1
|
Nasi GI, Georgakopoulou KI, Theodoropoulou MK, Papandreou NC, Chrysina ED, Tsiolaki PL, Iconomidou VA. Bacterial Lectin FimH and Its Aggregation Hot-Spots: An Alternative Strategy against Uropathogenic Escherichia coli. Pharmaceutics 2023; 15:pharmaceutics15031018. [PMID: 36986878 PMCID: PMC10058141 DOI: 10.3390/pharmaceutics15031018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/28/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Type I fimbriae are the main adhesive organelles of uropathogenic Escherichia coli (UPEC), consisting of four different subunits. Their component with the most important role in establishing bacterial infections is the FimH adhesin located at the fimbrial tip. This two-domain protein mediates adhesion to host epithelial cells through interaction with terminal mannoses on epithelial glycoproteins. Here, we propose that the amyloidogenic potential of FimH can be exploited for the development of therapeutic agents against Urinary Tract Infections (UTIs). Aggregation-prone regions (APRs) were identified via computational methods, and peptide-analogues corresponding to FimH lectin domain APRs were chemically synthesized and studied with the aid of both biophysical experimental techniques and molecular dynamic simulations. Our findings indicate that these peptide-analogues offer a promising set of antimicrobial candidate molecules since they can either interfere with the folding process of FimH or compete for the mannose-binding pocket.
Collapse
Affiliation(s)
- Georgia I Nasi
- Section of Cell Biology and Biophysics, Department of Biology, School of Sciences, National and Kapodistrian University of Athens, 15701 Athens, Greece
| | - Konstantina I Georgakopoulou
- Section of Cell Biology and Biophysics, Department of Biology, School of Sciences, National and Kapodistrian University of Athens, 15701 Athens, Greece
| | - Marilena K Theodoropoulou
- Section of Cell Biology and Biophysics, Department of Biology, School of Sciences, National and Kapodistrian University of Athens, 15701 Athens, Greece
| | - Nikos C Papandreou
- Section of Cell Biology and Biophysics, Department of Biology, School of Sciences, National and Kapodistrian University of Athens, 15701 Athens, Greece
| | - Evangelia D Chrysina
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
| | - Paraskevi L Tsiolaki
- Section of Cell Biology and Biophysics, Department of Biology, School of Sciences, National and Kapodistrian University of Athens, 15701 Athens, Greece
| | - Vassiliki A Iconomidou
- Section of Cell Biology and Biophysics, Department of Biology, School of Sciences, National and Kapodistrian University of Athens, 15701 Athens, Greece
| |
Collapse
|
2
|
Chontzopoulou E, Papaemmanouil CD, Chatziathanasiadou MV, Kolokouris D, Kiriakidi S, Konstantinidi A, Gerogianni I, Tselios T, Kostakis IK, Chrysina ED, Hadjipavlou-Litina D, Tzeli D, Tzakos AG, Mavromoustakos T. Molecular investigation of artificial and natural sweeteners as potential anti-inflammatory agents. J Biomol Struct Dyn 2022; 40:12608-12620. [PMID: 34499023 DOI: 10.1080/07391102.2021.1973565] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Repurposing existing drugs, as well as natural and artificial sweeteners for novel therapeutic indications could speed up the drug discovery process since numerous associated risks and costs for drug development can be surpassed. In this study, natural and artificial sweeteners have been evaluated by in silico and experimental studies for their potency to inhibit lipoxygenase enzyme, an enzyme participating in the inflammation pathway. A variety of different methods pinpointed that aspartame inhibits the lipoxygenase isoform 1 (LOX-1). In particular, "LOX-aspartame" complex, that was predicted by docking studies, was further evaluated by Molecular Dynamics (MD) simulations in order to assess the stability of the complex. The binding energy of the complex has been calculated after MD simulations using Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) method. Furthermore, Quantum Mechanics/Molecular Mechanics (QM/MM) calculations have been applied for geometry optimization of the "enzyme-ligand" complex. After having fully characterized the "LOX-aspartame" complex in silico, followed in vitro biological assays confirmed that aspartame inhibits LOX-1 (IC50=50 ± 3.0 μΜ) and blocks its biological response. The atomic details of aspartame's interaction profile with LOX-1 were revealed through Saturation Transfer Difference (STD) NMR (Nuclear Magnetic Resonance). Finally, aspartame was also tested with Molecular Docking and Molecular Dynamics studies for its potent binding to a number of different LOX isoforms of many organisms, including human. The in silico methods indicated that aspartame could serve as a novel starting point for drug design against LOX enzyme. Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Eleni Chontzopoulou
- Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
| | - Christina D Papaemmanouil
- Department of Chemistry, Section of Organic Chemistry and Biochemistry, University of Ioannina, Ioannina, Greece
| | - Maria V Chatziathanasiadou
- Department of Chemistry, Section of Organic Chemistry and Biochemistry, University of Ioannina, Ioannina, Greece
| | - Dimitrios Kolokouris
- Department of Pharmacy, National and Kapodistrian, University of Athens, Athens, Greece
| | - Sofia Kiriakidi
- Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
| | - Athina Konstantinidi
- Department of Pharmacy, National and Kapodistrian, University of Athens, Athens, Greece
| | - Ioanna Gerogianni
- Institute of Biology, Medicinal Chemistry and Biotechnology, Department of Pharmaceutical Chemistry, School of Pharmacy, Faculty of Health Sciences, National Hellenic Research Foundation, Athens, Greece.,Department of Pharmacy, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | - Ioannis K Kostakis
- Department of Pharmacy, National and Kapodistrian, University of Athens, Athens, Greece
| | - Evangelia D Chrysina
- Institute of Biology, Medicinal Chemistry and Biotechnology, Department of Pharmaceutical Chemistry, School of Pharmacy, Faculty of Health Sciences, National Hellenic Research Foundation, Athens, Greece.,Department of Pharmacy, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | - Demeter Tzeli
- Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
| | - Andreas G Tzakos
- Department of Chemistry, Section of Organic Chemistry and Biochemistry, University of Ioannina, Ioannina, Greece.,Institute of Materials Science and Computing, University Research Center of Ioannina (URCI), Ioannina, Greece
| | - Thomas Mavromoustakos
- Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
| |
Collapse
|
3
|
Neofytos DD, Papagiannopoulos A, Chrysina ED, Pispas S. Formation and physicochemical properties of glycogen phosphorylase in complex with a cationic polyelectrolyte. Int J Biol Macromol 2022; 206:371-380. [PMID: 35240213 DOI: 10.1016/j.ijbiomac.2022.02.136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 02/10/2022] [Accepted: 02/23/2022] [Indexed: 12/28/2022]
Abstract
The accumulation of rabbit muscle glycogen phosphorylase b (RMGPb) in electrostatic complexes with the cationic polyelectrolyte poly 2-(dimethylamino) ethyl methacrylate in its quenched form (QPDMAEMA) was studied in two buffer solutions. In the N-bis(2-hydroxyethyl)-2-aminoethanesulfonic acid (BES) buffer, large complexes of RMGPb-QPDMAEMA were formed which adopted smaller sizes as QPDMAEMA concentration increased. However, in N-(2-hydroxyethyl)piperazine-N'-(2-ethanesulfonic acid) (HEPES) buffer, the hydrodynamic radius of the formed complexes gradually increased as the polymer concentration increased. Zeta potential measurements (ζp) showed that RMGPb significantly changed the ζp of the QPDMAEMA aggregates. Fluorescence studies showed that the interaction between RMGPb and QPDMAEAMA was enhanced as polymer concentration increased. Specifically, 8-anilinonaphthalene-1-sulfonic acid (ANS) fluorescence indicated that in the BES buffer the aggregates became denser as more QPDMAEMA was added, while in the HEPES buffer the density of the formed structures decreased. RMGPb's secondary structure was examined by Attenuated Total Reflection - Fourier Transform Infrared (ATR-FTIR) and Circular Dichroism (CD) showing that QPDMAEMA interaction with RMGPb does not induce any changes to the secondary structure of the enzyme. These observations suggest that cationic polyelectrolytes may be utilized for the formulation of RMGPb in multifunctional nanostructures and be further exploited in innovative biotechnology applications and bioinspired materials development.
Collapse
Affiliation(s)
- Dionysios D Neofytos
- Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 11635 Athens, Greece; Institute of Chemical Biology, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 11635 Athens, Greece
| | - Aristeidis Papagiannopoulos
- Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 11635 Athens, Greece.
| | - Evangelia D Chrysina
- Institute of Chemical Biology, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 11635 Athens, Greece.
| | - Stergios Pispas
- Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 11635 Athens, Greece
| |
Collapse
|
4
|
Minadakis MP, Mavreas K, Neofytos DD, Paschou M, Kogkaki A, Athanasiou V, Mamais M, Veclani D, Iatrou H, Venturini A, Chrysina ED, Papazafiri P, Gimisis T. A glucose-based molecular rotor inhibitor of glycogen phosphorylase as a probe of cellular enzymatic function. Org Biomol Chem 2022; 20:2407-2423. [DOI: 10.1039/d1ob02211c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Molecular rotors belong to a family of fluorescent compounds characterized as molecular switches, where a fluorescence on/off signal signifies a change in the molecule’s microenvironment. Herein, the successful synthesis and...
Collapse
|
5
|
Mavreas KF, Neofytos DD, Chrysina ED, Venturini A, Gimisis T. Synthesis, Kinetic and Conformational Studies of 2-Substituted-5-(β-d-glucopyranosyl)-pyrimidin-4-ones as Potential Inhibitors of Glycogen Phosphorylase. Molecules 2020; 25:molecules25225463. [PMID: 33266408 PMCID: PMC7700572 DOI: 10.3390/molecules25225463] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/16/2020] [Accepted: 11/19/2020] [Indexed: 12/30/2022] Open
Abstract
Dysregulation of glycogen phosphorylase, an enzyme involved in glucose homeostasis, may lead to a number of pathological states such as type 2 diabetes and cancer, making it an important molecular target for the development of new forms of pharmaceutical intervention. Based on our previous work on the design and synthesis of 4-arylamino-1-(β-d-glucopyranosyl)pyrimidin-2-ones, which inhibit the activity of glycogen phosphorylase by binding at its catalytic site, we report herein a general synthesis of 2-substituted-5-(β-d-glucopyranosyl)pyrimidin-4-ones, a related class of metabolically stable, C-glucosyl-based, analogues. The synthetic development consists of a metallated heterocycle, produced from 5-bromo-2-methylthiouracil, in addition to protected d-gluconolactone, followed by organosilane reduction. The methylthio handle allowed derivatization through hydrolysis, ammonolysis and arylamine substitution, and the new compounds were found to be potent (μM) inhibitors of rabbit muscle glycogen phosphorylase. The results were interpreted with the help of density functional theory calculations and conformational analysis and were compared with previous findings.
Collapse
Affiliation(s)
- Konstantinos F. Mavreas
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15784 Athens, Greece;
| | - Dionysios D. Neofytos
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece;
| | - Evangelia D. Chrysina
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece;
- Correspondence: (E.D.C.); (A.V.); (T.G.)
| | - Alessandro Venturini
- Istituto ISOF, Consiglio Nazionale delle Ricerche, 40129 Bologna, Italy
- Correspondence: (E.D.C.); (A.V.); (T.G.)
| | - Thanasis Gimisis
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15784 Athens, Greece;
- Correspondence: (E.D.C.); (A.V.); (T.G.)
| |
Collapse
|
6
|
Zarafeta D, Galanopoulou AP, Leni ME, Kaili SI, Chegkazi MS, Chrysina ED, Kolisis FN, Hatzinikolaou DG, Skretas G. XynDZ5: A New Thermostable GH10 Xylanase. Front Microbiol 2020; 11:545. [PMID: 32390953 PMCID: PMC7193231 DOI: 10.3389/fmicb.2020.00545] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 03/12/2020] [Indexed: 12/27/2022] Open
Abstract
Xylanolytic enzymes have a broad range of applications in industrial biotechnology as biocatalytic components of various processes and products, such as food additives, bakery products, coffee extraction, agricultural silage and functional foods. An increasing market demand has driven the growing interest for the discovery of xylanases with specific industrially relevant characteristics, such as stability at elevated temperatures and in the presence of other denaturing factors, which will facilitate their incorporation into industrial processes. In this work, we report the discovery and biochemical characterization of a new thermostable GH10 xylanase, termed XynDZ5, exhibiting only 26% amino acid sequence identity to the closest characterized xylanolytic enzyme. This new enzyme was discovered in an Icelandic hot spring enrichment culture of a Thermoanaerobacterium species using a recently developed bioinformatic analysis platform. XynDZ5 was produced recombinantly in Escherichia coli, purified and characterized biochemically. This analysis revealed that it acts as an endo-1,4-β-xylanase that performs optimally at 65–75°C and pH 7.5. The enzyme is capable of retaining high levels of catalytic efficiency after several hours of incubation at high temperatures, as well as in the presence of significant concentrations of a range of metal ions and denaturing agents. Interestingly, the XynDZ5 biochemical profile was found to be atypical, as it also exhibits significant exo-activity. Computational modeling of its three-dimensional structure predicted a (β/α)8 TIM barrel fold, which is very frequently encountered among family GH10 enzymes. This modeled structure has provided clues about structural features that may explain aspects of its catalytic performance. Our results suggest that XynDZ5 represents a promising new candidate biocatalyst appropriate for several high-temperature biotechnological applications in the pulp, paper, baking, animal-feed and biofuel industries.
Collapse
Affiliation(s)
- Dimitra Zarafeta
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Anastasia P Galanopoulou
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece.,Department of Biology, Enzyme and Microbial Biotechnology Unit, National and Kapodistrian University of Athens, Athens, Greece
| | - Maria Evangelia Leni
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Stavroula I Kaili
- Department of Biology, Enzyme and Microbial Biotechnology Unit, National and Kapodistrian University of Athens, Athens, Greece
| | - Magda S Chegkazi
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Evangelia D Chrysina
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Fragiskos N Kolisis
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Dimitris G Hatzinikolaou
- Department of Biology, Enzyme and Microbial Biotechnology Unit, National and Kapodistrian University of Athens, Athens, Greece
| | - Georgios Skretas
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| |
Collapse
|
7
|
Dimarogona M, Topakas E, Christakopoulos P, Chrysina ED. The crystal structure of a Fusarium oxysporum feruloyl esterase that belongs to the tannase family. FEBS Lett 2020; 594:1738-1749. [PMID: 32297315 DOI: 10.1002/1873-3468.13776] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 03/13/2020] [Accepted: 03/17/2020] [Indexed: 12/31/2022]
Abstract
Feruloyl esterases are enzymes of industrial interest that catalyse the hydrolysis of the ester bond between hydroxycinnamic acids such as ferulic acid and sugars present in the plant cell wall. Although there are several structures of biochemically characterized feruloyl esterases available, the structural determinants of their substrate specificity are not yet fully understood. Here, we present the crystal structure of a feruloyl esterase from Fusarium oxysporum (FoFaeC) at 2.3 Å resolution. Similar to the two other tannase-like feruloyl esterases, FoFaeC features a large lid domain covering the active site with potential regulatory role and a disulphide bond that brings together the serine and histidine of the catalytic triad. Differences are mainly observed in the metal coordination site and the substrate binding pocket. ENZYMES: E.C.3.1.1.73. DATABASES: The sequence of FoFaeC has been deposited with UniProt with accession code A0A1D3S5H0_FUSOX and the atomic coordinates of the three-dimensional structure with Protein Data Bank, with PDB code: 6FAT.
Collapse
Affiliation(s)
- Maria Dimarogona
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece.,School of Chemical Engineering, National Technical University of Athens, Greece
| | - Evangelos Topakas
- School of Chemical Engineering, National Technical University of Athens, Greece
| | - Paul Christakopoulos
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, Sweden
| | - Evangelia D Chrysina
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| |
Collapse
|
8
|
Chountoulesi M, Pippa N, Chrysostomou V, Pispas S, Chrysina ED, Forys A, Otulakowski L, Trzebicka B, Demetzos C. Stimuli-Responsive Lyotropic Liquid Crystalline Nanosystems with Incorporated Poly(2-Dimethylamino Ethyl Methacrylate)-b-Poly(Lauryl Methacrylate) Amphiphilic Block Copolymer. Polymers (Basel) 2019; 11:polym11091400. [PMID: 31454966 PMCID: PMC6780812 DOI: 10.3390/polym11091400] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 08/09/2019] [Accepted: 08/18/2019] [Indexed: 12/18/2022] Open
Abstract
There is an emerging need to evolve the conventional lyotropic liquid crystalline nanoparticles to advanced stimuli-responsive, therapeutic nanosystems with upgraded functionality. Towards this effort, typically used stabilizers, such as Pluronics®, can be combined or replaced by smart, stimuli-responsive block copolymers. The aim of this study is to incorporate the stimuli-responsive amphiphilic block copolymer poly(2-(dimethylamino)ethyl methacrylate)-b-poly(lauryl methacrylate) (PDMAEMA-b-PLMA) as a stabilizer in lipidic liquid crystalline nanoparticles, in order to provide steric stabilization and simultaneous stimuli-responsiveness. The physicochemical and morphological characteristics of the prepared nanosystems were investigated by light scattering techniques, cryogenic-transmission electron microscopy (cryo-TEM), X-ray diffraction (XRD) and fluorescence spectroscopy. The PDMAEMA-b-PLMA, either individually or combined with Poloxamer 407, exhibited different modes of stabilization depending on the lipid used. Due to the protonation ability of PDMAEMA blocks in acidic pH, the nanoparticles exhibited high positive charge, as well as pH-responsive charge conversion, which can be exploited towards pharmaceutical applications. The ionic strength, temperature and serum proteins influenced the physicochemical behavior of the nanoparticles, while the polymer concentration differentiated their morphology; their micropolarity and microfluidity were also evaluated. The proposed liquid crystalline nanosystems can be considered as novel and attractive pH-responsive drug and gene delivery nanocarriers due to their polycationic content.
Collapse
Affiliation(s)
- Maria Chountoulesi
- Section of Pharmaceutical Technology, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 15771 Athens, Greece
| | - Natassa Pippa
- Section of Pharmaceutical Technology, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 15771 Athens, Greece
- Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 11635 Athens, Greece
| | - Varvara Chrysostomou
- Section of Pharmaceutical Technology, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 15771 Athens, Greece
- Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 11635 Athens, Greece
| | - Stergios Pispas
- Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 11635 Athens, Greece.
| | - Evangelia D Chrysina
- Institute of Chemical Biology, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 11635 Athens, Greece
| | - Aleksander Forys
- Centre of Polymer and Carbon Materials, Polish Academy of Sciences, 34 ul. M. Curie-Skłodowskiej, 34, 41-819 Zabrze, Poland
| | - Lukasz Otulakowski
- Centre of Polymer and Carbon Materials, Polish Academy of Sciences, 34 ul. M. Curie-Skłodowskiej, 34, 41-819 Zabrze, Poland
| | - Barbara Trzebicka
- Centre of Polymer and Carbon Materials, Polish Academy of Sciences, 34 ul. M. Curie-Skłodowskiej, 34, 41-819 Zabrze, Poland
| | - Costas Demetzos
- Section of Pharmaceutical Technology, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 15771 Athens, Greece.
| |
Collapse
|
9
|
Stathi A, Mamais M, Chrysina ED, Gimisis T. Anomeric Spironucleosides of β-d-Glucopyranosyl Uracil as Potential Inhibitors of Glycogen Phosphorylase. Molecules 2019; 24:E2327. [PMID: 31242546 PMCID: PMC6630470 DOI: 10.3390/molecules24122327] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 06/14/2019] [Accepted: 06/17/2019] [Indexed: 11/16/2022] Open
Abstract
In the case of type 2 diabetes, inhibitors of glycogen phosphorylase (GP) may prevent unwanted glycogenolysis under high glucose conditions and thus aim at the reduction of excessive glucose production by the liver. Anomeric spironucleosides, such as hydantocidin, present a rich synthetic chemistry and important biological function (e.g., inhibition of GP). For this study, the Suárez radical methodology was successfully applied to synthesize the first example of a 1,6-dioxa-4-azaspiro[4.5]decane system, not previously constructed via a radical pathway, starting from 6-hydroxymethyl-β-d-glucopyranosyluracil. It was shown that, in the rigid pyranosyl conformation, the required [1,5]-radical translocation was a minor process. The stereochemistry of the spirocycles obtained was unequivocally determined based on the chemical shifts of key sugar protons in the 1H-NMR spectra. The two spirocycles were found to be modest inhibitors of RMGPb.
Collapse
Affiliation(s)
- Aggeliki Stathi
- Organic Chemistry Laboratory, Department of Chemistry, National and Kapodistrian University of Athens, 10571 Athens, Greece.
| | - Michael Mamais
- Organic Chemistry Laboratory, Department of Chemistry, National and Kapodistrian University of Athens, 10571 Athens, Greece.
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece.
| | - Evangelia D Chrysina
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece.
| | - Thanasis Gimisis
- Organic Chemistry Laboratory, Department of Chemistry, National and Kapodistrian University of Athens, 10571 Athens, Greece.
| |
Collapse
|
10
|
Maffeis V, Mavreas K, Monti F, Mamais M, Gustavsson T, Chrysina ED, Markovitsi D, Gimisis T, Venturini A. Multiscale time-resolved fluorescence study of a glycogen phosphorylase inhibitor combined with quantum chemistry calculations. Phys Chem Chem Phys 2019; 21:7685-7696. [PMID: 30912774 DOI: 10.1039/c8cp07538g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A fluorescence study of N1-(β-d-glucopyranosyl)-N4-[2-acridin-9(10H)-onyl]-cytosine (GLAC), the first fluorescent potent inhibitor of glycogen phosphorylase (GP), in neutral aqueous solution, is presented herein. Quantum chemistry (TD-DFT) calculations show the existence of several conformers both in the ground and first excited states. They result from rotations of the acridone and cytosine moieties around an NH bridge which may lead to the formation of non-emitting charge-transfer states. The fingerprints of various conformers have been detected by time-resolved fluorescence spectroscopy (fluorescence upconversion and time-correlated single photon counting) and identified using as criteria their energy, polarization and relative population resulting from computations. Such an analysis should contribute to the design of new GP inhibitors with better fluorescence properties, suitable for imaging applications.
Collapse
Affiliation(s)
- Valentin Maffeis
- LIDYL, CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France.
| | | | | | | | | | | | | | | | | |
Collapse
|
11
|
Chountoulesi M, Pippa N, Pispas S, Chrysina ED, Forys A, Trzebicka B, Demetzos C. Cubic lyotropic liquid crystals as drug delivery carriers: Physicochemical and morphological studies. Int J Pharm 2018; 550:57-70. [PMID: 30121331 DOI: 10.1016/j.ijpharm.2018.08.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 07/15/2018] [Accepted: 08/01/2018] [Indexed: 12/22/2022]
Abstract
The self-assembly process of amphiphilic molecules into solvents results in different mesophases, such as inverse cubic and hexagonal that both belong to the wider category of lyotropic liquid crystals. The above mesophases can be further exploited upon the formation of liquid crystalline nanoparticles, cubosomes and hexosomes respectively, which may be utilized as drug delivery nanosystems, exhibiting major advantages. In the present study, liquid crystalline nanoparticles were prepared and evaluated in terms of morphology and physicochemical behavior. The goal of this study is to examine the effect of the different formulation parameters, as well as the effect of the different microenvironmental factors (temperature, ionic strength, pH, serum proteins presence) on their behavior. The physicochemical behavior and the morphology of the systems were investigated by X-Ray Diffraction (XRD), cryogenic-Transmission Electron Microscopy (cryo-TEM), fluorescence spectroscopy and a gamut of light scattering techniques. The formulation process was proved to influence strictly the physicochemical behavior of the prepared nanosystems. They presented colloidal stability over time and upon ionic strength increase, but they were affected by the presence of proteins and presented reversible structure alterations upon temperature increase. Their morphological structure and internal microenvironment, reflected by micropolarity and microfluidity, were also influenced by the formulation parameters.
Collapse
Affiliation(s)
- Maria Chountoulesi
- Section of Pharmaceutical Technology, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 15771 Athens, Greece
| | - Natassa Pippa
- Section of Pharmaceutical Technology, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 15771 Athens, Greece; Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 11635 Athens, Greece
| | - Stergios Pispas
- Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 11635 Athens, Greece
| | - Evangelia D Chrysina
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 11635 Athens, Greece
| | - Aleksander Forys
- Centre of Polymer and Carbon Materials, Polish Academy of Sciences, 34 ul. M. Curie-Skłodowskiej, Zabrze, Poland
| | - Barbara Trzebicka
- Centre of Polymer and Carbon Materials, Polish Academy of Sciences, 34 ul. M. Curie-Skłodowskiej, Zabrze, Poland
| | - Costas Demetzos
- Section of Pharmaceutical Technology, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 15771 Athens, Greece.
| |
Collapse
|
12
|
Abstract
Modern drug discovery and design approaches rely heavily on high-throughput methods and state-of-the-art infrastructures with robotic facilities and sophisticated platforms. However, the anticipated research output that would eventually lead to new drugs with minimal or no side effects to the market has not been achieved. Despite the vast amount of information generated, very little is converted to knowledge and even less is capitalized for cross-discipline research actions. Therefore, the need for re-launching rational approaches has become apparent. Here we present an overview of the new trends in rational drug design using integrative structural biology with emphasis on X-ray protein crystallography and small molecules as ligands. With the aim to increase researchers' awareness on the available possibilities to perform front line research, we also underline the benefits and enhanced prospects offered to the scientific community, through access to research infrastructures.
Collapse
Affiliation(s)
- Magda S Chegkazi
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece.,Faculty of Life Sciences and Medicine, Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | - Michael Mamais
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Anastasia I Sotiropoulou
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Evangelia D Chrysina
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece.
| |
Collapse
|
13
|
Mamais M, Degli Esposti A, Kouloumoundra V, Gustavsson T, Monti F, Venturini A, Chrysina ED, Markovitsi D, Gimisis T. Frontispiece: A New Potent Inhibitor of Glycogen Phosphorylase Reveals the Basicity of the Catalytic Site. Chemistry 2017. [DOI: 10.1002/chem.201783763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Michael Mamais
- Department of Chemistry; National and Kapodistrian University of Athens; Athens Greece
- Institute of Biology, Medicinal Chemistry and Biotechnology; National Hellenic Research Foundation; Athens Greece
| | | | | | | | - Filippo Monti
- Istituto ISOF; Consiglio Nazionale delle Ricerche; Bologna Italy
| | | | - Evangelia D. Chrysina
- Institute of Biology, Medicinal Chemistry and Biotechnology; National Hellenic Research Foundation; Athens Greece
| | | | - Thanasis Gimisis
- Department of Chemistry; National and Kapodistrian University of Athens; Athens Greece
| |
Collapse
|
14
|
Mamais M, Degli Esposti A, Kouloumoundra V, Gustavsson T, Monti F, Venturini A, Chrysina ED, Markovitsi D, Gimisis T. A New Potent Inhibitor of Glycogen Phosphorylase Reveals the Basicity of the Catalytic Site. Chemistry 2017; 23:8800-8805. [PMID: 28493496 DOI: 10.1002/chem.201701591] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Indexed: 11/08/2022]
Abstract
The design and synthesis of a glucose-based acridone derivative (GLAC), a potent inhibitor of glycogen phosphorylase (GP) are described. GLAC is the first inhibitor of glycogen phosphorylase, the electronic absorption properties of which are clearly distinguishable from those of the enzyme. This allows probing subtle interactions in the catalytic site. The GLAC absorption spectra, associated with X-ray crystallography and quantum chemistry calculations, reveal that part of the catalytic site of GP behaves as a highly basic environment in which GLAC exists as a bis-anion. This is explained by water-bridged hydrogen-bonding interactions with specific catalytic site residues.
Collapse
Affiliation(s)
- Michael Mamais
- Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece.,Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | | | | | | | - Filippo Monti
- Istituto ISOF, Consiglio Nazionale delle Ricerche, Bologna, Italy
| | | | - Evangelia D Chrysina
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | | | - Thanasis Gimisis
- Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
| |
Collapse
|
15
|
Zarafeta D, Moschidi D, Ladoukakis E, Gavrilov S, Chrysina ED, Chatziioannou A, Kublanov I, Skretas G, Kolisis FN. Metagenomic mining for thermostable esterolytic enzymes uncovers a new family of bacterial esterases. Sci Rep 2016; 6:38886. [PMID: 27991516 PMCID: PMC5171882 DOI: 10.1038/srep38886] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 11/14/2016] [Indexed: 11/09/2022] Open
Abstract
Biocatalysts exerting activity against ester bonds have a broad range of applications in modern biotechnology. Here, we have identified a new esterolytic enzyme by screening a metagenomic sample collected from a hot spring in Kamchatka, Russia. Biochemical characterization of the new esterase, termed EstDZ2, revealed that it is highly active against medium chain fatty acid esters at temperatures between 25 and 60 °C and at pH values 7-8. The new enzyme is moderately thermostable with a half-life of more than six hours at 60 °C, but exhibits exquisite stability against high concentrations of organic solvents. Phylogenetic analysis indicated that EstDZ2 is likely an Acetothermia enzyme that belongs to a new family of bacterial esterases, for which we propose the index XV. One distinctive feature of this new family, is the presence of a conserved GHSAG catalytic motif. Multiple sequence alignment, coupled with computational modelling of the three-dimensional structure of EstDZ2, revealed that the enzyme lacks the largest part of the "cap" domain, whose extended structure is characteristic for the closely related Family IV esterases. Thus, EstDZ2 appears to be distinct from known related esterolytic enzymes, both in terms of sequence characteristics, as well as in terms of three-dimensional structure.
Collapse
Affiliation(s)
- Dimitra Zarafeta
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Danai Moschidi
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Efthymios Ladoukakis
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Sergey Gavrilov
- Winogradsky Institute of Microbiology, Research Center for Biotechnology Russian Academy of Sciences, Moscow, Russian Federation
| | - Evangelia D. Chrysina
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Aristotelis Chatziioannou
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Ilya Kublanov
- Winogradsky Institute of Microbiology, Research Center for Biotechnology Russian Academy of Sciences, Moscow, Russian Federation
| | - Georgios Skretas
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Fragiskos N. Kolisis
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| |
Collapse
|
16
|
Zarafeta D, Szabo Z, Moschidi D, Phan H, Chrysina ED, Peng X, Ingham CJ, Kolisis FN, Skretas G. EstDZ3: A New Esterolytic Enzyme Exhibiting Remarkable Thermostability. Front Microbiol 2016; 7:1779. [PMID: 27899916 PMCID: PMC5110521 DOI: 10.3389/fmicb.2016.01779] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 10/24/2016] [Indexed: 11/25/2022] Open
Abstract
Lipolytic enzymes that retain high levels of catalytic activity when exposed to a variety of denaturing conditions are of high importance for a number of biotechnological applications. In this study, we aimed to identify new lipolytic enzymes, which are highly resistant to prolonged exposure to elevated temperatures. To achieve this, we searched for genes encoding for such proteins in the genomes of a microbial consortium residing in a hot spring located in China. After performing functional genomic screening on a bacterium of the genus Dictyoglomus, which was isolated from this hot spring following in situ enrichment, we identified a new esterolytic enzyme, termed EstDZ3. Detailed biochemical characterization of the recombinant enzyme, revealed that it constitutes a slightly alkalophilic and highly active esterase against esters of fatty acids with short to medium chain lengths. Importantly, EstDZ3 exhibits remarkable thermostability, as it retains high levels of catalytic activity after exposure to temperatures as high as 95°C for several hours. Furthermore, it exhibits very good stability against exposure to high concentrations of a variety of organic solvents. Interestingly, EstDZ3 was found to have very little similarity to previously characterized esterolytic enzymes. Computational modeling of the three-dimensional structure of this new enzyme predicted that it exhibits a typical α/β hydrolase fold that seems to include a “subdomain insertion”, which is similar to the one present in its closest homolog of known function and structure, the cinnamoyl esterase Lj0536 from Lactobacillus johnsonii. As it was found in the case of Lj0536, this structural feature is expected to be an important determinant of the catalytic properties of EstDZ3. The high levels of esterolytic activity of EstDZ3, combined with its remarkable thermostability and good stability against a range of organic solvents and other denaturing agents, render this new enzyme a candidate biocatalyst for high-temperature biotechnological applications.
Collapse
Affiliation(s)
- Dimitra Zarafeta
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research FoundationAthens, Greece; Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of AthensAthens, Greece
| | | | - Danai Moschidi
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens Athens, Greece
| | - Hien Phan
- Danish Archaea Centre, Department of Biology, Copenhagen University Copenhagen, Denmark
| | - Evangelia D Chrysina
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation Athens, Greece
| | - Xu Peng
- Danish Archaea Centre, Department of Biology, Copenhagen University Copenhagen, Denmark
| | | | - Fragiskos N Kolisis
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens Athens, Greece
| | - Georgios Skretas
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation Athens, Greece
| |
Collapse
|
17
|
Galal SA, Khattab M, Andreadaki F, Chrysina ED, Praly JP, Ragab FA, El Diwani HI. Synthesis of (benzimidazol-2-yl)aniline derivatives as glycogen phosphorylase inhibitors. Bioorg Med Chem 2016; 24:5423-5430. [DOI: 10.1016/j.bmc.2016.08.069] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 08/28/2016] [Accepted: 08/31/2016] [Indexed: 11/30/2022]
|
18
|
Louros NN, Chrysina ED, Baltatzis GE, Patsouris ES, Hamodrakas SJ, Iconomidou VA. A common 'aggregation-prone' interface possibly participates in the self-assembly of human zona pellucida proteins. FEBS Lett 2016; 590:619-30. [PMID: 26879157 DOI: 10.1002/1873-3468.12099] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 02/01/2016] [Accepted: 02/05/2016] [Indexed: 02/03/2023]
Abstract
Human zona pellucida (ZP) is composed of four glycoproteins, namely ZP1, ZP2, ZP3 and ZP4. ZP proteins form heterodimers, which are incorporated into filaments through a common bipartite polymerizing component, designated as the ZP domain. The latter is composed of two individually folded subdomains, named ZP-N and ZP-C. Here, we have synthesized six 'aggregation-prone' peptides, corresponding to a common interface of human ZP2, ZP3 and ZP4. Experimental results utilizing electron microscopy, X-ray diffraction, ATR FT-IR spectroscopy and polarizing microscopy indicate that these peptides self-assemble forming fibrils with distinct amyloid-like features. Finally, by performing detailed modeling and docking, we attempt to shed some light in the self-assembly mechanism of human ZP proteins.
Collapse
Affiliation(s)
- Nikolaos N Louros
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Greece
| | - Evangelia D Chrysina
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | | | | | - Stavros J Hamodrakas
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Greece
| | - Vassiliki A Iconomidou
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Greece
| |
Collapse
|
19
|
Mamais M, Kouloumoundra V, Smyrli E, Grammatopoulos P, Chrysina ED, Gimisis T. Synthesis of N4-aryl-β-d-glucopyranosylcytosines: a methodology study. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2015.08.037] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
20
|
Mavrokefalos N, Myrianthopoulos V, Chajistamatiou AS, Chrysina ED, Mikros E. Discovery of the glycogen phosphorylase-modulating activity of a resveratrol glucoside by using a virtual screening protocol optimized for solvation effects. Planta Med 2015; 81:507-516. [PMID: 25875507 DOI: 10.1055/s-0035-1545910] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The identification of natural products that can modulate blood glucose levels is of great interest as it can possibly facilitate the utilization of mild interventions such as herbal medicine or functional foods in the treatment of chronic diseases like diabetes. One of the established drug targets for antihyperglycemic therapy is glycogen phosphorylase. To evaluate the glycogen phosphorylase inhibitory properties of an in-house compound collection consisting to a large extent of natural products, a stepwise virtual and experimental screening protocol was devised and implemented. The fact that the active site of glycogen phosphorylase is highly hydrated emphasized that a methodological aspect needed to be efficiently addressed prior to an in silico evaluation of the compound collection. The effect of water molecules on docking calculations was regarded as a key parameter in terms of virtual screening protocol optimization. Statistical analysis of 125 structures of glycogen phosphorylase and solvent mapping focusing on the active site hydration motif in combination with a retrospective screening revealed the importance of a set of 29 crystallographic water molecules for achieving high enrichment as to the discrimination between active compounds and inactive decoys. The scaling of Van der Waals radii of system atoms had an additional effect on screening performance. Having optimized the in silico protocol, a prospective evaluation of the in-house compound collection derived a set of 18 top-ranked natural products that were subsequently evaluated in vitro for their activity as glycogen phosphorylase inhibitors. Two phenolic glucosides with glycogen phosphorylase-modulating activity were identified, whereas the most potent compound affording mid-micromolar inhibition was a glucosidic derivative of resveratrol, a stilbene well-known for its wide range of biological activities. Results show the possible phytotherapeutic and nutraceutical potential of products common in the Mediterranean countries, such as red wine and Vitis products in general or green raw salads and herbal preparations, where such compounds are abundant.
Collapse
Affiliation(s)
- Nikolaos Mavrokefalos
- Division of Pharmaceutical Chemistry, School of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
| | - Vassilios Myrianthopoulos
- Division of Pharmaceutical Chemistry, School of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
| | - Aikaterini S Chajistamatiou
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Evangelia D Chrysina
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Emmanuel Mikros
- Division of Pharmaceutical Chemistry, School of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
| |
Collapse
|
21
|
Czifrák K, Páhi A, Deák S, Kiss-Szikszai A, Kövér KE, Docsa T, Gergely P, Alexacou KM, Papakonstantinou M, Leonidas DD, Zographos SE, Chrysina ED, Somsák L. Glucopyranosylidene-spiro-iminothiazolidinone, a new bicyclic ring system: Synthesis, derivatization, and evaluation for inhibition of glycogen phosphorylase by enzyme kinetic and crystallographic methods. Bioorg Med Chem 2014; 22:4028-41. [DOI: 10.1016/j.bmc.2014.05.076] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 05/25/2014] [Accepted: 05/29/2014] [Indexed: 10/25/2022]
|
22
|
Goyard D, Chajistamatiou AS, Sotiropoulou AI, Chrysina ED, Praly JP, Vidal S. Efficient Atropodiastereoselective Access to 5,5′-Bis-1,2,3-triazoles: Studies on 1-Glucosylated 5-Halogeno 1,2,3-Triazoles and Their 5-Substituted Derivatives as Glycogen Phosphorylase Inhibitors. Chemistry 2014; 20:5423-32. [DOI: 10.1002/chem.201304989] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Indexed: 12/16/2022]
|
23
|
Louros NN, Iconomidou VA, Tsiolaki PL, Chrysina ED, Baltatzis GE, Patsouris ES, Hamodrakas SJ. An N-terminal pro-atrial natriuretic peptide (NT-proANP) 'aggregation-prone' segment involved in isolated atrial amyloidosis. FEBS Lett 2013; 588:52-7. [PMID: 24220659 DOI: 10.1016/j.febslet.2013.10.049] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 10/08/2013] [Accepted: 10/30/2013] [Indexed: 01/18/2023]
Abstract
Isolated atrial amyloidosis (IAA) is a common localized form of amyloid deposition within the atria of the aging heart. The main constituents of amyloid fibrils are atrial natriuretic peptide (ANP) and the N-terminal part of its precursor form (NT-proANP). An 'aggregation-prone' heptapeptide ((114)KLRALLT(120)) was located within the NT-proANP sequence. This peptide self-assembles into amyloid-like fibrils in vitro, as electron microscopy, X-ray fiber diffraction, ATR FT-IR spectroscopy and Congo red staining studies reveal. Consequently, remedies/drugs designed to inhibit the aggregation tendency of this 'aggregation-prone' segment of NT-proANP may assist in prevention/treatment of IAA, congestive heart failure (CHF) or atrial fibrillation (AF).
Collapse
Affiliation(s)
- Nikolaos N Louros
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, Athens 157 01, Greece
| | - Vassiliki A Iconomidou
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, Athens 157 01, Greece
| | - Paraskevi L Tsiolaki
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, Athens 157 01, Greece
| | - Evangelia D Chrysina
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, Athens 116 35, Greece
| | - Georgios E Baltatzis
- 1st Department of Pathology, Medical School, University of Athens, 75 Mikras Assias, Goudi 115 27, Greece
| | - Efstratios S Patsouris
- 1st Department of Pathology, Medical School, University of Athens, 75 Mikras Assias, Goudi 115 27, Greece
| | - Stavros J Hamodrakas
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, Athens 157 01, Greece.
| |
Collapse
|
24
|
Charavgi MD, Dimarogona M, Topakas E, Christakopoulos P, Chrysina ED. The structure of a novel glucuronoyl esterase from Myceliophthora thermophila gives new insights into its role as a potential biocatalyst. Acta Crystallogr D Biol Crystallogr 2012; 69:63-73. [PMID: 23275164 DOI: 10.1107/s0907444912042400] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Accepted: 10/10/2012] [Indexed: 11/10/2022]
Abstract
The increasing demand for the development of efficient biocatalysts is a consequence of their broad industrial applications. Typical difficulties that are encountered during their exploitation in a variety of processes are interconnected with factors such as temperature, pH, product inhibitors etc. To eliminate these, research has been directed towards the identification of new enzymes that would comply with the required standards. To this end, the recently discovered glucuronoyl esterases (GEs) are an enigmatic family within the carbohydrate esterase (CE) family. Structures of the thermophilic StGE2 esterase from Myceliophthora thermophila (synonym Sporotrichum thermophile), a member of the CE15 family, and its S213A mutant were determined at 1.55 and 1.9 Å resolution, respectively. The first crystal structure of the S213A mutant in complex with a substrate analogue, methyl 4-O-methyl-β-D-glucopyranuronate, was determined at 2.35 Å resolution. All of the three-dimensional protein structures have an α/β-hydrolase fold with a three-layer αβα-sandwich architecture and a Rossmann topology and comprise one molecule per asymmetric unit. These are the first crystal structures of a thermophilic GE both in an unliganded form and bound to a substrate analogue, thus unravelling the organization of the catalytic triad residues and their neighbours lining the active site. The knowledge derived offers novel insights into the key structural elements that drive the hydrolysis of glucuronic acid esters.
Collapse
Affiliation(s)
- Maria Despoina Charavgi
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | | | | | | | | |
Collapse
|
25
|
Goyard D, Baron M, Skourti PV, Chajistamatiou AS, Docsa T, Gergely P, Chrysina ED, Praly JP, Vidal S. Synthesis of 1,2,3-triazoles from xylosyl and 5-thioxylosyl azides: evaluation of the xylose scaffold for the design of potential glycogen phosphorylase inhibitors. Carbohydr Res 2012; 364:28-40. [DOI: 10.1016/j.carres.2012.09.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 09/24/2012] [Accepted: 09/26/2012] [Indexed: 10/27/2022]
|
26
|
Dimarogona M, Topakas E, Christakopoulos P, Chrysina ED. The structure of a GH10 xylanase fromFusarium oxysporumreveals the presence of an extended loop on top of the catalytic cleft. Acta Crystallogr D Biol Crystallogr 2012; 68:735-42. [DOI: 10.1107/s0907444912007044] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Accepted: 02/16/2012] [Indexed: 11/10/2022]
|
27
|
Nagy V, Felföldi N, Kónya B, Praly JP, Docsa T, Gergely P, Chrysina ED, Tiraidis C, Kosmopoulou MN, Alexacou KM, Konstantakaki M, Leonidas DD, Zographos SE, Oikonomakos NG, Kozmon S, Tvaroška I, Somsák L. N-(4-Substituted-benzoyl)-N′-(β-d-glucopyranosyl)ureas as inhibitors of glycogen phosphorylase: Synthesis and evaluation by kinetic, crystallographic, and molecular modelling methods. Bioorg Med Chem 2012; 20:1801-16. [DOI: 10.1016/j.bmc.2011.12.059] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Revised: 12/28/2011] [Accepted: 12/29/2011] [Indexed: 11/15/2022]
|
28
|
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] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Revised: 02/24/2011] [Accepted: 03/03/2011] [Indexed: 10/18/2022]
|
29
|
Alexacou KM, Zhang YZ, Praly JP, Zographos SE, Chrysina ED, Oikonomakos NG, Leonidas DD. Halogen-substituted (C-β-d-glucopyranosyl)-hydroquinone regioisomers: Synthesis, enzymatic evaluation and their binding to glycogen phosphorylase. Bioorg Med Chem 2011; 19:5125-36. [DOI: 10.1016/j.bmc.2011.07.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Revised: 07/12/2011] [Accepted: 07/13/2011] [Indexed: 11/24/2022]
|
30
|
Alexacou KM, Tenchiu (Deleanu) AC, Chrysina ED, Charavgi MD, Kostas ID, Zographos SE, Oikonomakos NG, Leonidas DD. The binding of β-d-glucopyranosyl-thiosemicarbazone derivatives to glycogen phosphorylase: A new class of inhibitors. Bioorg Med Chem 2010; 18:7911-22. [PMID: 20947361 DOI: 10.1016/j.bmc.2010.09.039] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Revised: 09/09/2010] [Accepted: 09/16/2010] [Indexed: 11/24/2022]
|
31
|
Felföldi N, Tóth M, Chrysina ED, Charavgi MD, Alexacou KM, Somsák L. Synthesis of new glycosyl biuret and urea derivatives as potential glycoenzyme inhibitors. Carbohydr Res 2010; 345:208-13. [DOI: 10.1016/j.carres.2009.10.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2009] [Revised: 10/11/2009] [Accepted: 10/20/2009] [Indexed: 11/30/2022]
|
32
|
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] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
|
33
|
Somsák L, Czifrák K, Tóth M, Bokor E, Chrysina ED, Alexacou KM, Hayes JM, Tiraidis C, Lazoura E, Leonidas DD, Zographos SE, Oikonomakos NG. New inhibitors of glycogen phosphorylase as potential antidiabetic agents. Curr Med Chem 2009; 15:2933-83. [PMID: 19075645 DOI: 10.2174/092986708786848659] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The protein glycogen phosphorylase has been linked to type 2 diabetes, indicating the importance of this target to human health. Hence, the search for potent and selective inhibitors of this enzyme, which may lead to antihyperglycaemic drugs, has received particular attention. Glycogen phosphorylase is a typical allosteric protein with five different ligand binding sites, thus offering multiple opportunities for modulation of enzyme activity. The present survey is focused on recent new molecules, potential inhibitors of the enzyme. The biological activity can be modified by these molecules through direct binding, allosteric effects or other structural changes. Progress in our understanding of the mechanism of action of these inhibitors has been made by the determination of high-resolution enzyme inhibitor structures (both muscle and liver). The knowledge of the three-dimensional structures of protein-ligand complexes allows analysis of how the ligands interact with the target and has the potential to facilitate structure-based drug design. In this review, the synthesis, structure determination and computational studies of the most recent inhibitors of glycogen phosphorylase at the different binding sites are presented and analyzed.
Collapse
Affiliation(s)
- L Somsák
- Department of Organic Chemistry, University of Debrecen, POB 20, H-4010 Debrecen, Hungary.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Alexacou KM, Hayes JM, Tiraidis C, Zographos SE, Leonidas DD, Chrysina ED, Archontis G, Oikonomakos NG, Paul JV, Varghese B, Loganathan D. Crystallographic and computational studies on 4-phenyl-N-(β-D-glucopyranosyl)-1H-1,2,3-triazole-1-acetamide, an inhibitor of glycogen phosphorylase: Comparison with α-D-glucose, N-acetyl-β-D-glucopyranosylamine and N-benzoyl-N′-β-D-glucopyranosyl urea bin. Proteins 2007; 71:1307-23. [DOI: 10.1002/prot.21837] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
35
|
He L, Zhi Zhang Y, Tanoh M, Chen GR, Praly JP, Chrysina ED, Tiraidis C, Kosmopoulou M, Leonidas DD, Oikonomakos NG. In the Search of Glycogen Phosphorylase Inhibitors: Synthesis of C-D-Glycopyranosylbenzo(hydro)quinones – Inhibition of and Binding to Glycogen Phosphorylase in the Crystal. European J Org Chem 2007. [DOI: 10.1002/ejoc.200600548] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
36
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
Affiliation(s)
- Evangelia I Petsalakis
- Institute of Organic and Pharmaceutical Chemistry, The National Hellenic Research Foundation, 48, Vas. Constantinou Ave., 116 35 Athens, Greece
| | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Hadjiloi T, Tiraidis C, Chrysina ED, Leonidas DD, Oikonomakos NG, Tsipos P, Gimisis T. Binding of oxalyl derivatives of β-d-glucopyranosylamine to muscle glycogen phosphorylase b. Bioorg Med Chem 2006; 14:3872-82. [PMID: 16464598 DOI: 10.1016/j.bmc.2006.01.045] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2005] [Revised: 01/13/2006] [Accepted: 01/17/2006] [Indexed: 11/29/2022]
Abstract
Five oxalyl derivatives of beta-d-glucopyranosylamine were synthesized as potential inhibitors of glycogen phosphorylase (GP). The compounds 1-4 were competitive inhibitors of rabbit muscle GPb (with respect to alpha-d-glucose-1-phosphate) with K(i) values of 0.2-1.4 mM, while compound 5 was not effective up to a concentration of 10 mM. In order to elucidate the structural basis of their inhibition, we analysed the structures of compounds 1-4 in complex with GPb at 1.93-1.96 Angstrom resolution. The complex structures reveal that the inhibitors can be accommodated at the catalytic site at approximately the same position as alpha-d-glucose and stabilize the T-state conformation of the 280 s loop by making several favourable contacts to Asp283 and Asn284 of this loop. Comparison with the lead compound N-acetyl-beta-d-glucopyranosylamine (6) shows that the hydrogen bonding interaction of the amide nitrogen with the main-chain carbonyl oxygen of His377 is not present in these complexes. The differences observed in the K(i) values of the four 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 interactions, conformational entropy and desolvation effects.
Collapse
Affiliation(s)
- Theodoros Hadjiloi
- Institute of Organic and Pharmaceutical Chemistry, The National Hellenic Research Foundation, 48 Vas. Constantinou Ave., 11635 Athens, Greece
| | | | | | | | | | | | | |
Collapse
|
38
|
Archontis G, Watson KA, Xie Q, Andreou G, Chrysina ED, Zographos SE, Oikonomakos NG, Karplus M. Glycogen phosphorylase inhibitors: a free energy perturbation analysis of glucopyranose spirohydantoin analogues. Proteins 2006; 61:984-98. [PMID: 16245298 DOI: 10.1002/prot.20641] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
GP catalyzes the phosphorylation of glycogen to Glc-1-P. Because of its fundamental role in the metabolism of glycogen, GP has been the target for a systematic structure-assisted design of inhibitory compounds, which could be of value in the therapeutic treatment of type 2 diabetes mellitus. The most potent catalytic-site inhibitor of GP identified to date is spirohydantoin of glucopyranose (hydan). In this work, we employ MD free energy simulations to calculate the relative binding affinities for GP of hydan and two spirohydantoin analogues, methyl-hydan and n-hydan, in which a hydrogen atom is replaced by a methyl- or amino group, respectively. The results are compared with the experimental relative affinities of these ligands, estimated by kinetic measurements of the ligand inhibition constants. The calculated binding affinity for methyl-hydan (relative to hydan) is 3.75 +/- 1.4 kcal/mol, in excellent agreement with the experimental value (3.6 +/- 0.2 kcal/mol). For n-hydan, the calculated value is 1.0 +/- 1.1 kcal/mol, somewhat smaller than the experimental result (2.3 +/- 0.1 kcal/mol). A free energy decomposition analysis shows that hydan makes optimum interactions with protein residues and specific water molecules in the catalytic site. In the other two ligands, structural perturbations of the active site by the additional methyl- or amino group reduce the corresponding binding affinities. The computed binding free energies are sensitive to the preference of a specific water molecule for two well-defined positions in the catalytic site. The behavior of this water is analyzed in detail, and the free energy profile for the translocation of the water between the two positions is evaluated. The results provide insights into the role of water molecules in modulating ligand binding affinities. A comparison of the interactions between a set of ligands and their surrounding groups in X-ray structures is often used in the interpretation of binding free energy differences and in guiding the design of new ligands. For the systems in this work, such an approach fails to estimate the order of relative binding strengths, in contrast to the rigorous free energy treatment.
Collapse
Affiliation(s)
- G Archontis
- Department of Physics, University of Cyprus, Cyprus.
| | | | | | | | | | | | | | | |
Collapse
|
39
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
Affiliation(s)
- Kimberly A Watson
- Laboratory of Molecular Biophysics, University of Oxford, Oxford, United Kingdom
| | | | | | | | | | | | | |
Collapse
|
40
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
Affiliation(s)
- Eleni Anagnostou
- Institute of Organic and Pharmaceutical Chemistry, The National Hellenic Research Foundation, 48, Vas. Constantinou Ave. 116 35 Athens, Greece
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Oikonomakos NG, Kosmopoulou MN, Chrysina ED, Leonidas DD, Kostas ID, Wendt KU, Klabunde T, Defossa E. Crystallographic studies on acyl ureas, a new class of glycogen phosphorylase inhibitors, as potential antidiabetic drugs. Protein Sci 2005; 14:1760-71. [PMID: 15987904 PMCID: PMC2253349 DOI: 10.1110/ps.051432405] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Acyl ureas were discovered as a novel class of inhibitors for glycogen phosphorylase, a molecular target to control hyperglycemia in type 2 diabetics. This series is exemplified by 6-{2,6-Dichloro- 4-[3-(2-chloro-benzoyl)-ureido]-phenoxy}-hexanoic acid, which inhibits human liver glycogen phosphorylase a with an IC(50) of 2.0 microM. Here we analyze four crystal structures of acyl urea derivatives in complex with rabbit muscle glycogen phosphorylase b to elucidate the mechanism of inhibition of these inhibitors. The structures were determined and refined to 2.26 Angstroms resolution and demonstrate that the inhibitors bind at the allosteric activator site, where the physiological activator AMP binds. Acyl ureas induce conformational changes in the vicinity of the allosteric site. Our findings suggest that acyl ureas inhibit glycogen phosphorylase by direct inhibition of AMP binding and by indirect inhibition of substrate binding through stabilization of the T' state.
Collapse
Affiliation(s)
- Nikos G Oikonomakos
- Institute of Organic and Pharmaceutical Chemistry, The National Hellenic Research Foundation, Athens, Greece.
| | | | | | | | | | | | | | | |
Collapse
|
42
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
Affiliation(s)
- Evangelia D Chrysina
- Institute of Organic and Pharmaceutical Chemistry, The National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 116 35 Athens, Greece
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Chrysina ED, Kosmopoulou MN, Kardakaris R, Bischler N, Leonidas DD, Kannan T, Loganathan D, Oikonomakos NG. Binding of β-d-glucopyranosyl bismethoxyphosphoramidate to glycogen phosphorylase b: kinetic and crystallographic studies. Bioorg Med Chem 2005; 13:765-72. [PMID: 15653344 DOI: 10.1016/j.bmc.2004.10.040] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2004] [Accepted: 10/18/2004] [Indexed: 11/20/2022]
Abstract
In an attempt to identify a new lead molecule that would enable the design of inhibitors with enhanced affinity for glycogen phosphorylase (GP), beta-D-glucopyranosyl bismethoxyphosphoramidate (phosphoramidate), a glucosyl phosphate analogue, was tested for inhibition of the enzyme. Kinetic experiments showed that the compound was a weak competitive inhibitor of rabbit muscle GPb (with respect to alpha-D-glucose-1-phosphate (Glc-1-P)) with a Ki value of 5.9 (+/-0.1) mM. In order to elucidate the structural basis of inhibition, we determined the structure of GPb complexed with the phosphoramidate at 1.83 A resolution. The complex structure reveals that the inhibitor binds at the catalytic site and induces significant conformational changes in the vicinity of this site. In particular, the 280s loop (residues 282-287) shifts 0.4-4.3 A (main-chain atoms) to accommodate the phosphoramidate, but these conformational changes do not lead to increased contacts between the inhibitor and the protein that would improve ligand binding.
Collapse
Affiliation(s)
- Evangelia D Chrysina
- Institute of Organic and Pharmaceutical Chemistry, The National Hellenic Research Foundation, 48 Vassileos Constantinou Ave., 11635 Athens, Greece
| | | | | | | | | | | | | | | |
Collapse
|
44
|
Skouridou V, Chrysina ED, Stamatis H, Oikonomakos NG, Kolisis FN. Kinetic and modelling studies on the lipase catalysed enantioselective esterification of (±)-perillyl alcohol. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/j.molcatb.2004.02.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
45
|
Kosmopoulou MN, Leonidas DD, Chrysina ED, Bischler N, Eisenbrand G, Sakarellos CE, Pauptit R, Oikonomakos NG. Binding of the potential antitumour agent indirubin-5-sulphonate at the inhibitor site of rabbit muscle glycogen phosphorylase b. ACTA ACUST UNITED AC 2004; 271:2280-90. [PMID: 15153119 DOI: 10.1111/j.1432-1033.2004.04173.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The binding of indirubin-5-sulphonate (E226), a potential anti-tumour agent and a potent inhibitor (IC(50) = 35 nm) of cyclin-dependent kinase 2 (CDK2) and glycogen phosphorylase (GP) has been studied by kinetic and crystallographic methods. Kinetic analysis revealed that E226 is a moderate inhibitor of GPb (K(i) = 13.8 +/- 0.2 micro m) and GPa (K(i) = 57.8 +/- 7.1 micro m) and acts synergistically with glucose. To explore the molecular basis of E226 binding we have determined the crystal structure of the GPb/E226 complex at 2.3 A resolution. Structure analysis shows clearly that E226 binds at the purine inhibitor site, where caffeine and flavopiridol also bind [Oikonomakos, N.G., Schnier, J.B., Zographos, S.E., Skamnaki, V.T., Tsitsanou, K.E. & Johnson, L.N. (2000) J. Biol. Chem.275, 34566-34573], by intercalating between the two aromatic rings of Phe285 and Tyr613. The mode of binding of E226 to GPb is similar, but not identical, to that of caffeine and flavopiridol. Comparative structural analyses of the GPb-E226, GPb-caffeine and GPb-flavopiridol complex structures reveal the structural basis of the differences in the potencies of the three inhibitors and indicate binding residues in the inhibitor site that can be exploited to obtain more potent inhibitors. Structural comparison of the GPb-E226 complex structure with the active pCDK2-cyclin A-E226 complex structure clearly shows the different binding modes of the ligand to GPb and CDK2; the more extensive interactions of E226 with the active site of CDK2 may explain its higher affinity towards the latter enzyme.
Collapse
Affiliation(s)
- Magda N Kosmopoulou
- Institute of Organic and Pharmaceutical Chemistry, The National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, 11635 Athens, Greece
| | | | | | | | | | | | | | | |
Collapse
|
46
|
Leonidas DD, Chavali GB, Oikonomakos NG, Chrysina ED, Kosmopoulou MN, Vlassi M, Frankling C, Acharya KR. High-resolution crystal structures of ribonuclease A complexed with adenylic and uridylic nucleotide inhibitors. Implications for structure-based design of ribonucleolytic inhibitors. Protein Sci 2003; 12:2559-74. [PMID: 14573867 PMCID: PMC2366950 DOI: 10.1110/ps.03196603] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The crystal structures of bovine pancreatic ribonuclease A (RNase A) in complex with 3',5'-ADP, 2',5'-ADP, 5'-ADP, U-2'-p and U-3'-p have been determined at high resolution. The structures reveal that each inhibitor binds differently in the RNase A active site by anchoring a phosphate group in subsite P1. The most potent inhibitor of all five, 5'-ADP (Ki = 1.2 microM), adopts a syn conformation (in contrast to 3',5'-ADP and 2',5'-ADP, which adopt an anti), and it is the beta- rather than the alpha-phosphate group that binds to P1. 3',5'-ADP binds with the 5'-phosphate group in P1 and the adenosine in the B2 pocket. Two different binding modes are observed in the two RNase A molecules of the asymmetric unit for 2',5'-ADP. This inhibitor binds with either the 3' or the 5' phosphate groups in subsite P1, and in each case, the adenosine binds in two different positions within the B2 subsite. The two uridilyl inhibitors bind similarly with the uridine moiety in the B1 subsite but the placement of a different phosphate group in P1 (2' versus 3') has significant implications on their potency against RNase A. Comparative structural analysis of the RNase A, eosinophil-derived neurotoxin (EDN), eosinophil cationic protein (ECP), and human angiogenin (Ang) complexes with these and other phosphonucleotide inhibitors provides a wealth of information for structure-based design of inhibitors specific for each RNase. These inhibitors could be developed to therapeutic agents that could control the biological activities of EDN, ECP, and ANG, which play key roles in human pathologies.
Collapse
Affiliation(s)
- Demetres D Leonidas
- Institute of Organic and Pharmaceutical Chemistry, The National Hellenic Research Foundation, 11635 Athens, Greece.
| | | | | | | | | | | | | | | |
Collapse
|
47
|
Pinotsis N, Leonidas DD, Chrysina ED, Oikonomakos NG, Mavridis IM. The binding of beta- and gamma-cyclodextrins to glycogen phosphorylase b: kinetic and crystallographic studies. Protein Sci 2003; 12:1914-24. [PMID: 12930991 PMCID: PMC2323989 DOI: 10.1110/ps.03149503] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A number of regulatory binding sites of glycogen phosphorylase (GP), such as the catalytic, the inhibitor, and the new allosteric sites are currently under investigation as targets for inhibition of hepatic glycogenolysis under high glucose concentrations; in some cases specific inhibitors are under evaluation in human clinical trials for therapeutic intervention in type 2 diabetes. In an attempt to investigate whether the storage site can be exploited as target for modulating hepatic glucose production, alpha-, beta-, and gamma-cyclodextrins were identified as moderate mixed-type competitive inhibitors of GPb (with respect to glycogen) with K(i) values of 47.1, 14.1, and 7.4 mM, respectively. To elucidate the structural basis of inhibition, we determined the structure of GPb complexed with beta- and gamma-cyclodextrins at 1.94 A and 2.3 A resolution, respectively. The structures of the two complexes reveal that the inhibitors can be accommodated in the glycogen storage site of T-state GPb with very little change of the tertiary structure and provide a basis for understanding their potency and subsite specificity. Structural comparisons of the two complexes with GPb in complex with either maltopentaose (G5) or maltoheptaose (G7) show that beta- and gamma-cyclodextrins bind in a mode analogous to the G5 and G7 binding with only some differences imposed by their cyclic conformations. It appears that the binding energy for stabilization of enzyme complexes derives from hydrogen bonding and van der Waals contacts to protein residues. The binding of alpha-cyclodextrin and octakis (2,3,6-tri-O-methyl)-gamma-cyclodextrin was also investigated, but none of them was bound in the crystal; moreover, the latter did not inhibit the phosphorylase reaction.
Collapse
Affiliation(s)
- Nikos Pinotsis
- Institute of Physical Chemistry, National Center for Scientific Research "Demokritos," Athens, Greece
| | | | | | | | | |
Collapse
|
48
|
Oikonomakos NG, Chrysina ED, Kosmopoulou MN, Leonidas DD. Crystal structure of rabbit muscle glycogen phosphorylase a in complex with a potential hypoglycaemic drug at 2.0 A resolution. Biochim Biophys Acta 2003; 1647:325-32. [PMID: 12686153 DOI: 10.1016/s1570-9639(03)00085-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
CP320626 has been identified as a potent inhibitor, synergistic with glucose, of human liver glycogen phosphorylase a (LGPa), a possible target for type 2 diabetes therapy. CP320626 is also a potent inhibitor of human muscle GPa. In order to elucidate the structural basis of the mechanism of CP320626 inhibition, the structures of T state rabbit muscle GPa (MGPa) in complex with glucose and in complex with both glucose and CP320626 were determined at 2.0 A resolution, and refined to crystallographic R values of 0.179 (R(free)=0.218) and 0.207 (R(free)=0.235), respectively. CP320626 binds at the new allosteric site, some 33 A from the catalytic site, where glucose binds. The binding of CP320626 to MGPa does not promote extensive conformational changes except for small shifts of the side chain atoms of residues R60, V64, and K191. Both CP320626 and glucose promote the less active T state, while structural comparisons of MGPa-glucose-CP320626 complex with LGPa complexed with a related compound (CP403700) and a glucose analogue inhibitor indicate that the residues of the new allosteric site, conserved in the two isozymes, show no significant differences in their positions.
Collapse
Affiliation(s)
- Nikos G Oikonomakos
- Institute of Biological Research and Biotechnology, The National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, Athens 11635, Greece.
| | | | | | | |
Collapse
|
49
|
Leonidas DD, Swamy BM, Bhat AG, Inamdar SR, Kosmopoulou MN, Chrysina ED, Oikonomakos NG. Crystallization and preliminary X-ray crystallographic analysis of Sclerotium rolfsii lectin. Acta Crystallogr D Biol Crystallogr 2003; 59:363-5. [PMID: 12554954 DOI: 10.1107/s0907444902021121] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2002] [Accepted: 11/18/2002] [Indexed: 11/10/2022]
Abstract
Sclerotium rolfsii lectin (SRL), from the soil-borne phytopathogenic fungus S. rolfsii, has been crystallized. SRL crystals were grown by the hanging-drop vapour-diffusion method using an MPD-ammonium acetate mixture in Tris-HCl buffer pH 8.5. A complete data set from a single crystal at 100 K was collected to 1.1 A resolution using synchrotron radiation. Preliminary crystallographic analysis showed that the crystals belong to the tetragonal space group P4(2)2(1)2, with unit-cell parameters a = b = 99.81, c = 63.99 A and two molecules per asymmetric unit.
Collapse
Affiliation(s)
- Demetres D Leonidas
- Institute of Biological Research and Biotechnology, The National Hellenic Research Foundation, 48 Vas. Constantinou Ave, 11635 Athens, Greece.
| | | | | | | | | | | | | |
Collapse
|
50
|
Cook A, Lowe ED, Chrysina ED, Skamnaki VT, Oikonomakos NG, Johnson LN. Structural studies on phospho-CDK2/cyclin A bound to nitrate, a transition state analogue: implications for the protein kinase mechanism. Biochemistry 2002; 41:7301-11. [PMID: 12044161 DOI: 10.1021/bi0201724] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Eukaryotic protein kinases catalyze the phosphoryl transfer of the gamma-phosphate of ATP to the serine, threonine, or tyrosine residue of protein substrates. The catalytic mechanism of phospho-CDK2/cyclin A (pCDK2/cyclin A) has been probed with structural and kinetic studies using the trigonal NO(3)(-) ion, which can be viewed as a mimic of the metaphosphate transition state. The crystal structure of pCDK2/cyclin A in complex with Mg(2+)ADP, nitrate, and a heptapeptide substrate has been determined at 2.7 A. The nitrate ion is located between the beta-phosphate of ADP and the hydroxyl group of the serine residue of the substrate. In one molecule of the asymmetric unit, the nitrate is close to the beta-phosphate of ADP (distance from the nitrate nitrogen to the nearest beta-phosphate oxygen of 2.5 A), while in the other subunit, the nitrate is closer to the substrate serine (distance of 2.1 A). Kinetic studies demonstrate that nitrate is not an effective inhibitor of protein kinases, consistent with the structural results that show the nitrate ion makes few stabilizing interactions with CDK2 at the catalytic site. The binding of orthovanadate was also investigated as a mimic of a pentavalent phosphorane intermediate of an associative mechanism for phosphoryl transfer. No vanadate was observed bound in a 3.4 A resolution structure of pCDK2/cyclin A in the presence of Mg(2+)ADP, and vanadate did not inhibit the kinase reaction. The results support the notion that the protein kinase reaction proceeds through a mostly dissociative mechanism with a trigonal planar metaphosphate intermediate rather than an associative mechanism that involves a pentavalent phosphorane intermediate.
Collapse
Affiliation(s)
- A Cook
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, Rex Richards Building, South Parks Road, Oxford OX1 3QU, U.K
| | | | | | | | | | | |
Collapse
|