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Klee LS, Gárdonyi M, Hüfner T, Heine A, Klebe G. Mutational Studies of Aldose Reductase to Trace a Transient Pocket Opening and to Explain Ligand Affinity Cliffs. ChemMedChem 2023; 18:e202300222. [PMID: 37278327 DOI: 10.1002/cmdc.202300222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/04/2023] [Accepted: 06/05/2023] [Indexed: 06/07/2023]
Abstract
Human aldose reductase, a target for the development of inhibitors for preventing diabetic complications, displays a transient specificity pocket which opens upon binding with specific, potent inhibitors. We investigated the opening mechanism of this pocket by mutating leucine residues involved in the gate keeping mechanism to alanine. Two isostructural inhibitors distinguished only by a single nitro to carboxy group replacement, have a 1000-fold difference in their binding affinity to the wild type. This difference is reduced to 10-fold in the mutated variants as the nitro derivative loses in affinity but conserves binding to the open transient pocket. The affinity of the carboxylate analog is minimally altered but the analog binding preference changes from the closed to open state of the transient pocket. Differences in the solvation properties of ligands and the transient pocket as well as changes from induced fit to conformational selections provide an explanation for the altered behavior of the ligands with respect to their binding to the different variants.
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Affiliation(s)
- Lea-Sophie Klee
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Marina Gárdonyi
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Tobias Hüfner
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Andreas Heine
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Gerhard Klebe
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032, Marburg, Germany
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2
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El-Gamil DS, ElHady AK, Chen PJ, Hwang TL, Abadi AH, Abdel-Halim M, Engel M. Development of novel conformationally restricted selective Clk1/4 inhibitors through creating an intramolecular hydrogen bond involving an imide linker. Eur J Med Chem 2022; 238:114411. [DOI: 10.1016/j.ejmech.2022.114411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 11/29/2022]
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3
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Qadir T, Amin A, Salhotra A, Sharma PK, Jeelani I, Abe H. Recent advances in the synthesis of benzothiazole and its derivatives. CURR ORG CHEM 2021. [DOI: 10.2174/1385272826666211229144446] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract:
Benzothiazoles have recognized pharmacophores in the field of research, predominantly in synthetic and medicinal chemistry, on account of their significant pharmaceutical properties. This important class of derivatives endows an extensive range of biological activities like anti-inflammatory, antidiabetic, anticancer, anticonvulsant, antibacterial, antiviral, antioxidant, antituberculosis, enzyme inhibitors, etc. Hence, various methodologies have been accomplished to synthesize benzothiazole compounds considering the purity, yield, and selectivity of the products. This review provides different reaction methods that are involved in the synthesis of a variety of benzothiazole derivatives.
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Affiliation(s)
- Tanzeela Qadir
- Department of Chemistry, School of Chemical Engineering and Physical Sciences, Lovely Professional University, Phagwara, Punjab, India
| | - Andleeb Amin
- Department of Chemistry, School of Chemical Engineering and Physical Sciences, Lovely Professional University, Phagwara, Punjab, India
| | - Alka Salhotra
- Department of Chemistry, School of Chemical Engineering and Physical Sciences, Lovely Professional University, Phagwara, Punjab, India
| | - Praveen Kumar Sharma
- Department of Chemistry, School of Chemical Engineering and Physical Sciences, Lovely Professional University, Phagwara, Punjab, India
| | - Ishtiaq Jeelani
- Graduate School of Innovative Life Science, University of Toyama, 3190 Gofuku 930-8555, Japan
| | - Hitoshi Abe
- Faculty of Engineering, University of Toyama, 3190 Gofuku 930-8555, Japan
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4
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Sandner A, Ngo K, Sager CP, Scheer F, Daude M, Diederich WE, Heine A, Klebe G. Which Properties Allow Ligands to Open and Bind to the Transient Binding Pocket of Human Aldose Reductase? Biomolecules 2021; 11:biom11121837. [PMID: 34944481 PMCID: PMC8699021 DOI: 10.3390/biom11121837] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/30/2021] [Accepted: 12/02/2021] [Indexed: 11/16/2022] Open
Abstract
The transient specificity pocket of aldose reductase only opens in response to specific ligands. This pocket may offer an advantage for the development of novel, more selective ligands for proteins with similar topology that lack such an adaptive pocket. Our aim was to elucidate which properties allow an inhibitor to bind in the specificity pocket. A series of inhibitors that share the same parent scaffold but differ in their attached aromatic substituents were screened using ITC and X-ray crystallography for their ability to occupy the pocket. Additionally, we investigated the electrostatic potentials and charge distribution across the attached terminal aromatic groups with respect to their potential to bind to the transient pocket of the enzyme using ESP calculations. These methods allowed us to confirm the previously established hypothesis that an electron-deficient aromatic group is an important prerequisite for opening and occupying the specificity pocket. We also demonstrated from our crystal structures that a pH shift between 5 and 8 does not affect the binding position of the ligand in the specificity pocket. This allows for a comparison between thermodynamic and crystallographic data collected at different pH values.
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Affiliation(s)
- Anna Sandner
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany; (A.S.); (K.N.); (A.H.)
| | - Khang Ngo
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany; (A.S.); (K.N.); (A.H.)
| | - Christoph P. Sager
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany; (A.S.); (K.N.); (A.H.)
| | - Frithjof Scheer
- Institut für Pharmazeutische Chemie, Zentrum für Tumor und Immunbiologie, Philipps-Universität Marburg, Hans-Meerwein-Straße 3, 35032 Marburg, Germany; (F.S.); (W.E.D.)
| | - Michael Daude
- Zentrum für Tumor und Immunbiologie, Core Facility Medicinal Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße 3, 35043 Marburg, Germany;
| | - Wibke E. Diederich
- Institut für Pharmazeutische Chemie, Zentrum für Tumor und Immunbiologie, Philipps-Universität Marburg, Hans-Meerwein-Straße 3, 35032 Marburg, Germany; (F.S.); (W.E.D.)
- Zentrum für Tumor und Immunbiologie, Core Facility Medicinal Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße 3, 35043 Marburg, Germany;
| | - Andreas Heine
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany; (A.S.); (K.N.); (A.H.)
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany; (A.S.); (K.N.); (A.H.)
- Correspondence: ; Tel.: +49-6421-28-21313
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5
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Benzothiazoles from Condensation of o-Aminothiophenoles with Carboxylic Acids and Their Derivatives: A Review. Molecules 2021; 26:molecules26216518. [PMID: 34770926 PMCID: PMC8587170 DOI: 10.3390/molecules26216518] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/14/2021] [Accepted: 10/21/2021] [Indexed: 01/27/2023] Open
Abstract
Nowadays, organic chemists are interested in the field of heterocyclic chemistry due to its use in the synthesis of a great variety of biologically active compounds. Heterocyclic compounds are widely found in nature and are essential for life. Among these, some natural nitrogen containing heterocyclic compounds have been used as chemotherapeutic agents. Their attachment to sugar molecules either as thioglycosides or as nucleosides analogues plays an important role in vital biological processes as well as in synthetic organic chemistry. Molecules containing benzothiazole (BT) nuclei are of this interesting class of compounds because some of them have been found to have a wide variety of biological activities. In this sense, we selected this topic to review and to then summarize the procedures related to the condensation reactions of o-aminothiophenoles (ATPs) as well as their disulfides with carboxylic acids, esters, orthoesters, acyl chlorides, amides, and nitriles. The condensation reactions with carbon dioxide (CO2) are included. Conventional methods with the use of acid and metal catalysts as well as recent green techniques, such as microwave irradiation, the use of ionic liquids, and ultrasound (US) chemistry, which have proven to have many advantages, were found in the review.
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6
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Lee DG, Lee JS, Quilantang NG, Jacinto SD, Lee S. Determination of Afzelin and Astragalin from Lespedeza cuneata on Aldose Reductase Inhibition. J Chromatogr Sci 2021; 59:381-387. [PMID: 33420504 DOI: 10.1093/chromsci/bmaa127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Indexed: 11/14/2022]
Abstract
The bioactive chemicals in L. cuneata were investigated by repeated column chromatography and their effect on aldose reductase (AR), obtained from rat lenses, was examined. Results showed that the ethyl acetate and n-butanol fractions of L. cuneata exhibited potential inhibitory effect against AR with IC50 values of 0.57 and 0.49 μg/mL, respectively. Phytochemical analysis of these two fractions resulted in the isolation of five flavonoids namely, acacetin (1), afzelin (2), astragalin (3), kaempferol (4) and scutellarein 7-O-glucoside (5). The AR inhibitory effect of compounds 1-5 was explored; compounds 2, 3 and 5 showed potential AR-inhibitory effects with IC50 values of 2.20, 1.91 and 12.87 μM, respectively. Quantitative analysis of afzelin (2) and astragalin (3) in L. cuneata by high performance liquid chromatography with ultraviolet detection revealed its content to be 0.722-11.828 and 2.054-7.006 mg/g, respectively. Overall, this study showed that L. cuneata is rich in flavonoids with promising AR-inhibitory activities, which can be utilized for the development of natural therapies for treating and managing diabetic complications.
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Affiliation(s)
- Dong Gu Lee
- BET Research Institute, Chung-Ang University, Seodongdaero, Daedukmyun, Anseong 17546, Republic of Korea
| | - Ju Sung Lee
- Department of Plant Science and Technology, Chung-Ang University, Seodongdaero, Daedukmyun, Anseong 17546, Republic of Korea
| | - Norman G Quilantang
- Department of Plant Science and Technology, Chung-Ang University, Seodongdaero, Daedukmyun, Anseong 17546, Republic of Korea
| | - Sonia D Jacinto
- Institute of Biology, University of the Philippines, Regidor St., Diliman, Quezon City 1101, Philippines
| | - Sanghyun Lee
- Department of Plant Science and Technology, Chung-Ang University, Seodongdaero, Daedukmyun, Anseong 17546, Republic of Korea
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Kousaxidis A, Petrou A, Lavrentaki V, Fesatidou M, Nicolaou I, Geronikaki A. Aldose reductase and protein tyrosine phosphatase 1B inhibitors as a promising therapeutic approach for diabetes mellitus. Eur J Med Chem 2020; 207:112742. [PMID: 32871344 DOI: 10.1016/j.ejmech.2020.112742] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 08/06/2020] [Indexed: 02/07/2023]
Abstract
Diabetes mellitus is a metabolic disease characterized by high blood glucose levels and usually associated with several chronic pathologies. Aldose reductase and protein tyrosine phosphatase 1B enzymes have identified as two novel molecular targets associated with the onset and progression of type II diabetes and related comorbidities. Although many inhibitors against these enzymes have already found in the field of diabetic mellitus, the research for discovering more effective and selective agents with optimal pharmacokinetic properties continues. In addition, dual inhibition of these target proteins has proved as a promising therapeutic approach. A variety of diverse scaffolds are presented in this review for the future design of potent and selective inhibitors of aldose reductase and protein tyrosine phosphatase 1B based on the most important structural features of both enzymes. The discovery of novel dual aldose reductase and protein tyrosine phosphatase 1B inhibitors could be effective therapeutic molecules for the treatment of insulin-resistant type II diabetes mellitus. The methods used comprise a literature survey and X-ray crystal structures derived from Protein Databank (PDB). Despite the available therapeutic options for type II diabetes mellitus, the inhibitors of aldose reductase and protein tyrosine phosphatase 1B could be two promising approaches for the effective treatment of hyperglycemia and diabetes-associated pathologies. Due to the poor pharmacokinetic profile and low in vivo efficacy of existing inhibitors of both targets, the research turned to more selective and cell-permeable agents as well as multi-target molecules.
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Affiliation(s)
- Antonios Kousaxidis
- School of Health, Department of Pharmacy, Aristotle University of Thessaloniki, 54124, Greece
| | - Anthi Petrou
- School of Health, Department of Pharmacy, Aristotle University of Thessaloniki, 54124, Greece
| | - Vasiliki Lavrentaki
- School of Health, Department of Pharmacy, Aristotle University of Thessaloniki, 54124, Greece
| | - Maria Fesatidou
- School of Health, Department of Pharmacy, Aristotle University of Thessaloniki, 54124, Greece
| | - Ioannis Nicolaou
- School of Health, Department of Pharmacy, Aristotle University of Thessaloniki, 54124, Greece
| | - Athina Geronikaki
- School of Health, Department of Pharmacy, Aristotle University of Thessaloniki, 54124, Greece.
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8
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Addressing selectivity issues of aldose reductase 2 inhibitors for the management of diabetic complications. Future Med Chem 2020; 12:1327-1358. [PMID: 32602375 DOI: 10.4155/fmc-2020-0032] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Aldose Reductase 2 (ALR2), the rate-limiting enzyme of the polyol pathway, plays an important role in detoxification of some toxic aldehydes. Under hyperglycemia, this enzyme overactivates and causes diabetic complications (DC). Therefore, ALR2 inhibition has been established as a potential approach to manage these complications. Several ALR2 inhibitors have been reported, but none of them could reach US FDA approval. One of the main reasons is their poor selectivity over ALR1, which leads to the toxicity. The current review underlines the molecular connectivity of ALR2 with DC and comparative analysis of the catalytic domains of ALR2 and ALR1, to better understand the selectivity issues. This report also discusses the key features required for ALR2 inhibition and to limit toxicity due to off-target activity.
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9
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Wu YQ, Lu HJ, Zhao WT, Zhao HY, Lin ZY, Zhang DF, Huang HH. A convenient and efficient H2SO4-promoted regioselective monobromination of phenol derivatives using N-bromosuccinimide. SYNTHETIC COMMUN 2020. [DOI: 10.1080/00397911.2019.1711415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Yong-Qi Wu
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hai-Jia Lu
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wen-Ting Zhao
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hong-Yi Zhao
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zi-Yun Lin
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Dong-Feng Zhang
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hai-Hong Huang
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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10
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Shchur IV, Shchegolkov EV, Burgart YV, Triandafilova GA, Maslova VV, Solodnikov SY, Krasnykh OP, Borisevich SS, Khursan SL, Saloutin VI. Synthesis and Biological Activity of 4-Cycloaminopolyfluorosalicylic Acids. ChemistrySelect 2019. [DOI: 10.1002/slct.201803523] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Irina V. Shchur
- The Ural Branch of the Russian Academy of Sciences; Postovsky Institute of Organic Synthesis; S. Kovalevskoy Str., 22 Ekaterinburg 620990 Russia
| | - Evgenii V. Shchegolkov
- The Ural Branch of the Russian Academy of Sciences; Postovsky Institute of Organic Synthesis; S. Kovalevskoy Str., 22 Ekaterinburg 620990 Russia
- Ural Federal University named after the First President of Russia B.N. Yeltsin; Mira Str., 19 Ekaterinburg 620002 Russia
| | - Yanina V. Burgart
- The Ural Branch of the Russian Academy of Sciences; Postovsky Institute of Organic Synthesis; S. Kovalevskoy Str., 22 Ekaterinburg 620990 Russia
- Ural Federal University named after the First President of Russia B.N. Yeltsin; Mira Str., 19 Ekaterinburg 620002 Russia
| | | | | | | | | | - Sophia S. Borisevich
- The Russian Academy of Sciences; Ufa Institute of Chemistry; Octyabrya Av., 71 Ufa 450078 Russia
| | - Sergey L. Khursan
- The Russian Academy of Sciences; Ufa Institute of Chemistry; Octyabrya Av., 71 Ufa 450078 Russia
| | - Victor I. Saloutin
- The Ural Branch of the Russian Academy of Sciences; Postovsky Institute of Organic Synthesis; S. Kovalevskoy Str., 22 Ekaterinburg 620990 Russia
- Ural Federal University named after the First President of Russia B.N. Yeltsin; Mira Str., 19 Ekaterinburg 620002 Russia
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11
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Yang X, Zhong J, Zhang Q, Qian J, Song K, Ruan C, Xu J, Ding K, Zhang J. Rational Design and Structure Validation of a Novel Peptide Inhibitor of the Adenomatous-Polyposis-Coli (APC)-Rho-Guanine-Nucleotide-Exchange-Factor-4 (Asef) Interaction. J Med Chem 2018; 61:8017-8028. [PMID: 30095910 DOI: 10.1021/acs.jmedchem.8b01112] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In colorectal cancer, adenomatous polyposis coli (APC) interacts with Rho guanine-nucleotide-exchange factor 4 (Asef), thereby stimulating aberrant colorectal-cancer-cell migration. Consequently, the APC-Asef interaction represents a promising therapeutic target for mitigating colorectal-cancer migration. In this study, we adopted the rational-design strategy involving the introduction of intramolecular hydrogen bonds and optimization of the lipophilic substituents to improve the binding affinities of peptides, leading to the discovery of MAI-400, the best inhibitor of the APC-Asef interaction known to date ( Kd = 0.012 μM, IC50 = 0.25 μM). Comprehensive evaluation of MAI-400 by biochemical and biophysical assays revealed the formation and effect of an intramolecular hydrogen bond. A cell-based assay showed MAI-400 efficiently blocking the APC-Asef interaction in a dose-dependent manner. Therefore, our study provides a best-in-class inhibitor, MAI-400, based on the rational drug design and structural validation, that can effectively inhibit the APC-Asef interaction.
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Affiliation(s)
| | | | | | | | | | | | | | - Ke Ding
- School of Pharmacy , Jinan University , 601 Huangpu Avenue West , Guangzhou 510632 , China
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12
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Johnson TW, Gallego RA, Edwards MP. Lipophilic Efficiency as an Important Metric in Drug Design. J Med Chem 2018; 61:6401-6420. [DOI: 10.1021/acs.jmedchem.8b00077] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Ted W. Johnson
- Oncology Medicinal Chemistry, Pfizer Inc., 10770 Science Center Drive, La Jolla, California 92121, United States
| | - Rebecca A. Gallego
- Oncology Medicinal Chemistry, Pfizer Inc., 10770 Science Center Drive, La Jolla, California 92121, United States
| | - Martin P. Edwards
- Oncology Medicinal Chemistry, Pfizer Inc., 10770 Science Center Drive, La Jolla, California 92121, United States
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13
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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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14
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Rechlin C, Scheer F, Terwesten F, Wulsdorf T, Pol E, Fridh V, Toth P, Diederich WE, Heine A, Klebe G. Price for Opening the Transient Specificity Pocket in Human Aldose Reductase upon Ligand Binding: Structural, Thermodynamic, Kinetic, and Computational Analysis. ACS Chem Biol 2017; 12:1397-1415. [PMID: 28287700 DOI: 10.1021/acschembio.7b00062] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Insights into the thermodynamic and kinetic signature of the transient opening of a protein-binding pocket resulting from accommodation of suitable substituents attached to a given parent ligand scaffold are presented. As a target, we selected human aldose reductase, an enzyme involved in the development of late-stage diabetic complications. To recognize a large scope of substrate molecules, this reductase opens a transient specificity pocket. The pocket-opening step was studied by X-ray crystallography, microcalorimetry, and surface plasmon resonance using a narrow series of 2-carbamoyl-phenoxy-acetic acid derivatives. Molecular dynamics simulations suggest that pocket opening occurs only once an appropriate substituent is attached to the parent scaffold. Transient pocket opening of the uncomplexed protein is hardly recorded. Hydration-site analysis suggests that up to five water molecules entering the opened pocket cannot stabilize this state. Sole substitution with a benzyl group stabilizes the opened state, and the energetic barrier for opening is estimated to be ∼5 kJ/mol. Additional decoration of the pocket-opening benzyl substituent with a nitro group results in a huge enthalpy-driven potency increase; on the other hand, an isosteric carboxylic acid group reduces the potency 1000-fold, and binding occurs without pocket opening. We suggest a ligand induced-fit mechanism for the pocket-opening step, which, however, does not represent the rate-determining step in binding kinetics.
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Affiliation(s)
- Chris Rechlin
- Institut
für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg
6, D-35032 Marburg, Germany
| | - Frithjof Scheer
- Institut
für Pharmazeutische Chemie, Zentrum für Tumor- und Immunbiologie (ZTI), Philipps-Universität Marburg, Hans-Meerwein-Straße
3, 35043 Marburg, Germany
| | - Felix Terwesten
- Institut
für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg
6, D-35032 Marburg, Germany
| | - Tobias Wulsdorf
- Institut
für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg
6, D-35032 Marburg, Germany
| | - Ewa Pol
- GE Healthcare Bio-Sciences AB, Björkgatan 30, SE-751 84 Uppsala, Sweden
| | - Veronica Fridh
- GE Healthcare Bio-Sciences AB, Björkgatan 30, SE-751 84 Uppsala, Sweden
| | - Philipp Toth
- Institut
für Pharmazeutische Chemie, Zentrum für Tumor- und Immunbiologie (ZTI), Philipps-Universität Marburg, Hans-Meerwein-Straße
3, 35043 Marburg, Germany
| | - Wibke E. Diederich
- Institut
für Pharmazeutische Chemie, Zentrum für Tumor- und Immunbiologie (ZTI), Philipps-Universität Marburg, Hans-Meerwein-Straße
3, 35043 Marburg, Germany
- Core
Facility Medicinal Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße 3, 35043 Marburg, Germany
| | - Andreas Heine
- Institut
für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg
6, D-35032 Marburg, Germany
| | - Gerhard Klebe
- Institut
für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg
6, D-35032 Marburg, Germany
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15
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Ke S. Novel amide-type ligand bearing bis-pyridine cores: Synthesis, spectral characterizations and X-ray structure analyses. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2016.04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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16
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Aberomand M, Parvank M, Mohammadzadeh G, Ramezani Z. Inhibition of Aldose Reductase and Sorbitol Accumulation by Hydroalcoholic Extract of Propolis. Jundishapur J Nat Pharm Prod 2016. [DOI: 10.17795/jjnpp-24594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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17
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Peng YH, Ueng SH, Tseng CT, Hung MS, Song JS, Wu JS, Liao FY, Fan YS, Wu MH, Hsiao WC, Hsueh CC, Lin SY, Cheng CY, Tu CH, Lee LC, Cheng MF, Shia KS, Shih C, Wu SY. Important Hydrogen Bond Networks in Indoleamine 2,3-Dioxygenase 1 (IDO1) Inhibitor Design Revealed by Crystal Structures of Imidazoleisoindole Derivatives with IDO1. J Med Chem 2015; 59:282-93. [PMID: 26642377 DOI: 10.1021/acs.jmedchem.5b01390] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Indoleamine 2,3-dioxygenase 1 (IDO1), promoting immune escape of tumors, is a therapeutic target for the cancer immunotherapy. A number of IDO1 inhibitors have been identified, but only limited structural biology studies of IDO1 inhibitors are available to provide insights on the binding mechanism of IDO1. In this study, we present the structure of IDO1 in complex with 24, a NLG919 analogue with potent activity. The complex structure revealed the imidazole nitrogen atom of 24 to coordinate with the heme iron, and the imidazoleisoindole core situated in pocket A with the 1-cyclohexylethanol moiety extended to pocket B to interact with the surrounding residues. Most interestingly, 24 formed an extensive hydrogen bond network with IDO1, which is a distinct feature of IDO1/24 complex structure and is not observed in the other IDO1 complex structures. Further structure-activity relationship, UV spectra, and structural biology studies of several analogues of 24 demonstrated that extensive hydrophobic interactions and the unique hydrogen bonding network contribute to the great potency of imidazoleisoindole derivatives. These results are expected to facilitate the structure-based drug design of new IDO inhibitors.
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Affiliation(s)
- Yi-Hui Peng
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan, Miaoli County 35053, Taiwan, ROC
| | - Shau-Hua Ueng
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan, Miaoli County 35053, Taiwan, ROC
| | - Chen-Tso Tseng
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan, Miaoli County 35053, Taiwan, ROC
| | - Ming-Shiu Hung
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan, Miaoli County 35053, Taiwan, ROC
| | - Jen-Shin Song
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan, Miaoli County 35053, Taiwan, ROC
| | - Jian-Sung Wu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan, Miaoli County 35053, Taiwan, ROC
| | - Fang-Yu Liao
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan, Miaoli County 35053, Taiwan, ROC
| | - Yu-Shiou Fan
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan, Miaoli County 35053, Taiwan, ROC
| | - Mine-Hsine Wu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan, Miaoli County 35053, Taiwan, ROC
| | - Wen-Chi Hsiao
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan, Miaoli County 35053, Taiwan, ROC
| | - Ching-Cheng Hsueh
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan, Miaoli County 35053, Taiwan, ROC
| | - Shu-Yu Lin
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan, Miaoli County 35053, Taiwan, ROC
| | - Chia-Yi Cheng
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan, Miaoli County 35053, Taiwan, ROC
| | - Chih-Hsiang Tu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan, Miaoli County 35053, Taiwan, ROC
| | - Lung-Chun Lee
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan, Miaoli County 35053, Taiwan, ROC
| | - Ming-Fu Cheng
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan, Miaoli County 35053, Taiwan, ROC
| | - Kak-Shan Shia
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan, Miaoli County 35053, Taiwan, ROC
| | - Chuan Shih
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan, Miaoli County 35053, Taiwan, ROC
| | - Su-Ying Wu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan, Miaoli County 35053, Taiwan, ROC
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18
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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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19
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Hu M, Ye W, Li J, Zhong G, He G, Xu Q, Zhang Y. Synthesis and Evaluation of Salicylanilide Derivatives as Potential Epidermal Growth Factor Receptor Inhibitors. Chem Biol Drug Des 2014; 85:280-9. [DOI: 10.1111/cbdd.12383] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Revised: 06/05/2014] [Accepted: 06/07/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Minhua Hu
- Anhui Key Laboratory of Traditional Chinese Medicine; Anhui University of Chinese Medicine; Hefei 230031 China
| | - Wenfeng Ye
- Anhui Key Laboratory of Traditional Chinese Medicine; Anhui University of Chinese Medicine; Hefei 230031 China
| | - Jiaming Li
- Anhui Key Laboratory of Traditional Chinese Medicine; Anhui University of Chinese Medicine; Hefei 230031 China
| | - Guochen Zhong
- Anhui Key Laboratory of Traditional Chinese Medicine; Anhui University of Chinese Medicine; Hefei 230031 China
| | - Guangwei He
- Hefei Medical Engineering Pharmaceutical Co., Ltd.; Hefei 230088 China
| | - Qinlong Xu
- Hefei Medical Engineering Pharmaceutical Co., Ltd.; Hefei 230088 China
| | - Yanchun Zhang
- Anhui Key Laboratory of Traditional Chinese Medicine; Anhui University of Chinese Medicine; Hefei 230031 China
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20
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Prajapati NP, Vekariya RH, Borad MA, Patel HD. Recent advances in the synthesis of 2-substituted benzothiazoles: a review. RSC Adv 2014. [DOI: 10.1039/c4ra07437h] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Recent advances in various synthetic protocols of 2-substituted benzothiazole derivatives.
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Affiliation(s)
| | - Rajesh H. Vekariya
- Department of Chemistry
- School of Sciences
- Gujarat University
- Ahmedabad, India
| | - Mayuri A. Borad
- Department of Chemistry
- School of Sciences
- Gujarat University
- Ahmedabad, India
| | - Hitesh D. Patel
- Department of Chemistry
- School of Sciences
- Gujarat University
- Ahmedabad, India
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21
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Małecka M, Mondal S, van Smaalen S, Paulmann C. Charge density distribution of 3-(1-aminoethylidene)-2-methoxy-2-oxo-2,3-dihydro-2λ(5)-benzo[e][1,2]oxaphosphinin-4-one. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2013; 69:621-628. [PMID: 24253088 DOI: 10.1107/s2052519213027267] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 10/03/2013] [Indexed: 06/02/2023]
Abstract
A combined experimental and theoretical study of one oxaphosphinane derivative was made on the basis of a topological analysis of its electron density distributions. The electron density was determined from a high-resolution X-ray diffraction data set measured with synchrotron radiation at 100 K, whereas theoretical calculations were performed using density functional theory (DFT) methods at the B3LYP\6-311++G(3df,3pd) level of approximation. The charge-density distribution and analysis of topological properties revealed that the P-O bond is of the transit closed-shell type. The crystal structure possesses one intra- and several intermolecular hydrogen bonds. They were characterized quantitatively by topological properties using Bader's Atoms in Molecules theory. All hydrogen bonds were classified as weak. Further analysis of the experimental electron density by the source function allowed the intramolecular hydrogen bond to be characterized as an isolated hydrogen bond, in contrast to the resonance-assisted hydrogen bond in related molecules, such as chromone derivatives.
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Affiliation(s)
- Magdalena Małecka
- Department of Crystallography and Crystal Chemistry, University of Łódź, Pomorska 163/165, 90-236 Łódź, Poland
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22
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23
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Li Z, Tan JH, He JH, Long Y, Ou TM, Li D, Gu LQ, Huang ZS. Disubstituted quinazoline derivatives as a new type of highly selective ligands for telomeric G-quadruplex DNA. Eur J Med Chem 2011; 47:299-311. [PMID: 22104971 DOI: 10.1016/j.ejmech.2011.10.057] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Revised: 10/25/2011] [Accepted: 10/28/2011] [Indexed: 12/12/2022]
Abstract
A series of 2,4-disubstituted quinazoline derivatives found to be a new type of highly selective ligand to bind with telomeric G-quadruplex DNA, and their biological properties were reported for the first time.Their interactions with telomeric G-quadruplex DNA were evaluated by using fluorescence resonance energy transfer (FRET) melting assay, circular dichroism (CD) spectroscopy, surface plasmon resonance (SPR), nuclear magnetic resonance (NMR), and molecular modeling. Our results showed that these derivatives could well recognize G-quadruplex and have high selectivity toward G-quadruplex over duplex DNA. The structure-activity relationships (SARs) study revealed that the disubstitution of quinazoline and the length of the amide side chain were important for its interaction with the G-quadruplex. Furthermore, telomerase inhibition of the quinazoline derivatives and their cellular effects were studied.
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Affiliation(s)
- Zeng Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People's Republic of China
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24
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Xu L, Cohen AE, Boxer SG. Electrostatic fields near the active site of human aldose reductase: 2. New inhibitors and complications caused by hydrogen bonds. Biochemistry 2011; 50:8311-22. [PMID: 21859105 DOI: 10.1021/bi200930f] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Vibrational Stark effect spectroscopy was used to measure electrostatic fields in the hydrophobic region of the active site of human aldose reductase (hALR2). A new nitrile-containing inhibitor was designed and synthesized, and the X-ray structure of its complex, along with cofactor NADP(+), with wild-type hALR2 was determined at 1.3 Å resolution. The nitrile is found to be in the proximity of T113, consistent with a hydrogen bond interaction. Two vibrational absorption peaks were observed at room temperature in the nitrile region when the inhibitor binds to wild-type hALR2, indicating that the nitrile probe experiences two different microenvironments, and these could be empirically separated into a hydrogen-bonded and non-hydrogen-bonded population by comparison with the T113A mutant, in which a hydrogen bond to the nitrile is not present. Classical molecular dynamics simulations based on the structure predict a double-peak distribution in protein electric fields projected along the nitrile probe. The interpretation of these two peaks as a hydrogen bond formation-dissociation process between the probe nitrile group and a nearby amino acid side chain is used to explain the observation of two IR bands, and the simulations were used to investigate the molecular details of this conformational change. Hydrogen bonding complicates the simplest analysis of vibrational frequency shifts as being due solely to electrostatic interactions through the vibrational Stark effect, and the consequences of this complication are discussed.
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Affiliation(s)
- Lin Xu
- Department of Chemistry, Stanford University, Stanford, California 94305-5080, United States
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25
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Kim JK, Lee YS, Kim SH, Bae YS, Lim SS. Inhibition of Aldose Reductase by Phenylethanoid Glycoside Isolated from the Seeds of Paulownia coreana. Biol Pharm Bull 2011; 34:160-3. [DOI: 10.1248/bpb.34.160] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Jin Kyu Kim
- Institute of Natural Medicine, Hallym University
| | - Yeon Sil Lee
- Center for Efficacy Assessment and Development of Functional Foods and Drugs, Hallym University
| | - Seon Ha Kim
- Center for Efficacy Assessment and Development of Functional Foods and Drugs, Hallym University
| | - Young Soo Bae
- Departement of Forest Biomaterials Engineering, Kangwon National University
| | - Soon Sung Lim
- Institute of Natural Medicine, Hallym University
- Center for Efficacy Assessment and Development of Functional Foods and Drugs, Hallym University
- Department of Food Science and Nutrition, Hallym University
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26
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Hattori T, Matsubara A, Taniguchi K, Ogura Y. Aldose reductase inhibitor fidarestat attenuates leukocyte-endothelial interactions in experimental diabetic rat retina in vivo. Curr Eye Res 2010; 35:146-54. [PMID: 20136425 DOI: 10.3109/02713680903447918] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
PURPOSE Dysregulation of the polyol pathway has been implicated as a major cause of diabetic retinopathy. The aldose reductase inhibitor fidarestat was recently reported to prevent retinal oxidative stress and overexpression of vascular endothelial growth factor (VEGF) protein in diabetic rats. In this study, we investigated the effect of fidarestat on leukocyte-endothelial cell interactions in an in vivo experimental model for diabetic retina. MATERIALS AND METHODS Diabetes was induced in six-week-old male Long-Evans rats by intraperitoneal injection of streptozotocin (STZ) (75 mg/kg). The rats were divided into four experimental groups: non-diabetic control rats, untreated diabetic rats, and diabetic rats treated with a low (4 mg/kg/day) or high (16 mg/kg/day) oral dose of fidarestat. After four weeks of treatment, accumulated leukocytes in the retina were counted in vivo by acridine orange digital fluorography. Intercellular adhesion molecule-1 (ICAM-1) and VEGF-164 mRNA levels in the retina were analyzed using the quantitative reverse transcription-polymerase chain reaction. ICAM-1 protein expression in the retina was investigated by immunohistochemistry. RESULTS Fidarestat treatment significantly decreased concentrations of sorbitol and fructose in the retinas of STZ-induced diabetic rats. Leukocyte accumulation in the retinas of fidarestat-treated rats was significantly less than in the untreated diabetic group (P < 0.01). Fidarestat treatment significantly reduced the expression ICAM-1 mRNA, but not VEGF-164 mRNA, in the retina of diabetic rats. Immunohistochemical study also revealed the suppressive effect of fidarestat on expression of ICAM-1. CONCLUSIONS Oral administration of fidarestat attenuated leukocyte accumulation in the retina of STZ induced-diabetic rats, suggesting that fidarestat may have a therapeutic role in preventing the progression of diabetic retinopathy.
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Affiliation(s)
- Tomoaki Hattori
- Department of Ophthalmology and Visual Sciences, Nagoya City University Graduate School of Medicine, 1 Kawasumi, Nagoya, Japan
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27
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Kuhn B, Mohr P, Stahl M. Intramolecular Hydrogen Bonding in Medicinal Chemistry. J Med Chem 2010; 53:2601-11. [DOI: 10.1021/jm100087s] [Citation(s) in RCA: 401] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Bernd Kuhn
- Discovery Chemistry, F. Hoffmann-La Roche AG, CH-4070 Basel, Switzerland
| | - Peter Mohr
- Discovery Chemistry, F. Hoffmann-La Roche AG, CH-4070 Basel, Switzerland
| | - Martin Stahl
- Discovery Chemistry, F. Hoffmann-La Roche AG, CH-4070 Basel, Switzerland
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28
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Van Zandt MC, Doan B, Sawicki DR, Sredy J, Podjarny AD. Discovery of [3-(4,5,7-trifluoro-benzothiazol-2-ylmethyl)-pyrrolo[2,3-b]pyridin-1-yl]acetic acids as highly potent and selective inhibitors of aldose reductase for treatment of chronic diabetic complications. Bioorg Med Chem Lett 2009; 19:2006-8. [DOI: 10.1016/j.bmcl.2009.02.037] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2008] [Revised: 02/05/2009] [Accepted: 02/09/2009] [Indexed: 10/21/2022]
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29
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Daş-Evcimen N, Bozdağ-Dündar O, Sarikaya M, Ertan R. In vitro aldose reductase inhibitory activity of some flavonyl-2,4-thiazolidinediones. J Enzyme Inhib Med Chem 2008; 23:297-301. [PMID: 18569331 DOI: 10.1080/14756360701475282] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Aldose reductase (AR) is implicated to play a critical role in diabetes and cardiovascular complications because of the reaction it catalyzes. AR enzyme appears to be the key factor in the reduction of glucose to sorbitol. Synthesis and accumulation of sorbitol in cells due to AR activity is the main cause of diabetic complications, such as diabetic cataract, retinopathy, neuropathy and nephropathy. Aldose reductase inhibitors have been found to prevent sorbitol accumulation in tissues. Numerous compounds have been prepared in order to improve the pharmacological prophile of inhibition of aldose reductase enzyme. In this study, seventeen flavonyl-2,4-thiazolidinediones (flavonyl-2,4-TZD) (Ia-e, IIa-e and IIIa-g) were tested for their ability to inhibit rat kidney AR. Compound Ib showed the highest inhibitory activity (88.69 +/- 1.46%) whereas Ia, IIa, IIIa, IIIb also showed significant inhibitory activity (49.26 +/- 2.85, 67.29 +/- 1.09, 71.11 +/- 1.95, 64.86 +/- 1.21%, respectively).
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Affiliation(s)
- Net Daş-Evcimen
- Department of Biochemistry, Faculty of Pharmacy, Ankara University.
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30
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Steuber H, Heine A, Podjarny A, Klebe G. Merging the binding sites of aldose and aldehyde reductase for detection of inhibitor selectivity-determining features. J Mol Biol 2008; 379:991-1016. [PMID: 18495158 DOI: 10.1016/j.jmb.2008.03.063] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2007] [Revised: 03/01/2008] [Accepted: 03/25/2008] [Indexed: 11/18/2022]
Abstract
Inhibition of human aldose reductase (ALR2) evolved as a promising therapeutic concept to prevent late complications of diabetes. As well as appropriate affinity and bioavailability, putative inhibitors should possess a high level of selectivity for ALR2 over the related aldehyde reductase (ALR1). We investigated the selectivity-determining features by gradually mapping the residues deviating between the binding pockets of ALR1 and ALR2 into the ALR2 binding pocket. The resulting mutational constructs of ALR2 (eight point mutations and one double mutant) were probed for their influence towards ligand selectivity by X-ray structure analysis of the corresponding complexes and isothermal titration calorimetry (ITC). The binding properties of these mutants were evaluated using a ligand set of zopolrestat, a related uracil derivative, IDD388, IDD393, sorbinil, fidarestat and tolrestat. Our study revealed induced-fit adaptations within the mutated binding site as an essential prerequisite for ligand accommodation related to the selectivity discrimination of the ligands. However, our study also highlights the limits of the present understanding of protein-ligand interactions. Interestingly, binding site mutations not involved in any direct interaction to the ligands in various cases show significant effects towards their binding thermodynamics. Furthermore, our results suggest the binding site residues deviating between ALR1 and ALR2 influence ligand affinity in a complex interplay, presumably involving changes of dynamic properties and differences of the solvation/desolvation balance upon ligand binding.
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Affiliation(s)
- Holger Steuber
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
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31
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Fafarman AT, Webb LJ, Chuang JI, Boxer SG. Site-specific conversion of cysteine thiols into thiocyanate creates an IR probe for electric fields in proteins. J Am Chem Soc 2007; 128:13356-7. [PMID: 17031938 PMCID: PMC2516909 DOI: 10.1021/ja0650403] [Citation(s) in RCA: 173] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The nitrile stretching mode of the thiocyanate moiety is a nearly ideal probe for measuring the local electric field arising from the organized environment of the interior of a protein. Nitriles were introduced into three proteins: ribonuclease S (RNase S), human aldose reductase (hALR2), and the reaction center (RC) of Rhodobacter capsulatus, through a facile synthetic scheme for the transformation of cysteine residues into thiocyanatoalanine. Vibrational Stark effect spectroscopy and Fourier transform infrared spectroscopy on the modified proteins demonstrated that thiocyanate residues are a highly general tool for probing electrostatic fields in proteins.
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Affiliation(s)
- Aaron T Fafarman
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA
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32
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Ferrari AM, Degliesposti G, Sgobba M, Rastelli G. Validation of an automated procedure for the prediction of relative free energies of binding on a set of aldose reductase inhibitors. Bioorg Med Chem 2007; 15:7865-77. [PMID: 17870536 DOI: 10.1016/j.bmc.2007.08.019] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2007] [Revised: 07/31/2007] [Accepted: 08/03/2007] [Indexed: 11/22/2022]
Abstract
Among the available methods for predicting free energies of binding of ligands to a protein, the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) and molecular mechanics generalized Born surface area (MM-GBSA) approaches have been validated for a relatively limited number of targets and compounds in the training set. Here, we report the results of an extensive study on a series of 28 inhibitors of aldose reductase with experimentally determined crystal structures and inhibitory activities, in which we evaluate the ability of MM-PBSA and MM-GBSA methods in predicting binding free energies using a number of different simulation conditions. While none of the methods proved able to predict absolute free energies of binding in quantitative agreement with the experimental values, calculated and experimental free energies of binding were significantly correlated. Comparing the predicted and experimental DeltaG of binding, MM-PBSA proved to perform better than MM-GBSA, and within the MM-PBSA methods, the PBSA of Amber performed similarly to Delphi. In particular, significant relationships between experimental and computed free energies of binding were obtained using Amber PBSA and structures minimized with a distance-dependent dielectric function. Importantly, while free energy predictions are usually made on large collections of equilibrated structures sampled during molecular dynamics in water, we have found that a single minimized structure is a reasonable approximation if relative free energies of binding are to be calculated. This finding is particularly relevant, considering that the generation of equilibrated MD ensembles and the subsequent free energy analysis on multiple snapshots is computationally intensive, while the generation and analysis of a single minimized structure of a protein-ligand complex is relatively fast, and therefore suited for high-throughput virtual screening studies. At this aim, we have developed an automated workflow that integrates all the necessary steps required to generate structures and calculate free energies of binding. The procedure is relatively fast and able to screen automatically and iteratively molecules contained in databases and libraries of compounds. Taken altogether, our results suggest that the workflow can be a valuable tool for ligand identification and optimization, being able to automatically and efficiently refine docking poses, which sometimes may not be accurate, and rank the compounds based on more accurate scoring functions.
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Affiliation(s)
- Anna Maria Ferrari
- Dipartimento di Scienze Farmaceutiche, Università di Modena e Reggio Emilia, Via Campi 183, 41100 Modena, Italy
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33
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Steuber H, Heine A, Klebe G. Structural and Thermodynamic Study on Aldose Reductase: Nitro-substituted Inhibitors with Strong Enthalpic Binding Contribution. J Mol Biol 2007; 368:618-38. [PMID: 17368668 DOI: 10.1016/j.jmb.2006.12.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2006] [Revised: 12/04/2006] [Accepted: 12/04/2006] [Indexed: 10/23/2022]
Abstract
To prevent diabetic complications derived from enhanced glucose flux via the polyol pathway the development of aldose reductase inhibitors (ARIs) has been established as a promising therapeutic concept. In order to identify novel lead compounds, a virtual screening (VS) was performed successfully suggesting carboxylate-type inhibitors of sub-micromolar to micromolar affinity. Here, we combine a structural characterization of the binding modes observed by X-ray crystallography with isothermal titration calorimetry (ITC) measurements providing insights into the driving forces of inhibitor binding, particularly of the first leads from VS. Characteristic features of this novel inhibitor type include a carboxylate head group connected via an alkyl spacer to a heteroaromatic moiety, which is linked to a further nitro-substituted aromatic portion. The crystal structures of two enzyme-inhibitor complexes have been determined at resolutions of 1.43 A and 1.55 A. Surprisingly, the carboxylic group of the most potent VS lead occupies the catalytic pocket differently compared to the interaction geometry observed in almost all other crystal structures with structurally related ligands and obtained under similar conditions, as an interstitial water molecule is picked up upon ligand binding. The nitro-aromatic moiety of both leads occupies the specificity pocket of the enzyme, however, adopting a different geometry compared to the docking prediction: unexpectedly, the nitro group binds to the bottom of the specificity pocket and provokes remarkable induced-fit adaptations. A peptide group located at the active site orients in such a way that H-bond formation to one nitro group oxygen atom is enabled, whereas a neighbouring tyrosine side-chain performs a slight rotation off from the binding cavity to accommodate the nitro group. Identically constituted ligands, lacking this nitro group, exhibit an affinity drop of one order of magnitude. In addition, thermodynamic data suggest a strongly favourable contribution to binding enthalpy in case the inhibitor is equipped with a nitro group at the corresponding position. To further investigate this phenomenon, we determined crystal structures and thermodynamic data of two similarly constituted IDD-type inhibitors addressing the specificity pocket with either a nitro or halogen-substituted aromatic moiety. As these data suggest, the nitro group provokes the enthalpic contribution, in addition to the H-bond mentioned above, by accepting two "non-classical" H-bonds donated by the aromatic tyrosine side-chain. In summary, this study provides the platform for further structure-guided design hypotheses of novel drug candidates with higher affinity and selectivity.
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Affiliation(s)
- Holger Steuber
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
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34
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Suydam IT, Snow CD, Pande VS, Boxer SG. Electric Fields at the Active Site of an Enzyme: Direct Comparison of Experiment with Theory. Science 2006; 313:200-4. [PMID: 16840693 DOI: 10.1126/science.1127159] [Citation(s) in RCA: 246] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The electric fields produced in folded proteins influence nearly every aspect of protein function. We present a vibrational spectroscopy technique that measures changes in electric field at a specific site of a protein as shifts in frequency (Stark shifts) of a calibrated nitrile vibration. A nitrile-containing inhibitor is used to deliver a unique probe vibration to the active site of human aldose reductase, and the response of the nitrile stretch frequency is measured for a series of mutations in the enzyme active site. These shifts yield quantitative information on electric fields that can be directly compared with electrostatics calculations. We show that extensive molecular dynamics simulations and ensemble averaging are required to reproduce the observed changes in field.
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Affiliation(s)
- Ian T Suydam
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA
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