1
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Stiller T, Merk D. Exploring Fatty Acid Mimetics as NR4A Ligands. J Med Chem 2023; 66:15362-15369. [PMID: 37918435 PMCID: PMC10683012 DOI: 10.1021/acs.jmedchem.3c01467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/14/2023] [Accepted: 10/17/2023] [Indexed: 11/04/2023]
Abstract
The ligand-activated transcription factors Nur77, Nurr1, and NOR-1 forming the NR4A family of nuclear receptors are considered as potential targets in various pathologies, including neurodegeneration and cancer. However, chemical tools for pharmacological NR4A modulation as a prerequisite for target validation are rare. Recent findings suggest that NR4As bind fatty acid metabolites and fatty acid mimetic (FAM) drugs, opening new opportunities for NR4A modulator development. We have explored the chemical space of FAM NR4A ligands by using fragment screening, in silico analysis, and systematic structure-activity relationship evaluation. From a chemically diverse library of 92 fragments, we identified 11 new FAM NR4A agonist and inverse agonist scaffolds. Structural optimization of the most active FAM fragment yielded NR4A agonists with submicromolar potency and binding affinity, demonstrating remarkable potential of FAM as NR4A-modulating tools and drugs.
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Affiliation(s)
- Tanja Stiller
- Department of Pharmacy, Ludwig-Maximilians-Universität (LMU) München, 81377 Munich, Germany
| | - Daniel Merk
- Department of Pharmacy, Ludwig-Maximilians-Universität (LMU) München, 81377 Munich, Germany
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2
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Kamata S, Honda A, Ishikawa R, Akahane M, Fujita A, Kaneko C, Miyawaki S, Habu Y, Shiiyama Y, Uchii K, Machida Y, Oyama T, Ishii I. Functional and Structural Insights into the Human PPARα/δ/γ Targeting Preferences of Anti-NASH Investigational Drugs, Lanifibranor, Seladelpar, and Elafibranor. Antioxidants (Basel) 2023; 12:1523. [PMID: 37627519 PMCID: PMC10451623 DOI: 10.3390/antiox12081523] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/19/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023] Open
Abstract
No therapeutic drugs are currently available for nonalcoholic steatohepatitis (NASH) that progresses from nonalcoholic fatty liver via oxidative stress-involved pathways. Three cognate peroxisome proliferator-activated receptor (PPAR) subtypes (PPARα/δ/γ) are considered as attractive targets. Although lanifibranor (PPARα/δ/γ pan agonist) and saroglitazar (PPARα/γ dual agonist) are currently under investigation in clinical trials for NASH, the development of seladelpar (PPARδ-selective agonist), elafibranor (PPARα/δ dual agonist), and many other dual/pan agonists has been discontinued due to serious side effects or little/no efficacies. This study aimed to obtain functional and structural insights into the potency, efficacy, and selectivity against PPARα/δ/γ of three current and past anti-NASH investigational drugs: lanifibranor, seladelpar, and elafibranor. Ligand activities were evaluated by three assays to detect different facets of the PPAR activation: transactivation assay, coactivator recruitment assay, and thermal stability assay. Seven high-resolution cocrystal structures (namely, those of the PPARα/δ/γ-ligand-binding domain (LBD)-lanifibranor, PPARα/δ/γ-LBD-seladelpar, and PPARα-LBD-elafibranor) were obtained through X-ray diffraction analyses, six of which represent the first deposit in the Protein Data Bank. Lanifibranor and seladelpar were found to bind to different regions of the PPARα/δ/γ-ligand-binding pockets and activated all PPAR subtypes with different potencies and efficacies in the three assays. In contrast, elafibranor induced transactivation and coactivator recruitment (not thermal stability) of all PPAR subtypes, but the PPARδ/γ-LBD-elafibranor cocrystals were not obtained. These results illustrate the highly variable PPARα/δ/γ activation profiles and binding modes of these PPAR ligands that define their pharmacological actions.
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Affiliation(s)
- Shotaro Kamata
- Department of Health Chemistry, Showa Pharmaceutical University, Machida 194-8543, Tokyo, Japan
| | - Akihiro Honda
- Department of Health Chemistry, Showa Pharmaceutical University, Machida 194-8543, Tokyo, Japan
| | - Ryo Ishikawa
- Department of Health Chemistry, Showa Pharmaceutical University, Machida 194-8543, Tokyo, Japan
| | - Makoto Akahane
- Department of Health Chemistry, Showa Pharmaceutical University, Machida 194-8543, Tokyo, Japan
| | - Ayane Fujita
- Department of Health Chemistry, Showa Pharmaceutical University, Machida 194-8543, Tokyo, Japan
| | - Chihiro Kaneko
- Department of Health Chemistry, Showa Pharmaceutical University, Machida 194-8543, Tokyo, Japan
| | - Saeka Miyawaki
- Department of Health Chemistry, Showa Pharmaceutical University, Machida 194-8543, Tokyo, Japan
| | - Yuki Habu
- Department of Health Chemistry, Showa Pharmaceutical University, Machida 194-8543, Tokyo, Japan
| | - Yui Shiiyama
- Department of Health Chemistry, Showa Pharmaceutical University, Machida 194-8543, Tokyo, Japan
| | - Kie Uchii
- Department of Health Chemistry, Showa Pharmaceutical University, Machida 194-8543, Tokyo, Japan
| | - Yui Machida
- Department of Health Chemistry, Showa Pharmaceutical University, Machida 194-8543, Tokyo, Japan
| | - Takuji Oyama
- Faculty of Life and Environmental Sciences, University of Yamanashi, Kofu 400-8510, Yamanashi, Japan
| | - Isao Ishii
- Department of Health Chemistry, Showa Pharmaceutical University, Machida 194-8543, Tokyo, Japan
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3
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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] [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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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] [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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Watanabe M, Nakamura-Nakayama M, Fujihara M, Kawasaki M, Nakano S, Kakuta H. Increased Molecular Flexibility Widens the Gap between K i and K d values in Screening for Retinoid X Receptor Modulators. ACS Med Chem Lett 2022; 13:211-217. [PMID: 35178177 PMCID: PMC8842113 DOI: 10.1021/acsmedchemlett.1c00575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 01/19/2022] [Indexed: 11/29/2022] Open
Abstract
Screening for small-molecule modulators targeting a particular receptor is frequently based on measurement of K d, i.e., the binding constant between the receptor and the compound of interest. However, K d values also reflect binding at receptor protein sites other than the modulatory site. We designed derivatives of retinoid X receptor (RXR) antagonist CBTF-EE (1) with modifications that altered their conformational flexibility. Compounds 6a,b and 7a,b showed quite similar K d values, but 7a,b exhibited 10-fold higher K i values than those of 6a,b. Further, 6a,b showed potent RXR-antagonistic activity, while 7a,b were inactive. These results suggest that increased conformational flexibility promotes binding at nontarget receptor sites. In this situation, conventional determination of K d is less effective for screening purposes than the determination of K i using a ligand that binds specifically to the site regulating transcriptional activity. Thus, the use of K i values for orthosteric ligands may increase the hit rate in screening active regulatory molecules.
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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
| | - Mariko Nakamura-Nakayama
- 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
K.K., Tri-Seven Roppongi
8F, 7-7-7 Roppongi, Minato-ku, Tokyo 106-0032, 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,. Phone: +81-(0)86-251-7963
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Galdadas I, Bonis V, Vgenopoulou P, Papadourakis M, Kakoulidis P, Stergiou G, Cournia Z, Klinakis A. The effect of S427F mutation on RXRα activity depends on its dimeric partner. Chem Sci 2021; 12:14700-14710. [PMID: 34820085 PMCID: PMC8597827 DOI: 10.1039/d1sc04465f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 09/18/2021] [Indexed: 12/24/2022] Open
Abstract
RXRs are nuclear receptors acting as transcription regulators that control key cellular processes in all tissues. All type II nuclear receptors require RXRs for transcriptional activity by forming heterodimeric complexes. Recent whole-exome sequencing studies have identified the RXRα S427F hotspot mutation in 5% of the bladder cancer patients, which is always located at the interface of RXRα with its obligatory dimerization partners. Here, we show that mutation of S427 deregulates transcriptional activity of RXRα dimers, albeit with diverse allosteric mechanisms of action depending on its dimeric partner. S427F acts by allosteric mechanisms, which range from inducing the collapse of the binding pocket to allosteric stabilization of active co-activator competent RXRα states. Unexpectedly, RXR S427F heterodimerization leads to either loss- or gain-of-function complexes, in both cases likely compromising its tumor suppressor activity. This is the first report of a cancer-associated single amino acid substitution that affects the function of the mutant protein variably depending on its dimerization partner.
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Affiliation(s)
| | - Vangelis Bonis
- Biomedical Research Foundation Academy of Athens Athens Greece
| | | | | | - Panos Kakoulidis
- Biomedical Research Foundation Academy of Athens Athens Greece
- Data Science and Information Technologies, Department of Informatics and Telecommunication, National and Kapodistrian University of Athens Athens Greece
| | - Georgia Stergiou
- Biomedical Research Foundation Academy of Athens Athens Greece
- Data Science and Information Technologies, Department of Informatics and Telecommunication, National and Kapodistrian University of Athens Athens Greece
| | - Zoe Cournia
- Biomedical Research Foundation Academy of Athens Athens Greece
- Data Science and Information Technologies, Department of Informatics and Telecommunication, National and Kapodistrian University of Athens Athens Greece
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