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Persico M, Sessa R, Cesaro E, Dini I, Costanzo P, Ritieni A, Fattorusso C, Grosso M. A multidisciplinary approach disclosing unexplored Aflatoxin B1 roles in severe impairment of vitamin D mechanisms of action. Cell Biol Toxicol 2023; 39:1275-1295. [PMID: 36066700 PMCID: PMC10425525 DOI: 10.1007/s10565-022-09752-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 06/20/2022] [Indexed: 11/02/2022]
Abstract
Aflatoxin B1 (AFB1), produced by fungi of the genus Aspergillus, is the most toxic and carcinogenic mycotoxin among the classes of aflatoxins. Previous research showed that AFB1 affects vitamin D receptor (VDR) expression. In the present study, integrated computational and experimental studies were carried out to investigate how AFB1 can interfere with Vitamin D signalling. A competitive antagonism of AFB1 toward RXRα and VDR was hypothesized by comparing the docked complex of AFB1/RXRα and AFB1/VDR ligand-binding domain (LBD) with the X-ray structures of RXRα and VDR bound to known ligands. Accordingly, we demonstrated that AFB1 can affect vitamin D-mediated transcriptional activation of VDR by impairing the formation of protein complexes containing both VDR-RXRα and RXRα/RAR and affecting the subcellular localization of VDR and RXRα. As a whole, our data indicate that AFB1 can interfere with different molecular pathways triggered by vitamin D with an antagonistic mechanism of action.
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Affiliation(s)
- Marco Persico
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano, Naples, Italy
| | - Raffaele Sessa
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Sergio Pansini, Naples, Italy
| | - Elena Cesaro
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Sergio Pansini, Naples, Italy
| | - Irene Dini
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano, Naples, Italy
| | - Paola Costanzo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Sergio Pansini, Naples, Italy
| | - Alberto Ritieni
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano, Naples, Italy.
- Staff of UNESCO Chair On Health Education and Sustainable Development, University of Naples Federico II, Naples, Italy.
| | - Caterina Fattorusso
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano, Naples, Italy
| | - Michela Grosso
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Sergio Pansini, Naples, Italy
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2
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Nagamani S, Jaiswal L, Sastry GN. Deciphering the importance of MD descriptors in designing Vitamin D Receptor agonists and antagonists using machine learning. J Mol Graph Model 2023; 118:108346. [PMID: 36208593 DOI: 10.1016/j.jmgm.2022.108346] [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: 04/27/2022] [Revised: 09/14/2022] [Accepted: 09/23/2022] [Indexed: 11/16/2022]
Abstract
The Vitamin D Receptor (VDR) ligand-binding domain undergoes conformation change upon the binding of VDR agonists/antagonists. Helix 12 ((H)12) is one of the important helices at VDR ligand binding and its conformational changes are controlled by the binding of agonists and antagonists molecules. Various molecular modeling studies are available to explain the agonistic and antagonistic activity of vitamin D analogs. In this work, for the first time, we attempted to generate a machine learning model with fingerprints, 2D, 3D and MD descriptors that are specific to Vitamin D analogs and VDR. Initially, 2D and 3D descriptors and fingerprints of 1003 vitamin D analogs were calculated using CDK and RDKit. The machine learning model was generated using descriptors and fingerprints. Further, 80 Vitamin D analogs (40 VDR agonists + 40 VDR antagonists) were docked in the VDR active site. 50ns MD simulation was performed for each protein-ligand complex. Different MD descriptors such as Solvent Accessible Surface Area (SASA), radius of gyration, PC1 and PC2 were calculated and considered along with CDK and RDKit descriptors as features for machine learning calculations. A few other descriptors that are related to VDR conformational changes such as conformation of the (H)12, the angle at kink were considered for machine learning model generation. It was observed that the descriptors calculated from VDR conformational changes i) were able to distinguish between agonists and antagonists ii) provide key and comprehensive information about the unique binding characteristics of agonists and antagonists iii) provide a strong basis for the machine learning model generation. Overall, this study attempts the utilization of descriptors that are specific to a protein conformation will be helpful for the generation of an efficient machine learning model.
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Affiliation(s)
- Selvaraman Nagamani
- Advanced Computation and Data Sciences Division, CSIR - North East Institute of Science and Technology, Jorhat, Assam, 785 006, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
| | - Lavi Jaiswal
- Advanced Computation and Data Sciences Division, CSIR - North East Institute of Science and Technology, Jorhat, Assam, 785 006, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - G Narahari Sastry
- Advanced Computation and Data Sciences Division, CSIR - North East Institute of Science and Technology, Jorhat, Assam, 785 006, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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3
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Takyo M, Sato Y, Hirata N, Tsuchiya K, Ishida H, Kurohara T, Yanase Y, Ito T, Kanda Y, Yamamoto K, Misawa T, Demizu Y. Oligoarginine-Conjugated Peptide Foldamers Inhibiting Vitamin D Receptor-Mediated Transcription. ACS OMEGA 2022; 7:46573-46582. [PMID: 36570290 PMCID: PMC9774327 DOI: 10.1021/acsomega.2c05409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 11/16/2022] [Indexed: 06/17/2023]
Abstract
The vitamin D receptor (VDR) is a nuclear receptor, which is involved in several physiological processes, including differentiation and bone homeostasis. The VDR is a promising target for the development of drugs against cancer and bone-related diseases. To date, several VDR antagonists, which bind to the ligand binding domain of the VDR and compete with the endogenous agonist 1α,25(OH)D3, have been reported. However, these ligands contain a secosteroidal skeleton, which is chemically unstable and complicated to synthesize. A few VDR antagonists with a nonsecosteroidal skeleton have been reported. Alternative inhibitors against VDR transactivation that act via different mechanisms are desirable. Here, we developed peptide-based VDR inhibitors capable of disrupting the VDR-coactivator interaction. It was reported that helical SRC2-3 peptides strongly bound to the VDR and competed with the coactivator in vitro. Therefore, we designed and synthesized a series of SRC2-3 derivatives by the introduction of nonproteinogenic amino acids, such as β-amino acids, and by side-chain stapling to stabilize helical structures and provide resistance against digestive enzymes. In addition, conjugation with a cell-penetrating peptide increased the cell membrane permeability and was a promising strategy for intracellular VDR inhibition. The nona-arginine-conjugated peptides 24 with side-chain stapling and 25 with cyclic β-amino acids showed strong intracellular VDR inhibitory activity, resulting in suppression of the target gene expression and inhibition of the cell differentiation of HL-60 cells. Herein, the peptide design, structure-activity relationship (SAR) study, and biological evaluation of the peptides are described.
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Affiliation(s)
- Mami Takyo
- National
Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki, Kanagawa 210-9501, Japan
- Graduate
School of Medical Life Science, Yokohama
City University, 1-7-29
Yokohama, Yokohama, Kanagawa 230-0045, Japan
| | - Yumi Sato
- National
Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki, Kanagawa 210-9501, Japan
- Graduate
School of Medical Life Science, Yokohama
City University, 1-7-29
Yokohama, Yokohama, Kanagawa 230-0045, Japan
| | - Naoya Hirata
- National
Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki, Kanagawa 210-9501, Japan
| | - Keisuke Tsuchiya
- National
Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki, Kanagawa 210-9501, Japan
- Graduate
School of Pharmacy, Showa University, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo 142-8555, Japan
| | - Hiroaki Ishida
- Laboratory
of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machidashi, Tokyo 194-8543, Japan
| | - Takashi Kurohara
- National
Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki, Kanagawa 210-9501, Japan
| | - Yuta Yanase
- National
Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki, Kanagawa 210-9501, Japan
- Graduate
School of Medical Life Science, Yokohama
City University, 1-7-29
Yokohama, Yokohama, Kanagawa 230-0045, Japan
| | - Takahito Ito
- National
Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki, Kanagawa 210-9501, Japan
- Graduate
School of Medical Life Science, Yokohama
City University, 1-7-29
Yokohama, Yokohama, Kanagawa 230-0045, Japan
| | - Yasunari Kanda
- National
Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki, Kanagawa 210-9501, Japan
| | - Keiko Yamamoto
- Laboratory
of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machidashi, Tokyo 194-8543, Japan
| | - Takashi Misawa
- National
Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki, Kanagawa 210-9501, Japan
| | - Yosuke Demizu
- National
Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki, Kanagawa 210-9501, Japan
- Graduate
School of Medical Life Science, Yokohama
City University, 1-7-29
Yokohama, Yokohama, Kanagawa 230-0045, Japan
- Graduate
School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushimanaka, Kita-ku, Okayama 700-8530, Japan
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4
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Maestro MA, Seoane S. The Centennial Collection of VDR Ligands: Metabolites, Analogs, Hybrids and Non-Secosteroidal Ligands. Nutrients 2022; 14:nu14224927. [PMID: 36432615 PMCID: PMC9692999 DOI: 10.3390/nu14224927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 11/23/2022] Open
Abstract
Since the discovery of vitamin D a century ago, a great number of metabolites, analogs, hybrids and nonsteroidal VDR ligands have been developed. An enormous effort has been made to synthesize compounds which present beneficial properties while attaining lower calcium serum levels than calcitriol. This structural review covers VDR ligands published to date.
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Affiliation(s)
- Miguel A. Maestro
- Department of Chemistry-CICA, University of A Coruña, Campus da Zapateira, s/n, 15008 A Coruña, Spain
- Correspondence:
| | - Samuel Seoane
- Department of Physiology-CIMUS, University of Santiago, Campus Vida, 15005 Santiago, Spain
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5
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Ekimoto T, Kudo T, Yamane T, Ikeguchi M. Mechanism of Vitamin D Receptor Ligand-Binding Domain Regulation Studied by gREST Simulations. J Chem Inf Model 2021; 61:3625-3637. [PMID: 34189910 DOI: 10.1021/acs.jcim.1c00534] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The vitamin D receptor ligand-binding domain (VDR-LBD) undergoes conformational changes upon ligand binding. In this nuclear receptor family, agonistic or antagonistic activities are controlled by the conformation of the helix (H)12. However, all crystal structures of VDR-LBD reported to date correspond to the active H12 conformation, regardless of agonist/antagonist binding. To understand the mechanism of VDR-LBD regulation structurally, conformational samplings of agonist- and antagonist-bound rat VDR-LBD were performed using the generalized replica exchange with solute tempering (gREST) method. The gREST simulations demonstrated different structural responses of rat VDR-LBD to agonist or antagonist binding, whereas in conventional molecular dynamics simulations, the conformation was the same as that of the crystal structures, regardless of agonist/antagonist binding. In the gREST simulations, a spontaneous conformational change of H12 was observed only for the antagonist complex. The different responses to agonist/antagonist binding were attributed to hydrophobic core formation at the ligand-binding pocket and cooperative rearrangements of H11. The gREST method can be applied to the examination of structure-activity relationships for multiple VDR-LBD ligands.
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Affiliation(s)
- Toru Ekimoto
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Takafumi Kudo
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Tsutomu Yamane
- Center for Computational Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Mitsunori Ikeguchi
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.,Center for Computational Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
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6
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Belorusova AY, Chalhoub S, Rovito D, Rochel N. Structural Analysis of VDR Complex with ZK168281 Antagonist. J Med Chem 2020; 63:9457-9463. [PMID: 32787090 DOI: 10.1021/acs.jmedchem.0c00656] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Vitamin D receptor (VDR) antagonists prevent the VDR activation function helix 12 from folding into its active conformation, thus affecting coactivator recruitment and antagonizing the transcriptional regulation induced by 1α,25-dihydroxyvitamin D3. Here, we report the crystal structure of the zebrafish VDR ligand-binding domain in complex with the ZK168281 antagonist, revealing that the ligand prevents optimal folding of the C-terminal region of VDR. This interference was confirmed by hydrogen-deuterium exchange mass spectrometry (HDX-MS) in solution.
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Affiliation(s)
- Anna Y Belorusova
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France.,Institut National de La Santé et de La Recherche Médicale (INSERM), U1258, 67400 Illkirch, France.,Centre National de Recherche Scientifique (CNRS), UMR7104, 67400 Illkirch, France.,Université de Strasbourg, 67400 Illkirch, France.,Medicinal Chemistry, Early Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, 431 83 Gothenburg, Sweden
| | - Sandra Chalhoub
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France.,Institut National de La Santé et de La Recherche Médicale (INSERM), U1258, 67400 Illkirch, France.,Centre National de Recherche Scientifique (CNRS), UMR7104, 67400 Illkirch, France.,Université de Strasbourg, 67400 Illkirch, France
| | - Daniela Rovito
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France.,Institut National de La Santé et de La Recherche Médicale (INSERM), U1258, 67400 Illkirch, France.,Centre National de Recherche Scientifique (CNRS), UMR7104, 67400 Illkirch, France.,Université de Strasbourg, 67400 Illkirch, France
| | - Natacha Rochel
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France.,Institut National de La Santé et de La Recherche Médicale (INSERM), U1258, 67400 Illkirch, France.,Centre National de Recherche Scientifique (CNRS), UMR7104, 67400 Illkirch, France.,Université de Strasbourg, 67400 Illkirch, France
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7
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Ibe K, Yamada T, Okamoto S. Synthesis and vitamin D receptor affinity of 16-oxa vitamin D 3 analogues. Org Biomol Chem 2019; 17:10188-10200. [PMID: 31769776 DOI: 10.1039/c9ob02339a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two novel 16-oxa-vitamin D3 analogues were synthesized using a tandem Ti(ii)-mediated enyne cyclization/Cu-catalyzed allylation, Ru-catalyzed ring-closing metathesis reaction, and a low-valent titanium (LVT)-mediated stereoselective radical reduction of 8α,14α-epoxide as the key steps for the synthesis of the 16-oxa-C,D ring unit. The vitamin D receptor-binding affinity of the synthesized analogues, 16-oxa-1α,25-(OH)2VD3 and 16-oxa-19-nor-1α,25-(OH)2VD3, was evaluated by fluorescence polarization vitamin D receptor competitor assay and time-resolved fluorescence energy transfer vitamin D receptor co-activator assay.
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Affiliation(s)
- Kouta Ibe
- Department of Materials and Life Chemistry, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan.
| | - Takeshi Yamada
- Department of Materials and Life Chemistry, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan.
| | - Sentaro Okamoto
- Department of Materials and Life Chemistry, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan.
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8
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Yamamoto K. Discovery of Nuclear Receptor Ligands and Elucidation of Their Mechanisms of Action. Chem Pharm Bull (Tokyo) 2019; 67:609-619. [DOI: 10.1248/cpb.c19-00131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Keiko Yamamoto
- Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University
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9
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Abstract
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For many individuals,
in particular during winter, supplementation
with the secosteroid vitamin D3 is essential for the prevention
of bone disorders, muscle weakness, autoimmune diseases, and possibly
also different types of cancer. Vitamin D3 acts via its
metabolite 1α,25-dihydroxyvitamin D3 [1,25(OH)2D3]
as potent agonist of the transcription factor vitamin D receptor (VDR).
Thus, vitamin D directly affects chromatin structure and gene regulation
at thousands of genomic loci, i.e., the epigenome and transcriptome
of its target tissues. Modifications of 1,25(OH)2D3 at its
side-chain, A-ring, triene system, or C-ring, alone and in combination,
as well as nonsteroidal mimics provided numerous potent VDR agonists
and some antagonists. The nearly 150 crystal structures of VDR’s
ligand-binding domain with various vitamin D compounds allow a detailed
molecular understanding of their action. This review discusses the
most important vitamin D analogs presented during the past 10 years
and molecular insight derived from new structural information on the
VDR protein.
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Affiliation(s)
- Miguel A Maestro
- Departamento de Química-CICA , Universidade da Coruña , ES-15071 A Coruña , Spain
| | - Ferdinand Molnár
- School of Science and Technology, Department of Biology , Nazarbayev University , KZ-010000 Astana , Kazakhstan
| | - Carsten Carlberg
- School of Medicine, Institute of Biomedicine , University of Eastern Finland , FI-70211 Kuopio , Finland
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