1
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Prieto-Díaz R, González-Gómez M, Fojo-Carballo H, Azuaje J, El Maatougui A, Majellaro M, Loza MI, Brea J, Fernández-Dueñas V, Paleo MR, Díaz-Holguín A, Garcia-Pinel B, Mallo-Abreu A, Estévez JC, Andújar-Arias A, García-Mera X, Gomez-Tourino I, Ciruela F, Salas CO, Gutiérrez-de-Terán H, Sotelo E. Exploring the Effect of Halogenation in a Series of Potent and Selective A 2B Adenosine Receptor Antagonists. J Med Chem 2022; 66:890-912. [PMID: 36517209 PMCID: PMC9841532 DOI: 10.1021/acs.jmedchem.2c01768] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The modulation of the A2B adenosine receptor is a promising strategy in cancer (immuno) therapy, with A2BAR antagonists emerging as immune checkpoint inhibitors. Herein, we report a systematic assessment of the impact of (di- and mono-)halogenation at positions 7 and/or 8 on both A2BAR affinity and pharmacokinetic properties of a collection of A2BAR antagonists and its study with structure-based free energy perturbation simulations. Monohalogenation at position 8 produced potent A2BAR ligands irrespective of the nature of the halogen. In contrast, halogenation at position 7 and dihalogenation produced a halogen-size-dependent decay in affinity. Eight novel A2BAR ligands exhibited remarkable affinity (Ki < 10 nM), exquisite subtype selectivity, and enantioselective recognition, with some eutomers eliciting sub-nanomolar affinity. The pharmacokinetic profile of representative derivatives showed enhanced solubility and microsomal stability. Finally, two compounds showed the capacity of reversing the antiproliferative effect of adenosine in activated primary human peripheral blood mononuclear cells.
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Affiliation(s)
- Rubén Prieto-Díaz
- Center
for Research in Biological Chemistry and Molecular Materials (CIQUS), University of Santiago de Compostela, 15782Santiago de
Compostela, Spain,Department
of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, 15782Santiago de Compostela, Spain,Department
of Cell and Molecular Biology, Uppsala University, Biomedical Center, 75124Uppsala, Sweden
| | - Manuel González-Gómez
- Center
for Research in Biological Chemistry and Molecular Materials (CIQUS), University of Santiago de Compostela, 15782Santiago de
Compostela, Spain,Department
of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, 15782Santiago de Compostela, Spain
| | - Hugo Fojo-Carballo
- Center
for Research in Biological Chemistry and Molecular Materials (CIQUS), University of Santiago de Compostela, 15782Santiago de
Compostela, Spain,Department
of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, 15782Santiago de Compostela, Spain
| | - Jhonny Azuaje
- Center
for Research in Biological Chemistry and Molecular Materials (CIQUS), University of Santiago de Compostela, 15782Santiago de
Compostela, Spain,Department
of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, 15782Santiago de Compostela, Spain
| | - Abdelaziz El Maatougui
- Center
for Research in Biological Chemistry and Molecular Materials (CIQUS), University of Santiago de Compostela, 15782Santiago de
Compostela, Spain,Department
of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, 15782Santiago de Compostela, Spain
| | - Maria Majellaro
- Center
for Research in Biological Chemistry and Molecular Materials (CIQUS), University of Santiago de Compostela, 15782Santiago de
Compostela, Spain,Department
of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, 15782Santiago de Compostela, Spain
| | - María I. Loza
- Center
for Research in Molecular Medicine and Chronic Diseases (CiMUS), University of Santiago de Compostela, 15782Santiago de
Compostela, Spain,Department
of Pharmacology, Pharmacy and Pharmaceutical Technology, Faculty of
Pharmacy, University of Santiago de Compostela, 15782Santiago de
Compostela, Spain
| | - José Brea
- Center
for Research in Molecular Medicine and Chronic Diseases (CiMUS), University of Santiago de Compostela, 15782Santiago de
Compostela, Spain,Department
of Pharmacology, Pharmacy and Pharmaceutical Technology, Faculty of
Pharmacy, University of Santiago de Compostela, 15782Santiago de
Compostela, Spain,. Tel: +34 881815459. Fax: +34-8818115474
| | - Víctor Fernández-Dueñas
- Pharmacology
Unit, Department of Pathology and Experimental Therapeutics, Faculty
of Medicine and Health Sciences, Institute of Neuroscience, University of Barcelona, 08907L’Hospitalet de Llobregat, Spain,Neuropharmacology
and Pain Group, Neuroscience Program, Institut
d’Investigació Biomèdica de Bellvitge, IDIBELL, 08907L’Hospitalet
de Llobregat, Spain
| | - M. Rita Paleo
- Center
for Research in Biological Chemistry and Molecular Materials (CIQUS), University of Santiago de Compostela, 15782Santiago de
Compostela, Spain,Department
of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, 15782Santiago de Compostela, Spain
| | - Alejandro Díaz-Holguín
- Department
of Cell and Molecular Biology, Uppsala University, Biomedical Center, 75124Uppsala, Sweden
| | - Beatriz Garcia-Pinel
- Center
for Research in Molecular Medicine and Chronic Diseases (CiMUS), University of Santiago de Compostela, 15782Santiago de
Compostela, Spain,Department
of Biochemistry and Molecular Biology, Faculty of Pharmacy, University of Santiago de Compostela, 15782Santiago de
Compostela, Spain
| | - Ana Mallo-Abreu
- Center
for Research in Biological Chemistry and Molecular Materials (CIQUS), University of Santiago de Compostela, 15782Santiago de
Compostela, Spain,Department
of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, 15782Santiago de Compostela, Spain
| | - Juan C. Estévez
- Center
for Research in Biological Chemistry and Molecular Materials (CIQUS), University of Santiago de Compostela, 15782Santiago de
Compostela, Spain,Department
of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, 15782Santiago de Compostela, Spain
| | - Antonio Andújar-Arias
- Center
for Research in Biological Chemistry and Molecular Materials (CIQUS), University of Santiago de Compostela, 15782Santiago de
Compostela, Spain,Department
of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, 15782Santiago de Compostela, Spain
| | - Xerardo García-Mera
- Department
of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, 15782Santiago de Compostela, Spain
| | - Iria Gomez-Tourino
- Center
for Research in Molecular Medicine and Chronic Diseases (CiMUS), University of Santiago de Compostela, 15782Santiago de
Compostela, Spain
| | - Francisco Ciruela
- Pharmacology
Unit, Department of Pathology and Experimental Therapeutics, Faculty
of Medicine and Health Sciences, Institute of Neuroscience, University of Barcelona, 08907L’Hospitalet de Llobregat, Spain,Neuropharmacology
and Pain Group, Neuroscience Program, Institut
d’Investigació Biomèdica de Bellvitge, IDIBELL, 08907L’Hospitalet
de Llobregat, Spain
| | - Cristian O. Salas
- Department
of Organic Chemistry, Faculty of Chemistry and Pharmacy, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Macul, Santiago7820436, Chile
| | - Hugo Gutiérrez-de-Terán
- Department
of Cell and Molecular Biology, Uppsala University, Biomedical Center, 75124Uppsala, Sweden,. Tel: +46 18
471 5056. Fax: +46 18 536971
| | - Eddy Sotelo
- Center
for Research in Biological Chemistry and Molecular Materials (CIQUS), University of Santiago de Compostela, 15782Santiago de
Compostela, Spain,Department
of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, 15782Santiago de Compostela, Spain,. Tel: +34 881815732. Fax: +34-881815704
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Enantiomeric Separation and Molecular Modelling of Bioactive 4-Aryl-3,4-dihydropyrimidin-2(1H)-one Ester Derivatives on Teicoplanin-Based Chiral Stationary Phase. SEPARATIONS 2021. [DOI: 10.3390/separations9010007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The enantiomeric separation of 15 racemic 4-aryl-3,4-dihydropyrimidin-2(1H)-one (DHP) alkoxycarbonyl esters, some of which proved to be highly active as A2B adenosine receptor antagonists, was carried out by HPLC on ChirobioticTM TAG, a chiral stationary phase (CSP) bearing teicoplanin aglycone (TAG) as the chiral selector. The racemic compounds were separated under polar organic (PO) conditions. Preliminarily, the same selectands were investigated on three different Pirkle-type CSPs in normal-phase (NP) conditions. A baseline separation was successfully obtained on TAG-based CSPs for the majority of compounds, some of which achieved high enantioselectivity ratios (α > 2) in contrast with the smaller α values (1–1.5) and the lack of baseline resolution observed with the Pirkle-type CSPs. In particular, the racemic tetrazole-fused DHP ester derivatives, namely compounds 8 and 9, were separated on TAG-based HPLC columns with noteworthy α values (8.8 and 6.0, respectively), demonstrating the potential of the method for preparative purposes. A competition experiment, carried out with a racemic analyte (6) by adding N-acetyl-d-alanine (NADA) to the mobile phase, suggested that H-bonding interactions involved in the recognition of the natural dipeptide ligand d-Ala-d-Ala into the TAG cleft should be critical for enantioselective recognition of 4-aryl DHPs by TAG. The X-ray crystal structure of TAG was elucidated at a 0.77 Å resolution, whereas the calculation of molecular descriptors of size, polar, and H-bond interactions, were complemented with molecular docking and molecular dynamics calculations, shedding light on repulsive (steric effects) and attractive (H-bond—polar and apolar) interactions between 4-aryl DHP selectands and TAG chiral selectors.
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3
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Majellaro M, Jespers W, Crespo A, Núñez MJ, Novio S, Azuaje J, Prieto-Díaz R, Gioé C, Alispahic B, Brea J, Loza MI, Freire-Garabal M, Garcia-Santiago C, Rodríguez-García C, García-Mera X, Caamaño O, Fernandez-Masaguer C, Sardina JF, Stefanachi A, El Maatougui A, Mallo-Abreu A, Åqvist J, Gutiérrez-de-Terán H, Sotelo E. 3,4-Dihydropyrimidin-2(1 H)-ones as Antagonists of the Human A 2B Adenosine Receptor: Optimization, Structure-Activity Relationship Studies, and Enantiospecific Recognition. J Med Chem 2020; 64:458-480. [PMID: 33372800 DOI: 10.1021/acs.jmedchem.0c01431] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We present and thoroughly characterize a large collection of 3,4-dihydropyrimidin-2(1H)-ones as A2BAR antagonists, an emerging strategy in cancer (immuno) therapy. Most compounds selectively bind A2BAR, with a number of potent and selective antagonists further confirmed by functional cyclic adenosine monophosphate experiments. The series was analyzed with one of the most exhaustive free energy perturbation studies on a GPCR, obtaining an accurate model of the structure-activity relationship of this chemotype. The stereospecific binding modeled for this scaffold was confirmed by resolving the two most potent ligands [(±)-47, and (±)-38 Ki = 10.20 and 23.6 nM, respectively] into their two enantiomers, isolating the affinity on the corresponding (S)-eutomers (Ki = 6.30 and 11.10 nM, respectively). The assessment of the effect in representative cytochromes (CYP3A4 and CYP2D6) demonstrated insignificant inhibitory activity, while in vitro experiments in three prostate cancer cells demonstrated that this pair of compounds exhibits a pronounced antimetastatic effect.
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Affiliation(s)
- María Majellaro
- Centro Singular de Investigación en Química Biolóxica y Materiais Moleculares (CIQUS), Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.,Departamento de Química Orgánica, Facultade de Farmacia, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Willem Jespers
- Department of Cell and Molecular Biology, Uppsala University, SE-75124 Uppsala, Sweden
| | - Abel Crespo
- Centro Singular de Investigación en Química Biolóxica y Materiais Moleculares (CIQUS), Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.,Departamento de Química Orgánica, Facultade de Farmacia, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - María J Núñez
- SNL, Departamento de Farmacología, Facultade de Medicina, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Silvia Novio
- SNL, Departamento de Farmacología, Facultade de Medicina, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Jhonny Azuaje
- Centro Singular de Investigación en Química Biolóxica y Materiais Moleculares (CIQUS), Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.,Departamento de Química Orgánica, Facultade de Farmacia, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Rubén Prieto-Díaz
- Centro Singular de Investigación en Química Biolóxica y Materiais Moleculares (CIQUS), Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.,Departamento de Química Orgánica, Facultade de Farmacia, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Claudia Gioé
- Centro Singular de Investigación en Química Biolóxica y Materiais Moleculares (CIQUS), Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.,Departamento de Química Orgánica, Facultade de Farmacia, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Belma Alispahic
- Department of Cell and Molecular Biology, Uppsala University, SE-75124 Uppsala, Sweden
| | - José Brea
- Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - María I Loza
- Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Manuel Freire-Garabal
- SNL, Departamento de Farmacología, Facultade de Medicina, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Carlota Garcia-Santiago
- SNL, Departamento de Farmacología, Facultade de Medicina, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Carlos Rodríguez-García
- Centro Singular de Investigación en Química Biolóxica y Materiais Moleculares (CIQUS), Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.,Departamento de Química Orgánica, Facultade de Farmacia, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Xerardo García-Mera
- Departamento de Química Orgánica, Facultade de Farmacia, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Olga Caamaño
- Departamento de Química Orgánica, Facultade de Farmacia, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Christian Fernandez-Masaguer
- Departamento de Química Orgánica, Facultade de Farmacia, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Javier F Sardina
- Centro Singular de Investigación en Química Biolóxica y Materiais Moleculares (CIQUS), Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Angela Stefanachi
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari ALDO MORO, via Orabona 4, 70125 Bari, Italy
| | - Abdelaziz El Maatougui
- Centro Singular de Investigación en Química Biolóxica y Materiais Moleculares (CIQUS), Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.,Departamento de Química Orgánica, Facultade de Farmacia, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Ana Mallo-Abreu
- Centro Singular de Investigación en Química Biolóxica y Materiais Moleculares (CIQUS), Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.,Departamento de Química Orgánica, Facultade de Farmacia, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Johan Åqvist
- Department of Cell and Molecular Biology, Uppsala University, SE-75124 Uppsala, Sweden
| | | | - Eddy Sotelo
- Centro Singular de Investigación en Química Biolóxica y Materiais Moleculares (CIQUS), Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.,Departamento de Química Orgánica, Facultade de Farmacia, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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Wang M, Jiang X, Cao C, Zhao S, Wan X. Green Synthesis and Structural Characterization of C6-Phenyl Substituted 3,4-Dihydropyrimidinones. ORG PREP PROCED INT 2020. [DOI: 10.1080/00304948.2020.1794222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Min Wang
- College of Chemistry and Chemical Engineering, Bohai University, Jinzhou, P. R. China
| | - Xiaoyu Jiang
- College of Chemistry and Chemical Engineering, Bohai University, Jinzhou, P. R. China
| | - Chunyan Cao
- College of Chemistry and Chemical Engineering, Bohai University, Jinzhou, P. R. China
| | - Shuang Zhao
- College of Chemistry and Chemical Engineering, Bohai University, Jinzhou, P. R. China
| | - Xin Wan
- College of Chemistry and Chemical Engineering, Bohai University, Jinzhou, P. R. China
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Mallo-Abreu A, Prieto-Díaz R, Jespers W, Azuaje J, Majellaro M, Velando C, García-Mera X, Caamaño O, Brea J, Loza MI, Gutiérrez-de-Terán H, Sotelo E. Nitrogen-Walk Approach to Explore Bioisosteric Replacements in a Series of Potent A 2B Adenosine Receptor Antagonists. J Med Chem 2020; 63:7721-7739. [PMID: 32573250 DOI: 10.1021/acs.jmedchem.0c00564] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A systematic exploration of bioisosteric replacements for furan and thiophene cores in a series of potent A2BAR antagonists has been carried out using the nitrogen-walk approach. A collection of 42 novel alkyl 4-substituted-2-methyl-1,4-dihydrobenzo[4,5]imidazo[1,2-a]pyrimidine-3-carboxylates, which contain 18 different pentagonal heterocyclic frameworks at position 4, was synthesized and evaluated. This study enabled the identification of new ligands that combine remarkable affinity (Ki < 30 nM) and exquisite selectivity. The structure-activity relationship (SAR) trends identified were substantiated by a molecular modeling study, based on a receptor-driven docking model and including a systematic free energy perturbation (FEP) study. Preliminary evaluation of the CYP3A4 and CYP2D6 inhibitory activity in optimized ligands evidenced weak and negligible activity, respectively. The stereospecific interaction between hA2BAR and the eutomer of the most attractive novel antagonist (S)-18g (Ki = 3.66 nM) was validated.
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Affiliation(s)
| | | | - Willem Jespers
- Department of Cell and Molecular Biology, Uppsala University, Uppsala SE 75124, Sweden
| | | | | | | | | | | | - José Brea
- Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - María I Loza
- Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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Vakhula AR, Horak YI, Lytvyn RZ, Lesyuk AI, Kinzhybalo V, Zubkov FI, Obushak MD. 5-Aryl-2-furaldehydes in the synthesis of tetrahydropyrimidinones by Biginelli reaction. Chem Heterocycl Compd (N Y) 2018. [DOI: 10.1007/s10593-018-2301-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Structure-Based Design of Potent and Selective Ligands at the Four Adenosine Receptors. Molecules 2017; 22:molecules22111945. [PMID: 29125553 PMCID: PMC6150288 DOI: 10.3390/molecules22111945] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 11/07/2017] [Accepted: 11/08/2017] [Indexed: 12/19/2022] Open
Abstract
The four receptors that signal for adenosine, A1, A2A, A2B and A3 ARs, belong to the superfamily of G protein-coupled receptors (GPCRs). They mediate a number of (patho)physiological functions and have attracted the interest of the biopharmaceutical sector for decades as potential drug targets. The many crystal structures of the A2A, and lately the A1 ARs, allow for the use of advanced computational, structure-based ligand design methodologies. Over the last decade, we have assessed the efficient synthesis of novel ligands specifically addressed to each of the four ARs. We herein review and update the results of this program with particular focus on molecular dynamics (MD) and free energy perturbation (FEP) protocols. The first in silico mutagenesis on the A1AR here reported allows understanding the specificity and high affinity of the xanthine-antagonist 8-Cyclopentyl-1,3-dipropylxanthine (DPCPX). On the A2AAR, we demonstrate how FEP simulations can distinguish the conformational selectivity of a recent series of partial agonists. These novel results are complemented with the revision of the first series of enantiospecific antagonists on the A2BAR, and the use of FEP as a tool for bioisosteric design on the A3AR.
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