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Lewandowski M, Carmina M, Knümann L, Sai M, Willems S, Kasch T, Pollinger J, Knapp S, Marschner JA, Chaikuad A, Merk D. Structure-Guided Design of a Highly Potent Partial RXR Agonist with Superior Physicochemical Properties. J Med Chem 2024; 67:2152-2164. [PMID: 38237049 DOI: 10.1021/acs.jmedchem.3c02095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Retinoid X receptors (RXRs, NR2B1-3) hold therapeutic potential in oncology, neurodegeneration, and metabolic diseases, but traditional RXR agonists mimicking the natural ligand 9-cis retinoic acid exhibit poor physicochemical properties, pharmacokinetics, and safety profiles. Improved RXR ligands are needed to exploit RXR modulation as a promising therapeutic concept in various indications beyond its current role in second-line cancer treatment. Here, we report the co-crystal structure of RXR in complex with a novel pyrimidine-based ligand and the structure-informed optimization of this scaffold to highly potent and highly soluble RXR agonists. Focused structure-activity relationship elucidation and rigidization resulted in a substantially optimized partial RXR agonist with low nanomolar potency, no cytotoxic activity, and very favorable physicochemical properties highlighting this promising scaffold for the development of next-generation RXR targeting drugs.
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Affiliation(s)
- Max Lewandowski
- Department of Pharmacy, Ludwig-Maximilians-Universität (LMU) München, 81377 Munich, Germany
| | - Melania Carmina
- Department of Pharmacy, Ludwig-Maximilians-Universität (LMU) München, 81377 Munich, Germany
- Department of Pharmaceutical Sciences, Università degli Studi di Perugia, 06123 Perugia, Italy
| | - Loris Knümann
- Department of Pharmacy, Ludwig-Maximilians-Universität (LMU) München, 81377 Munich, Germany
| | - Minh Sai
- Department of Pharmacy, Ludwig-Maximilians-Universität (LMU) München, 81377 Munich, Germany
| | - Sabine Willems
- Department of Pharmacy, Ludwig-Maximilians-Universität (LMU) München, 81377 Munich, Germany
| | - Till Kasch
- Department of Pharmacy, Ludwig-Maximilians-Universität (LMU) München, 81377 Munich, Germany
| | - Julius Pollinger
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Julian A Marschner
- Department of Pharmacy, Ludwig-Maximilians-Universität (LMU) München, 81377 Munich, Germany
| | - Apirat Chaikuad
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Daniel Merk
- Department of Pharmacy, Ludwig-Maximilians-Universität (LMU) München, 81377 Munich, Germany
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2
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Adouvi G, Nawa F, Ballarotto M, Rüger LA, Knümann L, Kasch T, Arifi S, Schubert-Zsilavecz M, Willems S, Marschner JA, Pabel J, Merk D. Structural Fusion of Natural and Synthetic Ligand Features Boosts RXR Agonist Potency. J Med Chem 2023; 66:16762-16771. [PMID: 38064686 DOI: 10.1021/acs.jmedchem.3c01435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
The retinoid X receptors (RXRs) are ligand-activated transcription factors involved in, for example, differentiation and apoptosis regulation. Currently used reference RXR agonists suffer from insufficient specificity and poor physicochemical properties, and improved tools are needed to capture the unexplored therapeutic potential of RXR. Endogenous vitamin A-derived RXR ligands and the natural product RXR agonist valerenic acid comprise acrylic acid residues with varying substitution patterns to engage the critical ionic contact with the binding site arginine. To mimic and exploit this natural ligand motif, we probed its structural fusion with synthetic RXR modulator scaffolds, which had profound effects on agonist activity and remarkably boosted potency of an oxaprozin-derived RXR agonist chemotype. Bioisosteric replacement of the acrylic acid to overcome its pan-assay interference compounds (PAINS) character enabled the development of a highly optimized RXR agonist chemical probe.
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Affiliation(s)
- Gustave Adouvi
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Felix Nawa
- Department of Pharmacy, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Marco Ballarotto
- Department of Pharmacy, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Lorena Andrea Rüger
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Loris Knümann
- Department of Pharmacy, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Till Kasch
- Department of Pharmacy, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Silvia Arifi
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | | | - Sabine Willems
- Department of Pharmacy, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Julian A Marschner
- Department of Pharmacy, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Jörg Pabel
- Department of Pharmacy, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Daniel Merk
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany
- Department of Pharmacy, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
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3
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Miura K, Fujihara M, Watanabe M, Takamura Y, Kawasaki M, Nakano S, Kakuta H. Direct evaluation of polarity of the ligand binding pocket in retinoid X receptor using a fluorescent solvatochromic agonist. Bioorg Med Chem Lett 2023; 96:129536. [PMID: 37913851 DOI: 10.1016/j.bmcl.2023.129536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 10/03/2023] [Accepted: 10/22/2023] [Indexed: 11/03/2023]
Abstract
High selectivity of small-molecule drug candidates for their target molecule is important to minimize potential side effects. One factor that contributes to the selectivity is the internal polarity of the ligand-binding pocket (LBP) in the target molecule, but this is difficult to measure. Here, we first confirmed that the retinoid X receptor (RXR) agonist 6-(ethyl(1-isobutyl-2-oxo-4-(trifluoromethyl)-1,2-dihydroquinolin-7-yl)amino)nicotinic acid (NEt-iFQ, 1) exhibits fluorescence solvatochromism, i.e., its Stokes shift depends on the polarity of the solvent, and then we utilized this property to directly measure the internal polarity of the RXRα-LBP. The Stokes shift of 1 when bound to the RXRα-LBP corresponded to that of 1 in chloroform solution. This finding is expected to be helpful for designing RXR-selective ligands. A similar approach should be appliable to evaluate the internal polarity of the LBPs of other receptors.
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Affiliation(s)
- Kizuku Miura
- Faculty of Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-naka, Kita-ku Okayama 700-8530, Japan
| | - Michiko Fujihara
- Division of Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 1-1-1, Tsushima-naka, Kita-ku Okayama 700-8530, Japan; Department of Liberal Arts, The Open University of Japan, 2-11 Wakaba, Mihama-ku, Chiba 261- 8586, Japan
| | - Masaki Watanabe
- Division of Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 1-1-1, Tsushima-naka, Kita-ku Okayama 700-8530, Japan
| | - Yuta Takamura
- Division of Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 1-1-1, Tsushima-naka, Kita-ku Okayama 700-8530, Japan
| | - Mayu Kawasaki
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, 52- 1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Shogo Nakano
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, 52- 1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Hiroki Kakuta
- Division of Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 1-1-1, Tsushima-naka, Kita-ku Okayama 700-8530, Japan.
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4
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Zaienne D, Isigkeit L, Marschner JA, Duensing-Kropp S, Höfner G, Merk D. Structural Modification of the Natural Product Valerenic Acid Tunes RXR Homodimer Agonism. ChemMedChem 2023; 18:e202300404. [PMID: 37697963 DOI: 10.1002/cmdc.202300404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 09/13/2023]
Abstract
Retinoid X receptors (RXR) are ligand-sensing transcription factors with a unique role in nuclear receptor signaling as universal heterodimer partners. RXR modulation holds potential in cancer, neurodegeneration and metabolic diseases but adverse effects of RXR activation and lack of selective modulators prevent further exploration as therapeutic target. The natural product valerenic acid has been discovered as RXR agonist with unprecedented preference for RXR subtype and homodimer activation. To capture structural determinants of this activity profile and identify potential for optimization, we have studied effects of structural modification of the natural product on RXR modulation and identified an analogue with enhanced RXR homodimer agonism.
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Affiliation(s)
- Daniel Zaienne
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Laura Isigkeit
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Julian A Marschner
- Department of Pharmacy, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Silke Duensing-Kropp
- Department of Pharmacy, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Georg Höfner
- Department of Pharmacy, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Daniel Merk
- Department of Pharmacy, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, Munich, Germany
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
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5
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Kawasaki M, Motoyama T, Yamada S, Watanabe M, Fujihara M, Kambe A, Nakano S, Kakuta H, Ito S. Ligand Screening System for the RXRα Heterodimer Using the Fluorescence RXR Agonist CU-6PMN. ACS Med Chem Lett 2023; 14:291-296. [PMID: 36923911 PMCID: PMC10009790 DOI: 10.1021/acsmedchemlett.2c00509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
Retinoid X receptor (RXR), a nuclear receptor (NR) that regulates transcription of target genes in a ligand binding-dependent manner, is of interest as a drug target. RXR agonists have been developed as therapeutic agents for cutaneous invasive T-cell lymphoma (e.g., bexarotene (1)) and investigated as potential anti-inflammatory agents. Screening systems for the binding of RXR alone have been reported. However, although RXRs function as RXR heterodimers, information on systems to evaluate the differential binding of RXR agonists as RXR heterodimers has not been available until recently. Here we show that the fluorescent RXR agonist CU-6PMN (3), designed by our group, can be useful for assessing RXR binding to PPARγ/RXRα, and that the binding data differ from those of RXRα alone. This screening method opens a new avenue for binding assays for RXR heterodimers.
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Affiliation(s)
- Mayu Kawasaki
- Graduate
School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Tomoharu Motoyama
- Graduate
School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Shoya Yamada
- Division
of Pharmaceutical Sciences, Okayama University
Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 1-1-1, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Masaki Watanabe
- Division
of Pharmaceutical Sciences, Okayama University
Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 1-1-1, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Michiko Fujihara
- Division
of Pharmaceutical Sciences, Okayama University
Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 1-1-1, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Akira Kambe
- Graduate
School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Shogo Nakano
- Graduate
School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
- PREST,
Japan Science and Technology Agency, Saitama 332-0012, Japan
| | - Hiroki Kakuta
- Division
of Pharmaceutical Sciences, Okayama University
Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 1-1-1, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Sohei Ito
- Graduate
School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
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6
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Adouvi G, Isigkeit L, López-García Ú, Chaikuad A, Marschner JA, Schubert-Zsilavecz M, Merk D. Rational Design of a New RXR Agonist Scaffold Enabling Single-Subtype Preference for RXRα, RXRβ, and RXRγ. J Med Chem 2023; 66:333-344. [PMID: 36533416 DOI: 10.1021/acs.jmedchem.2c01266] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The three retinoid X receptor subtypes (RXRα, RXRβ, RXRγ) exhibit critical regulatory roles in cell proliferation and differentiation, metabolism, and inflammation. Due to their importance in nuclear receptor signaling, RXRs are widely distributed and pan-RXR agonists cause adverse effects, but the three highly conserved RXR ligand binding sites render the development of subtype-selective ligands a major challenge. We have fused elements of known RXR ligands to obtain a new RXR agonist chemotype on which minor structural modifications enabled the development of tools with single-subtype preference for RXRα, RXRβ, and RXRγ. Molecular modeling indicated different binding conformations and interaction patterns with the RXR LBDs as factors of preferential binding. In a phenotypic adipocyte differentiation experiment, only the RXRα preferential tool enhanced the adipogenic effects of pioglitazone, suggesting this subtype as particularly relevant in adipogenesis and highlighting the set of subtype-preferential RXR agonist tools as suitable for functional cellular studies.
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Affiliation(s)
- Gustave Adouvi
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Laura Isigkeit
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Úrsula López-García
- Department of Pharmacy, Ludwig-Maximilians-Universität München,81377 Munich, Germany
| | - Apirat Chaikuad
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Julian A Marschner
- Department of Pharmacy, Ludwig-Maximilians-Universität München,81377 Munich, Germany
| | | | - Daniel Merk
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany.,Department of Pharmacy, Ludwig-Maximilians-Universität München,81377 Munich, Germany
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7
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Melo N, Belyaeva OV, Berger WK, Halasz L, Yu J, Pilli N, Yang Z, Klyuyeva AV, Elmets CA, Atigadda V, Muccio DD, Kane MA, Nagy L, Kedishvili NY, Renfrow MB. Next-generation retinoid X receptor agonists increase ATRA signaling in organotypic epithelium cultures and have distinct effects on receptor dynamics. J Biol Chem 2023; 299:102746. [PMID: 36436565 PMCID: PMC9807999 DOI: 10.1016/j.jbc.2022.102746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 11/26/2022] Open
Abstract
Retinoid X receptors (RXRs) are nuclear transcription factors that partner with other nuclear receptors to regulate numerous physiological processes. Although RXR represents a valid therapeutic target, only a few RXR-specific ligands (rexinoids) have been identified, in part due to the lack of clarity on how rexinoids selectively modulate RXR response. Previously, we showed that rexinoid UAB30 potentiates all-trans-retinoic acid (ATRA) signaling in human keratinocytes, in part by stimulating ATRA biosynthesis. Here, we examined the mechanism of action of next-generation rexinoids UAB110 and UAB111 that are more potent in vitro than UAB30 and the FDA-approved Targretin. Both UAB110 and UAB111 enhanced ATRA signaling in human organotypic epithelium at a 50-fold lower concentration than UAB30. This was consistent with the 2- to 5- fold greater increase in ATRA in organotypic epidermis treated with UAB110/111 versus UAB30. Furthermore, at 0.2 μM, UAB110/111 increased the expression of ATRA genes up to 16-fold stronger than Targretin. The less toxic and more potent UAB110 also induced more changes in differential gene expression than Targretin. Additionally, our hydrogen deuterium exchange mass spectrometry analysis showed that both ligands reduced the dynamics of the ligand-binding pocket but also induced unique dynamic responses that were indicative of higher affinity binding relative to UAB30, especially for Helix 3. UAB110 binding also showed increased dynamics towards the dimer interface through the Helix 8 and Helix 9 regions. These data suggest that UAB110 and UAB111 are potent activators of RXR-RAR signaling pathways but accomplish activation through different molecular responses to ligand binding.
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Affiliation(s)
- Nathalia Melo
- O'Neil Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama, USA; Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Olga V Belyaeva
- O'Neil Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama, USA; Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Wilhelm K Berger
- Departments of Medicine and Biological Chemistry, Johns Hopkins University School of Medicine Institute for Fundamental Biomedical Research, Johns Hopkins All Children's Hospital, St. Petersburg, Florida, USA
| | - Laszlo Halasz
- Departments of Medicine and Biological Chemistry, Johns Hopkins University School of Medicine Institute for Fundamental Biomedical Research, Johns Hopkins All Children's Hospital, St. Petersburg, Florida, USA
| | - Jianshi Yu
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland, USA
| | - Nagesh Pilli
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland, USA
| | - Zhengrong Yang
- O'Neil Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama, USA; Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Alla V Klyuyeva
- O'Neil Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Craig A Elmets
- O'Neil Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama, USA; Department of Dermatology, University of Alabama at Birmingham, Birmingham, Alabama, USA; Birmingham VA Medical Center, Birmingham, Alabama, USA
| | - Venkatram Atigadda
- O'Neil Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama, USA; Department of Dermatology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Donald D Muccio
- O'Neil Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama, USA; Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Maureen A Kane
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland, USA
| | - Laszlo Nagy
- Departments of Medicine and Biological Chemistry, Johns Hopkins University School of Medicine Institute for Fundamental Biomedical Research, Johns Hopkins All Children's Hospital, St. Petersburg, Florida, USA
| | - Natalia Y Kedishvili
- O'Neil Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama, USA; Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.
| | - Matthew B Renfrow
- O'Neil Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama, USA; Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.
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8
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Atigadda VR, Kashyap MP, Yang Z, Chattopadhyay D, Melo N, Sinha R, Belyaeva OV, Chou CF, Chang PL, Kedishvili NY, Grubbs CJ, Renfrow MB, Muccio DD, Elmets CA, Athar M. Conformationally Defined Rexinoids for the Prevention of Inflammation and Nonmelanoma Skin Cancers. J Med Chem 2022; 65:14409-14423. [PMID: 36318154 PMCID: PMC9942614 DOI: 10.1021/acs.jmedchem.2c00735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Compound 1 is a potent rexinoid that is highly effective in cancer chemoprevention but elevates serum triglycerides. In an effort to separate the lipid toxicity from the anticancer activity of 1, we synthesized four new analogs of rexinoid 1, of which three rexinoids did not elevate serum triglycerides. Rexinoids 3 and 4 are twice as potent as rexinoid 1 in binding to Retinoid X receptor (RXR). All-trans retinoic acid (ATRA) plays a key role in maintaining skin homeostasis, and rexinoids 3-6 are highly effective in upregulating the genes responsible for the biosynthesis of ATRA. Inflammation plays a key role in skin cancer, and rexinoids 3 and 4 are highly effective in diminishing LPS-induced inflammation. Rexinoids 3 and 4 are highly effective in preventing UVB-induced nonmelanoma skin cancer (NMSC) without displaying any overt toxicities. Biophysical studies of rexinoids 3 and 5 bound to hRXRα-ligand binding domain (LBD) reveal important conformational and dynamical differences in the ligand binding domain.
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9
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Yang Z, Muccio DD, Melo N, Atigadda VR, Renfrow MB. Stability of the Retinoid X Receptor-α Homodimer in the Presence and Absence of Rexinoid and Coactivator Peptide. Biochemistry 2021; 60:1165-1177. [PMID: 33792309 PMCID: PMC9949482 DOI: 10.1021/acs.biochem.0c00865] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Differential scanning calorimetry and differential scanning fluorimetry were used to measure the thermal stability of human retinoid X receptor-α ligand binding domain (RXRα LBD) homodimer in the absence or presence of rexinoid and coactivator peptide, GRIP-1. The apo-RXRα LBD homodimer displayed a single thermal unfolding transition with a Tm of 58.7 °C and an unfolding enthalpy (ΔH) of 673 kJ/mol (12.5 J/g), much lower than average value (35 J/g) of small globular proteins. Using a heat capacity change (ΔCp) of 15 kJ/(mol K) determined by measurements at different pH values, the free energy of unfolding (ΔG) of the native state was 33 kJ/mol at 37 °C. Rexinoid binding to the apo-homodimer increased Tm by 5 to 9 °C and increased the ΔG of the native homodimer by 12 to 20 kJ/mol at 37 °C, consistent with the nanomolar dissociation constant (Kd) of the rexinoids. GRIP-1 binding to holo-homodimers containing rexinoid resulted in additional increases in ΔG of 14 kJ/mol, a value that was the same for all three rexinoids. Binding of rexinoid and GRIP-1 resulted in a combined 50% increase in unfolding enthalpy, consistent with reduced structural fluidity and more compact folding observed in other published structural studies. The complexes of UAB110 and UAB111 are each more stable than the UAB30 complex by 8 kJ/mol due to enhanced hydrophobic interactions in the binding pocket because of their larger end groups. This increase in thermodynamic stability positively correlates with their improved RXR activation potency. Thermodynamic measurements are thus valuable in predicting agonist potency.
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Affiliation(s)
- Zhengrong Yang
- Department of Biochemistry & Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
| | - Donald D. Muccio
- Department of Biochemistry & Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
| | - Nathalia Melo
- Department of Biochemistry & Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
| | - Venkatram R. Atigadda
- Department of Dermatology, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
| | - Matthew B. Renfrow
- Department of Biochemistry & Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
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10
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Schierle S, Chaikuad A, Lillich FF, Ni X, Woltersdorf S, Schallmayer E, Renelt B, Ronchetti R, Knapp S, Proschak E, Merk D. Oxaprozin Analogues as Selective RXR Agonists with Superior Properties and Pharmacokinetics. J Med Chem 2021; 64:5123-5136. [PMID: 33793232 DOI: 10.1021/acs.jmedchem.1c00235] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The retinoid X receptors (RXR) are ligand-activated transcription factors involved in multiple regulatory networks as universal heterodimer partners for nuclear receptors. Despite their high therapeutic potential in many pathologies, targeting of RXR has only been exploited in cancer treatment as the currently available RXR agonists suffer from exceptional lipophilicity, poor pharmacokinetics (PK), and adverse effects. Aiming to overcome the limitations and to provide improved RXR ligands, we developed a new potent RXR ligand chemotype based on the nonsteroidal anti-inflammatory drug oxaprozin. Systematic structure-activity relationship analysis enabled structural optimization toward low nanomolar potency similar to the well-established rexinoids. Cocrystal structures of the most active derivatives demonstrated orthosteric binding, and in vivo profiling revealed superior PK properties compared to current RXR agonists. The optimized compounds were highly selective for RXR activation and induced RXR-regulated gene expression in native cellular and in vivo settings suggesting them as excellent chemical tools to further explore the therapeutic potential of RXR.
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Affiliation(s)
- Simone Schierle
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany
| | - Apirat Chaikuad
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany.,Structural Genomics Consortium, BMLS, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt, Germany
| | - Felix F Lillich
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany
| | - Xiaomin Ni
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany.,Structural Genomics Consortium, BMLS, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt, Germany
| | - Stefano Woltersdorf
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany
| | - Espen Schallmayer
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany
| | - Beatrice Renelt
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany
| | - Riccardo Ronchetti
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany.,Structural Genomics Consortium, BMLS, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt, Germany
| | - Ewgenij Proschak
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany
| | - Daniel Merk
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany
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11
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Xia L, Shen D, Zhang Y, Lu J, Wang M, Wang H, Chen Y, Xue D, Xie D, Li G. Targeting the TR4 nuclear receptor with antagonist bexarotene can suppress the proopiomelanocortin signalling in AtT-20 cells. J Cell Mol Med 2021; 25:2404-2417. [PMID: 33491272 PMCID: PMC7933964 DOI: 10.1111/jcmm.16074] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 09/29/2020] [Accepted: 10/25/2020] [Indexed: 01/12/2023] Open
Abstract
Drug options for the life‐threatening Cushing's disease are limited, and surgical resection or radiation therapy is not invariably effective. Testicular receptor 4 (TR4) has been identified as a novel drug target to treat Cushing's disease. We built the structure model of TR4 and searched the TR4 antagonist candidate via in silico virtual screening. Bexarotene was identified as an antagonist of TR4 that can directly interact with TR4 ligand binding domain (TR4‐LBD) and induces a conformational change in the secondary structure of TR4‐LBD. Bexarotene suppressed AtT‐20 cell growth, proopiomelanocortin (POMC) expression and adrenocorticotropin (ACTH) secretion. Mechanism dissection revealed that bexarotene could suppress TR4‐increased POMC expression via promoting the TR4 translocation from the nucleus to the cytoplasm. This TR4 translocation might then result in reducing the TR4 binding to the TR4 response element (TR4RE) on the 5’ promoter region of POMC. Results from in vivo mouse model also revealed that oral bexarotene administration markedly suppressed ACTH‐secreting tumour growth, adrenal enlargement and the secretion of ACTH and corticosterone in mice with already established tumours. Together, these results suggest that bexarotene may be developed as a potential novel therapeutic drug to better suppress Cushing's disease.
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Affiliation(s)
- Liqun Xia
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Danyang Shen
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Youyun Zhang
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jieyang Lu
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Mingchao Wang
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Huan Wang
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yuanlei Chen
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Dingwei Xue
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Dajiang Xie
- Department of Neurosurgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Gonghui Li
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
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12
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Watanabe M, Fujihara M, Motoyama T, Kawasaki M, Yamada S, Takamura Y, Ito S, Makishima M, Nakano S, Kakuta H. Discovery of a "Gatekeeper" Antagonist that Blocks Entry Pathway to Retinoid X Receptors (RXRs) without Allosteric Ligand Inhibition in Permissive RXR Heterodimers. J Med Chem 2020; 64:430-439. [PMID: 33356247 DOI: 10.1021/acs.jmedchem.0c01354] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Retinoid X receptor (RXR) heterodimers such as PPAR/RXR, LXR/RXR, and FXR/RXR can be activated by RXR agonists alone and are therefore designated as permissive. Similarly, existing RXR antagonists show allosteric antagonism toward partner receptor agonists in these permissive RXR heterodimers. Here, we show 1-(3-(2-ethoxyethoxy)-5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen-2-yl)-2-(trifluoromethyl)-1H-benzo[d]imidazole-5-carboxylic acid (14, CBTF-EE) as the first RXR antagonist that does not show allosteric inhibition in permissive RXR heterodimers. This compound was designed based on the hypothesis that RXR antagonists that do not induce conformational changes of RXR would not exhibit such allosteric inhibition. CD spectra and X-ray co-crystallography of the complex of 14 and the RXR ligand binding domain (LBD) confirmed that 14 does not change the conformation of hRXR-LBD. The X-ray structure analysis revealed that 14 binds at the entrance of the ligand binding pocket (LBP), blocking access to the LBP and thus serving as a "gatekeeper".
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Affiliation(s)
- Masaki Watanabe
- Division of Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 1-1-1, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Michiko Fujihara
- Division of Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 1-1-1, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan.,AIBIOS Company. Ltd., Tri-Seven Roppongi 8F 7-7-7 Roppongi, Minato-ku, Tokyo 106-0032, Japan
| | - Tomoharu Motoyama
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Mayu Kawasaki
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Shoya Yamada
- Division of Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 1-1-1, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan.,Research Fellowship Division, Japan Society for the Promotion of Science, Sumitomo-Ichibancho FS Bldg., 8 Ichibancho, Chiyoda-ku, Tokyo 102-8472, Japan
| | - Yuta Takamura
- Division of Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 1-1-1, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Sohei Ito
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Makoto Makishima
- Division of Biochemistry, Department of Biomedical Sciences, Nihon University School of Medicine, 30-1 Oyaguchi-kamicho, Itabashi-ku, Tokyo 173-8610, Japan
| | - Shogo Nakano
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Hiroki Kakuta
- Division of Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 1-1-1, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
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13
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Xia L, Shen D, Wang H, Ren L, Chen Y, Li G. Identification of Small-Molecule Regulators of Testicular Receptor 4 via a Drug Repurposing Screening. ACS Omega 2020; 5:30625-30632. [PMID: 33283111 PMCID: PMC7711931 DOI: 10.1021/acsomega.0c04623] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 11/03/2020] [Indexed: 06/12/2023]
Abstract
The testicular receptor 4 (TR4) is a nuclear receptor implicated in multiple pathological processes, including cancer development, chemotherapy, and radiotherapy resistance. However, no effective TR4 small-molecule regulator is available to date. Here, we assessed a physical-interaction-based surface plasmon resonance imaging assay for discovery of TR4 regulators. We screened 1018 FDA-approved drugs and obtained 126 drugs with K D values below 10-6 M. The dual-luciferase-based biological assay verified four activatory compounds and two inhibitory compounds against TR4. Among them, nilotinib exhibited the most potent inhibitor, with an EC50 of 1.05 μM, while genistein represented the most potent activator, with an EC50 of 2.42 μM. Both drugs were predicted to bind in the ligand binding pocket of TR4. The circular dichroism spectroscopic assay revealed differed conformation changes upon nilotinib or genistein binding. These results established our combined physical and biological approaches as a highly effective way to identify and develop new TR4 regulators.
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14
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Chaikuad A, Pollinger J, Rühl M, Ni X, Kilu W, Heering J, Merk D. Comprehensive Set of Tertiary Complex Structures and Palmitic Acid Binding Provide Molecular Insights into Ligand Design for RXR Isoforms. Int J Mol Sci 2020; 21:E8457. [PMID: 33187070 PMCID: PMC7697888 DOI: 10.3390/ijms21228457] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/06/2020] [Accepted: 11/09/2020] [Indexed: 01/10/2023] Open
Abstract
The retinoid X receptor (RXR) is a ligand-sensing transcription factor acting mainly as a universal heterodimer partner for other nuclear receptors. Despite presenting as a potential therapeutic target for cancer and neurodegeneration, adverse effects typically observed for RXR agonists, likely due to the lack of isoform selectivity, limit chemotherapeutic application of currently available RXR ligands. The three human RXR isoforms exhibit different expression patterns; however, they share high sequence similarity, presenting a major obstacle toward the development of subtype-selective ligands. Here, we report the discovery of the saturated fatty acid, palmitic acid, as an RXR ligand and disclose a uniform set of crystal structures of all three RXR isoforms in an active conformation induced by palmitic acid. A structural comparison revealed subtle differences among the RXR subtypes. We also observed an ability of palmitic acid as well as myristic acid and stearic acid to induce recruitment of steroid receptor co-activator 1 to the RXR ligand-binding domain with low micromolar potencies. With the high, millimolar endogenous concentrations of these highly abundant lipids, our results suggest their potential involvement in RXR signaling.
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Affiliation(s)
- Apirat Chaikuad
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany; (J.P.); (M.R.); (X.N.); (W.K.)
- Structural Genomics Consortium, BMLS, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt, Germany
| | - Julius Pollinger
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany; (J.P.); (M.R.); (X.N.); (W.K.)
| | - Michael Rühl
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany; (J.P.); (M.R.); (X.N.); (W.K.)
| | - Xiaomin Ni
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany; (J.P.); (M.R.); (X.N.); (W.K.)
- Structural Genomics Consortium, BMLS, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt, Germany
| | - Whitney Kilu
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany; (J.P.); (M.R.); (X.N.); (W.K.)
| | - Jan Heering
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology TMP, Theodor-Stern-Kai 7, 60596 Frankfurt, Germany;
| | - Daniel Merk
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany; (J.P.); (M.R.); (X.N.); (W.K.)
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15
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Abstract
This chapter has been conceived as an introductory text to aid in the understanding of the key design strategies for the development of synthetic analogs of endogenous retinoids as ligands for the retinoic acid receptors (RARs) and retinoid X receptors (RXRs). The structure and binding characteristics of the endogenous retinoids are first explained to put the main chemical design challenges in context. Existing biochemical and structural data is then used to describe the guiding principles used to develop agonists and antagonists of the RARs and RXRs. In light of the increasing proliferation of biophysical methods that employ fluorescence measurements or molecular tags, we also examine the application of retinoids as probes and the chemical principles required to develop these tools.
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Affiliation(s)
| | - Andrew Whiting
- Department of Chemistry, Durham University, Lower Mountjoy, Durham, United Kingdom
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16
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Shang J, Mosure SA, Zheng J, Brust R, Bass J, Nichols A, Solt LA, Griffin PR, Kojetin DJ. A molecular switch regulating transcriptional repression and activation of PPARγ. Nat Commun 2020; 11:956. [PMID: 32075969 PMCID: PMC7031403 DOI: 10.1038/s41467-020-14750-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 01/29/2020] [Indexed: 12/20/2022] Open
Abstract
Nuclear receptor (NR) transcription factors use a conserved activation function-2 (AF-2) helix 12 mechanism for agonist-induced coactivator interaction and NR transcriptional activation. In contrast, ligand-induced corepressor-dependent NR repression appears to occur through structurally diverse mechanisms. We report two crystal structures of peroxisome proliferator-activated receptor gamma (PPARγ) in an inverse agonist/corepressor-bound transcriptionally repressive conformation. Helix 12 is displaced from the solvent-exposed active conformation and occupies the orthosteric ligand-binding pocket enabled by a conformational change that doubles the pocket volume. Paramagnetic relaxation enhancement (PRE) NMR and chemical crosslinking mass spectrometry confirm the repressive helix 12 conformation. PRE NMR also defines the mechanism of action of the corepressor-selective inverse agonist T0070907, and reveals that apo-helix 12 exchanges between transcriptionally active and repressive conformations—supporting a fundamental hypothesis in the NR field that helix 12 exchanges between transcriptionally active and repressive conformations. Structural studies of nuclear receptor transcription factors revealed that nearly all nuclear receptors share a conserved helix 12 dependent transcriptional activation mechanism. Here the authors present two crystal structures of peroxisome proliferator-activated receptor gamma (PPARγ) in an inverse agonist/corepressor-bound transcriptionally repressive conformation, where helix 12 is located within the orthosteric ligand-binding pocket instead, and discuss mechanistic implications.
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Affiliation(s)
- Jinsai Shang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Sarah A Mosure
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL, 33458, USA.,Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, FL, 33458, USA.,Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Jie Zheng
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL, 33458, USA.,Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Richard Brust
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Jared Bass
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Ashley Nichols
- Summer Undergraduate Research Fellows (SURF) program, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Laura A Solt
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, 33458, USA.,Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Patrick R Griffin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL, 33458, USA.,Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Douglas J Kojetin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL, 33458, USA. .,Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA.
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17
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Kolesar JM, Andrews S, Green H, Havighurst TC, Wollmer BW, DeShong K, Laux DE, Krontiras H, Muccio DD, Kim K, Grubbs CJ, House MG, Parnes HL, Heckman-Stoddard BM, Bailey HH. A Randomized, Placebo-Controlled, Double-Blind, Dose Escalation, Single Dose, and Steady-State Pharmacokinetic Study of 9cUAB30 in Healthy Volunteers. Cancer Prev Res (Phila) 2019; 12:903-912. [PMID: 31484659 DOI: 10.1158/1940-6207.capr-19-0310] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 08/04/2019] [Accepted: 08/28/2019] [Indexed: 11/16/2022]
Abstract
9cUAB30 is a synthetic analogue of 9-cis retinoic acid with chemoprevention activity in cell lines and animal models. The purpose of this phase I placebo-controlled, double-blinded, dose escalation study of 9cUAB30 was to evaluate its safety, pharmacokinetics, and determine a dose for future phase II studies. Participants received a single dose of study drug (placebo or 9cUAB30) on day 1 followed by a 6-day drug-free period and then 28 days of continuous daily dosing starting on day 8. Fifty-three healthy volunteers were enrolled into five dose cohorts (20, 40, 80, 160, and 240 mg). Participants were randomized within each dose level to receive either 9cUAB30 (n = 8) or placebo (n = 2). 9cUAB30 was well tolerated, with no dose limiting toxicities reported and no evidence of persistent elevations in serum triglycerides or cholesterol. Treatment-emergent grade 3 hypertension occurred in 1 of 8 participants at the 20 mg dose level and in 2 of 8 at the 240 mg dose level, all considered unlikely related to study agent; no other grade 3 adverse events were observed. The AUC increased, as expected, between day 1 (single dose) and day 36 (steady state). Pharmacokinetics were linear in dose escalation through 160 mg. 9cUAB30 administered by daily oral dosing has a favorable safety and pharmacokinetic profile. On the basis of the observed safety profile and lack of linearity in pharmacokinetics at doses greater than 160 mg, the recommended phase II dose with the current formulation is 160 mg once daily.
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Affiliation(s)
- Jill M Kolesar
- College of Pharmacy, University of Kentucky, Lexington, Kentucky. .,University of Wisconsin Carbone Cancer Center, Madison, Wisconsin
| | - Shannon Andrews
- University of Wisconsin Carbone Cancer Center, Madison, Wisconsin
| | - Heather Green
- University of Wisconsin Carbone Cancer Center, Madison, Wisconsin
| | - Tom C Havighurst
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, Wisconsin
| | | | - Katina DeShong
- University of Wisconsin Carbone Cancer Center, Madison, Wisconsin
| | - Douglas E Laux
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa
| | - Helen Krontiras
- Department of Surgery, University of Alabama at Birmingham, Birmingham, Alabama
| | - Donald D Muccio
- Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - KyungMann Kim
- University of Wisconsin Carbone Cancer Center, Madison, Wisconsin.,Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, Wisconsin
| | - Clinton J Grubbs
- Department of Surgery, University of Alabama at Birmingham, Birmingham, Alabama
| | - Margaret G House
- Division of Cancer Prevention, National Cancer Institute, Rockville, Maryland
| | - Howard L Parnes
- Division of Cancer Prevention, National Cancer Institute, Rockville, Maryland
| | | | - Howard H Bailey
- University of Wisconsin Carbone Cancer Center, Madison, Wisconsin. .,Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
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18
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Schierle S, Merk D. Therapeutic modulation of retinoid X receptors – SAR and therapeutic potential of RXR ligands and recent patents. Expert Opin Ther Pat 2019; 29:605-621. [DOI: 10.1080/13543776.2019.1643322] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Simone Schierle
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
| | - Daniel Merk
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
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19
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Pollinger J, Gellrich L, Schierle S, Kilu W, Schmidt J, Kalinowsky L, Ohrndorf J, Kaiser A, Heering J, Proschak E, Merk D. Tuning Nuclear Receptor Selectivity of Wy14,643 towards Selective Retinoid X Receptor Modulation. J Med Chem 2019; 62:2112-2126. [PMID: 30702885 DOI: 10.1021/acs.jmedchem.8b01848] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The fatty acid sensing nuclear receptor families retinoid X receptors (RXRs) and peroxisome proliferator-activated receptors (PPARs) hold therapeutic potential in neurodegeneration. Valuable pleiotropic activities of Wy14,643 in models of such conditions exceed its known PPAR agonistic profile. Here, we characterize the compound as an RXR agonist explaining the pleiotropic effects and report its systematic structure-activity relationship analysis with the discovery of specific molecular determinants driving activity on PPARs and RXRs. We have designed close analogues of the drug comprising selective and dual agonism on RXRs and PPARs that may serve as superior pharmacological tools to study the role and interplay of the nuclear receptors in various pathologies. A systematically optimized high potency RXR agonist revealed activity in vivo and active concentrations in brain. With its lack of RXR/liver X receptor-mediated side effects and superior profile compared to classical rexinoids, it establishes a new class of innovative RXR modulators to overcome key challenges in RXR targeting drug discovery.
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Affiliation(s)
- Julius Pollinger
- Institute of Pharmaceutical Chemistry , Goethe University Frankfurt , Max-von-Laue-Str. 9 , D-60438 Frankfurt , Germany
| | - Leonie Gellrich
- Institute of Pharmaceutical Chemistry , Goethe University Frankfurt , Max-von-Laue-Str. 9 , D-60438 Frankfurt , Germany
| | - Simone Schierle
- Institute of Pharmaceutical Chemistry , Goethe University Frankfurt , Max-von-Laue-Str. 9 , D-60438 Frankfurt , Germany
| | - Whitney Kilu
- Institute of Pharmaceutical Chemistry , Goethe University Frankfurt , Max-von-Laue-Str. 9 , D-60438 Frankfurt , Germany
| | - Jurema Schmidt
- Institute of Pharmaceutical Chemistry , Goethe University Frankfurt , Max-von-Laue-Str. 9 , D-60438 Frankfurt , Germany
| | - Lena Kalinowsky
- Institute of Pharmaceutical Chemistry , Goethe University Frankfurt , Max-von-Laue-Str. 9 , D-60438 Frankfurt , Germany
| | - Julia Ohrndorf
- Institute of Pharmaceutical Chemistry , Goethe University Frankfurt , Max-von-Laue-Str. 9 , D-60438 Frankfurt , Germany
| | - Astrid Kaiser
- Institute of Pharmaceutical Chemistry , Goethe University Frankfurt , Max-von-Laue-Str. 9 , D-60438 Frankfurt , Germany
| | - Jan Heering
- Project Group Translational Medicine and Pharmacology TMP , Fraunhofer IME , Theodor-Stern-Kai 7 , D-60596 Frankfurt , Germany
| | - Ewgenij Proschak
- Institute of Pharmaceutical Chemistry , Goethe University Frankfurt , Max-von-Laue-Str. 9 , D-60438 Frankfurt , Germany
| | - Daniel Merk
- Institute of Pharmaceutical Chemistry , Goethe University Frankfurt , Max-von-Laue-Str. 9 , D-60438 Frankfurt , Germany
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20
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Heitel P, Gellrich L, Kalinowsky L, Heering J, Kaiser A, Ohrndorf J, Proschak E, Merk D. Computer-Assisted Discovery and Structural Optimization of a Novel Retinoid X Receptor Agonist Chemotype. ACS Med Chem Lett 2019; 10:203-208. [PMID: 30783504 PMCID: PMC6378677 DOI: 10.1021/acsmedchemlett.8b00551] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 12/27/2018] [Indexed: 12/21/2022] Open
Abstract
As universal heterodimer partners of many nuclear receptors, the retinoid X receptors (RXRs) constitute key transcription factors. They regulate cell proliferation, differentiation, inflammation, and metabolic homeostasis and have recently been proposed as potential drug targets for neurodegenerative and inflammatory diseases. Owing to the hydrophobic nature of RXR ligand binding sites, available synthetic RXR ligands are lipophilic, and their structural diversity is limited. Here, we disclose the computer-assisted discovery of a novel RXR agonist chemotype and its systematic optimization toward potent RXR modulators. We have developed a nanomolar RXR agonist with high selectivity among nuclear receptors and superior physicochemical properties compared to classical rexinoids that appears suitable for in vivo applications and as lead for future RXR-targeting medicinal chemistry.
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Affiliation(s)
- Pascal Heitel
- Institute
of Pharmaceutical Chemistry, Goethe University
Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Leonie Gellrich
- Institute
of Pharmaceutical Chemistry, Goethe University
Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Lena Kalinowsky
- Institute
of Pharmaceutical Chemistry, Goethe University
Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Jan Heering
- Project
Group Translational Medicine and Pharmacology TMP, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Theodor-Stern-Kai 7, D-60596 Frankfurt, Germany
| | - Astrid Kaiser
- Institute
of Pharmaceutical Chemistry, Goethe University
Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Julia Ohrndorf
- Institute
of Pharmaceutical Chemistry, Goethe University
Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Ewgenij Proschak
- Institute
of Pharmaceutical Chemistry, Goethe University
Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Daniel Merk
- Institute
of Pharmaceutical Chemistry, Goethe University
Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
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21
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Miyashita Y, Numoto N, Arulmozhiraja S, Nakano S, Matsuo N, Shimizu K, Shibahara O, Fujihara M, Kakuta H, Ito S, Ikura T, Ito N, Tokiwa H. Dual conformation of the ligand induces the partial agonistic activity of retinoid X receptor α (RXRα). FEBS Lett 2018; 593:242-250. [DOI: 10.1002/1873-3468.13301] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 11/01/2018] [Accepted: 11/14/2018] [Indexed: 01/29/2023]
Affiliation(s)
- Yurina Miyashita
- Department of Chemistry; Rikkyo University; Tokyo Japan
- AMED-CREST; Japan Agency for Medical Research and Development (AMED); Tokyo Japan
- Department of Structural Biology; Medical Research Institute; Tokyo Medical and Dental University (TMDU); Japan
| | - Nobutaka Numoto
- Department of Structural Biology; Medical Research Institute; Tokyo Medical and Dental University (TMDU); Japan
| | - Sundaram Arulmozhiraja
- Department of Chemistry; Rikkyo University; Tokyo Japan
- AMED; Japan Agency for Medical Research and Development (AMED); Tokyo Japan
| | - Shogo Nakano
- School of Food and Nutritional Sciences; University of Shizuoka; Japan
| | - Naoya Matsuo
- Department of Chemistry; Rikkyo University; Tokyo Japan
| | | | - Osamu Shibahara
- Division of Pharmaceutical Sciences; Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences; Japan
| | - Michiko Fujihara
- Division of Pharmaceutical Sciences; Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences; Japan
| | - Hiroki Kakuta
- Division of Pharmaceutical Sciences; Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences; Japan
| | - Sohei Ito
- School of Food and Nutritional Sciences; University of Shizuoka; Japan
| | - Teikichi Ikura
- Department of Structural Biology; Medical Research Institute; Tokyo Medical and Dental University (TMDU); Japan
| | - Nobutoshi Ito
- Department of Structural Biology; Medical Research Institute; Tokyo Medical and Dental University (TMDU); Japan
| | - Hiroaki Tokiwa
- Department of Chemistry; Rikkyo University; Tokyo Japan
- AMED-CREST; Japan Agency for Medical Research and Development (AMED); Tokyo Japan
- AMED; Japan Agency for Medical Research and Development (AMED); Tokyo Japan
- Research Center for Smart Molecules; Rikkyo University; Tokyo Japan
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22
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Wang W, Nakashima KI, Hirai T, Inoue M. Neuroprotective effect of naturally occurring RXR agonists isolated from Sophora tonkinensis Gagnep. on amyloid-β-induced cytotoxicity in PC12 cells. J Nat Med 2018; 73:154-162. [DOI: 10.1007/s11418-018-1257-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 10/13/2018] [Indexed: 01/08/2023]
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Hanish BJ, Hackney Price JF, Kaneko I, Ma N, van der Vaart A, Wagner CE, Jurutka PW, Marshall PA. A novel gene expression analytics-based approach to structure aided design of rexinoids for development as next-generation cancer therapeutics. Steroids 2018; 135:36-49. [PMID: 29704526 PMCID: PMC5977990 DOI: 10.1016/j.steroids.2018.04.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 04/09/2018] [Accepted: 04/18/2018] [Indexed: 12/20/2022]
Abstract
Rexinoids are powerful ligands that bind to retinoid-X-receptors (RXRs) and show great promise as therapeutics for a wide range of diseases, including cancer. However, only one rexinoid, bexarotene (Targretin TM) has been successfully transitioned from the bench to the clinic and used to treat cutaneous T-cell lymphoma (CTCL). Our goal is to develop novel potent rexinoids with a less untoward side effect profile than bexarotene. To this end, we have synthesized a wide array of rexinoids with EC50 values and biological activity similar to bexarotene. In order to determine their suitability for additional downstream analysis, and to identify potential candidate analogs for clinical translation, we treated human CTCL cells in culture and employed microarray technology to assess gene expression profiles. We analyzed twelve rexinoids and found they could be stratified into three distinct categories based on their gene expression: similar to bexarotene, moderately different from bexarotene, and substantially different from bexarotene. Surprisingly, small changes in the structure of the bexarotene parent compound led to marked differences in gene expression profiles. Furthermore, specific analogs diverged markedly from our hypothesis in expression of genes expected to be important for therapeutic promise. However, promoter analysis of genes whose expression was analyzed indicates general regulatory trends along structural frameworks. Our results suggest that certain structural motifs, particularly the basic frameworks found in analog 4 and analog 9, represent important starting points to exploit in generating additional rexinoids for future study and therapeutic applications.
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Affiliation(s)
- Bentley J Hanish
- New College of Interdisciplinary Arts and Sciences, Arizona State University, Glendale, AZ, United States
| | - Jennifer F Hackney Price
- New College of Interdisciplinary Arts and Sciences, Arizona State University, Glendale, AZ, United States
| | - Ichiro Kaneko
- New College of Interdisciplinary Arts and Sciences, Arizona State University, Glendale, AZ, United States; University of Arizona College of Medicine-Phoenix, Department of Basic Medical Sciences, Phoenix, AZ, United States; Department of Molecular Nutrition, Institution of Health Bioscience, University of Tokushima Graduate School, Kuramoto-cho, Japan
| | - Ning Ma
- Department of Chemistry, University of South Florida, Tampa, FL 33620, United States
| | - Arjan van der Vaart
- Department of Chemistry, University of South Florida, Tampa, FL 33620, United States
| | - Carl E Wagner
- New College of Interdisciplinary Arts and Sciences, Arizona State University, Glendale, AZ, United States
| | - Peter W Jurutka
- New College of Interdisciplinary Arts and Sciences, Arizona State University, Glendale, AZ, United States; University of Arizona College of Medicine-Phoenix, Department of Basic Medical Sciences, Phoenix, AZ, United States; University of Arizona Cancer Center, Tucson, AZ, United States
| | - Pamela A Marshall
- New College of Interdisciplinary Arts and Sciences, Arizona State University, Glendale, AZ, United States.
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Merk D, Grisoni F, Friedrich L, Gelzinyte E, Schneider G. Computer-Assisted Discovery of Retinoid X Receptor Modulating Natural Products and Isofunctional Mimetics. J Med Chem 2018; 61:5442-5447. [DOI: 10.1021/acs.jmedchem.8b00494] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Daniel Merk
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
| | - Francesca Grisoni
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza, 1, IT-20126 Milan, Italy
| | - Lukas Friedrich
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
| | - Elena Gelzinyte
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
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25
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Pham HDQ, Thai NQ, Bednarikova Z, Linh HQ, Gazova Z, Li MS. Bexarotene cannot reduce amyloid beta plaques through inhibition of production of amyloid beta peptides:in silicoandin vitrostudy. Phys Chem Chem Phys 2018; 20:24329-24338. [DOI: 10.1039/c8cp00049b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Recently, it has been reported that anti-cancer drug bexarotene can remarkably destroy amyloid beta (Aβ) plaques in mouse models suggesting therapeutic potential for Alzheimer's disease.
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Affiliation(s)
- Huy Dinh Quoc Pham
- Institute of Physics
- Polish Academy of Sciences
- 02-668 Warsaw
- Poland
- Institute for Computational Science and Technology
| | - Nguyen Quoc Thai
- Institute for Computational Science and Technology
- Quang Trung Software City
- Ho Chi Minh City
- Vietnam
- Biomedical Engineering Department
| | - Zuzana Bednarikova
- Department of Biophysics
- Institute of Experimental Physics
- Slovak Academy of Sciences
- 040 01 Kosice
- Slovakia
| | - Huynh Quang Linh
- Biomedical Engineering Department
- University of Technology
- Ho Chi Minh City
- Vietnam
| | - Zuzana Gazova
- Department of Biophysics
- Institute of Experimental Physics
- Slovak Academy of Sciences
- 040 01 Kosice
- Slovakia
| | - Mai Suan Li
- Institute of Physics
- Polish Academy of Sciences
- 02-668 Warsaw
- Poland
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26
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Affiliation(s)
- Tanaji T. Talele
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John’s University, Queens, New York 11439, United States
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27
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Thai NQ, Nguyen HL, Linh HQ, Li MS. Protocol for fast screening of multi-target drug candidates: Application to Alzheimer's disease. J Mol Graph Model 2017; 77:121-129. [PMID: 28850894 DOI: 10.1016/j.jmgm.2017.08.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 08/03/2017] [Accepted: 08/04/2017] [Indexed: 01/08/2023]
Abstract
The treatment of many diseases may require drugs that are capable to attack multiple targets simultaneously. Obviously, the virtual screening of multi-target drug candidates is much more time consuming compared to the single-target case. This, in particular, concerns the last step of virtual screening where the binding free energy is computed by conventional molecular dynamics simulation. To overcome this difficulty we propose a simple protocol which is relied on the fast steered molecular dynamics simulation and on available experimental data on binding affinity of reference ligand to a given target. Namely, first we compute non-equilibrium works generated during pulling ligands from the binding site using the steered molecular dynamics method. Then as top leads we choose only those compounds that have the non-equilibrium work larger than that of a reference compound for which the binding free energy has been already known from experiment. Despite many efforts no cures for AD (Alzheimer's disease) have been found. One of possible reasons for this failure is that drug candidates were developed for a single target, while there are exist many possible pathways to AD. Applying our new protocol to five targets including amyloid beta fibril, peroxisome proliferator-activated receptor γ, retinoic X receptor α, β- and γ-secretases, we have found two potential drugs (CID 16040294 and CID 9998128) for AD from the large PubChem database. We have also shown that these two ligands can interfere with the activity of popular Acetylcholinesterase target through strong binding towards it.
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Affiliation(s)
- Nguyen Quoc Thai
- Institute for Computational Sciences and Technology,SBI building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Viet Nam; Dong Thap University,783 Pham Huu Lau Street, Ward 6, Cao Lanh City, Dong Thap, Viet Nam; Biomedical Engineering Department, University of Technology -VNU HCM, 268 Ly Thuong Kiet Str., Distr. 10, Ho Chi Minh City, Viet Nam
| | - Hoang Linh Nguyen
- Institute for Computational Sciences and Technology,SBI building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Viet Nam
| | - Huynh Quang Linh
- Biomedical Engineering Department, University of Technology -VNU HCM, 268 Ly Thuong Kiet Str., Distr. 10, Ho Chi Minh City, Viet Nam
| | - Mai Suan Li
- Institute for Computational Sciences and Technology,SBI building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Viet Nam; Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland.
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28
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Abstract
INTRODUCTION Hydrogen deuterium exchange mass spectrometry (HDX-MS) is a powerful methodology to study protein dynamics, protein folding, protein-protein interactions, and protein small molecule interactions. The development of novel methodologies and technical advancements in mass spectrometers has greatly expanded the accessibility and acceptance of this technique within both academia and industry. Areas covered: This review examines the theoretical basis of how amide exchange occurs, how different mass spectrometer approaches can be used for HDX-MS experiments, as well as the use of HDX-MS in drug development, specifically focusing on how HDX-MS is used to characterize bio-therapeutics, and its use in examining protein-protein and protein small molecule interactions. Expert opinion: HDX-MS has been widely accepted within the pharmaceutical industry for the characterization of bio-therapeutics as well as in the mapping of antibody drug epitopes. However, there is room for this technique to be more widely used in the drug discovery process. This is particularly true in the use of HDX-MS as a complement to other high-resolution structural approaches, as well as in the development of small molecule therapeutics that can target both active-site and allosteric binding sites.
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Affiliation(s)
- Glenn R Masson
- a Protein and Nucleic Acid Chemistry Division , MRC Laboratory of Molecular Biology , Cambridge , UK
| | - Meredith L Jenkins
- b Department of Biochemistry and Microbiology , University of Victoria , Victoria , Canada
| | - John E Burke
- b Department of Biochemistry and Microbiology , University of Victoria , Victoria , Canada
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Abstract
Lipids are produced site-specifically in cells and then distributed nonrandomly among membranes via vesicular and nonvesicular trafficking mechanisms. The latter involves soluble amphitropic proteins extracting specific lipids from source membranes to function as molecular solubilizers that envelope their insoluble cargo before transporting it to destination sites. Lipid-binding and lipid transfer structural motifs range from multi-β-strand barrels, to β-sheet cups and baskets covered by α-helical lids, to multi-α-helical bundles and layers. Here, we focus on how α-helical proteins use amphipathic helical layering and bundling to form modular lipid-binding compartments and discuss the functional consequences. Preformed compartments generally rely on intramolecular disulfide bridging to maintain conformation (e.g., albumins, nonspecific lipid transfer proteins, saposins, nematode polyprotein allergens/antigens). Insights into nonpreformed hydrophobic compartments that expand and adapt to accommodate a lipid occupant are few and provided mostly by the three-layer, α-helical ligand-binding domain of nuclear receptors. The simple but elegant and nearly ubiquitous two-layer, α-helical glycolipid transfer protein (GLTP)-fold now further advances understanding.
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Affiliation(s)
- Lucy Malinina
- The Hormel Institute, University of Minnesota, Austin, Minnesota 55912; ,
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065;
| | - Rhoderick E Brown
- The Hormel Institute, University of Minnesota, Austin, Minnesota 55912; ,
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30
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Muccio DD, Atigadda VR, Brouillette WJ, Bland KI, Krontiras H, Grubbs CJ. Translation of a Tissue-Selective Rexinoid, UAB30, to the Clinic for Breast Cancer Prevention. Curr Top Med Chem 2017; 17:676-695. [PMID: 27320329 PMCID: PMC9904082 DOI: 10.2174/1568026616666160617093604] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 03/25/2016] [Accepted: 03/25/2016] [Indexed: 11/22/2022]
Abstract
This review focuses on our efforts to translate a low-toxicity retinoid X receptor-selective agonist, UAB30, to the clinic for the prevention of breast cancers. The review is divided into several sections. First, the current status of breast cancer prevention is discussed. Next, preclinical studies are presented that support translation of rexinoids to the clinic for cancer prevention. While current FDAapproved retinoids and rexinoids demonstrate profound effects in treating cancers, they lack sufficient safety for long term use in the high risk population that is otherwise disease free. The review stresses the need to identify cancer preventive drugs that are effective and safe in order to gain wide use in the clinic. Due to the heterogeneity of the disease, UAB30 is evaluated for the prevention of ER-positive and ER-negative mammary cancers. Since selective estrogen receptor modulators and aromatase inhibitors are used clinically to prevent and treat ER-positive breast cancers, preclinical studies also must demonstrate efficacy of UAB30 in combination with existing drugs under use in the clinic. To support an Investigational New Drug Application to the FDA, data on pharmacology and toxicity as well as mutagenicity is gathered prior to human trials. The review concludes with a discussion of the outcomes of human Phase 0/1 clinical trials that determine the safety and pharmacology of UAB30. These studies are essential before this agent is evaluated for efficacy in phase 2 trials. Success in phase 2 evaluation is critical before long-term and costly phase 3 trials are undertaken. The lack of surrogate biomarkers as endpoints for phase 2 evaluation of rexinoid preventive agents is discussed.
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Affiliation(s)
- Donald D. Muccio
- Department of Chemistry, University of Alabama at Birmingham, Birmingham Alabama 35294 USA
| | - Venkatram R Atigadda
- Department of Chemistry, University of Alabama at Birmingham, Birmingham Alabama 35294 USA
| | - Wayne J Brouillette
- Department of Chemistry, University of Alabama at Birmingham, Birmingham Alabama 35294 USA
| | - Kirby I Bland
- Department of Surgery, University of Alabama at Birmingham, Birmingham Alabama 35294 USA
| | - Helen Krontiras
- Department of Surgery, University of Alabama at Birmingham, Birmingham Alabama 35294 USA
| | - Clinton J Grubbs
- Department of Surgery, University of Alabama at Birmingham, Birmingham Alabama 35294 USA
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31
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Deng B, Lento C, Wilson DJ. Hydrogen deuterium exchange mass spectrometry in biopharmaceutical discovery and development – A review. Anal Chim Acta 2016; 940:8-20. [DOI: 10.1016/j.aca.2016.08.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 07/25/2016] [Accepted: 08/07/2016] [Indexed: 01/14/2023]
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Abstract
To develop strong vitamin D receptor (VDR) antagonists and reveal their antagonistic mechanism, we designed and synthesized vitamin D analogues with bulky side chains based on the "active antagonist" concept in which antagonist prevents helix 12 (H12) folding. Of the synthesized analogues, compounds 3a and 3b showed strong antagonistic activity. Dynamic hydrogen/deuterium exchange coupled with mass spectrometry (HDX-MS) and static X-ray crystal structure analyses indicated that compound 3a stabilizes H11-H12 but displaces H6-H7 so that 3a is a novel rather than "active" or "passive" type of antagonist. We classified 3a as a third type of antagonist and called it "H11-H12 stabilization antagonist". HDX-MS analysis indicated that antagonist 3b is an "active" antagonist. To date there are no reports relating to nuclear receptor antagonist that strongly stabilizes H12. In this study, we found first VDR antagonist that stabilizes H12 and we showed that antagonistic mechanism is diverse depending on each antagonist structure. Additionally, HDX-MS was proven to be very useful for investigations of protein structure alterations resulting from ligand binding.
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Affiliation(s)
- Akira Kato
- Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University , 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
| | - Toshimasa Itoh
- Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University , 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
| | - Yasuaki Anami
- Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University , 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
| | - Daichi Egawa
- Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University , 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
| | - Keiko Yamamoto
- Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University , 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
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Cummins DJ, Espada A, Novick SJ, Molina-Martin M, Stites RE, Espinosa JF, Broughton H, Goswami D, Pascal BD, Dodge JA, Chalmers MJ, Griffin PR. Two-Site Evaluation of the Repeatability and Precision of an Automated Dual-Column Hydrogen/Deuterium Exchange Mass Spectrometry Platform. Anal Chem 2016; 88:6607-14. [PMID: 27224086 DOI: 10.1021/acs.analchem.6b01650] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Hydrogen/deuterium exchange coupled with mass spectrometry (HDX-MS) is an information-rich biophysical method for the characterization of protein dynamics. Successful applications of differential HDX-MS include the characterization of protein-ligand binding. A single differential HDX-MS data set (protein ± ligand) is often comprised of more than 40 individual HDX-MS experiments. To eliminate laborious manual processing of samples, and to minimize random and gross errors, automated systems for HDX-MS analysis have become routine in many laboratories. However, an automated system, while less prone to random errors introduced by human operators, may have systematic errors that go unnoticed without proper detection. Although the application of automated (and manual) HDX-MS has become common, there are only a handful of studies reporting the systematic evaluation of the performance of HDX-MS experiments, and no reports have been published describing a cross-site comparison of HDX-MS experiments. Here, we describe an automated HDX-MS platform that operates with a parallel, two-trap, two-column configuration that has been installed in two remote laboratories. To understand the performance of the system both within and between laboratories, we have designed and completed a test-retest repeatability study for differential HDX-MS experiments implemented at each of two laboratories, one in Florida and the other in Spain. This study provided sufficient data to do both within and between laboratory variability assessments. Initial results revealed a systematic run-order effect within one of the two systems. Therefore, the study was repeated, and this time the conclusion was that the experimental conditions were successfully replicated with minimal systematic error.
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Affiliation(s)
- David J Cummins
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Alfonso Espada
- Analytical Technologies Department, Centro de Investigación Lilly, SA , Avenida de la Industria 30, 28108 Alcobendas, Spain
| | - Scott J Novick
- The Scripps Research Institute , Department of Molecular Therapeutics, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Manuel Molina-Martin
- Analytical Technologies Department, Centro de Investigación Lilly, SA , Avenida de la Industria 30, 28108 Alcobendas, Spain
| | - Ryan E Stites
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Juan Felix Espinosa
- Analytical Technologies Department, Centro de Investigación Lilly, SA , Avenida de la Industria 30, 28108 Alcobendas, Spain
| | - Howard Broughton
- Analytical Technologies Department, Centro de Investigación Lilly, SA , Avenida de la Industria 30, 28108 Alcobendas, Spain
| | - Devrishi Goswami
- The Scripps Research Institute , Department of Molecular Therapeutics, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Bruce D Pascal
- The Scripps Research institute, Informatics Core, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Jeffrey A Dodge
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Michael J Chalmers
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Patrick R Griffin
- The Scripps Research Institute , Department of Molecular Therapeutics, 130 Scripps Way, Jupiter, Florida 33458, United States
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Wu L, Chaudhary SC, Atigadda VR, Belyaeva OV, Harville SR, Elmets CA, Muccio DD, Athar M, Kedishvili NY. Retinoid X Receptor Agonists Upregulate Genes Responsible for the Biosynthesis of All-Trans-Retinoic Acid in Human Epidermis. PLoS One 2016; 11:e0153556. [PMID: 27078158 DOI: 10.1371/journal.pone.0153556] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 03/31/2016] [Indexed: 11/26/2022] Open
Abstract
UAB30 is an RXR selective agonist that has been shown to have potential cancer chemopreventive properties. Due to high efficacy and low toxicity, it is currently being evaluated in human Phase I clinical trials by the National Cancer Institute. While UAB30 shows promise as a low toxicity chemopreventive drug, the mechanism of its action is not well understood. In this study, we investigated the effects of UAB30 on gene expression in human organotypic skin raft cultures and mouse epidermis. The results of this study indicate that treatment with UAB30 results in upregulation of genes responsible for the uptake and metabolism of all-trans-retinol to all-trans-retinoic acid (ATRA), the natural agonist of RAR nuclear receptors. Consistent with the increased expression of these genes, the steady-state levels of ATRA are elevated in human skin rafts. In ultraviolet B (UVB) irradiated mouse skin, the expression of ATRA target genes is found to be reduced. A reduced expression of ATRA sensitive genes is also observed in epidermis of mouse models of UVB-induced squamous cell carcinoma and basal cell carcinomas. However, treatment of mouse skin with UAB30 prior to UVB irradiation prevents the UVB-induced decrease in expression of some of the ATRA-responsive genes. Considering its positive effects on ATRA signaling in the epidermis and its low toxicity, UAB30 could be used as a chemoprophylactic agent in the treatment of non-melanoma skin cancer, particularly in organ transplant recipients and other high risk populations.
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35
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Waters AM, Stewart JE, Atigadda VR, Mroczek-Musulman E, Muccio DD, Grubbs CJ, Beierle EA. Preclinical Evaluation of UAB30 in Pediatric Renal and Hepatic Malignancies. Mol Cancer Ther 2016; 15:911-21. [PMID: 26873726 DOI: 10.1158/1535-7163.mct-15-0521] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 02/06/2016] [Indexed: 12/13/2022]
Abstract
Rare tumors of solid organs remain some of the most difficult pediatric cancers to cure. These difficult tumors include rare pediatric renal malignancies, such as malignant rhabdoid kidney tumors (MRKT) and non-osseous renal Ewing sarcoma, and hepatoblastoma, a pediatric liver tumor that arises from immature liver cells. There are data in adult renal and hepatic malignancies demonstrating the efficacy of retinoid therapy. The investigation of retinoic acid therapy in cancer is not a new strategy, but the widespread adoption of this therapy has been hindered by toxicities. Our laboratory has been investigating a novel synthetic rexinoid, UAB30, which exhibits a more favorable side-effect profile. In this study, we hypothesized that UAB30 would diminish the growth of tumor cells from both rare renal and liver tumors in vitro and in vivo We successfully demonstrated decreased cellular proliferation, invasion and migration, cell-cycle arrest, and increased apoptosis after treatment with UAB30. Additionally, in in vivo murine models of human hepatoblastoma or rare human renal tumors, there were significantly decreased tumor xenograft growth and increased animal survival after UAB30 treatment. UAB30 should be further investigated as a developing therapeutic in these rare and difficult-to-treat pediatric solid organ tumors. Mol Cancer Ther; 15(5); 911-21. ©2016 AACR.
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Affiliation(s)
- Alicia M Waters
- Department of Surgery, University of Alabama, Birmingham, Birmingham, Alabama
| | - Jerry E Stewart
- Department of Surgery, University of Alabama, Birmingham, Birmingham, Alabama
| | | | | | - Donald D Muccio
- Department of Chemistry, University of Alabama, Birmingham, Birmingham, Alabama
| | - Clinton J Grubbs
- Department of Surgery, University of Alabama, Birmingham, Birmingham, Alabama
| | - Elizabeth A Beierle
- Department of Surgery, University of Alabama, Birmingham, Birmingham, Alabama.
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36
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Atigadda VR, Xia G, Deshpande A, Wu L, Kedishvili N, Smith CD, Krontiras H, Bland KI, Grubbs CJ, Brouillette WJ, Muccio DD. Conformationally Defined Rexinoids and Their Efficacy in the Prevention of Mammary Cancers. J Med Chem 2015; 58:7763-74. [PMID: 26331194 DOI: 10.1021/acs.jmedchem.5b00829] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
(2E,4E,6Z,8Z)-8-(3',4'-Dihydro-1'(2H)-naphthalen-1'-ylidene)-3,7-dimethyl-2,3,6-octatrienoinic acid (UAB30) is currently undergoing clinical evaluation as a novel cancer prevention agent. In efforts to develop even more highly potent rexinoids that prevent breast cancer without toxicity, we further explore here the structure-activity relationship of two separate classes of rexinoids. UAB30 belongs to the class II rexinoids and possesses a 9Z-tetraenoic acid chain bonded to a tetralone ring, whereas the class I rexinoids contain the same 9Z-tetraenoic acid chain bonded to a disubstituted cyclohexenyl ring. Among the 12 class I and class II rexinoids evaluated, the class I rexinoid 11 is most effective in preventing breast cancers in an in vivo rat model alone or in combination with tamoxifen. Rexinoid 11 also reduces the size of established tumors and exhibits a therapeutic effect. However, 11 induces hypertriglyceridemia at its effective dose. On the other hand rexinoid 10 does not increase triglyceride levels while being effective in the in vivo chemoprevention assay. X-ray studies of four rexinoids bound to the ligand binding domain of the retinoid X receptor reveal key structural aspects that enhance potency as well as those that enhance the synthesis of lipids.
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Affiliation(s)
- Venkatram R Atigadda
- Departments of †Chemistry, ‡Biochemistry and Molecular Genetics, §Vision Sciences, and ∥Surgery, University of Alabama at Birmingham , Birmingham, Alabama 35294, United States
| | - Gang Xia
- Departments of †Chemistry, ‡Biochemistry and Molecular Genetics, §Vision Sciences, and ∥Surgery, University of Alabama at Birmingham , Birmingham, Alabama 35294, United States
| | - Anil Deshpande
- Departments of †Chemistry, ‡Biochemistry and Molecular Genetics, §Vision Sciences, and ∥Surgery, University of Alabama at Birmingham , Birmingham, Alabama 35294, United States
| | - Lizhi Wu
- Departments of †Chemistry, ‡Biochemistry and Molecular Genetics, §Vision Sciences, and ∥Surgery, University of Alabama at Birmingham , Birmingham, Alabama 35294, United States
| | - Natalia Kedishvili
- Departments of †Chemistry, ‡Biochemistry and Molecular Genetics, §Vision Sciences, and ∥Surgery, University of Alabama at Birmingham , Birmingham, Alabama 35294, United States
| | - Craig D Smith
- Departments of †Chemistry, ‡Biochemistry and Molecular Genetics, §Vision Sciences, and ∥Surgery, University of Alabama at Birmingham , Birmingham, Alabama 35294, United States
| | - Helen Krontiras
- Departments of †Chemistry, ‡Biochemistry and Molecular Genetics, §Vision Sciences, and ∥Surgery, University of Alabama at Birmingham , Birmingham, Alabama 35294, United States
| | - Kirby I Bland
- Departments of †Chemistry, ‡Biochemistry and Molecular Genetics, §Vision Sciences, and ∥Surgery, University of Alabama at Birmingham , Birmingham, Alabama 35294, United States
| | - Clinton J Grubbs
- Departments of †Chemistry, ‡Biochemistry and Molecular Genetics, §Vision Sciences, and ∥Surgery, University of Alabama at Birmingham , Birmingham, Alabama 35294, United States
| | - Wayne J Brouillette
- Departments of †Chemistry, ‡Biochemistry and Molecular Genetics, §Vision Sciences, and ∥Surgery, University of Alabama at Birmingham , Birmingham, Alabama 35294, United States
| | - Donald D Muccio
- Departments of †Chemistry, ‡Biochemistry and Molecular Genetics, §Vision Sciences, and ∥Surgery, University of Alabama at Birmingham , Birmingham, Alabama 35294, United States
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Fratev F. Activation helix orientation of the estrogen receptor is mediated by receptor dimerization: evidence from molecular dynamics simulations. Phys Chem Chem Phys 2015; 17:13403-20. [DOI: 10.1039/c5cp00327j] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
ERα dimer formation reshapes the helix 12 conformational landscape and is a leading factor for the activation helix conformation.
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Affiliation(s)
- Filip Fratev
- Institute of Biophysics and Biomedical Engineering
- Bulgarian Academy of Sciences
- 1113 Sofia
- Bulgaria
- Micar21 Ltd
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Kawata K, Morishita KI, Nakayama M, Yamada S, Kobayashi T, Furusawa Y, Arimoto-Kobayashi S, Oohashi T, Makishima M, Naitou H, Ishitsubo E, Tokiwa H, Tai A, Kakuta H. RXR partial agonist produced by side chain repositioning of alkoxy RXR full agonist retains antitype 2 diabetes activity without the adverse effects. J Med Chem 2014; 58:912-26. [PMID: 25486327 DOI: 10.1021/jm501863r] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We previously reported RXR partial agonist CBt-PMN (1-(3,5,5,8,8-pentamethyl-5,6,7,8-tetrahydro-2-naphthyl)-1H-benzotriazole-5-carboxylic acid: 5, EC50 = 143 nM, Emax = 75%), which showed a potent glucose-lowering effect without causing serious adverse effects. However, it remains important to elucidate the structural requirements for RXR efficacy and the glucose-lowering effect because RXR-permissive heterodimers such as PPAR/RXR or LXR/RXR are reported to be activated differently depending upon the chemical structure of RXR agonists. In this work, we show that an RXR partial agonist, NEt-4IB (6-[ethyl-(4-isobutoxy-3-isopropylphenyl)amino]pyridine-3-carboxylic acid: 8b, EC50 = 169 nM, Emax = 55%), can be obtained simply by repositioning the side chains (interchanging the isobutoxy and isopropoxy groups) at the hydrophobic moiety of the RXR full agonist NEt-3IB (6-[ethyl-(3-isobutoxy-4-isopropylphenyl)amino]pyridine-3-carboxylic acid: 7b, EC50 = 19 nM). NEt-4IB (8b) showed antitype 2 diabetes activity without the above side effects upon repeated oral administration to mice at 10 mg/kg/day, similarly to 5.
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Affiliation(s)
- Kohei Kawata
- Division of Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences , 1-1-1, Tsushima-naka, Kita-ku Okayama 700-8530, Japan
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Affiliation(s)
- Gregory F Pirrone
- Department of Chemistry and Chemical Biology, Northeastern University , 360 Huntington Ave., Boston, Massachusetts 02115 United States
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Vedell PT, Townsend RR, You M, Malone JP, Grubbs CJ, Bland KI, Muccio DD, Atigadda VR, Chen Y, Vignola K, Lubet RA. Global molecular changes in rat livers treated with
RXR
agonists: a comparison using transcriptomics and proteomics. Pharmacol Res Perspect 2014. [DOI: 10.1002/prp2.74] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Peter T. Vedell
- Department of Pharmacology Medical College of Wisconsin Cancer Center Milwaukee Wisconsin 53226
| | - Reid R. Townsend
- Department of Internal Medicine Washington University School of Medicine St. Louis Missouri 63110
| | - Ming You
- Department of Pharmacology Medical College of Wisconsin Cancer Center Milwaukee Wisconsin 53226
| | - James P. Malone
- Department of Internal Medicine Washington University School of Medicine St. Louis Missouri 63110
| | - Clinton J. Grubbs
- Department of Surgery University of Alabama at Birmingham Birmingham Alabama 35294
| | - Kirby I. Bland
- Department of Surgery University of Alabama at Birmingham Birmingham Alabama 35294
| | - Donald D. Muccio
- Department of Chemistry University of Alabama at Birmingham Birmingham Alabama 35294
| | - Venkatram R. Atigadda
- Department of Chemistry University of Alabama at Birmingham Birmingham Alabama 35294
| | - Yang Chen
- Department of Science Development Metabolon Research Triangle Park North Carolina 27709
| | - Katie Vignola
- Department of Science Development Metabolon Research Triangle Park North Carolina 27709
| | - Ronald A. Lubet
- Chemoprevention Agent Development Research Group National Cancer Institute Rockville Maryland 20892
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Abstract
Technology often serves as a handmaiden and catalyst of invention. The discovery of safe, effective medications depends critically upon experimental approaches capable of providing high-impact information on the biological effects of drug candidates early in the discovery pipeline. This information can enable reliable lead identification, pharmacological compound differentiation and successful translation of research output into clinically useful therapeutics. The shallow preclinical profiling of candidate compounds promulgates a minimalistic understanding of their biological effects and undermines the level of value creation necessary for finding quality leads worth moving forward within the development pipeline with efficiency and prognostic reliability sufficient to help remediate the current pharma-industry productivity drought. Three specific technologies discussed herein, in addition to experimental areas intimately associated with contemporary drug discovery, appear to hold particular promise for strengthening the preclinical valuation of drug candidates by deepening lead characterization. These are: i) hydrogen-deuterium exchange mass spectrometry for characterizing structural and ligand-interaction dynamics of disease-relevant proteins; ii) activity-based chemoproteomics for profiling the functional diversity of mammalian proteomes; and iii) nuclease-mediated precision gene editing for developing more translatable cellular and in vivo models of human diseases. When applied in an informed manner congruent with the clinical understanding of disease processes, technologies such as these that span levels of biological organization can serve as valuable enablers of drug discovery and potentially contribute to reducing the current, unacceptably high rates of compound clinical failure.
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Affiliation(s)
- David R Janero
- Northeastern University, Bouvé College of Health Sciences, Center for Drug Discovery, Department of Pharmaceutical Sciences, Health Sciences Entrepreneurs , 360 Huntington Avenue, 116 Mugar Life Sciences Hall, Boston, MA 02115-5000 , USA +1 617 373 2208 ; +1 617 373 7493 ;
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Nakashima KI, Murakami T, Tanabe H, Inoue M. Identification of a naturally occurring retinoid X receptor agonist from Brazilian green propolis. Biochim Biophys Acta Gen Subj 2014; 1840:3034-41. [PMID: 24972164 DOI: 10.1016/j.bbagen.2014.06.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 06/06/2014] [Accepted: 06/17/2014] [Indexed: 01/01/2023]
Abstract
BACKGROUND Brazilian green propolis (BGP), a resinous substance produced from Baccharis dracunculifolia by Africanized honey bees (Apis mellifera), is used as a folk medicine. Our present study explores the retinoid X receptor (RXR) agonistic activity of BGP and the identification of an RXR agonist in its extract. METHODS RXRα agonistic activity was evaluated using a luciferase reporter gene assay. Isolation of the RXRα agonist from the ethanolic extract of BGP was performed using successive silica gel and a reversed phase column chromatography. The interaction between the isolated RXRα agonist and RXRα protein was predicted by a receptor-ligand docking simulation. The nuclear receptor (NR) cofactor assay was used to estimate whether the isolated RXRα agonist bound to various NRs, including RXRs and peroxisome proliferator-activated receptors (PPARs). We further examined its effect on adipogenesis in 3T3-L1 fibroblasts. RESULTS We identified drupanin as an RXRα agonist with an EC50 value of 4.8 ± 1.0 μM. Drupanin activated three RXR subtypes by a similar amount and activated PPARγ moderately. Additionally, drupanin induced adipogenesis and elevated aP2 mRNA levels in 3T3-L1 fibroblasts. CONCLUSIONS Drupanin, a component of BGP, is a novel RXR agonist with slight PPARγ agonistic activity. GENERAL SIGNIFICANCE This study revealed for the first time that BGP activates RXR and drupanin is an RXR agonist in its extract.
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Affiliation(s)
- Ken-Ichi Nakashima
- Laboratory of Natural Resources, School of Pharmacy, Aichi Gakuin University, 1-100 Kusumoto-cho, Chikusa-ku, Nagoya 464-8650, Japan
| | - Tohru Murakami
- Laboratory of Natural Resources, School of Pharmacy, Aichi Gakuin University, 1-100 Kusumoto-cho, Chikusa-ku, Nagoya 464-8650, Japan
| | - Hiroki Tanabe
- Laboratory of Natural Resources, School of Pharmacy, Aichi Gakuin University, 1-100 Kusumoto-cho, Chikusa-ku, Nagoya 464-8650, Japan
| | - Makoto Inoue
- Laboratory of Natural Resources, School of Pharmacy, Aichi Gakuin University, 1-100 Kusumoto-cho, Chikusa-ku, Nagoya 464-8650, Japan.
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Atigadda VR, Xia G, Desphande A, Boerma LJ, Lobo-Ruppert S, Grubbs CJ, Smith CD, Brouillette WJ, Muccio DD. Methyl substitution of a rexinoid agonist improves potency and reveals site of lipid toxicity. J Med Chem 2014; 57:5370-80. [PMID: 24801499 PMCID: PMC4216212 DOI: 10.1021/jm5004792] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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(2E,4E,6Z,8E)-8-(3′,4′-Dihydro-1′(2′H)-naphthalen-1′-ylidene)-3,7-dimethyl-2,4,6-octatrienoic
acid, 9cUAB30, is a selective rexinoid that displays substantial chemopreventive
capacity with little toxicity. 4-Methyl-UAB30, an analogue of 9cUAB30,
is a potent RXR agonist but caused increased lipid biosynthesis unlike
9cUAB30. To evaluate how methyl substitution influenced potency and
lipid biosynthesis, we synthesized four 9cUAB30 homologues with methyl
substitutions at the 5-, 6-, 7-, or 8-position of the tetralone ring.
The syntheses and biological evaluations of these new analogues are
reported here along with the X-ray crystal structures of each homologue
bound to the ligand binding domain of hRXRα. We demonstrate
that each homologue of 9cUAB30 is a more potent agonist, but only
the 7-methyl-9cUAB30 caused severe hyperlipidemia in rats. On the
basis of the X-ray crystal structures of these new rexinoids and bexarotene
(Targretin) bound to hRXRα-LBD, we reveal that each rexinoid,
which induced hyperlipidemia, had methyl groups that interacted with
helix 7 residues of the LBD.
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Affiliation(s)
- Venkatram R Atigadda
- Departments of †Chemistry, ‡Biochemistry and Molecular Genetics, §Medicine, and ∥Vision Sciences, University of Alabama at Birmingham , Birmingham, Alabama 35294, United States
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Desphande A, Xia G, Boerma LJ, Vines KK, Atigadda VR, Lobo-Ruppert S, Grubbs CJ, Moeinpour FL, Smith CD, Christov K, Brouillette WJ, Muccio DD. Methyl-substituted conformationally constrained rexinoid agonists for the retinoid X receptors demonstrate improved efficacy for cancer therapy and prevention. Bioorg Med Chem 2014; 22:178-85. [PMID: 24359708 DOI: 10.1016/j.bmc.2013.11.039] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 11/11/2013] [Accepted: 11/20/2013] [Indexed: 11/20/2022]
Abstract
(2E,4E,6Z,8Z)-8-(3',4'-Dihydro-1'(2H)-naphthalen-1'-ylidene)-3,7-dimethyl-2,3,6-octatrienoinic acid, 9cUAB30, is a selective rexinoid for the retinoid X nuclear receptors (RXR). 9cUAB30 displays substantial chemopreventive capacity with little toxicity and is being translated to the clinic as a novel cancer prevention agent. To improve on the potency of 9cUAB30, we synthesized 4-methyl analogs of 9cUAB30, which introduced chirality at the 4-position of the tetralone ring. The syntheses and biological evaluations of the racemic homolog and enantiomers are reported. We demonstrate that the S-enantiomer is the most potent and least toxic even though these enantiomers bind in a similar conformation in the ligand binding domain of RXR.
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