1
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Ciccone L, Petrarolo G, Barsuglia F, Fruchart-Gaillard C, Cassar Lajeunesse E, Adewumi AT, Soliman MES, La Motta C, Orlandini E, Nencetti S. Nature-Inspired O-Benzyl Oxime-Based Derivatives as New Dual-Acting Agents Targeting Aldose Reductase and Oxidative Stress. Biomolecules 2022; 12:biom12030448. [PMID: 35327641 PMCID: PMC8946157 DOI: 10.3390/biom12030448] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/02/2022] [Accepted: 03/05/2022] [Indexed: 02/04/2023] Open
Abstract
Aldose reductase (ALR2) is the enzyme in charge of developing cellular toxicity caused by diabetic hyperglycemia, which in turn leads to the generation of reactive oxygen species triggering oxidative stress. Therefore, inhibiting ALR2 while pursuing a concomitant anti-oxidant activity through dual-acting agents is now recognized as the gold standard treatment for preventing or at least delaying the progression of diabetic complications. Herein we describe a novel series of (E)-benzaldehyde O-benzyl oximes 6a–e, 7a–e, 8a–e, and 9–11 as ALR2 inhibitors endowed with anti-oxidant properties. Inspired by the natural products, the synthesized derivatives are characterized by a different polyhydroxy substitution pattern on their benzaldehyde fragment, which proved crucial for both the enzyme inhibitory activity and the anti-oxidant capacity. Derivatives (E)-2,3,4-trihydroxybenzaldehyde O-(3-methoxybenzyl) oxime (7b) and (E)-2,3,4-trihydroxybenzaldehyde O-(4-methoxybenzyl) oxime (8b) turned out to be the most effective dual-acting products, proving to combine the best ALR2 inhibitory properties with significant anti-oxidant efficacy.
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Affiliation(s)
- Lidia Ciccone
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy; (L.C.); (G.P.); (F.B.)
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, Commissariat à l’Énergie Atomique et aux Énergies Alternatives (CEA), Institut National de Recherche pour l’Agricolture, l’Alimentation et l’Environment (INRAE), SIMoS, 91191 Gif-sur-Yvette, France; (C.F.-G.); (E.C.L.)
- Centre for Instrumentation Sharing, University of Pisa (CISUP), Lungarno Pacinotti 43, 56126 Pisa, Italy;
| | - Giovanni Petrarolo
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy; (L.C.); (G.P.); (F.B.)
| | - Francesca Barsuglia
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy; (L.C.); (G.P.); (F.B.)
| | - Carole Fruchart-Gaillard
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, Commissariat à l’Énergie Atomique et aux Énergies Alternatives (CEA), Institut National de Recherche pour l’Agricolture, l’Alimentation et l’Environment (INRAE), SIMoS, 91191 Gif-sur-Yvette, France; (C.F.-G.); (E.C.L.)
| | - Evelyne Cassar Lajeunesse
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, Commissariat à l’Énergie Atomique et aux Énergies Alternatives (CEA), Institut National de Recherche pour l’Agricolture, l’Alimentation et l’Environment (INRAE), SIMoS, 91191 Gif-sur-Yvette, France; (C.F.-G.); (E.C.L.)
| | - Adeniyi T. Adewumi
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Science, Westville Campus, University of KwaZulu-Natal, Durban 4001, South Africa; (A.T.A.); (M.E.S.S.)
| | - Mahmoud E. S. Soliman
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Science, Westville Campus, University of KwaZulu-Natal, Durban 4001, South Africa; (A.T.A.); (M.E.S.S.)
| | - Concettina La Motta
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy; (L.C.); (G.P.); (F.B.)
- Centre for Instrumentation Sharing, University of Pisa (CISUP), Lungarno Pacinotti 43, 56126 Pisa, Italy;
- Correspondence: (C.L.M.); (S.N.)
| | - Elisabetta Orlandini
- Centre for Instrumentation Sharing, University of Pisa (CISUP), Lungarno Pacinotti 43, 56126 Pisa, Italy;
- Department of Earth Sciences, University of Pisa, Via Santa Maria 53, 56126 Pisa, Italy
- Research Center “E. Piaggio”, University of Pisa, Largo Lucio Lazzarino 1, 56122 Pisa, Italy
| | - Susanna Nencetti
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy; (L.C.); (G.P.); (F.B.)
- Centre for Instrumentation Sharing, University of Pisa (CISUP), Lungarno Pacinotti 43, 56126 Pisa, Italy;
- Correspondence: (C.L.M.); (S.N.)
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2
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Preparation of a Molecularly Imprinted Film on Quartz Crystal Microbalance Chip for Determination of Furanic Compounds. CHEMOSENSORS 2021. [DOI: 10.3390/chemosensors9120338] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The structural preferences of furanic compounds were studied using a combination of a molecularly imprinted film (MIF) on a piezoelectric-quartz chip. The furanic compounds and their derivatives were used as the templates. Owing to their similar heterocyclic structures, it is difficult to verify the structural differences between the templates. Therefore, a new cross-linker (Methacr-l-Cys-NHBn)2, was employed to generate a platform on a quartz crystal microbalance (QCM) chip. The cross-linker self-assembled to link the surface of the chip to copolymerize with other functional monomers. A layered film with chiral hydrophobicity and rigidity was thus fabricated. Subsequently, Acr-l-Ser-NHBn was utilized as a chiral monomer to construct MIF on a QCM chip. Forcomparison, we synthesized a more hydrophobic monomer, Methacr-l-Ser-NHBn, to enhance the binding ability of the MIF. The QCM flow injection system was handled in an organic solvent system. The proportion of the monomers was adjusted to optimize the recognition ability of these films. As the binding ability of the MIF toward model templates and structurally-related furanic compounds was improved, a MIF derived from 2-furaldehyde (FUL) achieved a lower detection limit (10 ng/mL). The binding properties of MIFs prepared against furanic compounds exhibited strong similarities to the binding properties of other compounds with heterocyclic ring structures. For example, 2-furaldehyde is very similar to 2-formylthiazole, 2-acetylfuran is similar to 2-acetylthiazole, and 2-furfuryl alcohol is similar to imidazole-2-methanol. Such recognition ability can help distinguish between the structural counterparts of other small heterocyclic compounds.
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3
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Elinson MN, Ryzhkova YE, Vereshchagin AN, Ryzhkov FV, Egorov MP. Electrocatalytic multicomponent one‐pot approach to tetrahydro‐2′
H
,
4
H
‐spiro[benzofuran‐2,5′‐pyrimidine] scaffold. J Heterocycl Chem 2021. [DOI: 10.1002/jhet.4274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Michail N. Elinson
- Department of Organic Chemistry N. D. Zelinsky Institute of Organic Chemistry Moscow Russian Federation
| | - Yuliya E. Ryzhkova
- Department of Organic Chemistry N. D. Zelinsky Institute of Organic Chemistry Moscow Russian Federation
| | - Anatoly N. Vereshchagin
- Department of Organic Chemistry N. D. Zelinsky Institute of Organic Chemistry Moscow Russian Federation
| | - Fedor V. Ryzhkov
- Department of Organic Chemistry N. D. Zelinsky Institute of Organic Chemistry Moscow Russian Federation
| | - Mikhail P. Egorov
- Department of Organic Chemistry N. D. Zelinsky Institute of Organic Chemistry Moscow Russian Federation
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4
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Efficient Electrocatalytic Approach to Spiro[Furo[3,2-b]pyran-2,5′-pyrimidine] Scaffold as Inhibitor of Aldose Reductase. ELECTROCHEM 2021. [DOI: 10.3390/electrochem2020021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
A continuously growing interest in convenient and ‘green’ reaction techniques encourages organic chemists to elaborate on new synthetic methodologies. Nowadays, organic electrochemistry is a new useful method with important synthetic and ecological advantages. The employment of an electrocatalytic methodology in cascade reactions is very promising because it provides the combination of the synthetic virtues of the cascade strategy with the ecological benefits and convenience of electrocatalytic procedures. In this research, a new type of the electrocatalytic cascade transformation was found: the electrochemical cyclization of 1,3-dimethyl-5-[[3-hydroxy-6-(hydroxymethyl)-4-oxo-4H-pyran-2-yl](aryl)methyl]pyrimidine-2,4,6(1H,3H,5H)-triones was carried out in alcohols in an undivided cell in the presence of sodium halides with the selective formation of spiro[furo[3,2-b]pyran-2,5′-pyrimidines] in 59-95% yields. This new electrocatalytic process is a selective, facile, and efficient way to create spiro[furo[3,2-b]pyran-2,5′-pyrimidines], which are pharmacologically active heterocyclic systems with different biomedical applications. Spiro[furo[3,2-b]pyran-2,5′-pyrimidines] were found to occupy the binding pocket of aldose reductase and inhibit it. The values of the binding energy and Lead Finder’s Virtual Screening scoring function showed that the formation of protein–ligand complexes was favorable. The synthesized compounds are promising for the inhibition of aldose reductase. This makes them interesting for study in the treatment of diabetes or similar diseases.
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5
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A supramolecular system that strictly follows the binding mechanism of conformational selection. Nat Commun 2020; 11:2740. [PMID: 32488094 PMCID: PMC7265396 DOI: 10.1038/s41467-020-16534-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 05/04/2020] [Indexed: 01/10/2023] Open
Abstract
Induced fit and conformational selection are two dominant binding mechanisms in biology. Although induced fit has been widely accepted by supramolecular chemists, conformational selection is rarely studied with synthetic systems. In the present research, we report a macrocyclic host whose binding mechanism is unambiguously assigned to conformational selection. The kinetic and thermodynamic aspects of this system are studied in great detail. It reveals that the kinetic equation commonly used for conformational selection is strictly followed here. In addition, two mathematical models are developed to determine the association constants of the same guest to the two host conformations. A “conformational selectivity factor” is defined to quantify the fidelity of conformational selection. Many details about the kinetic and thermodynamic aspects of conformational selection are revealed by this synthetic system. The conclusion and the mathematical models reported here should be helpful in understanding complex molecular recognition in both biological and synthetic systems. Conformational selection is one of the two dominant binding mechanisms in biology, but has rarely been studied in synthetic systems. Here, the authors report a supramolecular system that strictly follows the binding mechanism of conformational selection.
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6
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Saito R, Ishibashi K, Noumi M, Uno S, Higashi S, Goto M, Kuwahara S, Komatsu T. Synthesis and Aldose Reductase Inhibitory Activity of Botryllazine A Derivatives. Chem Pharm Bull (Tokyo) 2019; 67:556-565. [PMID: 31155561 DOI: 10.1248/cpb.c19-00003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Aldose reductase (AR) is associated with the onset of diabetic complications. Botryllazine A and its analogues were synthesized and evaluated for human AR inhibitory activity. Analogues possessing aromatic bicyclic systems at the C5 position of the central pyrazine ring exhibited superior AR inhibiting activity relative to the parent botryllazine A. In addition, the benzoyl groups at positions C2 and C3 of the pyrazine ring were dispensable for this improved inhibitory activity. Conversely, a benzoyl group-containing phenolic hydroxyl groups-at either position C2 or C3 of the pyrazine ring was essential for attainment of high inhibitory activity approaching that of sorbinil (a highly effective AR inhibitor).
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Affiliation(s)
- Ryota Saito
- Department of Chemistry, Toho University.,Research Center for Materials with Integrated Properties, Toho University
| | | | | | - Sota Uno
- Department of Chemistry, Toho University
| | | | - Masaru Goto
- Department of Biomolecular Science, Toho University
| | - Shunsuke Kuwahara
- Department of Chemistry, Toho University.,Research Center for Materials with Integrated Properties, Toho University
| | - Toshiya Komatsu
- Faculty of Pharmaceutical Sciences, Teikyo Heisei University
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7
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Abstract
INTRODUCTION Aldose reductase (ALR2) is both the key enzyme of the polyol pathway, whose activation under hyperglycemic conditions leads to the development of chronic diabetic complications, and the crucial promoter of inflammatory and cytotoxic conditions, even under a normoglycemic status. Accordingly, it represents an excellent drug target and a huge effort is being done to disclose novel compounds able to inhibit it. AREAS COVERED This literature survey summarizes patents and patent applications published over the last 5 years and filed for natural, semi-synthetic and synthetic ALR2 inhibitors. Compounds described have been discussed and analyzed from both chemical and functional angles. EXPERT OPINION Several ALR2 inhibitors with a promising pre-clinical ability to address diabetic complications and inflammatory diseases are being developed during the observed timeframe. Natural compounds and plant extracts are the prevalent ones, thus confirming the use of phytopharmaceuticals as an increasingly pursued therapeutic trend also in the ALR2 inhibitors field. Intriguing hints may be taken from synthetic derivatives, the most significant ones being represented by the differential inhibitors ARDIs. Differently from classical ARIs, these compounds should fire up the therapeutic efficacy of the class while minimizing its side effects, thus overcoming the existing limits of this kind of inhibitors.
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Affiliation(s)
- Luca Quattrini
- a Dipartimento di Farmacia , Università di Pisa , Pisa , Italy
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8
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Novel quinazolinone-based 2,4-thiazolidinedione-3-acetic acid derivatives as potent aldose reductase inhibitors. Future Med Chem 2017; 9:2147-2166. [DOI: 10.4155/fmc-2017-0149] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Aim: Targeting aldose reductase enzyme with 2,4-thiazolidinedione-3-acetic acid derivatives having a bulky hydrophobic 3-arylquinazolinone residue. Materials & methods: All the target compounds were structurally characterized by different spectroscopic methods and microanalysis, their aldose reductase inhibitory activities were evaluated, and binding modes were studied by molecular modeling. Results: All the synthesized compounds proved to inhibit the target enzyme potently, exhibiting IC50 values in the nanomolar/low nanomolar range. Compound 5i (IC50 = 2.56 nM), the most active of the whole series, turned out to be almost 70-fold more active than the only marketed aldose reductase inhibitor epalrestat. Conclusion: This work represents a promising matrix for developing new potential therapeutic candidates for prevention of diabetic complications through targeting aldose reductase enzyme. [Formula: see text]
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9
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Wang Z, Zhou S, Zhang S, Zhang S, Zhu F, Jin X, Chen Z, Xu X. Semi-rational engineering of a thermostable aldo-keto reductase from Thermotoga maritima for synthesis of enantiopure ethyl-2-hydroxy-4-phenylbutyrate (EHPB). Sci Rep 2017; 7:4007. [PMID: 28638047 PMCID: PMC5479831 DOI: 10.1038/s41598-017-03947-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 05/05/2017] [Indexed: 11/29/2022] Open
Abstract
A novel aldo-keto reductase Tm1743 characterized from Thermotoga maritima was explored as an effective biocatalyst in chiral alcohol production. Natural Tm1743 catalyzes asymmetric reduction of ethyl 2-oxo-4-phenylbutyrate (EOPB) at high efficiency, but the production of, ethyl (S)-2-hydroxy-4-phenylbutyrate ((S)-EHPB), which is less desirable, is preferred with an enantiomeric excess (ee) value of 76.5%. Thus, altering the enantioselectivity of Tm1743 to obtain the more valuable product (R)-EHPB for angiotensin drug synthesis is highly desired. In this work, we determined the crystal structure of Tm1743 in complex with its cofactor NADP+ at 2.0 Å resolution, and investigated the enantioselectivity of Tm1743 through semi-rational enzyme design. Molecular simulations based on the crystal structure obtained two binding models representing the pro-S and pro-R conformations of EOPB. Saturation mutagenesis studies revealed that Trp21 and Trp86 play important roles in determining the enantioselectivity of Tm1743. The best (R)- and (S)-EHPB preferring Tm1743 mutants, denoted as W21S/W86E and W21L/W118H, were identified; their ee values are 99.4% and 99.6% and the catalytic efficiencies are 0.81 and 0.12 mM-1s-1, respectively. Our work presents an efficient strategy to improve the enantioselectivity of a natural biocatalyst, which will serve as a guide for further exploration of new green catalysts for asymmetric reactions.
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Affiliation(s)
- Zhiguo Wang
- Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China
| | - Shuo Zhou
- Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China
| | | | - Sa Zhang
- Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China
| | - Fangmeng Zhu
- Apeloa Pharmaceutical Co., Ltd., Dongyang, Zhejiang, 322118, China
| | - Xiaolu Jin
- Yosemade Pharmaceutical Co., Ltd., Jinhua, Zhejiang, 321025, China
| | - Zhenming Chen
- Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China.
| | - Xiaoling Xu
- Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China.
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10
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Saito R, Tamura M, Kawano S, Yoshikawa Y, Kato A, Sasaki K, Yasui H. Synthesis and biological evaluation of 4-hydroxy-5-oxo-2,5-dihydro-1H-pyrrole-3-carboxamides and their zinc(ii) complexes as candidate antidiabetic agents. NEW J CHEM 2017. [DOI: 10.1039/c7nj00970d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Five new zinc(ii) complexes with 4-hydroxy-5-oxo-2,5-dihydro-1H-pyrrole-3-carboxamides were synthesized, and four of them exhibited insulin-mimetic activity in vitro.
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Affiliation(s)
- Ryota Saito
- Department of Chemistry
- Toho University
- Chiba 274-8510
- Japan
- Research Center for Materials with Integrated Properties
| | - Moe Tamura
- Department of Chemistry
- Toho University
- Chiba 274-8510
- Japan
| | - Saya Kawano
- Department of Chemistry
- Toho University
- Chiba 274-8510
- Japan
| | - Yutaka Yoshikawa
- Department of Health
- Sports and Nutrition
- Kobe Women's University
- Kobe 650-0046
- Japan
| | - Akihiro Kato
- Department of Chemistry
- Toho University
- Chiba 274-8510
- Japan
| | - Kaname Sasaki
- Department of Chemistry
- Toho University
- Chiba 274-8510
- Japan
| | - Hiroyuki Yasui
- Department of Analytical and Bioinorganic Chemistry
- Kyoto Pharmaceutical University
- Kyoto 607-8414
- Japan
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11
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Saito R, Hoshi M, Kato A, Ishikawa C, Komatsu T. Green fluorescent protein chromophore derivatives as a new class of aldose reductase inhibitors. Eur J Med Chem 2017; 125:965-974. [DOI: 10.1016/j.ejmech.2016.10.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 09/14/2016] [Accepted: 10/07/2016] [Indexed: 10/20/2022]
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12
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Cousido-Siah A, Ruiz FX, Fanfrlík J, Giménez-Dejoz J, Mitschler A, Kamlar M, Veselý J, Ajani H, Parés X, Farrés J, Hobza P, Podjarny AD. IDD388 Polyhalogenated Derivatives as Probes for an Improved Structure-Based Selectivity of AKR1B10 Inhibitors. ACS Chem Biol 2016; 11:2693-2705. [PMID: 27359042 DOI: 10.1021/acschembio.6b00382] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Human enzyme aldo-keto reductase family member 1B10 (AKR1B10) has evolved as a tumor marker and promising antineoplastic target. It shares high structural similarity with the diabetes target enzyme aldose reductase (AR). Starting from the potent AR inhibitor IDD388, we have synthesized a series of derivatives bearing the same halophenoxyacetic acid moiety with an increasing number of bromine (Br) atoms on its aryl moiety. Next, by means of IC50 measurements, X-ray crystallography, WaterMap analysis, and advanced binding free energy calculations with a quantum-mechanical (QM) approach, we have studied their structure-activity relationship (SAR) against both enzymes. The introduction of Br substituents decreases AR inhibition potency but improves it in the case of AKR1B10. Indeed, the Br atoms in ortho position may impede these drugs to fit into the AR prototypical specificity pocket. For AKR1B10, the smaller aryl moieties of MK181 and IDD388 can bind into the external loop A subpocket. Instead, the bulkier MK184, MK319, and MK204 open an inner specificity pocket in AKR1B10 characterized by a π-π stacking interaction of their aryl moieties and Trp112 side chain in the native conformation (not possible in AR). Among the three compounds, only MK204 can make a strong halogen bond with the protein (-4.4 kcal/mol, using QM calculations), while presenting the lowest desolvation cost among all the series, translated into the most selective and inhibitory potency AKR1B10 (IC50 = 80 nM). Overall, SAR of these IDD388 polyhalogenated derivatives have unveiled several distinctive AKR1B10 features (shape, flexibility, hydration) that can be exploited to design novel types of AKR1B10 selective drugs.
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Affiliation(s)
- Alexandra Cousido-Siah
- Department
of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS, INSERM, UdS, 1
rue Laurent Fries 67404 CEDEX Illkirch, France
| | - Francesc X. Ruiz
- Department
of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS, INSERM, UdS, 1
rue Laurent Fries 67404 CEDEX Illkirch, France
- Department
of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Barcelona, Spain
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Joan Giménez-Dejoz
- Department
of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Barcelona, Spain
| | - André Mitschler
- Department
of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS, INSERM, UdS, 1
rue Laurent Fries 67404 CEDEX Illkirch, France
| | - Martin Kamlar
- Department
of Organic Chemistry, Charles University in Prague, Hlavova 2030, 128 43 Prague 2, Czech Republic
| | - Jan Veselý
- Department
of Organic Chemistry, Charles University in Prague, Hlavova 2030, 128 43 Prague 2, Czech Republic
| | - Haresh Ajani
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Palacký University, Olomouc, 771 46 Olomouc, Czech Republic
| | - Xavier Parés
- Department
of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Barcelona, Spain
| | - Jaume Farrés
- Department
of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Barcelona, Spain
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Palacký University, Olomouc, 771 46 Olomouc, Czech Republic
| | - Alberto D. Podjarny
- Department
of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS, INSERM, UdS, 1
rue Laurent Fries 67404 CEDEX Illkirch, France
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13
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Pterin-7-carboxamides as a new class of aldose reductase inhibitors. Bioorg Med Chem Lett 2016; 26:4870-4874. [DOI: 10.1016/j.bmcl.2016.09.033] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 09/06/2016] [Accepted: 09/14/2016] [Indexed: 11/21/2022]
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14
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Kuhnert M, Köster H, Bartholomäus R, Park AY, Shahim A, Heine A, Steuber H, Klebe G, Diederich WE. Chamäleon-artige Bindungsmodi in der Leitstrukturoptimierung: wechselnde Bindungsgeometrien bei Aspartylprotease-Inhibitoren. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201411206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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15
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Kuhnert M, Köster H, Bartholomäus R, Park AY, Shahim A, Heine A, Steuber H, Klebe G, Diederich WE. Tracing binding modes in hit-to-lead optimization: chameleon-like poses of aspartic protease inhibitors. Angew Chem Int Ed Engl 2015; 54:2849-53. [PMID: 25630461 DOI: 10.1002/anie.201411206] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Indexed: 12/28/2022]
Abstract
Successful lead optimization in structure-based drug discovery depends on the correct deduction and interpretation of the underlying structure-activity relationships (SAR) to facilitate efficient decision-making on the next candidates to be synthesized. Consequently, the question arises, how frequently a binding mode (re)-validation is required, to ensure not to be misled by invalid assumptions on the binding geometry. We present an example in which minor chemical modifications within one inhibitor series lead to surprisingly different binding modes. X-ray structure determination of eight inhibitors derived from one core scaffold resulted in four different binding modes in the aspartic protease endothiapepsin, a well-established surrogate for e.g. renin and β-secretase. In addition, we suggest an empirical metrics that might serve as an indicator during lead optimization to qualify compounds as candidates for structural revalidation.
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Affiliation(s)
- Maren Kuhnert
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Hans-Meerwein-Strasse 3, 35032 Marburg (Germany)
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16
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Maccari R, Ottanà R. Targeting Aldose Reductase for the Treatment of Diabetes Complications and Inflammatory Diseases: New Insights and Future Directions. J Med Chem 2014; 58:2047-67. [DOI: 10.1021/jm500907a] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Rosanna Maccari
- Dipartimento
di Scienze del
Farmaco e dei Prodotti per la Salute, Università degli Studi di Messina, Polo Universitario dell’Annunziata, 98168 Messina, Italy
| | - Rosaria Ottanà
- Dipartimento
di Scienze del
Farmaco e dei Prodotti per la Salute, Università degli Studi di Messina, Polo Universitario dell’Annunziata, 98168 Messina, Italy
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17
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Could MM-GBSA be accurate enough for calculation of absolute protein/ligand binding free energies? J Mol Graph Model 2013; 46:41-51. [DOI: 10.1016/j.jmgm.2013.09.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 09/06/2013] [Accepted: 09/07/2013] [Indexed: 11/20/2022]
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18
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Avram SI, Crisan L, Pacureanu LM, Bora A, Seclaman E, Balint M, Kurunczi LG. Challenges in docking 2′-hydroxy and 2′,4′-dihydroxychalcones into the binding site of ALR2. Med Chem Res 2012. [DOI: 10.1007/s00044-012-0367-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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19
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Meslamani J, Li J, Sutter J, Stevens A, Bertrand HO, Rognan D. Protein–Ligand-Based Pharmacophores: Generation and Utility Assessment in Computational Ligand Profiling. J Chem Inf Model 2012; 52:943-55. [DOI: 10.1021/ci300083r] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Jamel Meslamani
- Laboratoire d’Innovation
Thérapeutique, UMR7200 Université de Strasbourg/CNRS,
74 route du Rhin, 67400 Illkirch, France
| | - Jiabo Li
- Accelrys, Inc., 10188 Telesis
Court, Suite 100, San Diego, California 92121, United States
| | - Jon Sutter
- Accelrys, Inc., 10188 Telesis
Court, Suite 100, San Diego, California 92121, United States
| | - Adrian Stevens
- Accelrys Ltd., 334 Cambridge Science
Park, Cambridge CB4 OWN, England
| | | | - Didier Rognan
- Laboratoire d’Innovation
Thérapeutique, UMR7200 Université de Strasbourg/CNRS,
74 route du Rhin, 67400 Illkirch, France
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20
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Avram S, Pacureanu LM, Seclaman E, Bora A, Kurunczi L. PLS-DA - Docking Optimized Combined Energetic Terms (PLSDA-DOCET) protocol: a brief evaluation. J Chem Inf Model 2011; 51:3169-79. [PMID: 22066983 DOI: 10.1021/ci2002268] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Docking studies have become popular approaches in drug design, where the binding energy of the ligand in the active site of the protein is estimated by a scoring function. Many promising techniques were developed to enhance the performance of scoring functions including the fusion of multiple scoring functions outcomes into a so-called consensus scoring function. Hereby, we evaluated the target oriented consensus technique using the energetic terms of several scoring functions. The approach was denoted PLSDA-DOCET. Optimization strategies for consensus energetic terms and scoring functions based on ROC metric were compared to classical rigid docking and to ligand-based similarity search methods comprising 2D fingerprints and ROCS. The ROCS results indicate large performance variations depending on the biological target. The AUC-based strategy of PLSDA-DOCET outperformed the other docking approaches regarding simple retrieval and scaffold-hopping. The superior performance of PLSDA-DOCET protocol relative to single and combined scoring functions was validated on an external test set. We found a relative low mean correlation of the ranks of the chemotypes retrieved by the PLSDA-DOCET protocol and all the other methods employed here.
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Affiliation(s)
- Sorin Avram
- Department of Computational Chemistry, Institute of Chemistry of Romanian Academy, Timisoara, Mihai Viteazul Avenue, 24, 300223 Timisoara, Romania
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21
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Pérez-Nueno VI, Ritchie DW. Identifying and characterizing promiscuous targets: implications for virtual screening. Expert Opin Drug Discov 2011; 7:1-17. [PMID: 22468890 DOI: 10.1517/17460441.2011.632406] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Ligand-based shape matching approaches have become established as important and popular virtual screening (VS) techniques. However, despite their relative success, the question of how to best choose the initial query compounds and their conformations remains largely unsolved. This issue gains importance when dealing with promiscuous targets, that is, proteins that bind multiple ligand scaffold families in one or more binding site. Conventional shape matching VS approaches assume that there is only one binding mode for a given protein target. This may be true for some targets, but it is certainly not true in all cases. Several recent studies have shown that some protein targets bind to different ligands in different ways. AREAS COVERED The authors discuss the concept of promiscuity in the context of virtual drug screening, and present and analyze several examples of promiscuous targets. The article also reports on the impact of the query conformation on the performance of shape-based VS and the potential to improve VS performance by using consensus shape clustering techniques. EXPERT OPINION The notion of polypharmacology is becoming highly relevant in drug discovery. Understanding and exploiting promiscuity present challenges and opportunities for drug discovery endeavors. The examples of promiscuity presented here suggest that promiscuous targets and ligands are much more common than previously assumed, and this should be taken into account in practical VS protocols. Although some progress has been made, there is a need to develop more sophisticated computational techniques and protocols that can identify and characterize promiscuous targets on a genomic scale.
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22
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Craig IR, Pfleger C, Gohlke H, Essex JW, Spiegel K. Pocket-space maps to identify novel binding-site conformations in proteins. J Chem Inf Model 2011; 51:2666-79. [PMID: 21910474 DOI: 10.1021/ci200168b] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The identification of novel binding-site conformations can greatly assist the progress of structure-based ligand design projects. Diverse pocket shapes drive medicinal chemistry to explore a broader chemical space and thus present additional opportunities to overcome key drug discovery issues such as potency, selectivity, toxicity, and pharmacokinetics. We report a new automated approach to diverse pocket selection, PocketAnalyzer(PCA), which applies principal component analysis and clustering to the output of a grid-based pocket detection algorithm. Since the approach works directly with pocket shape descriptors, it is free from some of the problems hampering methods that are based on proxy shape descriptors, e.g. a set of atomic positional coordinates. The approach is technically straightforward and allows simultaneous analysis of mutants, isoforms, and protein structures derived from multiple sources with different residue numbering schemes. The PocketAnalyzer(PCA) approach is illustrated by the compilation of diverse sets of pocket shapes for aldose reductase and viral neuraminidase. In both cases this allows identification of novel computationally derived binding-site conformations that are yet to be observed crystallographically. Indeed, known inhibitors capable of exploiting these novel binding-site conformations are subsequently identified, thereby demonstrating the utility of PocketAnalyzer(PCA) for rationalizing and improving the understanding of the molecular basis of protein-ligand interaction and bioactivity. A Python program implementing the PocketAnalyzer(PCA) approach is available for download under an open-source license ( http://sourceforge.net/projects/papca/ or http://cpclab.uni-duesseldorf.de/downloads ).
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Affiliation(s)
- Ian R Craig
- Novartis Institutes for Biomedical Research, Wimblehurst Road, Horsham, West Sussex RH12 5AB, UK.
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23
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Pérez-Nueno VI, Ritchie DW. Using Consensus-Shape Clustering To Identify Promiscuous Ligands and Protein Targets and To Choose the Right Query for Shape-Based Virtual Screening. J Chem Inf Model 2011; 51:1233-48. [DOI: 10.1021/ci100492r] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
| | - David W. Ritchie
- INRIA Nancy, LORIA, 615 rue du Jardin Botanique, 54600 Villers-lès-Nancy, France
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24
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Venkatraman V, Pérez-Nueno VI, Mavridis L, Ritchie DW. Comprehensive Comparison of Ligand-Based Virtual Screening Tools Against the DUD Data set Reveals Limitations of Current 3D Methods. J Chem Inf Model 2010; 50:2079-93. [DOI: 10.1021/ci100263p] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | - Lazaros Mavridis
- INRIA Nancy Grand Est, LORIA, 54506, Vandoeuvre-lès-Nancy, France
| | - David W. Ritchie
- INRIA Nancy Grand Est, LORIA, 54506, Vandoeuvre-lès-Nancy, France
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25
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Patra JC, Singh O. Artificial neural networks-based approach to design ARIs using QSAR for diabetes mellitus. J Comput Chem 2009; 30:2494-508. [DOI: 10.1002/jcc.21240] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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26
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Edwards AL, Batey RT. A structural basis for the recognition of 2'-deoxyguanosine by the purine riboswitch. J Mol Biol 2008; 385:938-48. [PMID: 19007790 DOI: 10.1016/j.jmb.2008.10.074] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2008] [Revised: 10/16/2008] [Accepted: 10/26/2008] [Indexed: 12/21/2022]
Abstract
Riboswitches are noncoding RNA elements that are commonly found in the 5'-untranslated region of bacterial mRNA. Binding of a small-molecule metabolite to the riboswitch aptamer domain guides the folding of the downstream sequence into one of two mutually exclusive secondary structures that directs gene expression. The purine riboswitch family, which regulates aspects of purine biosynthesis and transport, contains three distinct classes that specifically recognize guanine/hypoxanthine, adenine, or 2'-deoxyguanosine (dG). Structural analysis of the guanine and adenine classes revealed a binding pocket that almost completely buries the nucleobase within the core of the folded RNA. Thus, it is somewhat surprising that this family of RNA elements also recognizes dG. We have used a combination of structural and biochemical techniques to understand how the guanine riboswitch could be converted into a dG binder and the structural basis for dG recognition. These studies reveal that a limited number of sequence changes to a guanine-sensing RNA are required to cause a specificity switch from guanine to 2'-deoxyguanosine, and to impart an altered structure for accommodating the additional deoxyribose sugar moiety.
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Affiliation(s)
- Andrea L Edwards
- Department of Chemistry and Biochemistry, University of Colorado, 215 UCB, Boulder, CO 80309, USA
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27
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Davis AM, St-Gallay SA, Kleywegt GJ. Limitations and lessons in the use of X-ray structural information in drug design. Drug Discov Today 2008; 13:831-41. [PMID: 18617015 PMCID: PMC7185550 DOI: 10.1016/j.drudis.2008.06.006] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2008] [Revised: 05/23/2008] [Accepted: 06/04/2008] [Indexed: 12/04/2022]
Affiliation(s)
- Andrew M Davis
- Department of Medicinal Chemistry, AstraZeneca R&D Charnwood, Bakewell Road, Loughborough, Leicestershire LE11 5RH, United Kingdom.
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28
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Maccari R, Ottanà R, Ciurleo R, Rakowitz D, Matuszczak B, Laggner C, Langer T. Synthesis, induced-fit docking investigations, and in vitro aldose reductase inhibitory activity of non-carboxylic acid containing 2,4-thiazolidinedione derivatives. Bioorg Med Chem 2008; 16:5840-52. [PMID: 18492610 DOI: 10.1016/j.bmc.2008.04.072] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2008] [Revised: 04/23/2008] [Accepted: 04/30/2008] [Indexed: 01/12/2023]
Abstract
In continuation of our studies, we here report a series of non-carboxylic acid containing 2,4-thiazolidinedione derivatives, analogues of previously synthesized carboxylic acids which we had found to be very active in vitro aldose reductase (ALR2) inhibitors. Although the replacement of the carboxylic group with the carboxamide or N-hydroxycarboxamide one decreased the in vitro ALR2 inhibitory effect, this led to the identification of mainly non-ionized derivatives with micromolar ALR2 affinity. The 5-arylidene moiety deeply influenced the activity of these 2,4-thiazolidinediones. Our induced-fit docking studies suggested that 5-(4-hydroxybenzylidene)-substituted derivatives may bind the polar recognition region of the ALR2 active site by means of the deprotonated phenol group, while their acetic chain and carbonyl group at position 2 of the thiazolidinedione ring form a tight net of hydrogen bonds with amino acid residues of the lipophilic specificity pocket of the enzyme.
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Affiliation(s)
- Rosanna Maccari
- Dipartimento Farmaco-chimico, Facoltà di Farmacia, Università di Messina, Polo Universitario dell'Annunziata, 98168 Messina, Italy.
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29
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Xu Y, Colletier JP, Jiang H, Silman I, Sussman JL, Weik M. Induced-fit or preexisting equilibrium dynamics? Lessons from protein crystallography and MD simulations on acetylcholinesterase and implications for structure-based drug design. Protein Sci 2008; 17:601-5. [PMID: 18359854 DOI: 10.1110/ps.083453808] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Crystal structures of acetylcholinesterase complexed with ligands are compared with side-chain conformations accessed by native acetylcholinesterase in molecular dynamics (MD) simulations. Several crystallographic conformations of a key residue in a specific binding site are accessed in a simulation of native acetylcholinesterase, although not seen in rotomer plots. Conformational changes upon ligand binding thus involve preexisting equilibrium dynamics. Consequently, rational drug design could benefit significantly from conformations monitored by MD simulations of native targets.
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Affiliation(s)
- Yechun Xu
- Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
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30
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La Motta C, Sartini S, Salerno S, Simorini F, Taliani S, Marini AM, Da Settimo F, Marinelli L, Limongelli V, Novellino E. Acetic Acid Aldose Reductase Inhibitors Bearing a Five-Membered Heterocyclic Core with Potent Topical Activity in a Visual Impairment Rat Model. J Med Chem 2008; 51:3182-93. [DOI: 10.1021/jm701613h] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Concettina La Motta
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via D. Montesano 49, 80131 Napoli, Italy
| | - Stefania Sartini
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via D. Montesano 49, 80131 Napoli, Italy
| | - Silvia Salerno
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via D. Montesano 49, 80131 Napoli, Italy
| | - Francesca Simorini
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via D. Montesano 49, 80131 Napoli, Italy
| | - Sabrina Taliani
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via D. Montesano 49, 80131 Napoli, Italy
| | - Anna Maria Marini
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via D. Montesano 49, 80131 Napoli, Italy
| | - Federico Da Settimo
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via D. Montesano 49, 80131 Napoli, Italy
| | - Luciana Marinelli
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via D. Montesano 49, 80131 Napoli, Italy
| | - Vittorio Limongelli
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via D. Montesano 49, 80131 Napoli, Italy
| | - Ettore Novellino
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via D. Montesano 49, 80131 Napoli, Italy
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