title: Structural Determinants of the Selectivity of 3-Benzyluracil-1-acetic Acids toward Human Enzymes Aldose Reductase and AKR1B10.
abstract: The human enzymes aldose reductase (AR) and AKR1B10 have been thoroughly explored in terms of their roles in diabetes, inflammatory disorders, and cancer. In this study we identified two new lead compounds, 2-(3-(4-chloro-3-nitrobenzyl)-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)acetic acid (JF0048, 3) and 2-(2,4-dioxo-3-(2,3,4,5-tetrabromo-6-methoxybenzyl)-3,4-dihydropyrimidin-1(2H)-yl)acetic acid (JF0049, 4), which selectively target these enzymes. Although 3 and 4 share the 3-benzyluracil-1-acetic acid scaffold, they have different substituents in their aryl moieties. Inhibition studies along with thermodynamic and structural characterizations of both enzymes revealed that the chloronitrobenzyl moiety of compound 3 can open the AR specificity pocket but not that of the AKR1B10 cognate. In contrast, the larger atoms at the ortho and/or meta positions of compound 4 prevent the AR specificity pocket from opening due to steric hindrance and provide a tighter fit to the AKR1B10 inhibitor binding pocket, probably enhanced by the displacement of a disordered water molecule trapped in a hydrophobic subpocket, creating an enthalpic signature. Furthermore, this selectivity also occurs in the cell, which enables the development of a more efficient drug design strategy: compound 3 prevents sorbitol accumulation in human retinal ARPE-19 cells, whereas 4 stops proliferation in human lung cancer NCI-H460 cells.
authors.affiliation: Department of Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS, INSERM, UdS, rue Laurent Fries, 67404, Illkirch CEDEX, France. fxavier.ruiz@gmail.com.|Center for Advanced Biotechnology and Medicine, Department of Chemistry and Chemical Biology, Rutgers University, 08854-5627, Piscataway, NJ, (USA). fxavier.ruiz@gmail.com.
authors.forename: Francesc X
authors.initials: FX
authors.lastname: Ruiz
authors.affiliation: Department of Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS, INSERM, UdS, rue Laurent Fries, 67404, Illkirch CEDEX, France.
authors.forename: Alexandra
authors.initials: A
authors.lastname: Cousido-Siah
authors.affiliation: Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.
authors.forename: Sergio
authors.initials: S
authors.lastname: Porté
authors.affiliation: Departmento de Química Orgánica and Centro de Investigaciones Biomédicas (CINBIO), Universidade de Vigo, 363100, Vigo, Spain.
authors.forename: Marta
authors.initials: M
authors.lastname: Domínguez
authors.affiliation: Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.
authors.forename: Isidro
authors.identifier: http://orcid.org/0000-0001-7698-1720
authors.initials: I
authors.lastname: Crespo
authors.affiliation: Institute of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032, Marburg, Germany.
authors.forename: Chris
authors.initials: C
authors.lastname: Rechlin
authors.affiliation: Department of Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS, INSERM, UdS, rue Laurent Fries, 67404, Illkirch CEDEX, France.
authors.forename: André
authors.initials: A
authors.lastname: Mitschler
authors.affiliation: Departmento de Química Orgánica and Centro de Investigaciones Biomédicas (CINBIO), Universidade de Vigo, 363100, Vigo, Spain.
authors.forename: Ángel R
authors.initials: ÁR
authors.lastname: de Lera
authors.affiliation: Biomar Microbial Technologies S.A., Parque Tecnológico de León, 24009, León, Spain.
authors.forename: María Jesús
authors.initials: MJ
authors.lastname: Martín
authors.affiliation: Biomar Microbial Technologies S.A., Parque Tecnológico de León, 24009, León, Spain.
authors.forename: Jesús Ángel
authors.initials: JÁ
authors.lastname: de la Fuente
authors.affiliation: Institute of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032, Marburg, Germany.
authors.forename: Gerhard
authors.initials: G
authors.lastname: Klebe
authors.affiliation: Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.
authors.forename: Xavier
authors.initials: X
authors.lastname: Parés
authors.affiliation: Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.
authors.forename: Jaume
authors.identifier: http://orcid.org/0000-0001-9069-3987
authors.initials: J
authors.lastname: Farrés
authors.affiliation: Department of Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS, INSERM, UdS, rue Laurent Fries, 67404, Illkirch CEDEX, France. podjarny@igbmc.fr.
authors.forename: Alberto
authors.initials: A
authors.lastname: Podjarny
mesh_terms: D000085:Acetates / Q000737:chemistry* / Q000378:metabolism / Q000494:pharmacology; D000449:Aldehyde Reductase / Q000037:antagonists & inhibitors* / Q000378:metabolism; D000074408:Aldo-Keto Reductases; D001665:Binding Sites; D045744:Cell Line, Tumor; D049109:Cell Proliferation / Q000187:drug effects; D018360:Crystallography, X-Ray; D015195:Drug Design; D004791:Enzyme Inhibitors / Q000737:chemistry* / Q000378:metabolism / Q000494:pharmacology; D006801:Humans; D006860:Hydrogen Bonding; D020128:Inhibitory Concentration 50; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D013329:Structure-Activity Relationship; D013816:Thermodynamics; D014498:Uracil / Q000031:analogs & derivatives* / Q000737:chemistry
chemical_list: C403911:5-benzyluracil; D000085:Acetates; D004791:Enzyme Inhibitors; D014498:Uracil; C120471:AKR1B10 protein, human; D000074408:Aldo-Keto Reductases; D000449:Aldehyde Reductase
keywords: AKR1B10; aldose reductase; buried water molecule; drug design; steric hindrance