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Traverssi MG, Manzano VE, Varela O, Colomer JP. Synthesis of N-glycosyl amides: conformational analysis and evaluation as inhibitors of β-galactosidase from E. coli. RSC Adv 2024; 14:2659-2672. [PMID: 38229710 PMCID: PMC10790283 DOI: 10.1039/d3ra07763b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 01/08/2024] [Indexed: 01/18/2024] Open
Abstract
The synthesis of N-glycosyl amides typically involves the use of glycosyl amines as direct precursors, resulting in low yields due to hydrolysis and the loss of stereocontrol through anomerization processes. In this study, a sequential synthesis of N-glycosyl amides is proposed, employing glycosyl amines as intermediates obtained from glycosyl azides. Derivatives with gluco, galacto, or xylo configurations were synthesized. Hexose derivatives were obtained under stereocontrol to give only the β anomer, while the xylo derivatives provided a mixture of α and β anomers. Conformational analysis revealed that all β anomers adopted the 4C1 conformation, while α anomers were found in the 1C4 chair as the major conformer. After de-O-acetylation, the derivatives containing a galactose unit were evaluated as inhibitors of β-galactosidase from E. coli and were found to be moderate inhibitors.
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Affiliation(s)
- Miqueas G Traverssi
- Departamento de Química Orgánica, Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Ciudad Universitaria Edificio de Ciencias II Córdoba Argentina
- Instituto de Investigaciones en Fisico-Química de Córdoba (INFIQC), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) UNC Argentina
| | - Verónica E Manzano
- Departamento de Química Orgánica, Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Ciudad Universitaria Pab. 2 C1428EHA Buenos Aires Argentina
- Centro de Investigación en Hidratos de Carbono (CIHIDECAR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) UBA Argentina
| | - Oscar Varela
- Departamento de Química Orgánica, Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Ciudad Universitaria Pab. 2 C1428EHA Buenos Aires Argentina
- Centro de Investigación en Hidratos de Carbono (CIHIDECAR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) UBA Argentina
| | - Juan P Colomer
- Departamento de Química Orgánica, Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Ciudad Universitaria Edificio de Ciencias II Córdoba Argentina
- Instituto de Investigaciones en Fisico-Química de Córdoba (INFIQC), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) UNC Argentina
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2
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Kyriakis E, Karra AG, Papaioannou O, Solovou T, Skamnaki VT, Liggri PGV, Zographos SE, Szennyes E, Bokor É, Kun S, Psarra AMG, Somsák L, Leonidas DD. The architecture of hydrogen and sulfur σ-hole interactions explain differences in the inhibitory potency of C-β-d-glucopyranosyl thiazoles, imidazoles and an N-β-d glucopyranosyl tetrazole for human liver glycogen phosphorylase and offer new insights to structure-based design. Bioorg Med Chem 2019; 28:115196. [PMID: 31767404 DOI: 10.1016/j.bmc.2019.115196] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 10/24/2019] [Accepted: 10/30/2019] [Indexed: 01/10/2023]
Abstract
C-Glucopyranosyl imidazoles, thiazoles, and an N-glucopyranosyl tetrazole were assessed in vitro and ex vivo for their inhibitory efficiency against isoforms of glycogen phosphorylase (GP; a validated pharmacological target for the development of anti-hyperglycaemic agents). Imidazoles proved to be more potent inhibitors than the corresponding thiazoles or the tetrazole. The most potent derivative has a 2-naphthyl substituent, a Ki value of 3.2 µM for hepatic glycogen phosphorylase, displaying also 60% inhibition of GP activity in HepG2 cells, compared to control vehicle treated cells, at 100 μM. X-Ray crystallography studies of the protein - inhibitor complexes revealed the importance of the architecture of inhibitor associated hydrogen bonds or sulfur σ-hole bond interactions to Asn284 OD1, offering new insights to structure-based design efforts. Moreover, while the 2-glucopyranosyl-tetrazole seems to bind differently from the corresponding 1,2,3-triazole compound, the two inhibitors are equipotent.
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Affiliation(s)
- Efthimios Kyriakis
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece
| | - Aikaterini G Karra
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece
| | - Olga Papaioannou
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece
| | - Theodora Solovou
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece
| | - Vassiliki T Skamnaki
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece
| | - Panagiota G V Liggri
- Department of Organic Chemistry, University of Debrecen, H-4002 POB 400 Debrecen, Hungary; Institute of Chemical Biology, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 11635 Athens, Greece
| | - Spyros E Zographos
- Institute of Chemical Biology, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 11635 Athens, Greece
| | - Eszter Szennyes
- Department of Organic Chemistry, University of Debrecen, H-4002 POB 400 Debrecen, Hungary
| | - Éva Bokor
- Department of Organic Chemistry, University of Debrecen, H-4002 POB 400 Debrecen, Hungary
| | - Sándor Kun
- Department of Organic Chemistry, University of Debrecen, H-4002 POB 400 Debrecen, Hungary
| | - Anna-Maria G Psarra
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece.
| | - László Somsák
- Department of Organic Chemistry, University of Debrecen, H-4002 POB 400 Debrecen, Hungary.
| | - Demetres D Leonidas
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece.
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3
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Pałasz A, Cież D, Trzewik B, Miszczak K, Tynor G, Bazan B. In the Search of Glycoside-Based Molecules as Antidiabetic Agents. Top Curr Chem (Cham) 2019; 377:19. [PMID: 31165274 PMCID: PMC6548768 DOI: 10.1007/s41061-019-0243-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 05/14/2019] [Indexed: 02/06/2023]
Abstract
This review is an effort to summarize recent developments in synthesis of O-glycosides and N-, C-glycosyl molecules with promising antidiabetic potential. Articles published after 2000 are included. First, the O-glycosides used in the treatment of diabetes are presented, followed by the N-glycosides and finally the C-glycosides constituting the largest group of antidiabetic drugs are described. Within each group of glycosides, we presented how the structure of compounds representing potential drugs changes and when discussing chemical compounds of a similar structure, achievements are presented in the chronological order. C-Glycosyl compounds mimicking O-glycosides structure, exhibit the best features in terms of pharmacodynamics and pharmacokinetics. Therefore, the largest part of the article is concerned with the description of the synthesis and biological studies of various C-glycosides. Also N-glycosides such as N-(β-d-glucopyranosyl)-amides, N-(β-d-glucopyranosyl)-ureas, and 1,2,3-triazolyl derivatives belong to the most potent classes of antidiabetic agents. In order to indicate which of the compounds presented in the given sections have the best inhibitory properties, a list of the best inhibitors is presented at the end of each section. In summary, the best inhibitors were selected from each of the summarizing figures and the results of the ranking were placed. In this way, the reader can learn about the structure of the compounds having the best antidiabetic activity. The compounds, whose synthesis was described in the article but did not appear on the figures presenting the structures of the most active inhibitors, did not show proper activity as inhibitors. Thus, the article also presents studies that have not yielded the desired results and show directions of research that should not be followed. In order to show the directions of the latest research, articles from 2018 to 2019 are described in a separate Sect. 5. In Sect. 6, biological mechanisms of action of the glycosides and patents of marketed drugs are described.
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Affiliation(s)
- Aleksandra Pałasz
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Kraków, Poland.
| | - Dariusz Cież
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Kraków, Poland
| | - Bartosz Trzewik
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Kraków, Poland
| | - Katarzyna Miszczak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Kraków, Poland
| | - Grzegorz Tynor
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Kraków, Poland
| | - Bartłomiej Bazan
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Kraków, Poland
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Abstract
Abstract
Glycomimetics are compounds that resemble carbohydrate molecules in their chemical structure and/or biological effect. A large variety of compounds can be designed and synthesized to get glycomimetics, however, C-glycosyl derivatives represent one of the most frequently studied subgroup. In the present survey syntheses of a range of five- and six membered C-glycopyranosyl heterocycles, anhydro-aldimine type compounds, exo-glycals, C-glycosyl styrenes, carbon-sulfur bonded oligosaccharide mimics are described. Some of the C-glycopyranosyl azoles, namely 1,2,4-triazoles and imidazoles belong to the most efficient glucose analog inhibitors of glycogen phosphorylase known to date. Biological studies revealed the therapeutical potential of such inhibitors. Other synthetic derivatives offer versatile possibilities to get further glycomimetics.
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5
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High Consistency of Structure-Based Design and X-Ray Crystallography: Design, Synthesis, Kinetic Evaluation and Crystallographic Binding Mode Determination of Biphenyl- N-acyl-β-d-Glucopyranosylamines as Glycogen Phosphorylase Inhibitors. Molecules 2019; 24:molecules24071322. [PMID: 30987252 PMCID: PMC6479789 DOI: 10.3390/molecules24071322] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 03/30/2019] [Accepted: 04/01/2019] [Indexed: 11/17/2022] Open
Abstract
Structure-based design and synthesis of two biphenyl-N-acyl-β-d-glucopyranosylamine derivatives as well as their assessment as inhibitors of human liver glycogen phosphorylase (hlGPa, a pharmaceutical target for type 2 diabetes) is presented. X-ray crystallography revealed the importance of structural water molecules and that the inhibitory efficacy correlates with the degree of disturbance caused by the inhibitor binding to a loop crucial for the catalytic mechanism. The in silico-derived models of the binding mode generated during the design process corresponded very well with the crystallographic data.
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6
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Synthesis of New C- and N-β-d-Glucopyranosyl Derivatives of Imidazole, 1,2,3-Triazole and Tetrazole, and Their Evaluation as Inhibitors of Glycogen Phosphorylase. Molecules 2018; 23:molecules23030666. [PMID: 29543771 PMCID: PMC6017874 DOI: 10.3390/molecules23030666] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 03/07/2018] [Accepted: 03/13/2018] [Indexed: 12/13/2022] Open
Abstract
The aim of the present study was to broaden the structure-activity relationships of C- and N-β-d-glucopyranosyl azole type inhibitors of glycogen phosphorylase. 1-Aryl-4-β-d-gluco-pyranosyl-1,2,3-triazoles were prepared by copper catalyzed azide-alkyne cycloadditions between O-perbenzylated or O-peracetylated β-d-glucopyranosyl ethynes and aryl azides. 1-β-d-Gluco-pyranosyl-4-phenyl imidazole was obtained in a glycosylation of 4(5)-phenylimidazole with O-peracetylated α-d-glucopyranosyl bromide. C-β-d-Glucopyranosyl-N-substituted-tetrazoles were synthesized by alkylation/arylation of O-perbenzoylated 5-β-d-glucopyranosyl-tetrazole or from a 2,6-anhydroheptose tosylhydrazone and arenediazonium salts. 5-Substituted tetrazoles were glycosylated by O-peracetylated α-d-glucopyranosyl bromide to give N-β-d-glucopyranosyl-C-substituted-tetrazoles. Standard deprotections gave test compounds which were assayed against rabbit muscle glycogen phosphorylase b. Most of the compounds proved inactive, the best inhibitor was 2-β-d-glucopyranosyl-5-phenyltetrazole (IC50 600 μM). These studies extended the structure-activity relationships of β-d-glucopyranosyl azole type inhibitors and revealed the extreme sensitivity of such type of inhibitors towards the structure of the azole moiety.
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7
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Bokor É, Kyriakis E, Solovou TGA, Koppány C, Kantsadi AL, Szabó KE, Szakács A, Stravodimos GA, Docsa T, Skamnaki VT, Zographos SE, Gergely P, Leonidas DD, Somsák L. Nanomolar Inhibitors of Glycogen Phosphorylase Based on β-d-Glucosaminyl Heterocycles: A Combined Synthetic, Enzyme Kinetic, and Protein Crystallography Study. J Med Chem 2017; 60:9251-9262. [PMID: 28925695 DOI: 10.1021/acs.jmedchem.7b01056] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Aryl substituted 1-(β-d-glucosaminyl)-1,2,3-triazoles as well as C-β-d-glucosaminyl 1,2,4-triazoles and imidazoles were synthesized and tested as inhibitors against muscle and liver isoforms of glycogen phosphorylase (GP). While the N-β-d-glucosaminyl 1,2,3-triazoles showed weak or no inhibition, the C-β-d-glucosaminyl derivatives had potent activity, and the best inhibitor was the 2-(β-d-glucosaminyl)-4(5)-(2-naphthyl)-imidazole with a Ki value of 143 nM against human liver GPa. An X-ray crystallography study of the rabbit muscle GPb inhibitor complexes revealed structural features of the strong binding and offered an explanation for the differences in inhibitory potency between glucosyl and glucosaminyl derivatives and also for the differences between imidazole and 1,2,4-triazole analogues.
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Affiliation(s)
- Éva Bokor
- Department of Organic Chemistry, University of Debrecen , POB 400, H-4002 Debrecen, Hungary
| | - Efthimios Kyriakis
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis , 41500 Larissa, Greece
| | - Theodora G A Solovou
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis , 41500 Larissa, Greece
| | - Csenge Koppány
- Department of Organic Chemistry, University of Debrecen , POB 400, H-4002 Debrecen, Hungary
| | - Anastassia L Kantsadi
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis , 41500 Larissa, Greece
| | - Katalin E Szabó
- Department of Organic Chemistry, University of Debrecen , POB 400, H-4002 Debrecen, Hungary
| | - Andrea Szakács
- Department of Organic Chemistry, University of Debrecen , POB 400, H-4002 Debrecen, Hungary
| | - George A Stravodimos
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis , 41500 Larissa, Greece
| | - Tibor Docsa
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen , Egyetem tér 1, H-4032 Debrecen, Hungary
| | - Vassiliki T Skamnaki
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis , 41500 Larissa, Greece
| | - Spyros E Zographos
- Institute of Biology, Pharmaceutical Chemistry and Biotechnology, National Hellenic Research Foundation , 48 Vassileos Constantinou Avenue, 11635 Athens, Greece
| | - Pál Gergely
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen , Egyetem tér 1, H-4032 Debrecen, Hungary
| | - Demetres D Leonidas
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis , 41500 Larissa, Greece
| | - László Somsák
- Department of Organic Chemistry, University of Debrecen , POB 400, H-4002 Debrecen, Hungary
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8
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Murugavel S, Jacob Prasanna Stephen CS, Subashini R, AnanthaKrishnan D. Synthesis, structural elucidation, antioxidant, CT-DNA binding and molecular docking studies of novel chloroquinoline derivatives: Promising antioxidant and anti-diabetic agents. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2017; 173:216-230. [PMID: 28599239 DOI: 10.1016/j.jphotobiol.2017.05.043] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 05/29/2017] [Accepted: 05/30/2017] [Indexed: 12/15/2022]
Abstract
The synthesized novel chloroquinoline derivatives 1-(2-chloro-4-phenylquinolin-3-yl)ethanone (CPQE), 1-(2,6-dichloro-4-phenylquinolin-3-yl)ethanone (DCPQE), methyl 2,6-dichloro-4-phenylquinoline-3-carboxylate (MDCPQC),methyl 2-chloro-4-methylquinoline-3-carboxylate (MCMQC) were subjected to the elementary analysis like FT-IR, NMR and Mass spectra using GCMS. Also, single crystal X-ray diffraction study was executed for the compound MDCPQC. The crystal packing is stabilized by C-H…π and π-π interactions and also Chlorine-Chlorine short intermolecular contacts generating a three-dimensional supramolecular network. The antioxidant activity reduces high glucose level in the human body and hence the synthesized compounds were subjected for the estimation of antioxidant activity using DPPH method which exhibited good percentage of inhibition in comparison with ascorbic acid, a well-known anti-oxidant. The binding interaction of the chloroquinoline derivatives with calf thymus DNA (CT-DNA) has been explored by fluorescence quenching studies and molecular docking analysis has been employed to confirm the nature of binding. The prediction of pharmacological properties such as drug-likeness, molecular properties like absorption, distribution, metabolism, excretion and toxicity (ADMET) was carried out by computational studies to compare chloroquinoline derivatives with standard drug. Owing to the various potential biological activities of the quinoline compounds, molecular docking studies were also further carried out for the chloroquinoline derivatives, showing that they may act as effective anti-diabetic agents by inhibiting Glycogen Phosphorylase a protein.
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Affiliation(s)
- S Murugavel
- Department of Physics, Thanthai Periyar Government Institute of Technology, Vellore 632 002, Tamilnadu, India.
| | - C S Jacob Prasanna Stephen
- Department of Physics, Global Institute of Engineering and Technology, Melvisharam, Vellore 632 509, Tamilnadu, India
| | - R Subashini
- Department of Chemistry, Arignar Anna Government Arts College for Women, Walajapet, Vellore, Tamilnadu, India
| | - Dhanabalan AnanthaKrishnan
- Bioinformatics infrastructure facility, University of Madras, Guindy Campus, Chennai 600 025, Tamilnadu, India
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9
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Kundoor G, Rao DS, Kashyap S. Regioselective Direct Difunctionalization of Glycals: Convenient Access to 2-Deoxyglycoconjugates Mediated by Tetra-n-butylammonium Iodide/Sodium Periodate. ASIAN J ORG CHEM 2015. [DOI: 10.1002/ajoc.201500470] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Govindareddy Kundoor
- Discovery Laboratory, Organic and Biomolecular Chemistry Division; Indian Institute of Chemical Technology (CSIR), Tarnaka; Uppal Road Hyderabad- 500007 India
| | - Dodla Sivanageswara Rao
- Discovery Laboratory, Organic and Biomolecular Chemistry Division; Indian Institute of Chemical Technology (CSIR), Tarnaka; Uppal Road Hyderabad- 500007 India
| | - Sudhir Kashyap
- Discovery Laboratory, Organic and Biomolecular Chemistry Division; Indian Institute of Chemical Technology (CSIR), Tarnaka; Uppal Road Hyderabad- 500007 India
- Academy of Scientific and Innovative Research; Indian Institute of Chemical Technology (CSIR); Hyderabad- 500 007 India
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10
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Meyerhoefer TJ, Kershaw S, Caliendo N, Eltayeb S, Hanawa-Romero E, Bykovskaya P, Huang V, Marzabadi CH, De Castro M. A Practical Synthesis of Various 2-Deoxy-N-glycosides by UsingD-Glucal. European J Org Chem 2015. [DOI: 10.1002/ejoc.201500001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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11
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Polyák M, Varga G, Szilágyi B, Juhász L, Docsa T, Gergely P, Begum J, Hayes JM, Somsák L. Synthesis, enzyme kinetics and computational evaluation of N-(β-d-glucopyranosyl) oxadiazolecarboxamides as glycogen phosphorylase inhibitors. Bioorg Med Chem 2013; 21:5738-47. [DOI: 10.1016/j.bmc.2013.07.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 07/08/2013] [Accepted: 07/10/2013] [Indexed: 11/15/2022]
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12
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Bokor É, Docsa T, Gergely P, Somsák L. C-Glucopyranosyl-1,2,4-triazoles As New Potent Inhibitors of Glycogen Phosphorylase. ACS Med Chem Lett 2013; 4:612-5. [PMID: 24900719 DOI: 10.1021/ml4001529] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 05/17/2013] [Indexed: 11/29/2022] Open
Abstract
Glycogen phosphorylase inhibitors are considered as potential antidiabetic agents. 3-(β-d-Glucopyranosyl)-5-substituted-1,2,4-triazoles were prepared by acylation of O-perbenzoylated N (1)-tosyl-C-β-d-glucopyranosyl formamidrazone and subsequent removal of the protecting groups. The best inhibitor was 3-(β-d-glucopyranosyl)-5-(2-naphthyl)-1,2,4-triazole (K i = 0.41 μM against rabbit muscle glycogen phosphorylase b).
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Affiliation(s)
- Éva Bokor
- Department of Organic Chemistry, University of Debrecen, POB 20, H-4010 Debrecen, Hungary
| | - Tibor Docsa
- Department of Medical Chemistry,
Medical and Health Science Centre, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - Pál Gergely
- Department of Medical Chemistry,
Medical and Health Science Centre, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - László Somsák
- Department of Organic Chemistry, University of Debrecen, POB 20, H-4010 Debrecen, Hungary
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13
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Kun S, Nagy GZ, Tóth M, Czecze L, Van Nhien AN, Docsa T, Gergely P, Charavgi MD, Skourti PV, Chrysina ED, Patonay T, Somsák L. Synthesis of variously coupled conjugates of d-glucose, 1,3,4-oxadiazole, and 1,2,3-triazole for inhibition of glycogen phosphorylase. Carbohydr Res 2011; 346:1427-38. [DOI: 10.1016/j.carres.2011.03.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Revised: 02/24/2011] [Accepted: 03/03/2011] [Indexed: 10/18/2022]
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14
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Tsirkone VG, Tsoukala E, Lamprakis C, Manta S, Hayes JM, Skamnaki VT, Drakou C, Zographos SE, Komiotis D, Leonidas DD. 1-(3-Deoxy-3-fluoro-β-d-glucopyranosyl) pyrimidine derivatives as inhibitors of glycogen phosphorylase b: Kinetic, crystallographic and modelling studies. Bioorg Med Chem 2010; 18:3413-25. [DOI: 10.1016/j.bmc.2010.04.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Revised: 03/26/2010] [Accepted: 04/01/2010] [Indexed: 10/19/2022]
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15
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Synthesis of 1-(d-glucopyranosyl)-1,2,3-triazoles and their evaluation as glycogen phosphorylase inhibitors. Bioorg Med Chem 2010; 18:1171-80. [DOI: 10.1016/j.bmc.2009.12.043] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2009] [Revised: 12/09/2009] [Accepted: 12/15/2009] [Indexed: 11/23/2022]
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16
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Czakó Z, Juhász L, Kenéz Á, Czifrák K, Somsák L, Docsa T, Gergely P, Antus S. Synthesis and glycogen phosphorylase inhibitory activity of N-(β-d-glucopyranosyl)amides possessing 1,4-benzodioxane moiety. Bioorg Med Chem 2009; 17:6738-41. [DOI: 10.1016/j.bmc.2009.07.052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2009] [Revised: 07/14/2009] [Accepted: 07/22/2009] [Indexed: 11/25/2022]
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17
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Tóth M, Kun S, Bokor É, Benltifa M, Tallec G, Vidal S, Docsa T, Gergely P, Somsák L, Praly JP. Synthesis and structure–activity relationships of C-glycosylated oxadiazoles as inhibitors of glycogen phosphorylase. Bioorg Med Chem 2009; 17:4773-85. [DOI: 10.1016/j.bmc.2009.04.036] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2009] [Revised: 04/15/2009] [Accepted: 04/17/2009] [Indexed: 12/22/2022]
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18
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Chrysina ED, Bokor É, Alexacou KM, Charavgi MD, Oikonomakos GN, Zographos SE, Leonidas DD, Oikonomakos NG, Somsák L. Amide-1,2,3-triazole bioisosterism: the glycogen phosphorylase case. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.tetasy.2009.03.021] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Somsák L, Felföldi N, Kónya B, Hüse C, Telepó K, Bokor É, Czifrák K. Assessment of synthetic methods for the preparation of N-β-d-glucopyranosyl-N′-substituted ureas, -thioureas and related compounds. Carbohydr Res 2008; 343:2083-93. [DOI: 10.1016/j.carres.2008.01.045] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2007] [Revised: 01/24/2008] [Accepted: 01/29/2008] [Indexed: 11/26/2022]
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20
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Ali MMN, Aich U, Varghese B, Imberty A. Conformational Preferences of the Aglycon Moiety in Models and Analogs of GlcNAc-Asn Linkage: Crystal Structures and ab Initio Quantum Chemical Calculations of N-(β-d-Glycopyranosyl)haloacetamides. J Am Chem Soc 2008; 130:8317-25. [DOI: 10.1021/ja800335m] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mohamed Mohamed Naseer Ali
- CERMAV-CNRS (affiliated to Université Joseph Fourier and ICMG), BP 53, 38041 Grenoble cedex 9, France, Department of Chemistry and Sophisticated Analytical Instrumentation Facility, Indian Institute of Technology Madras, Chennai, 600036, India
| | - Udayanath Aich
- CERMAV-CNRS (affiliated to Université Joseph Fourier and ICMG), BP 53, 38041 Grenoble cedex 9, France, Department of Chemistry and Sophisticated Analytical Instrumentation Facility, Indian Institute of Technology Madras, Chennai, 600036, India
| | - Babu Varghese
- CERMAV-CNRS (affiliated to Université Joseph Fourier and ICMG), BP 53, 38041 Grenoble cedex 9, France, Department of Chemistry and Sophisticated Analytical Instrumentation Facility, Indian Institute of Technology Madras, Chennai, 600036, India
| | - Anne Imberty
- CERMAV-CNRS (affiliated to Université Joseph Fourier and ICMG), BP 53, 38041 Grenoble cedex 9, France, Department of Chemistry and Sophisticated Analytical Instrumentation Facility, Indian Institute of Technology Madras, Chennai, 600036, India
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21
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Approaches to Three-Dimensional Quantitative Structure-Activity Relationships. REVIEWS IN COMPUTATIONAL CHEMISTRY 2007. [DOI: 10.1002/9780470125885.ch4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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Petsalakis EI, Chrysina ED, Tiraidis C, Hadjiloi T, Leonidas DD, Oikonomakos NG, Aich U, Varghese B, Loganathan D. Crystallographic studies on N-azidoacetyl-β-d-glucopyranosylamine, an inhibitor of glycogen phosphorylase: Comparison with N-acetyl-β-d-glucopyranosylamine. Bioorg Med Chem 2006; 14:5316-24. [PMID: 16616506 DOI: 10.1016/j.bmc.2006.03.044] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2005] [Revised: 03/20/2006] [Accepted: 03/24/2006] [Indexed: 11/25/2022]
Abstract
N-acetyl-beta-D-glucopyranosylamine (NAG) is a potent inhibitor (Ki=32 microM) of glycogen phosphorylase b (GPb), and has been employed as a lead compound for the structure-based design of new analogues, in an effort to utilize its potential as a hypoglycaemic agent. Replacement of the acetamido group by azidoacetamido group resulted in an inhibitor, N-azidoacetyl-beta-D-glucopyranosylamine (azido-NAG), with a Ki value of 48.7 microM, in the direction of glycogen synthesis. In order to elucidate the mechanism of inhibition, we determined the ligand structure in complex with GPb at 2.03 A resolution, and the structure of the fully acetylated derivative in the free form. The molecular packing of the latter is stabilized by a number of bifurcated hydrogen bonds of which the one involving a bifurcated C-H...N...H-C type hydrogen bonding is rather unique in organic azides. Azido-NAG can be accommodated in the catalytic site of T-state GPb at approximately the same position as that of NAG and stabilizes the T-state conformation of the 280 s loop by making several favourable contacts to residues of this loop. The difference observed in the Ki values of the two analogues can be interpreted in terms of desolvation effects, subtle structural changes of protein residues and changes in water structure.
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Affiliation(s)
- Evangelia I Petsalakis
- Institute of Organic and Pharmaceutical Chemistry, The National Hellenic Research Foundation, 48, Vas. Constantinou Ave., 116 35 Athens, Greece
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23
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Baker DJ, Greenhaff PL, Timmons JA. Glycogen phosphorylase inhibition as a therapeutic target: a review of the recent patent literature. Expert Opin Ther Pat 2006. [DOI: 10.1517/13543776.16.4.459] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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24
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Watson KA, Chrysina ED, Tsitsanou KE, Zographos SE, Archontis G, Fleet GWJ, Oikonomakos NG. Kinetic and crystallographic studies of glucopyranose spirohydantoin and glucopyranosylamine analogs inhibitors of glycogen phosphorylase. Proteins 2005; 61:966-83. [PMID: 16222658 DOI: 10.1002/prot.20653] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Glycogen phosphorylase (GP) is currently exploited as a target for inhibition of hepatic glycogenolysis under high glucose conditions. Spirohydantoin of glucopyranose and N-acetyl-beta-D-glucopyranosylamine have been identified as the most potent inhibitors of GP that bind at the catalytic site. Four spirohydantoin and three beta-D-glucopyranosylamine analogs have been designed, synthesized and tested for inhibition of GP in kinetic experiments. Depending on the functional group introduced, the K(i) values varied from 16.5 microM to 1200 microM. In order to rationalize the kinetic results, we determined the crystal structures of the analogs in complex with GP. All the inhibitors bound at the catalytic site of the enzyme, by making direct and water-mediated hydrogen bonds with the protein and by inducing minor movements of the side chains of Asp283 and Asn284, of the 280s loop that blocks access of the substrate glycogen to the catalytic site, and changes in the water structure in the vicinity of the site. The differences observed in the Ki values of the analogs can be interpreted in terms of variations in hydrogen bonding and van der Waals interactions, desolvation effects, ligand conformational entropy, and displacement of water molecules on ligand binding to the catalytic site.
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Affiliation(s)
- Kimberly A Watson
- Laboratory of Molecular Biophysics, University of Oxford, Oxford, United Kingdom
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25
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Anagnostou E, Kosmopoulou MN, Chrysina ED, Leonidas DD, Hadjiloi T, Tiraidis C, Zographos SE, Györgydeák Z, Somsák L, Docsa T, Gergely P, Kolisis FN, Oikonomakos NG. Crystallographic studies on two bioisosteric analogues, N-acetyl-beta-D-glucopyranosylamine and N-trifluoroacetyl-beta-D-glucopyranosylamine, potent inhibitors of muscle glycogen phosphorylase. Bioorg Med Chem 2005; 14:181-9. [PMID: 16213146 DOI: 10.1016/j.bmc.2005.08.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2005] [Accepted: 08/02/2005] [Indexed: 10/25/2022]
Abstract
Structure-based inhibitor design has led to the discovery of a number of potent inhibitors of glycogen phosphorylase b (GPb), N-acyl derivatives of beta-D-glucopyranosylamine, that bind at the catalytic site of the enzyme. The first good inhibitor in this class of compounds, N-acetyl-beta-D-glucopyranosylamine (NAG) (K(i) = 32 microM), has been previously characterized by biochemical, biological and crystallographic experiments at 2.3 angstroms resolution. Bioisosteric replacement of the acetyl group by trifluoroacetyl group resulted in an inhibitor, N-trifluoroacetyl-beta-D-glucopyranosylamine (NFAG), with a K(i) = 75 microM. To elucidate the structural basis of its reduced potency, we determined the ligand structure in complex with GPb at 1.8 angstroms resolution. To compare the binding mode of N-trifluoroacetyl derivative with that of the lead molecule, we also determined the structure of GPb-NAG complex at a higher resolution (1.9 angstroms). NFAG can be accommodated in the catalytic site of T-state GPb at approximately the same position as that of NAG and stabilize the T-state conformation of the 280 s loop by making several favourable contacts to Asn284 of this loop. The difference observed in the K(i) values of the two analogues can be interpreted in terms of subtle conformational changes of protein residues and shifts of water molecules in the vicinity of the catalytic site, variations in van der Waals interaction, and desolvation effects.
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Affiliation(s)
- Eleni Anagnostou
- Institute of Organic and Pharmaceutical Chemistry, The National Hellenic Research Foundation, 48, Vas. Constantinou Ave. 116 35 Athens, Greece
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26
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Chrysina ED, Kosmopoulou MN, Tiraidis C, Kardakaris R, Bischler N, Leonidas DD, Hadady Z, Somsak L, Docsa T, Gergely P, Oikonomakos NG. Kinetic and crystallographic studies on 2-(beta-D-glucopyranosyl)-5-methyl-1, 3, 4-oxadiazole, -benzothiazole, and -benzimidazole, inhibitors of muscle glycogen phosphorylase b. Evidence for a new binding site. Protein Sci 2005; 14:873-88. [PMID: 15741340 PMCID: PMC2253430 DOI: 10.1110/ps.041216105] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
In an attempt to identify leads that would enable the design of inhibitors with enhanced affinity for glycogen phosphorylase (GP), that might control hyperglycaemia in type 2 diabetes, three new analogs of beta-D-glucopyranose, 2-(beta-D-glucopyranosyl)-5-methyl-1, 3, 4-oxadiazole, -benzothiazole, and -benzimidazole were assessed for their potency to inhibit GPb activity. The compounds showed competitive inhibition (with respect to substrate Glc-1-P) with K(i) values of 145.2 (+/-11.6), 76 (+/-4.8), and 8.6 (+/-0.7) muM, respectively. In order to establish the mechanism of this inhibition, crystallographic studies were carried out and the structures of GPb in complex with the three analogs were determined at high resolution (GPb-methyl-oxadiazole complex, 1.92 A; GPb-benzothiazole, 2.10 A; GPb-benzimidazole, 1.93 A). The complex structures revealed that the inhibitors can be accommodated in the catalytic site of T-state GPb with very little change of the tertiary structure, and provide a rationalization for understanding variations in potency of the inhibitors. In addition, benzimidazole bound at the new allosteric inhibitor or indole binding site, located at the subunit interface, in the region of the central cavity, and also at a novel binding site, located at the protein surface, far removed (approximately 32 A) from the other binding sites, that is mostly dominated by the nonpolar groups of Phe202, Tyr203, Val221, and Phe252.
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Affiliation(s)
- Evangelia D Chrysina
- Institute of Organic and Pharmaceutical Chemistry, The National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 116 35 Athens, Greece
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27
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Gohlke H, Klebe G. DrugScore meets CoMFA: adaptation of fields for molecular comparison (AFMoC) or how to tailor knowledge-based pair-potentials to a particular protein. J Med Chem 2002; 45:4153-70. [PMID: 12213058 DOI: 10.1021/jm020808p] [Citation(s) in RCA: 100] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The development of a new tailor-made scoring function to predict binding affinities of protein-ligand complexes is described. Knowledge-based pair-potentials are specifically adapted to a particular protein by considering additional ligand-based information. The formalism applied to derive the new function is similar to the well-known CoMFA approach, however, the fields used in the approach originate from the protein environment (and not from the aligned ligands as in CoMFA, thus, a "reverse" CoMFA (= AFMoC) named Adaptation of Fields for Molecular Comparison is performed). A regular-spaced grid is placed into the binding site and knowledge-based pair-potentials between protein atoms and ligand atom probes are mapped onto the grid intersections resulting in "potential fields". By multiplying distance-dependent atom-type properties of actual ligands docked into the binding site with the neighboring grid values, "interaction fields" are produced from the original "potential fields". In a PLS analysis, these atom-type specific interaction fields are correlated to the actual binding affinities of the embedded ligands, resulting in individual weighting factors for each field value. As in CoMFA, the results of the analysis can be interpreted in graphical terms by contribution maps, and binding affinities of novel ligands are predicted by applying the derived 3D QSAR equation. The scope of the new method is demonstrated using thermolysin and glycogen phosphorylase b as test examples. Impressive improvements of the predictive power for affinity prediction can be achieved compared to the application of the original knowledge-based potentials by considering a sample set of only 15 known training ligands. Thus, with growing information about the drug target studied, the new method allows one to move gradually from generally valid to protein-specifically adapted pair-potentials, depending on the amount of training information available and its degree of structural diversity. In addition, convincing predictive power is also achieved for ligand poses generated by automatic docking tools.
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Affiliation(s)
- Holger Gohlke
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
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Affiliation(s)
- L N Johnson
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU.
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29
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So SS, Karplus M. Evaluation of designed ligands by a multiple screening method: application to glycogen phosphorylase inhibitors constructed with a variety of approaches. J Comput Aided Mol Des 2001; 15:613-47. [PMID: 11688944 DOI: 10.1023/a:1011945119287] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Glycogen phosphorylase (GP) is an important enzyme that regulates blood glucose level and a key therapeutic target for the treatment of type II diabetes. In this study, a number of potential GP inhibitors are designed with a variety of computational approaches. They include the applications of MCSS, LUDI and CoMFA to identify additional fragments that can be attached to existing lead molecules; the use of 2D and 3D similarity-based QSAR models (HQSAR and SMGNN) and of the LUDI program to identify novel molecules that may bind to the glucose binding site. The designed ligands are evaluated by a multiple screening method, which is a combination of commercial and in-house ligand-receptor binding affinity prediction programs used in a previous study (So and Karplus, J. Comp.-Aid. Mol. Des., 13 (1999), 243-258). Each method is used at an appropriate point in the screening, as determined by both the accuracy of the calculations and the computational cost. A comparison of the strengths and weaknesses of the ligand design approaches is made.
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Affiliation(s)
- S S So
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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Oikonomakos NG, Schnier JB, Zographos SE, Skamnaki VT, Tsitsanou KE, Johnson LN. Flavopiridol inhibits glycogen phosphorylase by binding at the inhibitor site. J Biol Chem 2000; 275:34566-73. [PMID: 10924512 DOI: 10.1074/jbc.m004485200] [Citation(s) in RCA: 93] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Flavopiridol (L86-8275) ((-)-cis-5, 7-dihydroxy-2-(2-chlorophenyl)-8-[4-(3-hydroxy-1-methyl)-piperidinyl] -4H-benzopyran-4-one), a potential antitumor drug, currently in phase II trials, has been shown to be an inhibitor of muscle glycogen phosphorylase (GP) and to cause glycogen accumulation in A549 non-small cell lung carcinoma cells (Kaiser, A., Nishi, K., Gorin, F.A., Walsh, D.A., Bradbury, E. M., and Schnier, J. B., unpublished data). Kinetic experiments reported here show that flavopiridol inhibits GPb with an IC(50) = 15.5 microm. The inhibition is synergistic with glucose resulting in a reduction of IC(50) for flavopiridol to 2.3 microm and mimics the inhibition of caffeine. In order to elucidate the structural basis of inhibition, we determined the structures of GPb complexed with flavopiridol, GPb complexed with caffeine, and GPa complexed with both glucose and flavopiridol at 1.76-, 2.30-, and 2.23-A resolution, and refined to crystallographic R values of 0.216 (R(free) = 0.247), 0.189 (R(free) = 0.219), and 0.195 (R(free) = 0.252), respectively. The structures provide a rational for flavopiridol potency and synergism with glucose inhibitory action. Flavopiridol binds at the allosteric inhibitor site, situated at the entrance to the catalytic site, the site where caffeine binds. Flavopiridol intercalates between the two aromatic rings of Phe(285) and Tyr(613). Both flavopiridol and glucose promote the less active T-state through localization of the closed position of the 280s loop which blocks access to the catalytic site, thereby explaining their synergistic inhibition. The mode of interactions of flavopiridol with GP is different from that of des-chloro-flavopiridol with CDK2, illustrating how different functional parts of the inhibitor can be used to provide specific and potent binding to two different enzymes.
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Affiliation(s)
- N G Oikonomakos
- Institute of Biological Research and Biotechnology, The National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, Athens 11635, Greece.
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31
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Oikonomakos NG, Skamnaki VT, Tsitsanou KE, Gavalas NG, Johnson LN. A new allosteric site in glycogen phosphorylase b as a target for drug interactions. Structure 2000; 8:575-84. [PMID: 10873856 DOI: 10.1016/s0969-2126(00)00144-1] [Citation(s) in RCA: 106] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND In muscle and liver, glycogen concentrations are regulated by the coordinated activities of glycogen phosphorylase (GP) and glycogen synthase. GP exists in two forms: the dephosphorylated low-activity form GPb and the phosphorylated high-activity form GPa. In both forms, allosteric effectors can promote equilibrium between a less active T state and a more active R state. GP is a possible target for drugs that aim to prevent unwanted glycogen breakdown and to stimulate glycogen synthesis in non-insulin-dependent diabetes. As a result of a data bank search, 5-chloro-1H-indole-2-carboxylic acid (1-(4-fluorobenzyl)-2-(4-hydroxypiperidin-1-yl)-2-oxoethy l)amide, CP320626, was identified as a potent inhibitor of human liver GP. Structural studies have been carried out in order to establish the mechanism of this unusual inhibitor. RESULTS The structure of the cocrystallised GPb-CP320626 complex has been determined to 2.3 A resolution. CP320626 binds at a site located at the subunit interface in the region of the central cavity of the dimeric structure. The site has not previously been observed to bind ligands and is some 15 A from the AMP allosteric site and 33 A from the catalytic site. The contacts between GPb and CP320626 comprise six hydrogen bonds and extensive van der Waals interactions that create a tight binding site in the T-state conformation of GPb. In the R-state conformation of GPa these interactions are significantly diminished. CONCLUSIONS CP320626 inhibits GPb by binding at a new allosteric site. Although over 30 A from the catalytic site, the inhibitor exerts its effects by stabilising the T state at the expense of the R state and thereby shifting the allosteric equilibrium between the two states. The new allosteric binding site offers a further recognition site in the search for improved GP inhibitors.
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Affiliation(s)
- N G Oikonomakos
- Institute of Biological Research and Biotechnology, The National Hellenic Research Foundation, Athens, 11635, Greece. nikos@krokees. eie.gr
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So SS, Karplus M. A comparative study of ligand-receptor complex binding affinity prediction methods based on glycogen phosphorylase inhibitors. J Comput Aided Mol Des 1999; 13:243-58. [PMID: 10216832 DOI: 10.1023/a:1008073215919] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Finding an accurate method for estimating the affinity of protein ligands activity is the most challenging task in computer-aided molecular design. In this study we investigate and compare seven different prediction methods for a set of 30 glycogen phosphorylase (GP) inhibitors with known crystal structures. Five of the methods involve quantitative structure-activity relationships (QSAR) based on the 2D or 3D structures of the GP ligands alone. They are hologram QSAR (HQSAR), receptor surface model (RSM), comparative molecular field analysis (CoMFA), and applications of genetic neural network to similarity matrix (SM/GNN) or conventional descriptors (C2GNN). All five QSAR-based models have good predictivity and yield q2 values ranging from 0.60 to 0.82. The other two methods, LUDI and a structure-based binding energy predictor (SBEP) system, make use of the structures of the ligand-receptor complexes. The weak correlation between biological activities and the LUDI scores of this set of inhibitors suggests that the LUDI scoring function, by itself, may not be a general method for reliable ranking of a congeneric series of compounds. The SBEP system is derived from a set of physical properties that characterizes ligand-receptor interactions. The final neural network model, which yields a q2 value of 0.60, employs four descriptors. A jury method that combines the predictions of the five QSAR-based models leads to an increase in predictivity. A multi-layer scoring system that utilizes all seven prediction methods is proposed for the evaluation of novel GP ligands.
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Affiliation(s)
- S S So
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
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Tsitsanou KE, Oikonomakos NG, Zographos SE, Skamnaki VT, Gregoriou M, Watson KA, Johnson LN, Fleet GW. Effects of commonly used cryoprotectants on glycogen phosphorylase activity and structure. Protein Sci 1999; 8:741-9. [PMID: 10211820 PMCID: PMC2144310 DOI: 10.1110/ps.8.4.741] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The effects of a number of cryoprotectants on the kinetic and structural properties of glycogen phosphorylase b have been investigated. Kinetic studies showed that glycerol, one of the most commonly used cryoprotectants in X-ray crystallographic studies, is a competitive inhibitor with respect to substrate glucose-1-P with an apparent Ki value of 3.8% (v/v). Cryogenic experiments, with the enzyme, have shown that glycerol binds at the catalytic site and competes with glucose analogues that bind at the catalytic site, thus preventing the formation of complexes. This necessitated a change in the conditions for cryoprotection in crystallographic binding experiments with glycogen phosphorylase. It was found that 2-methyl-2,4-pentanediol (MPD), polyethylene glycols (PEGs) of various molecular weights, and dimethyl sulfoxide (DMSO) activated glycogen phosphorylase b to different extents, by stabilizing its most active conformation, while sucrose acted as a noncompetitive inhibitor and ethylene glycol as an uncompetitive inhibitor with respect to glucose-1-P. A parallel experimental investigation by X-ray crystallography showed that, at 100 K, both MPD and DMSO do not bind at the catalytic site, do not induce any significant conformational change on the enzyme molecule, and hence, are more suitable cryoprotectants than glycerol for binding studies with glycogen phosphorylase.
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Affiliation(s)
- K E Tsitsanou
- Institute of Biological Research and Biotechnology, The National Hellenic Research Foundation, Athens, Greece
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Board M. N-Acetyl-beta-D-glucopyranosylamine 6-phosphate is a specific inhibitor of glycogen-bound protein phosphatase 1. Biochem J 1997; 328 ( Pt 2):695-700. [PMID: 9371733 PMCID: PMC1218973 DOI: 10.1042/bj3280695] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Previous work has shown that the C-1-substituted glucose-analogue N-acetyl-beta-D-glucopyranosylamine (1-GlcNAc) is a competitive inhibitor of glycogen phosphorylase (GP) and stimulates the inactivation of this enzyme by GP phosphatase. In addition to its effects on GP, 1-GlcNAc also prevents the glucose-led activation of glycogen synthase (GS) in whole hepatocytes. Such an effect on GS was thought to be due to the formation of 1-GlcNAc-6-P by the action of glucokinase within the hepatocyte [Board, Bollen, Stalmans, Kim, Fleet and Johnson (1995) Biochem. J. 311, 845-852]. To investigate this possibility further, a pure preparation of 1-GlcNAc-6-P was synthesized. The effects of the phosphorylated glucose analogue on the activity of protein phosphatase 1 (PP1), the enzyme responsible for dephosphorylation and activation of GS, are reported. During the present study, 1-GlcNAc-6-P inhibited the activity of the glycogen-bound form of PP1, affecting both the GSb phosphatase and GPa phosphatase activities. A level of 50% inhibition of GSb phosphatase activity was achieved with 85 microM 1-GlcNAc-6-P in the absence of Glc-6-P and with 135 microM in the presence of 10 mM Glc-6-P. At either Glc-6-P concentration, 500 microM 1-GlcNAc-6-P completely inhibited activity. The Glc-6-P stimulation of the GPa phosphatase activity of PP1 was negated by 1-GlcNAc-6-P but there was no inhibition of the basal rate in the absence of Glc-6-P. 1-GlcNAc-6-P inhibition was specific for the glycogen-bound form of PP1 and did not inhibit the GSb phosphatase activity of the cytosolic form of the enzyme. The present work explains our previous observations on the inactivating effects on GS of incubating whole hepatocytes with 1-GlcNAc. These observations have their basis in the inhibition of glycogen-bound PP1 by 1-GlcNAc-6-P. A novel inhibitor of PP1, specific for the glycogen-bound form of the enzyme, is presented.
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Affiliation(s)
- M Board
- Catholic University of Leuven, Faculty of Medicine, Biochemistry Section, Herestraat, 49, B3000 Leuven, Belgium
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Zographos SE, Oikonomakos NG, Tsitsanou KE, Leonidas DD, Chrysina ED, Skamnaki VT, Bischoff H, Goldmann S, Watson KA, Johnson LN. The structure of glycogen phosphorylase b with an alkyldihydropyridine-dicarboxylic acid compound, a novel and potent inhibitor. Structure 1997; 5:1413-25. [PMID: 9384557 DOI: 10.1016/s0969-2126(97)00292-x] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND In muscle and liver, glycogen concentrations are regulated by the reciprocal activities of glycogen phosphorylase (GP) and glycogen synthase. An alkyl-dihydropyridine-dicarboxylic acid has been found to be a potent inhibitor of GP, and as such has potential to contribute to the regulation of glycogen metabolism in the non-insulin-dependent diabetes diseased state. The inhibitor has no structural similarity to the natural regulators of GP. We have carried out structural studies in order to elucidate the mechanism of inhibition. RESULTS Kinetic studies with rabbit muscle glycogen phosphorylase b (GPb) show that the compound (-)(S)-3-isopropyl 4-(2-chlorophenyl)-1,4-dihydro-1-ethyl-2-methyl-pyridine-3,5, 6-tricarboxylate (Bay W1807) has a Ki = 1.6 nM and is a competitive inhibitor with respect to AMP. The structure of the cocrystallised GPb-W1807 complex has been determined at 100K to 2.3 A resolution and refined to an R factor of 0.198 (Rfree = 0.287). W1807 binds at the GPb allosteric effector site, the site which binds AMP, glucose-6-phosphate and a number of other phosphorylated ligands, and induces conformational changes that are characteristic of those observed with the naturally occurring allosteric inhibitor, glucose-6-phosphate. The dihydropyridine-5,6-dicarboxylate groups mimic the phosphate group of ligands that bind to the allosteric site and contact three arginine residues. CONCLUSIONS The high affinity of W1807 for GP appears to arise from the numerous nonpolar interactions made between the ligand and the protein. Its potency as an inhibitor results from the induced conformational changes that lock the enzyme in a conformation known as the T' state. Allosteric enzymes, such as GP, offer a new strategy for structure-based drug design in which the allosteric site can be exploited. The results reported here may have important implications in the design of new therapeutic compounds.
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Affiliation(s)
- S E Zographos
- Institute of Biological Research and Biotechnology, The National Hellenic Research Foundation 48, vas Constantinou Avenue, Athens, 11635, Greece
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Blériot Y, Smelt KH, Cadefau J, Bollen M, Stalmans W, Biggadike K, Johnson LN, Oikonomakos NG, Lane AL, Crook S, Watkin DJ, Fleet GW. 7-Carbon mimics of D-glucose and L-fucose: Activation by 6R-, and inactivation by 6S, -6C-methylglucose of glycogen synthase: Inhibition of glucokinase and/or glucose-6-phosphatase. Tetrahedron Lett 1996. [DOI: 10.1016/0040-4039(96)01565-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Blériot Y, Veighey CR, Smelt KH, Cadefau J, Stalmans W, Biggadike K, Lane AL, Müller M, Watkin DJ, Fleet GW. The first example of a : Inhibition of glucokinase. ACTA ACUST UNITED AC 1996. [DOI: 10.1016/0957-4166(96)00356-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Brandstetter TW, Wormald MR, Dwek RA, Butters TD, Platt FM, Tsitsanou KE, Zographos SE, Oikonomakos NG, Fleet GW. A galactopyranose analogue of hydantocidin. ACTA ACUST UNITED AC 1996. [DOI: 10.1016/0957-4166(95)00432-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Oikonomakos NG, Kontou M, Zographos SE, Watson KA, Johnson LN, Bichard CJ, Fleet GW, Acharya KR. N-acetyl-beta-D-glucopyranosylamine: a potent T-state inhibitor of glycogen phosphorylase. A comparison with alpha-D-glucose. Protein Sci 1995; 4:2469-77. [PMID: 8580837 PMCID: PMC2143045 DOI: 10.1002/pro.5560041203] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Structure-based drug design has led to the discovery of a number of glucose analogue inhibitors of glycogen phosphorylase that have an increased affinity compared to alpha-D-glucose (Ki = 1.7 mM). The best inhibitor in the class of N-acyl derivatives of beta-D-glucopyranosylamine, N-acetyl-beta-D-glucopyranosylamine (1-GlcNAc), has been characterized by kinetic, ultracentrifugation, and crystallographic studies. 1-GlcNAc acts as a competitive inhibitor for both the b (Ki = 32 microM) and the a (Ki = 35 microM) forms of the enzyme with respect to glucose 1-phosphate and in synergism with caffeine, mimicking the binding of glucose. Sedimentation velocity experiments demonstrated that 1-GlcNAc was able to induce dissociation of tetrameric phosphorylase a and stabilization of the dimeric T-state conformation. Co-crystals of the phosphorylase b-1-GlcNAc-IMP complex were grown in space group P4(3)2(1)2, with native-like unit cell dimensions, and the complex structure has been refined to give a crystallographic R factor of 18.1%, for data between 8 and 2.3 A resolution. 1-GlcNAc binds tightly at the catalytic site of T-state phosphorylase b at approximately the same position as that of alpha-D-glucose. The ligand can be accommodated in the catalytic site with very little change in the protein structure and stabilizes the T-state conformation of the 280s loop by making several favorable contacts to Asn 284 of this loop. Structural comparisons show that the T-state phosphorylase b-1-GlcNAc-IMP complex structure is overall similar to the T-state phosphorylase b-alpha-D-glucose complex structure. The structure of the 1-GlcNAc complex provides a rational for the biochemical properties of the inhibitor.
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Affiliation(s)
- N G Oikonomakos
- Institute of Biological Research and Biotechnology, National Hellenic Research Foundation, Athens, Greece.
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