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Güleç Ö, Türkeş C, Arslan M, Demir Y, Dincer B, Ece A, İrfan Küfrevioğlu Ö, Beydemir Ş. Novel spiroindoline derivatives targeting aldose reductase against diabetic complications: Bioactivity, cytotoxicity, and molecular modeling studies. Bioorg Chem 2024; 145:107221. [PMID: 38387398 DOI: 10.1016/j.bioorg.2024.107221] [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: 10/30/2023] [Revised: 02/01/2024] [Accepted: 02/16/2024] [Indexed: 02/24/2024]
Abstract
Despite significant developments in therapeutic strategies, Diabetes Mellitus remains an increasing concern, leading to various complications, e.g., cataracts, neuropathy, retinopathy, nephropathy, and several cardiovascular diseases. The polyol pathway, which involves Aldose reductase (AR) as a critical enzyme, has been focused on by many researchers as a target for intervention. On the other hand, spiroindoline-based compounds possess remarkable biological properties. This guided us to synthesize novel spiroindoline oxadiazolyl-based acetate derivatives and investigate their biological activities. The synthesized molecules' structures were confirmed herein, using IR, NMR (1H and 13C), and Mass spectroscopy. All compounds were potent inhibitors with KI constants spanning from 0.186 ± 0.020 μM to 0.662 ± 0.042 μM versus AR and appeared as better inhibitors than the clinically used drug, Epalrestat (EPR, KI: 0.841 ± 0.051 μM). Besides its remarkable inhibitory profile compared to EPR, compound 6k (KI: 0.186 ± 0.020 μM) was also determined to have an unusual pharmacokinetic profile. The results showed that 6k had less cytotoxic effect on normal mouse fibroblast (L929) cells (IC50 of 569.58 ± 0.80 μM) and reduced the viability of human breast adenocarcinoma (MCF-7) cells (IC50 of 110.87 ± 0.42 μM) more than the reference drug Doxorubicin (IC50s of 98.26 ± 0.45 μM and 158.49 ± 2.73 μM, respectively), thus exhibiting more potent anticancer activity. Moreover, molecular dynamic simulations for 200 ns were conducted to predict the docked complex's stability and reveal significant amino acid residues that 6k interacts with throughout the simulation.
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Affiliation(s)
- Özcan Güleç
- Department of Chemistry, Faculty of Arts and Sciences, Sakarya University, 54187 Sakarya, Turkey
| | - Cüneyt Türkeş
- Department of Biochemistry, Faculty of Pharmacy, Erzincan Binali Yıldırım University, 24002 Erzincan, Turkey.
| | - Mustafa Arslan
- Department of Chemistry, Faculty of Arts and Sciences, Sakarya University, 54187 Sakarya, Turkey.
| | - Yeliz Demir
- Department of Pharmacy Services, Nihat Delibalta Göle Vocational High School, Ardahan University, 75700 Ardahan, Turkey
| | - Busra Dincer
- Department of Pharmacology, Faculty of Pharmacy, Ondokuz Mayıs University, 55020 Samsun, Turkey
| | - Abdulilah Ece
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Biruni University, 34010 İstanbul, Turkey
| | | | - Şükrü Beydemir
- Department of Biochemistry, Faculty of Pharmacy, Anadolu University, 26470 Eskişehir, Turkey; Bilecik Şeyh Edebali University, 11230 Bilecik, Turkey
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2
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Türkeş C, Demir Y, Beydemir Ş. In Vitro
Inhibitory Activity and Molecular Docking Study of Selected Natural Phenolic Compounds as AR and SDH Inhibitors**. ChemistrySelect 2022. [DOI: 10.1002/slct.202204050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Cüneyt Türkeş
- Department of Biochemistry Faculty of Pharmacy Erzincan Binali Yıldırım University Erzincan 24002 Turkey
| | - Yeliz Demir
- Department of Pharmacy Services Nihat Delibalta Göle Vocational High School Ardahan University Ardahan 75700 Turkey
| | - Şükrü Beydemir
- Department of Biochemistry Faculty of Pharmacy Anadolu University Eskişehir 26470 Turkey
- The Rectorate of Bilecik Şeyh Edebali University Bilecik 11230 Turkey
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3
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Türkeş C, Arslan M, Demir Y, Çoçaj L, Nixha AR, Beydemir Ş. N-substituted phthalazine sulfonamide derivatives as non-classical aldose reductase inhibitors. J Mol Recognit 2022; 35:e2991. [PMID: 36073557 DOI: 10.1002/jmr.2991] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 08/23/2022] [Accepted: 09/05/2022] [Indexed: 01/05/2023]
Abstract
Aldose reductase (AR, AKR1B1; EC 1.1.1.21) is an aldo-keto reductase that has been widely investigated as an enzyme crucially involved in the pathogenesis of several chronic complications, including nephropathy, neuropathy, retinopathy, and cataracts associated with diabetes mellitus. Although sulfonamides have been reported to possess many other biological activities, in continuation of our interest in designing and discovering potent inhibitors of AR, herein, we have evaluated the AR inhibitory potential of N-substituted phthalazine sulfonamide derivatives 5a-l. The biological studies revealed that all the derivatives show excellent activity against AR, with KI constants ranging from 67.73 to 495.20 nM. Among these agents, 4-(6-nitro-1,4-dioxo-1,2,3,4-tetrahydrophthalazine-2-carbonyl)benzenesulfonamide (5e) and 1,4-dioxo-3-(4-sulfamoylbenzoyl)-1,2,3,4-tetrahydrophthalazine-6-carboxylic acid (5f) showed prominent inhibitory activity with KI values of 67.73 and 148.20 nM, respectively, vs AR and were found to be more potent than epalrestat (KI = 852.50 nM), the only AR inhibitor currently used in the therapy. Moreover, molecular docking studies were also performed to rationalize binding site interactions of these sulfonamides (5a-l) with the target enzyme AR. According to ADME-Tox, predicts were also determined that these derivatives be ARIs displaying suitable drug-like properties. The sulfonamides identified in this study may be used to develop lead therapeutic agents inhibiting diabetic complications.
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Affiliation(s)
- Cüneyt Türkeş
- Department of Biochemistry, Faculty of Pharmacy, Erzincan Binali Yıldırım University, Erzincan, Turkey
| | - Mustafa Arslan
- Department of Chemistry, Faculty of Arts and Sciences, Sakarya University, Sakarya, Turkey
| | - Yeliz Demir
- Department of Pharmacy Services, Nihat Delibalta Göle Vocational High School, Ardahan University, Ardahan, Turkey
| | - Liridon Çoçaj
- Department of Chemistry, Faculty of Mathematical and Natural Sciences, Prishtina University, Republic of Kosova, Serbia
| | - Arleta Rifati Nixha
- Department of Chemistry, Faculty of Mathematical and Natural Sciences, Prishtina University, Republic of Kosova, Serbia
| | - Şükrü Beydemir
- Department of Biochemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey.,The Rectorate of Bilecik Şeyh Edebali University, Bilecik, Turkey
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4
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Abudayah A, Daoud S, Al-Sha'er M, Taha M. Pharmacophore Modeling of Targets Infested with Activity Cliffs via Molecular Dynamics Simulation Coupled with QSAR and Comparison with other Pharmacophore Generation Methods: KDR as Case Study. Mol Inform 2022; 41:e2200049. [PMID: 35973966 DOI: 10.1002/minf.202200049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 08/15/2022] [Indexed: 11/07/2022]
Abstract
Activity cliffs (ACs) are defined as pairs of structurally similar compounds with large difference in their potencies against certain biotarget. We recently proposed that potent AC members induce significant entropically-driven conformational modifications of the target that unveil additional binding interactions, while their weakly-potent counterparts are enthalpically-driven binders with little influence on the protein target. We herein propose to extract pharmacophores for ACs-infested target(s) from molecular dynamics (MD) frames of purely "enthalpic" potent binder(s) complexed within the particular target. Genetic function algorithm/machine learning (GFA/ML) can then be employed to search for the best possible combination of MD pharmacophore(s) capable of explaining bioactivity variations within a list of inhibitors. We compared the performance of this approach with established ligand-based and structure-based methods. Kinase inserts domain receptor (KDR) was used as a case study. KDR plays a crucial role in angiogenic signaling and its inhibitors have been approved in cancer treatment. Interestingly, GFA/ML selected, MD-based, pharmacophores were of comparable performances to ligand-based and structure-based pharmacophores. The resulting pharmacophores and QSAR models were used to capture hits from the national cancer institute list of compounds. The most active hit showed anti-KDR IC50 of 2.76 µM.
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Affiliation(s)
| | | | | | - Mutasem Taha
- Faculty of pharmacy,University of jordan, JORDAN
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5
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Exploiting activity cliffs for building pharmacophore models and comparison with other pharmacophore generation methods: sphingosine kinase 1 as case study. J Comput Aided Mol Des 2022; 36:39-62. [DOI: 10.1007/s10822-021-00435-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 11/24/2021] [Indexed: 12/20/2022]
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6
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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: 31] [Impact Index Per Article: 7.8] [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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Bajusz D, Rácz A, Héberger K. Comparison of Data Fusion Methods as Consensus Scores for Ensemble Docking. Molecules 2019; 24:E2690. [PMID: 31344902 PMCID: PMC6695709 DOI: 10.3390/molecules24152690] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 07/18/2019] [Accepted: 07/22/2019] [Indexed: 12/05/2022] Open
Abstract
Ensemble docking is a widely applied concept in structure-based virtual screening-to at least partly account for protein flexibility-usually granting a significant performance gain at a modest cost of speed. From the individual, single-structure docking scores, a consensus score needs to be produced by data fusion: this is usually done by taking the best docking score from the available pool (in most cases- and in this study as well-this is the minimum score). Nonetheless, there are a number of other fusion rules that can be applied. We report here the results of a detailed statistical comparison of seven fusion rules for ensemble docking, on five case studies of current drug targets, based on four performance metrics. Sevenfold cross-validation and variance analysis (ANOVA) allowed us to highlight the best fusion rules. The results are presented in bubble plots, to unite the four performance metrics into a single, comprehensive image. Notably, we suggest the use of the geometric and harmonic means as better alternatives to the generally applied minimum fusion rule.
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Affiliation(s)
- Dávid Bajusz
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2, H-1117 Budapest, Hungary
| | - Anita Rácz
- Plasma Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2, H-1117 Budapest, Hungary.
| | - Károly Héberger
- Plasma Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2, H-1117 Budapest, Hungary
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8
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Sun Z, Wang X, Zhao Q, Zhu T. Understanding Aldose Reductase-Inhibitors interactions with free energy simulation. J Mol Graph Model 2019; 91:10-21. [PMID: 31128525 DOI: 10.1016/j.jmgm.2019.05.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 05/13/2019] [Accepted: 05/14/2019] [Indexed: 12/15/2022]
Abstract
Aldose Reductase (AR) reduces a variety of substrates, such as aldehydes, aldoses and corticosteroids. It is the first and rate-limiting enzyme of the polyol pathway and is an important target enzyme for diabetes-associated complications, including retinopathy, neuropathy, and nephropathy. Inhibitors targeting this enzyme are structurally different and some of them have side effects. In existing publications, computational techniques are applied to investigate the binding affinities of existing inhibitors and predicting the affinities of newly designed ligands. However, these calculations only employ coarse and approximated methods such as docking and MM/PBSA. Brute force simulations are employed to study the dynamics of the system but no converged statistics is obtained. As a result, these computations provide results not consistent with experimental values and large discrepancies exist. In the current work, we employ the enhanced sampling technique of alchemical free energy simulation to calculate the binding affinities of several ligands targeting AR. The statistical error is defined with care and the correlation in the time-series data is fully considered. The statistically optimal estimators are used to extract the free energy estimates and the predicted results are in agreement with the experimental values. Less computationally demanding end-point free energy methods are also performed to compare their efficiency with the alchemical methods. As is expected, the end-point methods are of less accuracy and reliability compared with the alchemical free energy methods. The decomposition of the free energy difference in each alchemical transformation into the enthalpic and entropic components gives further insights on the thermodynamics. The enthalpy-entropy compensation is observed in this case. As the structural data obtained from experiments are only snapshots and more details are needed to understand the dynamics of the protein-ligand system, the conformational ensemble is analyzed. We identify important residues involved in the protein-ligand binding case and short-lived interactions formed due to fluctuations in the conformational ensemble. The current work shed light on the atomic detailed understanding of the dynamics of AR-inhibitors interactions.
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Affiliation(s)
- Zhaoxi Sun
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China; Computational Biomedicine (IAS-5/INM-9), Forschungszentrum Jülich, Jülich, 52425, Germany.
| | - Xiaohui Wang
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China; Institute of Computational Science, Università della Svizzera italiana (USI), Via Giuseppe Buffi 13, CH-6900, Lugano, Ticino, Switzerland
| | - Qianqian Zhao
- Computational Biomedicine (IAS-5/INM-9), Forschungszentrum Jülich, Jülich, 52425, Germany; College of Chemistry, Fuzhou University, Fuzhou, 350002, China
| | - Tong Zhu
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China
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9
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Mu Y, Yang M, Li H, Wu F, Luo S. 3D-QSARs and molecular dynamics simulation studies on induced fit binding of flavones to human aldose reductase. J Biomol Struct Dyn 2019; 38:1234-1241. [PMID: 30880629 DOI: 10.1080/07391102.2019.1592023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yunsong Mu
- School of Environment and Natural Resources, Renmin University of China, Beijing, China.,State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Mingru Yang
- College of Environmental Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Huixian Li
- School of Environment and Natural Resources, Renmin University of China, Beijing, China
| | - Fengchang Wu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Si Luo
- College of Resources and Environment, Hunan Agricultural University, Changsha, China
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10
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Wang Z, Zhou S, Zhang S, Zhang S, Zhu F, Jin X, Chen Z, Xu X. Semi-rational engineering of a thermostable aldo-keto reductase from Thermotoga maritima for synthesis of enantiopure ethyl-2-hydroxy-4-phenylbutyrate (EHPB). Sci Rep 2017; 7:4007. [PMID: 28638047 PMCID: PMC5479831 DOI: 10.1038/s41598-017-03947-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 05/05/2017] [Indexed: 11/29/2022] Open
Abstract
A novel aldo-keto reductase Tm1743 characterized from Thermotoga maritima was explored as an effective biocatalyst in chiral alcohol production. Natural Tm1743 catalyzes asymmetric reduction of ethyl 2-oxo-4-phenylbutyrate (EOPB) at high efficiency, but the production of, ethyl (S)-2-hydroxy-4-phenylbutyrate ((S)-EHPB), which is less desirable, is preferred with an enantiomeric excess (ee) value of 76.5%. Thus, altering the enantioselectivity of Tm1743 to obtain the more valuable product (R)-EHPB for angiotensin drug synthesis is highly desired. In this work, we determined the crystal structure of Tm1743 in complex with its cofactor NADP+ at 2.0 Å resolution, and investigated the enantioselectivity of Tm1743 through semi-rational enzyme design. Molecular simulations based on the crystal structure obtained two binding models representing the pro-S and pro-R conformations of EOPB. Saturation mutagenesis studies revealed that Trp21 and Trp86 play important roles in determining the enantioselectivity of Tm1743. The best (R)- and (S)-EHPB preferring Tm1743 mutants, denoted as W21S/W86E and W21L/W118H, were identified; their ee values are 99.4% and 99.6% and the catalytic efficiencies are 0.81 and 0.12 mM-1s-1, respectively. Our work presents an efficient strategy to improve the enantioselectivity of a natural biocatalyst, which will serve as a guide for further exploration of new green catalysts for asymmetric reactions.
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Affiliation(s)
- Zhiguo Wang
- Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China
| | - Shuo Zhou
- Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China
| | | | - Sa Zhang
- Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China
| | - Fangmeng Zhu
- Apeloa Pharmaceutical Co., Ltd., Dongyang, Zhejiang, 322118, China
| | - Xiaolu Jin
- Yosemade Pharmaceutical Co., Ltd., Jinhua, Zhejiang, 321025, China
| | - Zhenming Chen
- Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China.
| | - Xiaoling Xu
- Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China.
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11
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Salentin S, Schreiber S, Haupt VJ, Adasme MF, Schroeder M. PLIP: fully automated protein-ligand interaction profiler. Nucleic Acids Res 2015; 43:W443-7. [PMID: 25873628 PMCID: PMC4489249 DOI: 10.1093/nar/gkv315] [Citation(s) in RCA: 1173] [Impact Index Per Article: 130.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 03/28/2015] [Indexed: 11/14/2022] Open
Abstract
The characterization of interactions in protein-ligand complexes is essential for research in structural bioinformatics, drug discovery and biology. However, comprehensive tools are not freely available to the research community. Here, we present the protein-ligand interaction profiler (PLIP), a novel web service for fully automated detection and visualization of relevant non-covalent protein-ligand contacts in 3D structures, freely available at projects.biotec.tu-dresden.de/plip-web. The input is either a Protein Data Bank structure, a protein or ligand name, or a custom protein-ligand complex (e.g. from docking). In contrast to other tools, the rule-based PLIP algorithm does not require any structure preparation. It returns a list of detected interactions on single atom level, covering seven interaction types (hydrogen bonds, hydrophobic contacts, pi-stacking, pi-cation interactions, salt bridges, water bridges and halogen bonds). PLIP stands out by offering publication-ready images, PyMOL session files to generate custom images and parsable result files to facilitate successive data processing. The full python source code is available for download on the website. PLIP's command-line mode allows for high-throughput interaction profiling.
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Affiliation(s)
- Sebastian Salentin
- Biotechnology Center (BIOTEC), TU Dresden, Tatzberg 47-49, 01307 Dresden, Germany
| | - Sven Schreiber
- Biotechnology Center (BIOTEC), TU Dresden, Tatzberg 47-49, 01307 Dresden, Germany
| | - V Joachim Haupt
- Biotechnology Center (BIOTEC), TU Dresden, Tatzberg 47-49, 01307 Dresden, Germany
| | - Melissa F Adasme
- Biotechnology Center (BIOTEC), TU Dresden, Tatzberg 47-49, 01307 Dresden, Germany Escuela de Ingeniería en Bioinformática, Universidad de Talca, Avda. Lircay s/n Talca, 3460000, Chile
| | - Michael Schroeder
- Biotechnology Center (BIOTEC), TU Dresden, Tatzberg 47-49, 01307 Dresden, Germany
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12
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Ivanova ME, Fletcher GC, O’Reilly N, Purkiss AG, Thompson BJ, McDonald NQ. Structures of the human Pals1 PDZ domain with and without ligand suggest gated access of Crb to the PDZ peptide-binding groove. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:555-64. [PMID: 25760605 PMCID: PMC4356366 DOI: 10.1107/s139900471402776x] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 12/19/2014] [Indexed: 12/21/2022]
Abstract
Many components of epithelial polarity protein complexes possess PDZ domains that are required for protein interaction and recruitment to the apical plasma membrane. Apical localization of the Crumbs (Crb) transmembrane protein requires a PDZ-mediated interaction with Pals1 (protein-associated with Lin7, Stardust, MPP5), a member of the p55 family of membrane-associated guanylate kinases (MAGUKs). This study describes the molecular interaction between the Crb carboxy-terminal motif (ERLI), which is required for Drosophila cell polarity, and the Pals1 PDZ domain using crystallography and fluorescence polarization. Only the last four Crb residues contribute to Pals1 PDZ-domain binding affinity, with specificity contributed by conserved charged interactions. Comparison of the Crb-bound Pals1 PDZ structure with an apo Pals1 structure reveals a key Phe side chain that gates access to the PDZ peptide-binding groove. Removal of this side chain enhances the binding affinity by more than fivefold, suggesting that access of Crb to Pals1 may be regulated by intradomain contacts or by protein-protein interaction.
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Affiliation(s)
- Marina E. Ivanova
- Structural Biology Laboratories, Cancer Research UK, 44 Lincoln’s Inn Fields, London WC2A 3LY, England
| | - Georgina C. Fletcher
- Epithelial Biology Laboratories, Cancer Research UK, 44 Lincoln’s Inn Fields, London WC2A 3LY, England
| | - Nicola O’Reilly
- Peptide Chemistry Laboratories, Cancer Research UK, 44 Lincoln’s Inn Fields, London WC2A 3LY, England
| | - Andrew G. Purkiss
- Structural Biology Laboratories, Cancer Research UK, 44 Lincoln’s Inn Fields, London WC2A 3LY, England
| | - Barry J. Thompson
- Epithelial Biology Laboratories, Cancer Research UK, 44 Lincoln’s Inn Fields, London WC2A 3LY, England
| | - Neil Q. McDonald
- Structural Biology Laboratories, Cancer Research UK, 44 Lincoln’s Inn Fields, London WC2A 3LY, England
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, Malet Street, London WC1E 7HX, England
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13
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Fanfrlík J, Kolář M, Kamlar M, Hurný D, Ruiz FX, Cousido-Siah A, Mitschler A, Řezáč J, Munusamy E, Lepšík M, Matějíček P, Veselý J, Podjarny A, Hobza P. Modulation of aldose reductase inhibition by halogen bond tuning. ACS Chem Biol 2013; 8:2484-92. [PMID: 23988122 DOI: 10.1021/cb400526n] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
In this paper, we studied a designed series of aldose reductase (AR) inhibitors. The series was derived from a known AR binder, which had previously been shown to form a halogen bond between its bromine atom and the oxygen atom of the Thr-113 side chain of AR. In the series, the strength of the halogen bond was modulated by two factors, namely bromine-iodine substitution and the fluorination of the aromatic ring in several positions. The role of the single halogen bond in AR-ligand binding was elucidated by advanced binding free energy calculations involving the semiempirical quantum chemical Hamiltonian. The results were complemented with ultrahigh-resolution X-ray crystallography and IC50 measurements. All of the AR inhibitors studied were shown by X-ray crystallography to bind in an identical manner. Further, it was demonstrated that it was possible to decrease the IC50 value by about 1 order of magnitude by tuning the strength of the halogen bond by a monoatomic substitution. The calculations revealed that the protein-ligand interaction energy increased upon the substitution of iodine for bromine or upon the addition of electron-withdrawing fluorine atoms to the ring. However, the effect on the binding affinity was found to be more complex due to the change of the solvation/desolvation properties within the ligand series. The study shows that it is possible to modulate the strength of a halogen bond in a protein-ligand complex as was designed based on the previous studies of low-molecular-weight complexes.
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Affiliation(s)
- Jindřich Fanfrlík
- Institute of Organic
Chemistry and Biochemistry and Gilead Science Research Center, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
| | - Michal Kolář
- Institute of Organic
Chemistry and Biochemistry and Gilead Science Research Center, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
| | - Martin Kamlar
- Department
of Organic Chemistry, Charles University in Prague, Hlavova 2030, 128 43 Prague 2, Czech Republic
| | - David Hurný
- Department
of Organic Chemistry, Charles University in Prague, Hlavova 2030, 128 43 Prague 2, Czech Republic
| | - Francesc X. Ruiz
- Department
of Integrative Biology, IGBMC, CNRS, INSERM, UdS, 1 rue Laurent Fries, 67404 Illkirch CEDEX, France
| | - Alexandra Cousido-Siah
- Department
of Integrative Biology, IGBMC, CNRS, INSERM, UdS, 1 rue Laurent Fries, 67404 Illkirch CEDEX, France
| | - André Mitschler
- Department
of Integrative Biology, IGBMC, CNRS, INSERM, UdS, 1 rue Laurent Fries, 67404 Illkirch CEDEX, France
| | - Jan Řezáč
- Institute of Organic
Chemistry and Biochemistry and Gilead Science Research Center, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
| | - Elango Munusamy
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Martin Lepšík
- Institute of Organic
Chemistry and Biochemistry and Gilead Science Research Center, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
| | - Pavel Matějíček
- Department
of Physical and Macromolecular Chemistry, Charles University in Prague, Hlavova 2030, 128 43 Prague 2, Czech Republic
| | - Jan Veselý
- Department
of Organic Chemistry, Charles University in Prague, Hlavova 2030, 128 43 Prague 2, Czech Republic
| | - Alberto Podjarny
- Department
of Integrative Biology, IGBMC, CNRS, INSERM, UdS, 1 rue Laurent Fries, 67404 Illkirch CEDEX, France
| | - Pavel Hobza
- Institute of Organic
Chemistry and Biochemistry and Gilead Science Research Center, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
- Regional Centre of Advanced
Technologies and Materials, Department of Physical Chemistry, Palacký University, Olomouc, 771 46 Olomouc, Czech Republic
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The molecular basis for inhibition of sulindac and its metabolites towards human aldose reductase. FEBS Lett 2011; 586:55-9. [DOI: 10.1016/j.febslet.2011.11.023] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Revised: 11/15/2011] [Accepted: 11/17/2011] [Indexed: 01/26/2023]
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15
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Steuber H. An Old NSAID Revisited: Crystal Structure of Aldose Reductase in Complex with Sulindac at 1.0 Å Supports a Novel Mechanism for its Anticancer and Antiproliferative Effects. ChemMedChem 2011; 6:2155-7. [DOI: 10.1002/cmdc.201100374] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Indexed: 12/12/2022]
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