemistry, University of Illinois, 600 S. Goodwin Avenue, Urbana, Illinois 61801
| | - Adriano Martinelli
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy, and Department of Molecular and Integrative Physiology and Department of Chemistry, University of Illinois, 600 S. Goodwin Avenue, Urbana, Illinois 61801
| | - Fabio Stossi
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy, and Department of Molecular and Integrative Physiology and Department of Chemistry, University of Illinois, 600 S. Goodwin Avenue, Urbana, Illinois 61801
| | - Kathryn E. Carlson
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy, and Department of Molecular and Integrative Physiology and Department of Chemistry, University of Illinois, 600 S. Goodwin Avenue, Urbana, Illinois 61801
| | - Benita S. Katzenellenbogen
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy, and Department of Molecular and Integrative Physiology and Department of Chemistry, University of Illinois, 600 S. Goodwin Avenue, Urbana, Illinois 61801
| | - John A. Katzenellenbogen
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy, and Department of Molecular and Integrative Physiology and Department of Chemistry, University of Illinois, 600 S. Goodwin Avenue, Urbana, Illinois 61801
| | - Marco Macchia
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy, and Department of Molecular and Integrative Physiology and Department of Chemistry, University of Illinois, 600 S. Goodwin Avenue, Urbana, Illinois 61801
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