1
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Celestina SK, Sundaram K, Ravi S. In vitro studies of potent aldose reductase inhibitors: Synthesis, characterization, biological evaluation and docking analysis of rhodanine-3-hippuric acid derivatives. Bioorg Chem 2020; 97:103640. [PMID: 32086051 DOI: 10.1016/j.bioorg.2020.103640] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 11/28/2019] [Accepted: 01/28/2020] [Indexed: 01/31/2023]
Abstract
Inhibitors of aldose reductase are rate-limiting enzymes and could play a key role to prevent the complications of diabetes. In our attempt to develop novel inhibitors of aldose reductase, the derivatives of rhodanine-3-hippuric acid-pyrazole hybrid were synthesized and characterised by spectral data. The biological studies reveal that all the compounds show an excellent activity against ALR2 with IC50 values ranging from 0.04 to 1.36 µM. Among these the synthesised compounds 6a-m, 6g and 6e showed specific inhibitory activity with IC50 values of 0.04 and 0.06 µM respectively against ALR2 and found to be more potent than epalrestat (IC50 = 0.87 μM), the only aldose reductase inhibitor currently used in the therapy. Molecular docking analysis using the AR-NADP+ complex as a receptor was performed with all the synthesized compounds. All the compounds exhibit a well-defined binding mode within the AR active site, similarly to previous described AR inhibitors, with the anion head group bound to the catalytic center, blocking thus its activity. By forming hydrogen bonds with Tyr48 and His110 of the protein from ALR2 (PDB ID: 2FZD), the compounds 6g and 6e interrupt the proton donation mechanism, which is necessary for the catalytic activity of ALR2.
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Affiliation(s)
- Stephen Kumar Celestina
- Department of Chemistry, Karpagam Academy of Higher Education, Coimbatore 641021, Tamil Nadu, India
| | - Kaveri Sundaram
- Department of Chemistry, Karpagam Academy of Higher Education, Coimbatore 641021, Tamil Nadu, India.
| | - Subban Ravi
- Department of Chemistry, Karpagam Academy of Higher Education, Coimbatore 641021, Tamil Nadu, India
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2
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Zhang C, Min Z, Liu X, Wang C, Wang Z, Shen J, Tang W, Zhang X, Liu D, Xu X. Tolrestat acts atypically as a competitive inhibitor of the thermostable aldo-keto reductase Tm1743 from Thermotoga maritima. FEBS Lett 2019; 594:564-580. [PMID: 31573681 DOI: 10.1002/1873-3468.13630] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/17/2019] [Accepted: 09/29/2019] [Indexed: 12/28/2022]
Abstract
Tolrestat and epalrestat have been characterized as noncompetitive inhibitors of aldo-ketone reductase 1B1 (AKR1B1), a leading drug target for the treatment of type 2 diabetes complications. However, clinical applications are limited for most AKR1B1 inhibitors due to adverse effects of cross-inhibition with other AKRs. Here, we report an atypical competitive binding and inhibitory effect of tolrestat on the thermostable AKR Tm1743 from Thermotoga maritima. Analysis of the Tm1743 crystal structure in complex with tolrestat alone and epalrestat-NADP+ shows that tolrestat, but not epalrestat, binding triggers dramatic conformational changes in the anionic site and cofactor binding pocket that prevents accommodation of NADP+ . Enzymatic and molecular dynamics simulation analyses further confirm tolrestat as a competitive inhibitor of Tm1743.
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Affiliation(s)
- Chenyun Zhang
- School of Medicine, Hangzhou Normal University, China
| | - Zhenzhen Min
- School of Medicine, Hangzhou Normal University, China
| | - Xuemeng Liu
- School of Medicine, Hangzhou Normal University, China
| | - Chao Wang
- School of Medicine, Hangzhou Normal University, China
| | - Zhiguo Wang
- School of Medicine, Hangzhou Normal University, China
| | - Jiejie Shen
- School of Medicine, Hangzhou Normal University, China
| | - Wanrong Tang
- School of Medicine, Hangzhou Normal University, China
| | - Xin Zhang
- School of Medicine, Hangzhou Normal University, China
| | - Dan Liu
- School of Medicine, Hangzhou Normal University, China
| | - Xiaoling Xu
- School of Medicine, Hangzhou Normal University, China.,Institute of Cardiovascular Disease Research, The Affiliated Hospital of Hangzhou Normal University, China
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3
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Elhenawy AA, Al-Harbi LM, El-Gazzar MA, Khowdiary MM, Moustfa A. Synthesis, molecular properties and comparative docking and QSAR of new 2-(7-hydroxy-2-oxo-2H-chromen-4-yl)acetic acid derivatives as possible anticancer agents. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 218:248-262. [PMID: 31003050 DOI: 10.1016/j.saa.2019.02.074] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 02/10/2019] [Accepted: 02/17/2019] [Indexed: 06/09/2023]
Abstract
Novel coumarin amino acid derivatives were synthesized. The structure of synthesized compounds has established on basis of different spectral data. The optimization geometry, frontier molecular orbitals (FMOs), thermodynamic parameters and chemical reactivity, were discussed using DFT\B3LYP by 6-311G* basis set, to identify a clear view for inter and intramolecular interaction of tested compounds. The molecular electrostatic potential (MEP) has plotted to investigate a recognition manner of synthesized compounds upon COX-2 receptor. All tested compounds showed a promising (NLOs) nonlinear optical properties. Bond dissociation energy (BDE) has studied to investigate a potency of these molecules against autoxidation mechanism Polynomial molecular docking logarithms have performed into the COX-2 active site for tested compounds. The docking protocol that has low RMSD has selected for discussion the binding affinity. The compounds with a high docking score 3,4,6-8,10 and 11 were selected for additional study against ADMET insilico, which showed that these compounds are a good oral bioavailability without observed carcinogenesis affect. The compounds (3,4,6-8,10 and 11) which that passed through docking and ADMET profile have examined their potency against (MCF-7) breast cancer cell in vitro. The compound 7 showed a highest potency against MCF-7 with IC50 value 0.39 μM. The QSAR model has created to discover the structural necessity inhibition of MCF-7. The derived QSAR model has a statistically significant with a good predictive power.
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Affiliation(s)
- Ahmed A Elhenawy
- Chemistry Department, Faculty of Science, Al-Azhar University (Boys Branch), Nasr City, Cairo, Egypt.
| | - L M Al-Harbi
- King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - M A El-Gazzar
- Chemistry Department, Faculty of Science, Al-Azhar University (Boys Branch), Nasr City, Cairo, Egypt
| | - Manal M Khowdiary
- Egyptian Petroleum Research Institute, Applied Surfactant Laboratory, Nasr City 11727, Cairo, Egypt; Chemistry Department, Faculty of Applied Sciences, Um El Qura University, Makkah, Saudi Arabia
| | - A Moustfa
- Chemistry Department, Faculty of Science, Al-Azhar University (Boys Branch), Nasr City, Cairo, Egypt
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4
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Elhenawy AA, Al-Harbi LM, Moustafa GO, El-Gazzar MA, Abdel-Rahman RF, Salim AE. Synthesis, comparative docking, and pharmacological activity of naproxen amino acid derivatives as possible anti-inflammatory and analgesic agents. Drug Des Devel Ther 2019; 13:1773-1790. [PMID: 31213767 PMCID: PMC6540076 DOI: 10.2147/dddt.s196276] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 04/04/2019] [Indexed: 11/23/2022] Open
Abstract
Background and aim: Naproxen is a member of the Nonsteroidal anti-inflammatory drugs (NSAIDs). This work aimed to synthesize a safe NSAID agent based on a peptide derivative. Methods: The structure of compounds 5–20 was established on the basis of spectral data. Frontier molecular orbitals and chemical reactivity were discussed to clarify inter- and intramolecular interactions among tested compounds. We applied competitive molecular docking using polynomial logarithms to identify the most accurate algorithm for pharmacological activity prediction for the tested compounds. The docking protocol with the lowest RMSD was selected for analyzing binding affinity. Results: Docking results illustrated that the binding interaction increased after introduction of an acidic fragment to the parent compound. These compounds were selected for additional study against adsorption, distribution, metabolism, excretion, and toxicity (ADMET) in silico. The compounds tested had good oral bioavailability without any carcinogenesis effect; no marked health effects were observed via rodent toxicity. Compounds passed through docking and ADMET profiles for them (5–16) were examined as anti-inflammatory and analgesic agents. Compounds 8 and 16 showed higher anti-inflammatory potency than the reference drug and tested compounds. Compounds 8, 10, and 14 exhibited the highest analgesic potency compared to the other tested compounds. Conclusion: The tested compounds have shown negligible ulcerogenic effects, and may be considered safer drugs than naproxen for treating inflammatory conditions.
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Affiliation(s)
- Ahmed A Elhenawy
- Chemistry Department, Faculty of Science, Al-Azhar University (Boys' Branch), Nasr City, Cairo, Egypt
| | - L M Al-Harbi
- King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Gaber O Moustafa
- Peptide Chemistry Department, Chemical Industries Research Division, National Research Centre, Dokki, Giza 12622, Egypt
| | - M A El-Gazzar
- Chemistry Department, Faculty of Science, Al-Azhar University (Boys' Branch), Nasr City, Cairo, Egypt
| | | | - Abd Elhamid Salim
- Chemistry Department, Faculty of Science, Al-Azhar University (Boys' Branch), Nasr City, Cairo, Egypt
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5
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A series of pyrido[2,3-b]pyrazin-3(4H)-one derivatives as aldose reductase inhibitors with antioxidant activity. Eur J Med Chem 2016; 121:308-317. [DOI: 10.1016/j.ejmech.2016.05.036] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 05/16/2016] [Accepted: 05/18/2016] [Indexed: 01/05/2023]
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6
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Andleeb H, Tehseen Y, Ali Shah SJ, Khan I, Iqbal J, Hameed S. Identification of novel pyrazole–rhodanine hybrid scaffolds as potent inhibitors of aldose reductase: design, synthesis, biological evaluation and molecular docking analysis. RSC Adv 2016. [DOI: 10.1039/c6ra14531k] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A series of novel pyrazole–rhodanine derivatives was designed, synthesized, and biologically evaluated for their potential inhibitory effect on both aldehyde reductase (ALR1) and aldose reductase (ALR2).
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Affiliation(s)
- Hina Andleeb
- Department of Chemistry
- Quaid-i-Azam University
- Islamabad-45320
- Pakistan
| | - Yildiz Tehseen
- Centre for Advanced Drug Research
- COMSATS Institute of Information Technology
- Abbottabad-22060
- Pakistan
| | - Syed Jawad Ali Shah
- Centre for Advanced Drug Research
- COMSATS Institute of Information Technology
- Abbottabad-22060
- Pakistan
| | - Imtiaz Khan
- Department of Chemistry
- Quaid-i-Azam University
- Islamabad-45320
- Pakistan
| | - Jamshed Iqbal
- Centre for Advanced Drug Research
- COMSATS Institute of Information Technology
- Abbottabad-22060
- Pakistan
| | - Shahid Hameed
- Department of Chemistry
- Quaid-i-Azam University
- Islamabad-45320
- Pakistan
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7
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8
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Endo S, Matsunaga T, Soda M, Tajima K, Zhao HT, El-Kabbani O, Hara A. Selective inhibition of the tumor marker AKR1B10 by antiinflammatory N-phenylanthranilic acids and glycyrrhetic acid. Biol Pharm Bull 2010; 33:886-90. [PMID: 20460771 DOI: 10.1248/bpb.33.886] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A human aldose reductase-like protein, AKR1B10 in the aldo-keto reductase (AKR) superfamily, was recently identified as a tumor marker of several types of cancer. Tolrestat, an aldose reductase inhibitor (ARI), is known to be the most potent inhibitor of the enzyme. In this study, we compared the inhibitory effects of other ARIs including flavonoids on AKR1B10 and aldose reductase to evaluate their specificity. However, ARIs showed lower inhibitory potency for AKR1B10 than for aldose reductase. In the search for potent and selective inhibitors of AKR1B10 from other drugs used clinically, we found that non-steroidal antiinflammatory N-phenylanthranilic acids, diclofenac and glycyrrhetic acid competitively inhibited AKR1B10, showing K(i) values of 0.35-2.9 microM and high selectivity to this enzyme (43-57 fold versus aldose reductase). Molecular docking studies of mefenamic acid and glycyrrhetic acid in the AKR1B10-nicotinamide adenine dinucleotide phosphate (NADP(+)) complex and site-directed mutagenesis of the putative binding residues suggest that the side chain of Val301 and a hydrogen-bonding network among residues Val301, Gln114 and Ser304 are important for determining the inhibitory potency and selectivity of the non-steroidal antiinflammatory drugs. Thus, the potent and selective inhibition may be related to the cancer chemopreventive roles of the drugs, and their structural features may facilitate the design of new anti-cancer agents targeting AKR1B10.
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Affiliation(s)
- Satoshi Endo
- Laboratory of Biochemistry, Gifu Pharmaceutical University, Daigaku-Nishi, Gifu 501-1196, Japan
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9
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Experimental validation and docking studies of flavone derivatives on aldose reductase involved in diabetic retinopathy, neuropathy, and nephropathy. Med Chem Res 2010. [DOI: 10.1007/s00044-010-9412-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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10
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Soni LK, Gupta AK, Kaskhedikar SG. Exploration of QSAR modelling techniques and their combination to rationalize the physicochemical characters of nitrophenyl derivatives towards aldose reductase inhibition. J Enzyme Inhib Med Chem 2009; 24:1002-7. [DOI: 10.1080/14756360802565486] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Affiliation(s)
- Love Kumar Soni
- Molecular Modelling Study Group CADD Laboratory, Computational Chemistry Research Department of Pharmacy, Shri G.S. Institute of Technology & Science 23 Park Road, Indore 452 003, India
| | - Arun Kumar Gupta
- Molecular Modelling Study Group CADD Laboratory, Computational Chemistry Research Department of Pharmacy, Shri G.S. Institute of Technology & Science 23 Park Road, Indore 452 003, India
| | - S. G Kaskhedikar
- Molecular Modelling Study Group CADD Laboratory, Computational Chemistry Research Department of Pharmacy, Shri G.S. Institute of Technology & Science 23 Park Road, Indore 452 003, India
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11
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Kato A, Higuchi Y, Goto H, Kizu H, Okamoto T, Asano N, Hollinshead J, Nash RJ, Adachi I. Inhibitory effects of Zingiber officinale Roscoe derived components on aldose reductase activity in vitro and in vivo. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2006; 54:6640-4. [PMID: 16939321 DOI: 10.1021/jf061599a] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Ginger (Zingiber officinale Roscoe) continues to be used as an important cooking spice and herbal medicine around the world. Scientific research has gradually verified the antidiabetic effects of ginger. Especially gingerols, which are the major components of ginger, are known to improve diabetes including the effect of enhancement against insulin-sensitivity. Aldose reductase inhibitors have considerable potential for the treatment of diabetes, without increased risk of hypoglycemia. The assay for aldose reductase inhibitors in ginger led to the isolation of five active compounds including 2-(4-hydroxy-3-methoxyphenyl)ethanol (2) and 2-(4-hydroxy-3-methoxyphenyl)ethanoic acid (3). Compounds 2 and 3 were good inhibitors of recombinant human aldose reductase, with IC50 values of 19.2 +/- 1.9 and 18.5 +/- 1.1 microM, respectively. Furthermore, these compounds significantly suppressed not only sorbitol accumulation in human erythrocytes but also lens galactitol accumulation in 30% of galactose-fed cataract rat model. A structure-activity relationship study revealed that the applicable side alkyl chain length and the presence of a C3 OCH3 group in the aromatic ring are essential features for enzyme recognition and binding. These results suggested that it would contribute to the protection against or improvement of diabetic complications for a dietary supplement of ginger or its extract containing aldose reductase inhibitors.
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Affiliation(s)
- Atsushi Kato
- Department of Hospital Pharmacy, University of Toyama, Toyama 930-0194, Japan.
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12
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Hofstadler SA, Sannes-Lowery KA. Applications of ESI-MS in drug discovery: interrogation of noncovalent complexes. Nat Rev Drug Discov 2006; 5:585-95. [PMID: 16816839 DOI: 10.1038/nrd2083] [Citation(s) in RCA: 171] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
For many years, analytical mass spectrometry has had numerous supporting roles in the drug development process, including the assessment of compound purity; quantitation of absorption, distribution, metabolism and excretion; and compound-specific pharmacokinetic analyses. More recently, mass spectrometry has emerged as an effective technique for identifying lead compounds on the basis of the characterization of noncovalent ligand-macromolecular target interactions. This approach offers several attractive properties for screening applications in drug discovery compared with other strategies, including the small quantities of target and ligands required, and the capacity to study ligands or targets without having to label them. Here, we review the application of electrospray ionization mass spectrometry to the interrogation of noncovalent complexes, highlighting examples from drug discovery efforts aimed at a range of target classes.
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Affiliation(s)
- Steven A Hofstadler
- Ibis Therapeutics, A Division of ISIS Pharmaceuticals, 1891 Rutherford Road, Carlsbad, California 92008, USA.
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13
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Rakowitz D, Maccari R, Ottanà R, Vigorita MG. In vitro aldose reductase inhibitory activity of 5-benzyl-2,4-thiazolidinediones. Bioorg Med Chem 2006; 14:567-74. [PMID: 16202614 DOI: 10.1016/j.bmc.2005.08.056] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2005] [Revised: 08/06/2005] [Accepted: 08/19/2005] [Indexed: 11/26/2022]
Abstract
Several 5-benzyl-2,4-thiazolidinediones (5-7) were synthesised and tested as in vitro aldose reductase (ALR2) inhibitors. Most of them, particularly N-unsubstituted 5-benzyl-2,4-thiazolidinediones 5 and (5-benzyl-2,4-dioxothiazolidin-3-yl)acetic acids 7, displayed moderate to high inhibitory activity levels. In detail, the insertion of an acetic chain on N-3 significantly enhanced ALR2 inhibitory potency, leading to acids 7 which proved to be the most effective among the tested compounds. In addition, in N-unsubstituted derivatives 5 the presence of an additional aromatic ring on the 5-benzyl moiety was generally beneficial. In fact, the ALR2 inhibition results of compounds 5-7, compared to those of the previously assayed corresponding 5-arylidene-2,4-thiazolidinediones, indicated that N-unsubstituted derivatives 5b, c and d, which bore an additional aromatic group in the para position of the 5-benzyl residue, were significantly more effective than their 5-arylidene counterparts; in all other cases, the saturation of the exocyclic double bond CC in 5 brought about a moderate decrease in activity.
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Affiliation(s)
- Dietmar Rakowitz
- Institute of Pharmacy, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
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14
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Maccari R, Ottanà R, Curinga C, Vigorita MG, Rakowitz D, Steindl T, Langer T. Structure–activity relationships and molecular modelling of 5-arylidene-2,4-thiazolidinediones active as aldose reductase inhibitors. Bioorg Med Chem 2005; 13:2809-23. [PMID: 15781392 DOI: 10.1016/j.bmc.2005.02.026] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2004] [Revised: 02/04/2005] [Accepted: 02/15/2005] [Indexed: 11/27/2022]
Abstract
The structure-activity relationships (SARs) of 5-arylidene-2,4-thiazolidinediones active as aldose reductase inhibitors (ARIs) were extended by varying the substitution pattern on the 5-arylidene moiety and on N-3. In particular, the introduction of an additional aromatic ring or an H-bond donor group on the 5-benzylidene ring enhanced ALR2 inhibitory potency. Moreover, the presence of a carboxylic anionic chain on N-3 was shown to be an important, although not essential, structural requisite to produce high levels of ALR2 inhibition. The length of this carboxylic chain was critical and acetic acids 4 were the most effective inhibitors among the tested derivatives. Molecular docking simulations into the ALR2 active site accorded with the in vitro inhibition data. They allowed the rationalization of the observed SARs and provided a pharmacophoric model for this class of ARIs.
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Affiliation(s)
- Rosanna Maccari
- Dipartimento Farmaco-chimico, Facoltà di Farmacia, Università di Messina, Viale SS. Annunziata, 98168 Messina, Italy.
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15
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Costantino L, Rastelli G, Cignarella G, Vianello P, Barlocco D. New aldose reductase inhibitors as potential agents for the prevention of long-term diabetic complications. Expert Opin Ther Pat 2005. [DOI: 10.1517/13543776.7.8.843] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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16
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Teodoro ML, Phillips GN, Kavraki LE. Understanding protein flexibility through dimensionality reduction. J Comput Biol 2004; 10:617-34. [PMID: 12935348 DOI: 10.1089/10665270360688228] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
This work shows how to decrease the complexity of modeling flexibility in proteins by reducing the number of dimensions necessary to model important macromolecular motions such as the induced-fit process. Induced fit occurs during the binding of a protein to other proteins, nucleic acids, or small molecules (ligands) and is a critical part of protein function. It is now widely accepted that conformational changes of proteins can affect their ability to bind other molecules and that any progress in modeling protein motion and flexibility will contribute to the understanding of key biological functions. However, modeling protein flexibility has proven a very difficult task. Experimental laboratory methods, such as x-ray crystallography, produce rather limited information, while computational methods such as molecular dynamics are too slow for routine use with large systems. In this work, we show how to use the principal component analysis method, a dimensionality reduction technique, to transform the original high-dimensional representation of protein motion into a lower dimensional representation that captures the dominant modes of motions of proteins. For a medium-sized protein, this corresponds to reducing a problem with a few thousand degrees of freedom to one with less than fifty. Although there is inevitably some loss in accuracy, we show that we can obtain conformations that have been observed in laboratory experiments, starting from different initial conformations and working in a drastically reduced search space.
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Affiliation(s)
- Miguel L Teodoro
- Department of Biochemistry and Cell Biology and Department of Computer Science, Rice University, 6100 Main Street, MS 140, Houston, TX 77005, USA
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17
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Bruno G, Costantino L, Curinga C, Maccari R, Monforte F, Nicoló F, Ottanà R, Vigorita MG. Synthesis and aldose reductase inhibitory activity of 5-arylidene-2,4-thiazolidinediones. Bioorg Med Chem 2002; 10:1077-84. [PMID: 11836118 DOI: 10.1016/s0968-0896(01)00366-2] [Citation(s) in RCA: 179] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Several (Z)-5-arylidene-2,4-thiazolidinediones were synthesized and tested as aldose reductase inhibitors (ARIs). The most active of the N-unsubstituted derivatives (2) exerted the same inhibitory activity of Sorbinil. The introduction of an acetic side chain on N-3 of the thiazolidinedione moiety led to a marked increase in lending inhibitory activity, conducting to the discovery of a very potent ARI (4c), whose activity level (IC50=0.13 microM) was in the same range of Tolrestat. Moreover, the corresponding methyl esters (3), devoid of any acidic functionality, showed appreciable inhibitory activity similar to that of the N-unsubstituted compounds. It was also found that the substitution pattern on the 5-benzylidene moiety markedly influenced the activity of N-unsubstituted 2,4-thiazolidinediones 2, compounds with substituents at the meta position being generally more effective than the para-substituted ones; however, this SAR was not evidenced in acetates 3 and acids 4.
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Affiliation(s)
- G Bruno
- Dipartimento Ch. Inorg., Chim. Anal. e Ch.-Fis, Facoltà Scienze MMFFNN, Università di Messina, Salita Sperone 31, 98166, Messina, Italy
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18
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Schlitzer M, Rodriguez L, Kador PF. Synthesis of potential aldose reductase inhibitors based on minimal pharmacophore requirements. J Pharm Pharmacol 2001; 53:831-9. [PMID: 11428659 DOI: 10.1211/0022357011776180] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A series of 17 compounds were synthesized based on the premise that the minimal pharmacophore for aldose reductase inhibition requires the presence of both an aryl group and polar group connected by a linking structure. Three groups of compounds were synthesized, the first possessing an aniline-4-(2'-6'-methylbenzothiazole) or 2-aminobenzothiazole group as the aryl group, the second possessing a 2-naphthyl as the aryl group and the third possessing either a 4-(2-phenylthiazole) or 2-(5-2'-nitrophenylfuran) as the aryl group. In all three of these groups the carboxylate or its methyl ester are linked to the aryl group through various lengths of methylene carbons and amide or cinnamide groups. Optimal activity was observed when the carboxylic group was separated from the aryl group by a linking structure of five atoms in length. Both a double bond and an amide moiety are well tolerated in the linking structure.
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Affiliation(s)
- M Schlitzer
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Germany
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19
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Rogniaux H, Van Dorsselaer A, Barth P, Biellmann JF, Barbanton J, van Zandt M, Chevrier B, Howard E, Mitschler A, Potier N, Urzhumtseva L, Moras D, Podjarny A. Binding of aldose reductase inhibitors: correlation of crystallographic and mass spectrometric studies. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 1999; 10:635-647. [PMID: 10384727 DOI: 10.1016/s1044-0305(99)00030-6] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Aldose reductase is a NADP(H)-dependent enzyme, believed to be strongly implicated in the development of degenerative complications of Diabetes Mellitus. The search for specific inhibitors of this enzyme has thus become a major pharmaceutic challenge. In this study, we applied both X-ray crystallography and mass spectrometry to characterize the interactions between aldose reductase and four representative inhibitors: AminoSNM, Imirestat, LCB3071, and IDD384. If crystallography remains obviously the only way to get an extensive description of the contacts between an inhibitor and the enzymatic site, the duration of the crystallographic analysis makes this technique incompatible with high throughput screenings of inhibitors. On the other hand, dissociation experiments monitored by mass spectrometry permitted us to evaluate rapidly the relative gas-phase stabilities of the aldose reductase-inhibitor noncovalent complexes. In our experiments, dissociation in the gas-phase was provoked by increasing the accelerating voltage of the ions (Vc) in the source-analyzer interface region: the Vc value needed to dissociate 50% of the noncovalent complex initially present (Vc50) was taken as a gas-phase stability parameter of the enzyme-inhibitor complex. Interestingly, the Vc50 were found to correlate with the energy of the electrostatic and H-bond interactions involved in the contact aldose reductase/inhibitor (Eel-H), computed from the crystallographic model. This finding may be specially interesting in a context of drug development. Actually, during a drug design optimization phase, the binding of the drug to the target enzyme is often optimized by modifying its interatomic electrostatic and H-bond contacts; because they usually depend on a single atom change on the drug, and are easier to introduce than the hydrophobic interactions. Therefore, the Vc50 may help to monitor the chemical modifications introduced in new inhibitors. X-ray crystallography is clearly needed to get the details of the contacts and to rationalize the design. Nevertheless, once the cycle of chemical modification is engaged, mass spectrometry can be used to select a priori the drug candidates which are worthy of further crystallographic investigation. We thus propose to use the two techniques in a complementary way, to improve the screening of large collections of inhibitors.
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Affiliation(s)
- H Rogniaux
- Laboratoire de Spectrométrie de Masse Bio-Organique, Institut de Chimie, Université Louis Pasteur, Strasbourg, France
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20
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Costantino L, Rastelli G, Gamberini MC, Vinson JA, Bose P, Iannone A, Staffieri M, Antolini L, Del Corso A, Mura U, Albasini A. 1-Benzopyran-4-one antioxidants as aldose reductase inhibitors. J Med Chem 1999; 42:1881-93. [PMID: 10354396 DOI: 10.1021/jm980441h] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Starting from the inhibitory activity of the flavonoid Quercetin, a series of 4H-1-benzopyran-4-one derivatives was synthesized and tested for inhibition of aldose reductase, an enzyme involved in the appearance of diabetic complications. Some of the compounds obtained display inhibitory activity similar to that of Sorbinil but are more selective than Quercetin and Sorbinil with respect to the closely related enzyme, aldehyde reductase, and also possess antioxidant activity. Remarkably, these compounds possess higher pKa values than carboxylic acids, a characteristic which could make the pharmacokinetics of these compounds very interesting. Molecular modeling investigations on the structures of inhibitors bound at the active site of aldose reductase were performed in order to suggest how these new inhibitors might bind to the enzyme and also to interpret structure-activity relationships.
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Affiliation(s)
- L Costantino
- Dipartimento di Scienze Farmaceutiche, Dipartimento di Scienze Biomediche, and Dipartimento di Chimica, Università di Modena, Via Campi 183, 41100 Modena, Italy
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21
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Fresneau P, Cussac M, Morand JM, Szymonski B, Tranqui D, Leclerc G. Synthesis, activity, and molecular modeling of new 2, 4-dioxo-5-(naphthylmethylene)-3-thiazolidineacetic acids and 2-thioxo analogues as potent aldose reductase inhibitors. J Med Chem 1998; 41:4706-15. [PMID: 9822541 DOI: 10.1021/jm9801399] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A series of 2,4-dioxo-5-(2-naphthylmethylene)-3-thiazolidineacetic acids and 2-thioxo analogues have been prepared as aldose reductase inhibitors. In vitro inhibitory activities of bovine lens aldose reductase were determined by a conventional method. 1-Naphthyl-substituted derivatives of the 2-thioxo series were the more potent inhibitors (IC50 congruent with 10 nM) with similar activity to that of Epalrestat. Structural analysis, especially by X-ray crystallography of two selected compounds, and molecular modeling comparisons with Zopolrestat were performed. These results provide explanations of the good activity of the inhibitor, the preference for 1-naphthyl-substituted compounds, and the nature of molecular interactions in these systems.
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Affiliation(s)
- P Fresneau
- Laboratoire de Chimie Thérapeutique and Laboratoire de Chimie Organique, Groupe de Pharmacochimie Moléculaire, EP811-CNRS, France
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22
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Urzhumtsev A, Tête-Favier F, Mitschler A, Barbanton J, Barth P, Urzhumtseva L, Biellmann JF, Podjarny A, Moras D. A 'specificity' pocket inferred from the crystal structures of the complexes of aldose reductase with the pharmaceutically important inhibitors tolrestat and sorbinil. Structure 1997; 5:601-12. [PMID: 9195881 DOI: 10.1016/s0969-2126(97)00216-5] [Citation(s) in RCA: 194] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
BACKGROUND Aldose reductase (AR) is an NADPH-dependent enzyme implicated in long-term diabetic complications. Buried at the bottom of a deep hydrophobic cleft, the NADPH coenzyme is surrounded by the conserved hydrophilic residues of the AR active site. The existence of an anionic binding site near the NADP+ has been determined from the structures of the complexes of AR with citrate, cacodylate and glucose-6-phosphate. The inhibitor zopolrestat binds to this anionic site, and in the hydrophobic cleft, after a change of conformation which opens a 'specificity' pocket. RESULTS The crystal structures of the porcine AR holoenzyme and its complexes with the inhibitors tolrestat and sorbinil have been solved; these structures are important as tolrestat and sorbinil are, pharmaceutically, the most well-studied AR inhibitors. The active site of the holoenzyme was analyzed, and binding of the inhibitors was found to involve two contact zones in the active site: first, a recognition region for hydrogen-bond acceptors near the coenzyme, with three centers, including the anionic site; and second, a hydrophobic contact zone in the active-site cleft, which in the case of tolrestat includes the specificity pocket. The conformational change leading to the opening of the specificity pocket upon tolrestat binding is different to the one seen upon zopolrestat binding; this pocket binds inhibitors that are more effective against AR than against aldehyde reductase. CONCLUSIONS The active site of AR adapts itself to bind tightly to different inhibitors; this happens both upon binding to the inhibitor's hydrophilic heads, and at the hydrophobic and specificity pockets of AR, which can change their shape through different conformational changes of the same residues. This flexibility could explain the large variety of possible substrates of AR.
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Affiliation(s)
- A Urzhumtsev
- UPR-de Biologie Structurale 9004 IGMBC CNRS/INSERM/ULP 1 rue Laurent Fries, B.P. 163, 67404, Illkirch, France
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23
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Nakano T, Petrash JM. Kinetic and spectroscopic evidence for active site inhibition of human aldose reductase. Biochemistry 1996; 35:11196-202. [PMID: 8780524 DOI: 10.1021/bi9608121] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Aldose reductase is an NADPH-dependent oxidoreductase that catalyzes the reduction of a variety of aldehydes and carbonyls, including monosaccharides. Intense interest in the discovery and characterization of inhibitors has developed since the action of this enzyme has been linked to the pathogenesis of some diabetic complications. Since past studies indicated that most inhibitors act noncompetitively or uncompetitively versus substrate in the direction of aldehyde reduction, it was assumed that they bind at one or more sites distinct from the active site. However, the crystal structure of aldose reductase complexed with inhibitor [Wilson et al. (1993) Proc. Natl. Acad. Sci. U.S.A. 90, 9847-9851] unambiguously revealed the inhibitor bound at the active site. The present study was undertaken to address this apparent discrepancy. Using a fluorometric assay, it was determined that zopolrestat, an acetic acid-type inhibitor, bound to aldose reductase complexed with either NADPH or NADP+. In contrast, the spirohydantoin-type inhibitor sorbinil demonstrated preferential binding to the binary enzyme.NADPH complex. Prior incubation of the enzyme.NADPH complex with zopolrestat prevented subsequent sorbinil binding. These results, together with the published structure of the ternary enzyme.NADPH.zopolrestat complex, are consistent with the conclusion that both sorbinil and zopolrestat bind at the active site. We propose that mixed inhibition patterns previously observed with sorbinil are due to inhibitor binding to both structural isomers of the enzyme.NADPH complex. Similar patterns for inhibition by zopolrestat are due to tight binding of the inhibitor. Substrate inhibition in the direction of aldehyde reduction occurs as a result of substrate binding to the enzyme.NADP+ complex.
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Affiliation(s)
- T Nakano
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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24
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Kador PF, Lee YS, Rodriguez L, Sato S, Bartoszko-Malik A, Abdel-Ghany YS, Miller DD. Identification of an aldose reductase inhibitor site by affinity labeling. Bioorg Med Chem 1995; 3:1313-24. [PMID: 8564397 DOI: 10.1016/0968-0896(95)00118-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Animal studies indicate that aldose reductase inhibitors represent a pharmacological method for inhibiting the onset of diabetic complications that is independent of blood sugar control. This has spurred the development of aldose reductase inhibitors (ARIs). To facilitate the rational development of more potent and direct ARIs, more specific knowledge of the structural and pharmacophoric requirements of the site at which ARIs interact are required. Co-crystallization of human placental aldose reductase with the inhibitor zopolrestat has been reported to result in a complex where the inhibitor is almost completely sequestered in the hydrophobic pocket which forms the substrate site. Zopolrestat's observed location, which makes the active site pocket inaccessible to solvent or further productive binding of substrate, is not supported by published inhibitor structure-activity relationships (SAR) studies or kinetic results which indicate that aldose reductase inhibitors such as zopolrestat are either non-competitive or uncompetitive inhibitors. Using a 5-iodoacetamido analog of alrestatin as an affinity labeled aldose reductase inhibitor, an inhibitor binding site on aldose reductase has been located. This inhibitor binding site contains a number of pharmacophoric elements previously proposed for the inhibitor site. Its location and composition is consistent with reported kinetic data, SAR observations, stereochemical requirements, and quantum chemical calculations.
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Affiliation(s)
- P F Kador
- Laboratory of Ocular Therapeutics, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
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25
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Bhatnagar A, Srivastava SK. Aldose reductase: congenial and injurious profiles of an enigmatic enzyme. BIOCHEMICAL MEDICINE AND METABOLIC BIOLOGY 1992; 48:91-121. [PMID: 1419150 DOI: 10.1016/0885-4505(92)90055-4] [Citation(s) in RCA: 122] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- A Bhatnagar
- Department of Human Biological Chemistry and Genetics, University of Texas Medical Branch, Galveston 77550
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26
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Hall IH, Izydore RA, Simlot R, Wong OT. Potential aldose reductase inhibitors: 1,2,4-triazolidine-3,5-diones and 2-(3,4,5-trimethoxybenzoyl)-4,4-diethyl-3,5-isoxazolidinedione . EXPERIENTIA 1992; 48:383-6. [PMID: 1582496 DOI: 10.1007/bf01923435] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
1,2,4-Triazolidine-3,5-diones and the 3,5-isoxazolidinedione were observed to be potent inhibitors of rat lens aldose reductase activity. In vivo in streptozotocin-diabetic rats, selected agents at 20 mg/kg/day, orally for 21 days reduced significantly the sorbitol levels of rbc, lens and sciatic nerves, suggesting that these derivatives may have some usefulness to treat clinical complications of diabetes mellitus.
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Affiliation(s)
- I H Hall
- Division of Medicinal Chemistry and Natural Products, School of Pharmacy, University of North Carolina, Chapel Hill 27599
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27
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Abstract
Aldose reductase is an NADPH-dependent enzyme which catalyzes the reduction of glucose to sorbitol. Specific potent inhibitors of aldose reductase are of potential pharmacological use because elevated levels of sorbitol produced by this enzyme in lens, peripheral nerve, retina, and renal glomeruli may be responsible for the pathogenesis associated with chronic diabetes. These inhibitors could also serve as probes of the mechanism of action of aldose reductase. anti-Oximes of aromatic aldehydes (e.g., benzaldoxime and 4-fluorobenzaldoxime) have proved to be effective inhibitors of aldose reductase rivaling pharmacological agents currently used to inhibit this enzyme in vivo. The kinetic patterns of inhibition in which benzyl alcohol is used as the oxidizable substrate suggest that the inhibition is due to the formation of a stable ternary complex composed of aldose reductase, NADP+, and the anti-oxime. Analogus ternary complexes are formed at the active site of horse liver alcohol dehydrogenase which is also inhibited by anti-oximes of efficient substrates.
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Affiliation(s)
- C Shen
- Department of Biological Chemistry School of Medicine, University of California, Los Angeles 90024
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28
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Mylari BL, Zembrowski WJ. Synthesis of aldose reductase inhibitor, 3,4-dihydro-4-oxo-3-[[5-(trifluoromethyl)-214C benzothiazolyl]methyl]-1-phthalazineacetic acid. J Labelled Comp Radiopharm 1991. [DOI: 10.1002/jlcr.2580290204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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29
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Lipinski CA, Fiese EF, Korst RJ. pKa, Log P and MedChem CLOGP Fragment Values of Acidic Heterocyclic Potential Bioisosteres. ACTA ACUST UNITED AC 1991. [DOI: 10.1002/qsar.19910100205] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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30
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Mayfield CA, DeRuiter J. Studies of the inhibition of aldose reductase: evidence for multiple site binding. THE INTERNATIONAL JOURNAL OF BIOCHEMISTRY 1989; 21:1275-85. [PMID: 2515079 DOI: 10.1016/0020-711x(89)90015-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
1. Comparison of structure-inhibition relationships and kinetic data between the N-[(4-benzoylamino)phenyl]sulfonyl]amino acids (BAPS-amino acids) and phenylsulfonylamino acids (PS-amino acids) suggests that the additional benzoyl moiety present in the BAPS-amino acids enhances inhibition by direct interaction with aldose reductase (EC 1.1.1.21) without altering the mode of interaction with the enzyme. 2. Also the 2-, 3- and 4-nitro regioisomers of BAPS-glycine (NBAPSG) display parallel structure- inhibition relationships with the 2-, 3- and 4-nitrobenzaldehyde substrates and the 2-, 3- and 4-nitroacetophenone competitive inhibitors. 3. Competition studies and multiple inhibition analyses demonstrate that the 4-nitrobenzoyl group of 4-NBAPSG binds at the substrate site of aldose reductase, while the PS-glycine moiety of 4-NBAPSG binds cooperatively at a distinct site.
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