1
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Mpakali A, Barla I, Lu L, Ramesh KM, Thomaidis N, Stern LJ, Giastas P, Stratikos E. Mechanisms of Allosteric Inhibition of Insulin-Regulated Aminopeptidase. J Mol Biol 2024; 436:168449. [PMID: 38244767 DOI: 10.1016/j.jmb.2024.168449] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 01/12/2024] [Accepted: 01/14/2024] [Indexed: 01/22/2024]
Abstract
Inhibition of Insulin-Regulated Aminopeptidase is being actively explored for the treatment of several human diseases and several classes of inhibitors have been developed although no clinical applications have been reported yet. Here, we combine enzymological analysis with x-ray crystallography to investigate the mechanism employed by two of the most studied inhibitors of IRAP, an aryl sulfonamide and a 2-amino-4H-benzopyran named HFI-419. Although both compounds have been hypothesized to target the enzyme's active site by competitive mechanisms, we discovered that they instead target previously unidentified proximal allosteric sites and utilize non-competitive inhibition mechanisms. X-ray crystallographic analysis demonstrated that the aryl sulfonamide stabilizes the closed, more active, conformation of the enzyme whereas HFI-419 locks the enzyme in a semi-open, and likely less active, conformation. HFI-419 potency is substrate-dependent and fails to effectively block the degradation of the physiological substrate cyclic peptide oxytocin. Our findings demonstrate alternative mechanisms for inhibiting IRAP through allosteric sites and conformational restricting and suggest that the pharmacology of HFI-419 may be more complicated than initially considered. Such conformation-specific interactions between IRAP and small molecules can be exploited for the design of more effective second-generation allosteric inhibitors.
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Affiliation(s)
- Anastasia Mpakali
- Laboratory of Biochemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens 15771, Greece; National Centre for Scientific Research Demokritos, Athens 15341, Greece
| | - Ioanna Barla
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens 15771, Greece
| | - Liying Lu
- Department of Pathology, UMass Chan Medical School, Worcester, MA 01650, USA
| | - Karthik M Ramesh
- Department of Pathology, UMass Chan Medical School, Worcester, MA 01650, USA
| | - Nikolaos Thomaidis
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens 15771, Greece
| | - Lawrence J Stern
- Department of Pathology, UMass Chan Medical School, Worcester, MA 01650, USA
| | - Petros Giastas
- Department of Biotechnology, School of Applied Biology & Biotechnology, Agricultural University of Athens, Athens 11855, Greece
| | - Efstratios Stratikos
- Laboratory of Biochemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens 15771, Greece; National Centre for Scientific Research Demokritos, Athens 15341, Greece.
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2
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Camberlein V, Fléau C, Sierocki P, Li L, Gealageas R, Bosc D, Guillaume V, Warenghem S, Leroux F, Rosell M, Cheng K, Medve L, Prigent M, Decanter M, Piveteau C, Biela A, Eveque M, Dumont J, Mpakali A, Giastas P, Herledan A, Couturier C, Haupenthal J, Lesire L, Hirsch AKH, Deprez B, Stratikos E, Bouvier M, Deprez‐Poulain R. Discovery of the First Selective Nanomolar Inhibitors of ERAP2 by Kinetic Target-Guided Synthesis. Angew Chem Int Ed Engl 2022; 61:e202203560. [PMID: 35904863 PMCID: PMC9558494 DOI: 10.1002/anie.202203560] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Indexed: 01/07/2023]
Abstract
Endoplasmic reticulum aminopeptidase 2 (ERAP2) is a key enzyme involved in the trimming of antigenic peptides presented by Major Histocompatibility Complex class I. It is a target of growing interest for the treatment of autoimmune diseases and in cancer immunotherapy. However, the discovery of potent and selective ERAP2 inhibitors is highly challenging. Herein, we have used kinetic target-guided synthesis (KTGS) to identify such inhibitors. Co-crystallization experiments revealed the binding mode of three different inhibitors with increasing potency and selectivity over related enzymes. Selected analogues engage ERAP2 in cells and inhibit antigen presentation in a cellular context. 4 d (BDM88951) displays favorable in vitro ADME properties and in vivo exposure. In summary, KTGS allowed the discovery of the first nanomolar and selective highly promising ERAP2 inhibitors that pave the way of the exploration of the biological roles of this enzyme and provide lead compounds for drug discovery efforts.
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Affiliation(s)
- Virgyl Camberlein
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems3 rue du Pr Laguesse59000LilleFrance,European Genomic Institute for Diabetes, EGID, Pôle Recherche1 place de Verdun59045Lille CedexFrance
| | - Charlotte Fléau
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems3 rue du Pr Laguesse59000LilleFrance,European Genomic Institute for Diabetes, EGID, Pôle Recherche1 place de Verdun59045Lille CedexFrance
| | - Pierre Sierocki
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems3 rue du Pr Laguesse59000LilleFrance,European Genomic Institute for Diabetes, EGID, Pôle Recherche1 place de Verdun59045Lille CedexFrance
| | - Lenong Li
- Department of Microbiology and ImmunologyUniversity of Illinois at Chicago909 S Wolcott AvenueChicagoIL 60612USA
| | - Ronan Gealageas
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems3 rue du Pr Laguesse59000LilleFrance,European Genomic Institute for Diabetes, EGID, Pôle Recherche1 place de Verdun59045Lille CedexFrance
| | - Damien Bosc
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems3 rue du Pr Laguesse59000LilleFrance,European Genomic Institute for Diabetes, EGID, Pôle Recherche1 place de Verdun59045Lille CedexFrance
| | - Valentin Guillaume
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems3 rue du Pr Laguesse59000LilleFrance,European Genomic Institute for Diabetes, EGID, Pôle Recherche1 place de Verdun59045Lille CedexFrance
| | - Sandrine Warenghem
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems3 rue du Pr Laguesse59000LilleFrance,European Genomic Institute for Diabetes, EGID, Pôle Recherche1 place de Verdun59045Lille CedexFrance
| | - Florence Leroux
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems3 rue du Pr Laguesse59000LilleFrance,European Genomic Institute for Diabetes, EGID, Pôle Recherche1 place de Verdun59045Lille CedexFrance
| | - Melissa Rosell
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems3 rue du Pr Laguesse59000LilleFrance,European Genomic Institute for Diabetes, EGID, Pôle Recherche1 place de Verdun59045Lille CedexFrance
| | - Keguang Cheng
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems3 rue du Pr Laguesse59000LilleFrance,European Genomic Institute for Diabetes, EGID, Pôle Recherche1 place de Verdun59045Lille CedexFrance
| | - Laura Medve
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems3 rue du Pr Laguesse59000LilleFrance,European Genomic Institute for Diabetes, EGID, Pôle Recherche1 place de Verdun59045Lille CedexFrance
| | - Mathilde Prigent
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems3 rue du Pr Laguesse59000LilleFrance,European Genomic Institute for Diabetes, EGID, Pôle Recherche1 place de Verdun59045Lille CedexFrance
| | - Myriam Decanter
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems3 rue du Pr Laguesse59000LilleFrance,European Genomic Institute for Diabetes, EGID, Pôle Recherche1 place de Verdun59045Lille CedexFrance
| | - Catherine Piveteau
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems3 rue du Pr Laguesse59000LilleFrance,European Genomic Institute for Diabetes, EGID, Pôle Recherche1 place de Verdun59045Lille CedexFrance
| | - Alexandre Biela
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems3 rue du Pr Laguesse59000LilleFrance,European Genomic Institute for Diabetes, EGID, Pôle Recherche1 place de Verdun59045Lille CedexFrance
| | - Maxime Eveque
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems3 rue du Pr Laguesse59000LilleFrance,European Genomic Institute for Diabetes, EGID, Pôle Recherche1 place de Verdun59045Lille CedexFrance
| | - Julie Dumont
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems3 rue du Pr Laguesse59000LilleFrance,European Genomic Institute for Diabetes, EGID, Pôle Recherche1 place de Verdun59045Lille CedexFrance
| | - Anastasia Mpakali
- National Center for Scientific Research DemokritosAgia Paraskevi15341Greece
| | - Petros Giastas
- National Center for Scientific Research DemokritosAgia Paraskevi15341Greece
| | - Adrien Herledan
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems3 rue du Pr Laguesse59000LilleFrance,European Genomic Institute for Diabetes, EGID, Pôle Recherche1 place de Verdun59045Lille CedexFrance
| | - Cyril Couturier
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems3 rue du Pr Laguesse59000LilleFrance,European Genomic Institute for Diabetes, EGID, Pôle Recherche1 place de Verdun59045Lille CedexFrance
| | - Jörg Haupenthal
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI)Campus E8 166123SaarbrückenGermany
| | - Laetitia Lesire
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems3 rue du Pr Laguesse59000LilleFrance,European Genomic Institute for Diabetes, EGID, Pôle Recherche1 place de Verdun59045Lille CedexFrance
| | - Anna K. H. Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI)Campus E8 166123SaarbrückenGermany,Department for Pharmacy, Saarland UniversityCampus E8 166123SaarbrückenGermany
| | - Benoit Deprez
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems3 rue du Pr Laguesse59000LilleFrance,European Genomic Institute for Diabetes, EGID, Pôle Recherche1 place de Verdun59045Lille CedexFrance
| | - Efstratios Stratikos
- National Center for Scientific Research DemokritosAgia Paraskevi15341Greece,Laboratory of BiochemistryDepartment of ChemistryNational and Kapodistrian University of AthensPanepistimiopolisZographou15784Greece
| | - Marlene Bouvier
- Department of Microbiology and ImmunologyUniversity of Illinois at Chicago909 S Wolcott AvenueChicagoIL 60612USA
| | - Rebecca Deprez‐Poulain
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems3 rue du Pr Laguesse59000LilleFrance,European Genomic Institute for Diabetes, EGID, Pôle Recherche1 place de Verdun59045Lille CedexFrance
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3
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Zouridakis M, Papakyriakou A, Ivanov IA, Kasheverov IE, Tsetlin V, Tzartos S, Giastas P. Corrigendum: Crystal structure of the monomeric extracellular domain of α9 nicotinic receptor subunit in complex with α-conotoxin RgIA: Molecular dynamics insights into RgIA binding to α9α10 nicotinic receptors. Front Pharmacol 2022; 13:980202. [PMID: 36091796 PMCID: PMC9455631 DOI: 10.3389/fphar.2022.980202] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 07/28/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Marios Zouridakis
- Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece
- *Correspondence: Marios Zouridakis, ; Petros Giastas,
| | | | - Igor A. Ivanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Igor E. Kasheverov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Victor Tsetlin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- PhysBio of MEPhI, Moscow, Russia
| | - Socrates Tzartos
- Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece
- Department of Pharmacy, University of Patras, Patras, Greece
| | - Petros Giastas
- Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece
- *Correspondence: Marios Zouridakis, ; Petros Giastas,
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4
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Camberlein V, Fleau-Tabey C, Sierocki P, Li L, Gealageas R, Bosc D, Guillaume V, Warenghem S, Leroux F, Rosell M, Cheng K, Medve L, Prigent M, Decanter M, Piveteau C, Biela A, Eveque M, Dumont J, Mpakali A, Giastas P, Herledan A, Couturier C, Haupenthal J, Lesire L, Hirsch AK, Deprez B, Stratikos E, Bouvier M, Deprez-Poulain R. Discovery of the First Selective Nanomolar Inhibitors of Endoplasmic Reticulum Aminopeptidase 2 by Kinetic Target‐Guided Synthesis. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203560] [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: 11/12/2022]
Affiliation(s)
- Virgyl Camberlein
- University of Lille: Universite de Lille M2SV: Drugs and molecules for living systems Lille FRANCE
| | - Charlotte Fleau-Tabey
- University of Lille: Universite de Lille M2SV: Drugs and Molecules for Living systems Lille FRANCE
| | - Pierre Sierocki
- University of Lille: Universite de Lille M2SV: Drugs and Molecules for Living Systems LILLE FRANCE
| | - Lenong Li
- University of Illinois at Chicago Microbiology and Immunology chicago UNITED STATES
| | - Ronan Gealageas
- University of Lille: Universite de Lille M2SV: Drugs and molecules for Living Systems Lille FRANCE
| | - Damien Bosc
- University of Lille: Universite de Lille M2SV: Drugs and Molecules for Living Systems Lille FRANCE
| | - Valentin Guillaume
- Institut Pasteur de Lille M2SV: Drugs and molecules for Living Systems Lille FRANCE
| | - Sandrine Warenghem
- Institut Pasteur de Lille M2SV: Drugs and Molecules for Living Systems Lille FRANCE
| | - Florence Leroux
- INSERM U1177 Drugs and Molecules for Living Systems M2SV Drugs and Moelcules for Living Systems Lille FRANCE
| | - Melissa Rosell
- Universite de Lille M2SV: Drugs and molecules for living systems Lille FRANCE
| | - Keguang Cheng
- University of Lille: Universite de Lille M2SV: Drugs and molecules for Living systems Lille FRANCE
| | - Laura Medve
- Institut Pasteur de Lille M2SV: Drugs and Molecules for Living systems Lille FRANCE
| | - Mathilde Prigent
- Pasteur Institute Lille: Institut Pasteur de Lille M2SV: Drugs and Molecules for Living Systems FRANCE
| | - Myriam Decanter
- Pasteur Institute Lille: Institut Pasteur de Lille M2SV: Drugs and Molecules for Living Systems FRANCE
| | - Catherine Piveteau
- University of Lille: Universite de Lille M2SV: Drugs and molecules for living systems Lille FRANCE
| | - Alexandre Biela
- Institut Pasteur de Lille M2SV: Drugs and Molecules for Living Systems Lille FRANCE
| | - Maxime Eveque
- University of Lille: Universite de Lille M2SV: Drugs and Molecules for Living Systems Lille FRANCE
| | - Julie Dumont
- University of Lille: Universite de Lille M2SV: Drugs and Molecules for Living Systems Lille FRANCE
| | - Anastasia Mpakali
- National Centre for Scientific Research-Demokritos: Ethniko Kentro Ereunas Physikon Epistemon Demokritos Protein Chemistry laboratory Athens GREECE
| | - Petros Giastas
- NCSR Demokritos: Ethniko Kentro Ereunas Physikon Epistemon Demokritos Protein Chemistry laboratory Athens GREECE
| | - Adrien Herledan
- INSERM U1177 Drugs and Molecules for Living Systems M2SV: Drugs and Moelcules for Living systems Lille FRANCE
| | - Cyril Couturier
- University of Lille: Universite de Lille M2SV: Drugs and Molecules for Living Systems Lille FRANCE
| | - Jörg Haupenthal
- Helmholtz-Institut fur Pharmazeutische Forschung Saarland HIPS Saarbrücken GERMANY
| | - Laetitia Lesire
- Institut Pasteur de Lille M2SV: Drugs and Molecules for Living Systems Lille FRANCE
| | - Anna K Hirsch
- Helmholtz-Institut fur Pharmazeutische Forschung Saarland HIPS Saarbrücken GERMANY
| | - Benoit Deprez
- University of Lille: Universite de Lille M2SV: Drugs and Molecules for Living Systems Lille FRANCE
| | - Efstratios Stratikos
- National and Kapodistrian University of Athens: Ethniko kai Kapodistriako Panepistemio Athenon biochemistry Athens GREECE
| | - Marlene Bouvier
- University of Illinois at Chicago Microbiology and Immunology Chicago UNITED STATES
| | - Rebecca Deprez-Poulain
- University of Lille: Universite de Lille U1177 M2SV Drugs and molecules for Living systems 3 rue du Pr Laguesse 59000 LILLE FRANCE
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5
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Vourloumis D, Mavridis I, Athanasoulis A, Temponeras I, Koumantou D, Giastas P, Mpakali A, Magrioti V, Leib J, van Endert P, Stratikos E, Papakyriakou A. Discovery of Selective Nanomolar Inhibitors for Insulin-Regulated Aminopeptidase Based on α-Hydroxy-β-amino Acid Derivatives of Bestatin. J Med Chem 2022; 65:10098-10117. [PMID: 35833347 DOI: 10.1021/acs.jmedchem.2c00904] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The oxytocinase subfamily of M1 zinc aminopeptidases comprises emerging drug targets, including the ER-resident aminopeptidases 1 and 2 (ERAP1 and ERAP2) and insulin-regulated aminopeptidase (IRAP); however, reports on clinically relevant inhibitors are limited. Here we report a new synthetic approach of high diastereo- and regioselectivity for functionalization of the α-hydroxy-β-amino acid scaffold of bestatin. Stereochemistry and mechanism of inhibition were investigated by a high-resolution X-ray crystal structure of ERAP1 in complex with a micromolar inhibitor. By exploring the P1 side-chain functionalities, we achieve significant potency and selectivity, and we report a cell-active, low-nanomolar inhibitor of IRAP with >120-fold selectivity over homologous enzymes. X-ray crystallographic analysis of IRAP in complex with this inhibitor suggest that interactions with the GAMEN loop is an unappreciated key determinant for potency and selectivity. Overall, our results suggest that α-hydroxy-β-amino acid derivatives may constitute useful chemical tools and drug leads for this group of aminopeptidases.
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Affiliation(s)
- Dionisios Vourloumis
- National Centre for Scientific Research "Demokritos", Ag. Paraskevi, GR-15341 Athens, Greece
| | - Ioannis Mavridis
- National Centre for Scientific Research "Demokritos", Ag. Paraskevi, GR-15341 Athens, Greece
| | - Alexandros Athanasoulis
- National Centre for Scientific Research "Demokritos", Ag. Paraskevi, GR-15341 Athens, Greece
| | - Ioannis Temponeras
- National Centre for Scientific Research "Demokritos", Ag. Paraskevi, GR-15341 Athens, Greece.,Department of Pharmacy, University of Patras, 26504 Patra, Greece
| | - Despoina Koumantou
- National Centre for Scientific Research "Demokritos", Ag. Paraskevi, GR-15341 Athens, Greece
| | - Petros Giastas
- Department of Biotechnology, Agricultural University of Athens, GR-11855 Athens, Greece
| | - Anastasia Mpakali
- National Centre for Scientific Research "Demokritos", Ag. Paraskevi, GR-15341 Athens, Greece.,Department of Chemistry, National and Kapodistrian University of Athens, GR-15784 Athens, Greece
| | - Victoria Magrioti
- Department of Chemistry, National and Kapodistrian University of Athens, GR-15784 Athens, Greece
| | - Jacqueline Leib
- Université Paris Cité, INSERM, CNRS, Institut Necker Enfants Malades, F-75015 Paris, France
| | - Peter van Endert
- Université Paris Cité, INSERM, CNRS, Institut Necker Enfants Malades, F-75015 Paris, France.,Service Immunologie Biologique, AP-HP, Hôpital Universitaire Necker-Enfants Malades, F-75015 Paris, France
| | - Efstratios Stratikos
- National Centre for Scientific Research "Demokritos", Ag. Paraskevi, GR-15341 Athens, Greece.,Department of Chemistry, National and Kapodistrian University of Athens, GR-15784 Athens, Greece
| | - Athanasios Papakyriakou
- National Centre for Scientific Research "Demokritos", Ag. Paraskevi, GR-15341 Athens, Greece
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6
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Mpakali A, Georgiadis D, Stratikos E, Giastas P. Inhibitor-Dependent Usage of the S1' Specificity Pocket of ER Aminopeptidase 2. ACS Med Chem Lett 2022; 13:218-224. [PMID: 35178178 PMCID: PMC8842112 DOI: 10.1021/acsmedchemlett.1c00582] [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: 10/22/2021] [Accepted: 01/10/2022] [Indexed: 01/16/2023] Open
Abstract
Endoplasmic reticulum aminopeptidase 2 (ERAP2) is an intracellular enzyme involved in the processing of antigenic peptides intended for presentation by major histocompatibility complex class I (MHCI) molecules. Because of its role in regulating immune responses, ERAP2 is an emerging pharmacological target. Phosphinic pseudopeptides are potent transition-state analogue inhibitors of ERAP2. Previous structure-activity studies have revealed a complex but ambiguous relationship between the occupation of putative specificity pockets and the inhibitor efficacy. To address these problems, we solved crystal structures of ERAP2 in complex with two phosphinic pseudotripeptide inhibitors. Both compounds are found in the catalytic site in a canonical orientation for transition-state analogues and utilize the S1 and S2' pockets in a similar fashion. Strikingly, their P1' side chains exhibit different orientations and make interactions with distinct shallow pockets near the ERAP2 active site. These structures suggest that S1' pocket usage in ERAP2 may be inhibitor-dependent and constitute useful starting templates for the further optimization of this class of compounds.
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Affiliation(s)
- Anastasia Mpakali
- National
Centre for Scientific Research Demokritos, Agia Paraskevi, Athens 15341, Greece,
| | - Dimitris Georgiadis
- Laboratory
of Organic Chemistry, Chemistry Department, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, Athens 15771, Greece
| | - Efstratios Stratikos
- National
Centre for Scientific Research Demokritos, Agia Paraskevi, Athens 15341, Greece,Laboratory
of Biochemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, Athens 15771 Greece
| | - Petros Giastas
- Department
of Neurobiology, Hellenic Pasteur Institute, Athens 11521, Greece,Department
of Biotechnology, School of Applied Biology & Biotechnology, Agricultural University of Athens, Athens 11855, Greece,
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7
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Chiniadis L, Giastas P, Bratsos I, Papakyriakou A. Insights into the Protein Ruthenation Mechanism by Antimetastatic Metallodrugs: High-Resolution X-ray Structures of the Adduct Formed between Hen Egg-White Lysozyme and NAMI-A at Various Time Points. Inorg Chem 2021; 60:10729-10737. [PMID: 34197115 DOI: 10.1021/acs.inorgchem.1c01441] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The pharmacological profile of medicinally relevant Ru(III) coordination compounds has been ascribed to their interactions with proteins, as several studies have provided evidence that DNA is not the primary target. In this regard, numerous spectroscopic and crystallographic studies have indicated that the Ru(III) ligands play an important role in determining the metal binding site, acting as the recognition element in the early stages of the protein-complex formation. Herein, we present a series of near-atomic-resolution X-ray crystal structures of the adducts formed between the antimetastatic metallodrug imidazolium trans-[tetrachlorido(S-dimethyl sufoxide)(1H-imidazole)ruthenate(III)] (NAMI-A) and hen egg-white lysozyme (HEWL). These structures elucidate a series of binding events starting from the noncovalent interaction of intact NAMI-A ions with HEWL (1.5 h), followed by the stepwise exchange of all Ru ligands except for 1H-imidazole (26 h) to the final "ruthenated" protein comprising one aquated Ru ion coordinated to histidine-15 of HEWL (98 h). Our structural data clearly support a two-step mechanism of protein ruthenation, illustrating the ligand-mediated recognition step of the process.
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Affiliation(s)
| | - Petros Giastas
- Department of Neurobiology, Hellenic Pasteur Institute, 11521 Athens, Greece.,Department of Biotechnology, School of Applied Biology & Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
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8
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Mpakali A, Saridakis E, Giastas P, Maben Z, Stern LJ, Larhed M, Hallberg M, Stratikos E. Structural Basis of Inhibition of Insulin-Regulated Aminopeptidase by a Macrocyclic Peptidic Inhibitor. ACS Med Chem Lett 2020; 11:1429-1434. [PMID: 32676150 PMCID: PMC7357224 DOI: 10.1021/acsmedchemlett.0c00172] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 06/02/2020] [Indexed: 12/15/2022] Open
Abstract
Insulin-regulated aminopeptidase (IRAP) is a transmembrane zinc metallopeptidase with many important biological functions and an emerging pharmacological target. Although previous structural studies have given insight on how IRAP recognizes linear peptides, how it recognizes its physiological cyclic ligands remains elusive. Here, we report the first crystal structure of IRAP with the macrocyclic peptide inhibitor HA08 that combines structural elements from angiotensin IV and the physiological substrates oxytocin and vasopressin. The compound is found in the catalytic site in a near canonical substrate-like configuration and inhibits by a competitive mechanism. Comparison with previously solved structures of IRAP along with small-angle X-ray scattering experiments suggests that IRAP is in an open conformation in solution but undergoes a closing conformational change upon inhibitor binding. Stabilization of the closed conformation in combination with catalytic water exclusion by the tightly juxtaposed GAMEN loop is proposed as a mechanism of inhibition.
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Affiliation(s)
- Anastasia Mpakali
- National
Center for Scientific Research Demokritos, Agia Paraskevi, Athens 15341, Greece
| | - Emmanuel Saridakis
- National
Center for Scientific Research Demokritos, Agia Paraskevi, Athens 15341, Greece
| | - Petros Giastas
- National
Center for Scientific Research Demokritos, Agia Paraskevi, Athens 15341, Greece
| | - Zachary Maben
- Department
of Pathology, University of Massachusetts
Medical School, Worcester, Massachusetts 01655, United States
| | - Lawrence J. Stern
- Department
of Pathology, University of Massachusetts
Medical School, Worcester, Massachusetts 01655, United States
| | - Mats Larhed
- Department
of Medicinal Chemistry, Science for Life Laboratory, BMC, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden
| | - Mathias Hallberg
- The
Beijer Laboratory, Division of Biological Research on Drug Dependence,
Department of Pharmaceutical Biosciences, BMC, Uppsala University, P.O. Box 591, SE-751 24 Uppsala, Sweden
| | - Efstratios Stratikos
- National
Center for Scientific Research Demokritos, Agia Paraskevi, Athens 15341, Greece
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9
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Giastas P, Neu M, Rowland P, Stratikos E. High-Resolution Crystal Structure of Endoplasmic Reticulum Aminopeptidase 1 with Bound Phosphinic Transition-State Analogue Inhibitor. ACS Med Chem Lett 2019; 10:708-713. [PMID: 31097987 PMCID: PMC6511960 DOI: 10.1021/acsmedchemlett.9b00002] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 02/13/2019] [Indexed: 01/25/2023] Open
Abstract
Endoplasmic reticulum aminopeptidase 1 (ERAP1) is an intracellular enzyme that helps generate peptides presented by Major Histocompatibility Complex Class I (MHC class I) molecules and is an emerging target for immunotherapy applications. Despite almost two decades of research on ERAP1, lack of high-resolution crystal structures has hampered drug-development efforts. By optimizing the protein construct, we obtained a high-resolution (1.60 Å) crystal structure of the closed-conformation of ERAP1 with a potent phosphinic pseudopeptide inhibitor bound in its active site. The structure provides key insight on the mechanism of inhibition as well as selectivity toward homologous enzymes and allows detailed mapping of the internal cavity of the enzyme that accommodates peptide-substrates. Bis-tris propane and malic acid molecules, found bound in pockets in the internal cavity, reveal potential druggable secondary binding sites. The ability to obtain high-resolution crystal structures of ERAP1 removes a major bottleneck in the development of compounds that regulate its activity and will greatly accelerate drug-discovery efforts.
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Affiliation(s)
- Petros Giastas
- National Center for Scientific Research Demokritos, Agia
Paraskevi, Athens 15310, Greece
| | - Margarete Neu
- Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Paul Rowland
- Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Efstratios Stratikos
- National Center for Scientific Research Demokritos, Agia
Paraskevi, Athens 15310, Greece
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10
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Zouridakis M, Papakyriakou A, Ivanov IA, Kasheverov IE, Tsetlin V, Tzartos S, Giastas P. Crystal Structure of the Monomeric Extracellular Domain of α9 Nicotinic Receptor Subunit in Complex With α-Conotoxin RgIA: Molecular Dynamics Insights Into RgIA Binding to α9α10 Nicotinic Receptors. Front Pharmacol 2019; 10:474. [PMID: 31118896 PMCID: PMC6504684 DOI: 10.3389/fphar.2019.00474] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [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: 11/15/2018] [Accepted: 04/15/2019] [Indexed: 12/20/2022] Open
Abstract
The α9 subunit of nicotinic acetylcholine receptors (nAChRs) exists mainly in heteropentameric assemblies with α10. Accumulating data indicate the presence of three different binding sites in α9α10 nAChRs: the α9(+)/α9(−), the α9(+)/α10(−), and the α10(+)/α9(−). The major role of the principal (+) side of the extracellular domain (ECD) of α9 subunit in binding of the antagonists methyllylcaconitine and α-bungarotoxin was shown previously by the crystal structures of the monomeric α9-ECD with these molecules. Here we present the 2.26-Å resolution crystal structure of α9-ECD in complex with α-conotoxin (α-Ctx) RgIA, a potential drug for chronic pain, the first structure reported for a complex between an nAChR domain and an α-Ctx. Superposition of this structure with those of other α-Ctxs bound to the homologous pentameric acetylcholine binding proteins revealed significant similarities in the orientation of bound conotoxins, despite the monomeric state of the α9-ECD. In addition, ligand-binding studies calculated a binding affinity of RgIA to the α9-ECD at the low micromolar range. Given the high identity between α9 and α10 ECDs, particularly at their (+) sides, the presented structure was used as template for molecular dynamics simulations of the ECDs of the human α9α10 nAChR in pentameric assemblies. Our results support a favorable binding of RgIA at α9(+)/α9(−) or α10(+)/α9(−) rather than the α9(+)/α10(−) interface, in accordance with previous mutational and functional data.
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Affiliation(s)
- Marios Zouridakis
- Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece
| | | | - Igor A Ivanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Igor E Kasheverov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Victor Tsetlin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,PhysBio of MEPhI, Moscow, Russia
| | - Socrates Tzartos
- Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece.,Department of Pharmacy, University of Patras, Patras, Greece
| | - Petros Giastas
- Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece
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11
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Andreou A, Giastas P, Arnaouteli S, Tzanodaskalaki M, Tzartos SJ, Bethanis K, Bouriotis V, Eliopoulos EE. The putative polysaccharide deacetylase Ba0331: cloning, expression, crystallization and structure determination. Acta Crystallogr F Struct Biol Commun 2019; 75:312-320. [PMID: 30950833 DOI: 10.1107/s2053230x19001766] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 01/30/2019] [Indexed: 11/10/2022]
Abstract
Ba0331 is a putative polysaccharide deacetylase from Bacillus anthracis, the etiological agent of the disease anthrax, that contributes to adaptation of the bacterium under extreme conditions and to maintenance of the cell shape. In the present study, the crystal structure of Ba0331 was determined at 2.6 Å resolution. The structure consists of two domains: a fibronectin type 3-like (Fn3-like) domain and a NodB catalytic domain. The latter is present in all carbohydrate esterase family 4 enzymes, while a comparative analysis of the Fn3-like domain revealed structural plasticity despite the retention of the conserved Fn3-like domain characteristics.
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Affiliation(s)
- Athena Andreou
- Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Petros Giastas
- Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Sofia Arnaouteli
- Department of Biology, Enzyme Biotechnology Group, University of Crete, Vasilika Vouton, 70013 Heraklion, Crete, Greece
| | - Mary Tzanodaskalaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Hellas N. Plastira 100, 70013 Heraklion, Crete, Greece
| | - Socrates J Tzartos
- Department of Neurobiology, Hellenic Pasteur Institute, Vasilissis Sofias 127, 11521 Athens, Greece
| | - Kostas Bethanis
- Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Vassilis Bouriotis
- Department of Biology, Enzyme Biotechnology Group, University of Crete, Vasilika Vouton, 70013 Heraklion, Crete, Greece
| | - Elias E Eliopoulos
- Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
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12
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Andreou A, Giastas P, Christoforides E, Eliopoulos EE. Structural and Evolutionary Insights within the Polysaccharide Deacetylase Gene Family of Bacillus anthracis and Bacillus cereus. Genes (Basel) 2018; 9:E386. [PMID: 30065210 PMCID: PMC6115787 DOI: 10.3390/genes9080386] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [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: 05/31/2018] [Revised: 07/24/2018] [Accepted: 07/25/2018] [Indexed: 02/06/2023] Open
Abstract
Functional and folding constraints impose interdependence between interacting sites along the protein chain that are envisaged through protein sequence evolution. Studying the influence of structure in phylogenetic models requires detailed and reliable structural models. Polysaccharide deacetylases (PDAs), members of the carbohydrate esterase family 4, perform mainly metal-dependent deacetylation of O- or N-acetylated polysaccharides such as peptidoglycan, chitin and acetylxylan through a conserved catalytic core termed the NodB homology domain. Genomes of Bacillus anthracis and its relative Bacillus cereus contain multiple genes of putative or known PDAs. A comparison of the functional domains of the recently determined PDAs from B. anthracis and B. cereus and multiple amino acid and nucleotide sequence alignments and phylogenetic analysis performed on these closely related species showed that there were distinct differences in binding site formation, despite the high conservation on the protein sequence, the folding level and the active site assembly. This may indicate that, subject to biochemical verification, the binding site-forming sequence fragments are under functionally driven evolutionary pressure to accommodate and recognize distinct polysaccharide residues according to cell location, use, or environment. Finally, we discuss the suggestion of the paralogous nature of at least two genes of B. anthracis, ba0330 and ba0331, via specific differences in gene sequence, protein structure, selection pressure and available localization patterns. This study may contribute to understanding the mechanisms under which sequences evolve in their structures and how evolutionary processes enable structural variations.
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Affiliation(s)
- Athena Andreou
- Department of Biotechnology, Laboratory of Genetics, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece.
| | - Petros Giastas
- Department of Neurobiology, Hellenic Pasteur Institute, Vasilissis Sofias 127, 11521 Athens, Greece.
| | - Elias Christoforides
- Department of Biotechnology, Laboratory of Genetics, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece.
| | - Elias E Eliopoulos
- Department of Biotechnology, Laboratory of Genetics, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece.
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13
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Giastas P, Andreou A, Papakyriakou A, Koutsioulis D, Balomenou S, Tzartos SJ, Bouriotis V, Eliopoulos EE. Structures of the Peptidoglycan N-Acetylglucosamine Deacetylase Bc1974 and Its Complexes with Zinc Metalloenzyme Inhibitors. Biochemistry 2018; 57:753-763. [PMID: 29257674 DOI: 10.1021/acs.biochem.7b00919] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The cell wall peptidoglycan is recognized as a primary target of the innate immune system, and usually its disintegration results in bacterial lysis. Bacillus cereus, a close relative of the highly virulent Bacillus anthracis, contains 10 polysaccharide deacetylases. Among these, the peptidoglycan N-acetylglucosamine deacetylase Bc1974 is the highest homologue to the Bacillus anthracis Ba1977 that is required for full virulence and is involved in resistance to the host's lysozyme. These metalloenzymes belong to the carbohydrate esterase family 4 (CE4) and are attractive targets for the development of new anti-infective agents. Herein we report the first X-ray crystal structures of the NodB domain of Bc1974, the conserved catalytic core of CE4s, in the unliganded form and in complex with four known metalloenzyme inhibitors and two amino acid hydroxamates that target the active site metal. These structures revealed the presence of two conformational states of a catalytic loop known as motif-4 (MT4), which were not observed previously for peptidoglycan deacetylases, but were recently shown in the structure of a Vibrio clolerae chitin deacetylase. By employing molecular docking of a substrate model, we describe a catalytic mechanism that probably involves initial binding of the substrate in a receptive, more open state of MT4 and optimal catalytic activity in the closed state of MT4, consistent with the previous observations. The ligand-bound structures presented here, in addition to the five Bc1974 inhibitors identified, provide a valuable basis for the design of antibacterial agents that target the peptidoglycan deacetylase Ba1977.
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Affiliation(s)
- Petros Giastas
- Department of Biotechnology, Laboratory of Genetics, Agricultural University of Athens , Iera Odos 75, 11855 Athens, Greece.,Department of Neurobiology, Hellenic Pasteur Institute , Vasilissis Sofias 127, 11521 Athens, Greece
| | - Athena Andreou
- Department of Biotechnology, Laboratory of Genetics, Agricultural University of Athens , Iera Odos 75, 11855 Athens, Greece
| | - Athanasios Papakyriakou
- Department of Biotechnology, Laboratory of Genetics, Agricultural University of Athens , Iera Odos 75, 11855 Athens, Greece.,Institute of Biosciences and Applications, NCSR "Demokritos" , 15310 Aghia Paraskevi, Athens, Greece
| | - Dimitris Koutsioulis
- Institute of Molecular Biology and Biotechnology, FORTH , 70013 Heraklion, Crete, Greece
| | - Stavroula Balomenou
- Institute of Molecular Biology and Biotechnology, FORTH , 70013 Heraklion, Crete, Greece.,Department of Biology, Enzyme Biotechnology Group, University of Crete , Vasilika Vouton, 70013 Heraklion, Crete, Greece
| | - Socrates J Tzartos
- Department of Neurobiology, Hellenic Pasteur Institute , Vasilissis Sofias 127, 11521 Athens, Greece
| | - Vassilis Bouriotis
- Institute of Molecular Biology and Biotechnology, FORTH , 70013 Heraklion, Crete, Greece.,Department of Biology, Enzyme Biotechnology Group, University of Crete , Vasilika Vouton, 70013 Heraklion, Crete, Greece
| | - Elias E Eliopoulos
- Department of Biotechnology, Laboratory of Genetics, Agricultural University of Athens , Iera Odos 75, 11855 Athens, Greece
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14
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Chatziefthimiou SD, Inclán M, Giastas P, Papakyriakou A, Yannakopoulou K, Mavridis IM. Molecular recognition of N-acetyltryptophan enantiomers by β-cyclodextrin. Beilstein J Org Chem 2017; 13:1572-1582. [PMID: 28904606 PMCID: PMC5564276 DOI: 10.3762/bjoc.13.157] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [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: 02/14/2017] [Accepted: 07/18/2017] [Indexed: 01/08/2023] Open
Abstract
The enantioselectivity of β-cyclodextrin (β-CD) towards L- and D-N-acetyltryptophan (NAcTrp) has been studied in aqueous solution and the crystalline state. NMR studies in solution show that β-CD forms complexes of very similar but not identical geometry with both L- and D-NAcTrp and exhibits stronger binding with L-NAcTrp. In the crystalline state, only β-CD–L-NAcTrp crystallizes readily from aqueous solutions as a dimeric complex (two hosts enclosing two guest molecules). In contrast, crystals of the complex β-CD–D-NAcTrp were never obtained, although numerous conditions were tried. In aqueous solution, the orientation of the guest in both complexes is different than in the β-CD–L-NAcTrp complex in the crystal. Overall, the study shows that subtle differences observed between the β-CD–L,D-NAcTrp complexes in aqueous solution are magnified at the onset of crystallization, as a consequence of accumulation of many soft host–guest interactions and of the imposed crystallographic order, thus resulting in very dissimilar propensity of each enantiomer to produce crystals with β-CD.
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Affiliation(s)
- Spyros D Chatziefthimiou
- Institute of Nanoscience & Nanotechnology, National Center for Scientific Research "Demokritos", Patriarchou Gregoriou E' & Neapoleos 27, 15310 Aghia Paraskevi Attikis, Greece
| | - Mario Inclán
- Institute of Nanoscience & Nanotechnology, National Center for Scientific Research "Demokritos", Patriarchou Gregoriou E' & Neapoleos 27, 15310 Aghia Paraskevi Attikis, Greece
| | - Petros Giastas
- Institute of Nanoscience & Nanotechnology, National Center for Scientific Research "Demokritos", Patriarchou Gregoriou E' & Neapoleos 27, 15310 Aghia Paraskevi Attikis, Greece
| | - Athanasios Papakyriakou
- Institute of Nanoscience & Nanotechnology, National Center for Scientific Research "Demokritos", Patriarchou Gregoriou E' & Neapoleos 27, 15310 Aghia Paraskevi Attikis, Greece
| | - Konstantina Yannakopoulou
- Institute of Nanoscience & Nanotechnology, National Center for Scientific Research "Demokritos", Patriarchou Gregoriou E' & Neapoleos 27, 15310 Aghia Paraskevi Attikis, Greece
| | - Irene M Mavridis
- Institute of Nanoscience & Nanotechnology, National Center for Scientific Research "Demokritos", Patriarchou Gregoriou E' & Neapoleos 27, 15310 Aghia Paraskevi Attikis, Greece
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15
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Giastas P, Zouridakis M, Tzartos SJ. Understanding structure-function relationships of the human neuronal acetylcholine receptor: insights from the first crystal structures of neuronal subunits. Br J Pharmacol 2017; 175:1880-1891. [PMID: 28452148 DOI: 10.1111/bph.13838] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 04/13/2017] [Accepted: 04/20/2017] [Indexed: 01/27/2023] Open
Abstract
Nicotinic ACh receptors (nAChRs) are the best studied members of the superfamily of pentameric ligand-gated ion channels (pLGICs). Neuronal nAChRs regulate neuronal excitability and neurotransmitter release in the nervous system and form either homo- or hetero-pentameric complexes with various combinations of the 11 neuronal nAChR subunits (α2-7, α9, α10 and β2-4) known to exist in humans. In addition to their wide distribution in the nervous system, neuronal nAChRs have been also found in immune cells and many peripheral tissues. These nAChRs are important drug targets for neurological and neuropsychiatric diseases (e.g. Alzheimer's, schizophrenia) and substance addiction (e.g. nicotine), as well as in a variety of diseases such as chronic pain, auditory disorders and some cancers. To decipher the functional mechanisms of human nAChRs and develop efficient and specific therapeutic drugs, elucidation of their high-resolution structures is needed. Recent studies, including the X-ray crystal structures of the near-intact α4β2 nAChR and of the ligand-binding domains of the α9 and α2 subunits, have advanced our knowledge on the detailed structure of the ligand-binding sites formed between the same and different subunits and revealed many other functionally important interactions. The aim of this review is to highlight some of the structural and functional findings of these studies and to compare them with recent breakthrough findings on other pLGIC members and earlier data from their homologous ACh-binding proteins. LINKED ARTICLES This article is part of a themed section on Nicotinic Acetylcholine Receptors. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v175.11/issuetoc.
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Affiliation(s)
- Petros Giastas
- Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece
| | - Marios Zouridakis
- Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece
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16
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Mpakali A, Saridakis E, Harlos K, Zhao Y, Kokkala P, Georgiadis D, Giastas P, Papakyriakou A, Stratikos E. Ligand-Induced Conformational Change of Insulin-Regulated Aminopeptidase: Insights on Catalytic Mechanism and Active Site Plasticity. J Med Chem 2017; 60:2963-2972. [PMID: 28328206 DOI: 10.1021/acs.jmedchem.6b01890] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Insulin-regulated aminopeptidase (IRAP) is an enzyme with several important biological functions that is known to process a large variety of different peptidic substrates, although the mechanism behind this wide specificity is not clearly understood. We describe a crystal structure of IRAP in complex with a recently developed bioactive and selective inhibitor at 2.53 Å resolution. In the presence of this inhibitor, the enzyme adopts a novel conformation in which domains II and IV are juxtaposed, forming a hollow structure that excludes external solvent access to the catalytic center. A loop adjacent to the enzyme's GAMEN motif undergoes structural reconfiguration, allowing the accommodation of bulky inhibitor side chains. Atomic interactions between the inhibitor and IRAP that are unique to this conformation can explain the strong selectivity compared to homologous aminopeptidases ERAP1 and ERAP2. This conformation provides insight on IRAP's catalytic cycle and reveals significant active-site plasticity that may underlie its substrate permissiveness.
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Affiliation(s)
- Anastasia Mpakali
- National Center for Scientific Research Demokritos, Agia Paraskevi , Athens 15310, Greece
| | - Emmanuel Saridakis
- National Center for Scientific Research Demokritos, Agia Paraskevi , Athens 15310, Greece
| | - Karl Harlos
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Oxford University , Oxford OX3 7BN, United Kingdom
| | - Yuguang Zhao
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Oxford University , Oxford OX3 7BN, United Kingdom
| | - Paraskevi Kokkala
- Department of Chemistry, University of Athens , Athens 15771, Greece
| | | | - Petros Giastas
- National Center for Scientific Research Demokritos, Agia Paraskevi , Athens 15310, Greece
| | | | - Efstratios Stratikos
- National Center for Scientific Research Demokritos, Agia Paraskevi , Athens 15310, Greece
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17
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Mpakali A, Giastas P, Deprez-Poulain R, Papakyriakou A, Koumantou D, Gealageas R, Tsoukalidou S, Vourloumis D, Mavridis IM, Stratikos E, Saridakis E. Crystal Structures of ERAP2 Complexed with Inhibitors Reveal Pharmacophore Requirements for Optimizing Inhibitor Potency. ACS Med Chem Lett 2017; 8:333-337. [PMID: 28337326 DOI: 10.1021/acsmedchemlett.6b00505] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [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: 12/14/2016] [Accepted: 02/21/2017] [Indexed: 11/29/2022] Open
Abstract
Endoplasmic reticulum aminopeptidase 2 assists with the generation of antigenic peptides for presentation onto Major Histocompatibility Class I molecules in humans. Recent evidence has suggested that the activity of ERAP2 may contribute to the generation of autoimmunity, thus making ERAP2 a possible pharmacological target for the regulation of adaptive immune responses. To better understand the structural elements of inhibitors that govern their binding affinity to the ERAP2 active site, we cocrystallized ERAP2 with a medium activity 3,4-diaminobenzoic acid inhibitor and a poorly active hydroxamic acid derivative. Comparison of these two crystal structures with a previously solved structure of ERAP2 in complex with a potent phosphinic pseudopeptide inhibitor suggests that engaging the substrate N-terminus recognition properties of the active site is crucial for inhibitor binding even in the absence of a potent zinc-binding group. Proper utilization of all five major pharmacophores is necessary, however, to optimize inhibitor potency.
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Affiliation(s)
- Anastasia Mpakali
- National Center for Scientific Research Demokritos, Agia Paraskevi, GR-15310 Athens, Greece
| | - Petros Giastas
- National Center for Scientific Research Demokritos, Agia Paraskevi, GR-15310 Athens, Greece
| | - Rebecca Deprez-Poulain
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177−Drugs & Molecules for Living Systems, F-59000 Lille, France
| | | | - Despoina Koumantou
- National Center for Scientific Research Demokritos, Agia Paraskevi, GR-15310 Athens, Greece
| | - Ronan Gealageas
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177−Drugs & Molecules for Living Systems, F-59000 Lille, France
| | - Sofia Tsoukalidou
- National Center for Scientific Research Demokritos, Agia Paraskevi, GR-15310 Athens, Greece
| | - Dionisios Vourloumis
- National Center for Scientific Research Demokritos, Agia Paraskevi, GR-15310 Athens, Greece
| | - Irene M. Mavridis
- National Center for Scientific Research Demokritos, Agia Paraskevi, GR-15310 Athens, Greece
| | - Efstratios Stratikos
- National Center for Scientific Research Demokritos, Agia Paraskevi, GR-15310 Athens, Greece
| | - Emmanuel Saridakis
- National Center for Scientific Research Demokritos, Agia Paraskevi, GR-15310 Athens, Greece
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18
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Kaloudi-Chantzea A, Martinou E, Seintis K, Karakostas N, Giastas P, Pitterl F, Oberacher H, Fakis M, Pistolis G. Formation of a highly-ordered rigid multichromophoric 3D supramolecular network by combining ionic and coordination-driven self-assembly. Chem Commun (Camb) 2016; 52:3388-91. [DOI: 10.1039/c5cc10335e] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A highly-ordered supramolecular network for energy transfer and polarization switching.
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Affiliation(s)
| | - Elisabeth Martinou
- NCSR “Demokritos” Institute of Nanoscience and Nanotechnology
- 153 10 Athens
- Greece
| | - Kostas Seintis
- Department of Physics
- University of Patras
- 26500 Patras
- Greece
| | - Nikolaos Karakostas
- NCSR “Demokritos” Institute of Nanoscience and Nanotechnology
- 153 10 Athens
- Greece
| | | | - Florian Pitterl
- Inst. of Legal Medicine and Core Facility Metabolomics
- Medical Univ. of Innsbruck
- 6020 Innsbruck
- Austria
| | - Herbert Oberacher
- Inst. of Legal Medicine and Core Facility Metabolomics
- Medical Univ. of Innsbruck
- 6020 Innsbruck
- Austria
| | - Mihalis Fakis
- Department of Physics
- University of Patras
- 26500 Patras
- Greece
| | - George Pistolis
- NCSR “Demokritos” Institute of Nanoscience and Nanotechnology
- 153 10 Athens
- Greece
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19
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Mpakali A, Giastas P, Mathioudakis N, Mavridis IM, Saridakis E, Stratikos E. Structural Basis for Antigenic Peptide Recognition and Processing by Endoplasmic Reticulum (ER) Aminopeptidase 2. J Biol Chem 2015; 290:26021-32. [PMID: 26381406 DOI: 10.1074/jbc.m115.685909] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [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: 08/17/2015] [Indexed: 01/26/2023] Open
Abstract
Endoplasmic reticulum (ER) aminopeptidases process antigenic peptide precursors to generate epitopes for presentation by MHC class I molecules and help shape the antigenic peptide repertoire and cytotoxic T-cell responses. To perform this function, ER aminopeptidases have to recognize and process a vast variety of peptide sequences. To understand how these enzymes recognize substrates, we determined crystal structures of ER aminopeptidase 2 (ERAP2) in complex with a substrate analogue and a peptidic product to 2.5 and 2.7 Å, respectively, and compared them to the apo-form structure determined to 3.0 Å. The peptides were found within the internal cavity of the enzyme with no direct access to the outside solvent. The substrate analogue extends away from the catalytic center toward the distal end of the internal cavity, making interactions with several shallow pockets along the path. A similar configuration was evident for the peptidic product, although decreasing electron density toward its C terminus indicated progressive disorder. Enzymatic analysis confirmed that visualized interactions can either positively or negatively impact in vitro trimming rates. Opportunistic side-chain interactions and lack of deep specificity pockets support a limited-selectivity model for antigenic peptide processing by ERAP2. In contrast to proposed models for the homologous ERAP1, no specific recognition of the peptide C terminus by ERAP2 was evident, consistent with functional differences in length selection and self-activation between these two enzymes. Our results suggest that ERAP2 selects substrates by sequestering them in its internal cavity and allowing opportunistic interactions to determine trimming rates, thus combining substrate permissiveness with sequence bias.
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Affiliation(s)
- Anastasia Mpakali
- From the National Center for Scientific Research Demokritos, Agia Paraskevi, Athens 15310, Greece
| | - Petros Giastas
- From the National Center for Scientific Research Demokritos, Agia Paraskevi, Athens 15310, Greece
| | - Nikolas Mathioudakis
- From the National Center for Scientific Research Demokritos, Agia Paraskevi, Athens 15310, Greece
| | - Irene M Mavridis
- From the National Center for Scientific Research Demokritos, Agia Paraskevi, Athens 15310, Greece
| | - Emmanuel Saridakis
- From the National Center for Scientific Research Demokritos, Agia Paraskevi, Athens 15310, Greece
| | - Efstratios Stratikos
- From the National Center for Scientific Research Demokritos, Agia Paraskevi, Athens 15310, Greece
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Arnaouteli S, Giastas P, Andreou A, Tzanodaskalaki M, Aldridge C, Tzartos SJ, Vollmer W, Eliopoulos E, Bouriotis V. Two Putative Polysaccharide Deacetylases Are Required for Osmotic Stability and Cell Shape Maintenance in Bacillus anthracis. J Biol Chem 2015; 290:13465-78. [PMID: 25825488 PMCID: PMC4505593 DOI: 10.1074/jbc.m115.640029] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [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: 01/25/2015] [Indexed: 11/26/2022] Open
Abstract
Membrane-anchored lipoproteins have a broad range of functions and play key roles in several cellular processes in Gram-positive bacteria. BA0330 and BA0331 are the only lipoproteins among the 11 known or putative polysaccharide deacetylases of Bacillus anthracis. We found that both lipoproteins exhibit unique characteristics. BA0330 and BA0331 interact with peptidoglycan, and BA0330 is important for the adaptation of the bacterium to grow in the presence of a high concentration of salt, whereas BA0331 contributes to the maintenance of a uniform cell shape. They appear not to alter the peptidoglycan structure and do not contribute to lysozyme resistance. The high resolution x-ray structure of BA0330 revealed a C-terminal domain with the typical fold of a carbohydrate esterase 4 and an N-terminal domain unique for this family, composed of a two-layered (4 + 3) β-sandwich with structural similarity to fibronectin type 3 domains. Our data suggest that BA0330 and BA0331 have a structural role in stabilizing the cell wall of B. anthracis.
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Affiliation(s)
- Sofia Arnaouteli
- From the Department of Biology, Enzyme Biotechnology Group, University of Crete, Vasilika Vouton, 70013 Heraklion, Crete, Greece
| | - Petros Giastas
- the Department of Neurobiology, Hellenic Pasteur Institute, Vasilissis Sofias 127, 11521 Athens, Greece
| | - Athina Andreou
- the Department of Biotechnology, Laboratory of Genetics, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Mary Tzanodaskalaki
- the Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece
| | - Christine Aldridge
- the Institute for Cell and Molecular Biosciences, Centre for Bacterial Cell Biology, Newcastle University, NE2 4AX Newcastle upon Tyne, United Kingdom, and
| | - Socrates J Tzartos
- the Department of Neurobiology, Hellenic Pasteur Institute, Vasilissis Sofias 127, 11521 Athens, Greece, the Department of Pharmacy, University of Patras, 26504, Patras, Greece
| | - Waldemar Vollmer
- the Institute for Cell and Molecular Biosciences, Centre for Bacterial Cell Biology, Newcastle University, NE2 4AX Newcastle upon Tyne, United Kingdom, and
| | - Elias Eliopoulos
- the Department of Biotechnology, Laboratory of Genetics, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Vassilis Bouriotis
- From the Department of Biology, Enzyme Biotechnology Group, University of Crete, Vasilika Vouton, 70013 Heraklion, Crete, Greece, the Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece,
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Azam L, Papakyriakou A, Zouridakis M, Giastas P, Tzartos SJ, McIntosh JM. Molecular interaction of α-conotoxin RgIA with the rat α9α10 nicotinic acetylcholine receptor. Mol Pharmacol 2015; 87:855-64. [PMID: 25740413 DOI: 10.1124/mol.114.096511] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The α9α10 nicotinic acetylcholine receptor (nAChR) was first identified in the auditory system, where it mediates synaptic transmission between efferent olivocochlear cholinergic fibers and cochlea hair cells. This receptor gained further attention due to its potential role in chronic pain and breast and lung cancers. We previously showed that α-conotoxin (α-CTx) RgIA, one of the few α9α10 selective ligands identified to date, is 300-fold less potent on human versus rat α9α10 nAChR. This species difference was conferred by only one residue in the (-), rather than (+), binding region of the α9 subunit. In light of this unexpected discovery, we sought to determine other interacting residues with α-CTx RgIA. A previous molecular modeling study, based on the structure of the homologous molluscan acetylcholine-binding protein, predicted that RgIA interacts with three residues on the α9(+) face and two residues on the α10(-) face of the α9α10 nAChR. However, mutations of these residues had little or no effect on toxin block of the α9α10 nAChR. In contrast, mutations of homologous residues in the opposing nAChR subunits (α10 Ε197, P200 and α9 T61, D121) resulted in 19- to 1700-fold loss of toxin activity. Based on the crystal structure of the extracellular domain (ECD) of human α9 nAChR, we modeled the rat α9α10 ECD and its complexes with α-CTx RgIA and acetylcholine. Our data support the interaction of α-CTx RgIA at the α10/α9 rather than the α9/α10 nAChR subunit interface, and may facilitate the development of selective ligands with therapeutic potential.
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Affiliation(s)
- Layla Azam
- Departments of Biology (L.A., J.M.M.) and Psychiatry (J.M.M.), University of Utah, Salt Lake City, Utah; George E. Wahlen Veterans Affair Medical Center, Salt Lake City, Utah (J.M.M.); National Center for Scientific Research "Demokritos," Athens, Greece (A.P.); and Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece (M.Z., P.G., S.J.T.)
| | - Athanasios Papakyriakou
- Departments of Biology (L.A., J.M.M.) and Psychiatry (J.M.M.), University of Utah, Salt Lake City, Utah; George E. Wahlen Veterans Affair Medical Center, Salt Lake City, Utah (J.M.M.); National Center for Scientific Research "Demokritos," Athens, Greece (A.P.); and Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece (M.Z., P.G., S.J.T.)
| | - Marios Zouridakis
- Departments of Biology (L.A., J.M.M.) and Psychiatry (J.M.M.), University of Utah, Salt Lake City, Utah; George E. Wahlen Veterans Affair Medical Center, Salt Lake City, Utah (J.M.M.); National Center for Scientific Research "Demokritos," Athens, Greece (A.P.); and Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece (M.Z., P.G., S.J.T.)
| | - Petros Giastas
- Departments of Biology (L.A., J.M.M.) and Psychiatry (J.M.M.), University of Utah, Salt Lake City, Utah; George E. Wahlen Veterans Affair Medical Center, Salt Lake City, Utah (J.M.M.); National Center for Scientific Research "Demokritos," Athens, Greece (A.P.); and Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece (M.Z., P.G., S.J.T.)
| | - Socrates J Tzartos
- Departments of Biology (L.A., J.M.M.) and Psychiatry (J.M.M.), University of Utah, Salt Lake City, Utah; George E. Wahlen Veterans Affair Medical Center, Salt Lake City, Utah (J.M.M.); National Center for Scientific Research "Demokritos," Athens, Greece (A.P.); and Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece (M.Z., P.G., S.J.T.)
| | - J Michael McIntosh
- Departments of Biology (L.A., J.M.M.) and Psychiatry (J.M.M.), University of Utah, Salt Lake City, Utah; George E. Wahlen Veterans Affair Medical Center, Salt Lake City, Utah (J.M.M.); National Center for Scientific Research "Demokritos," Athens, Greece (A.P.); and Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece (M.Z., P.G., S.J.T.)
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Zouridakis M, Giastas P, Zarkadas E, Chroni-Tzartou D, Bregestovski P, Tzartos SJ. Crystal structures of free and antagonist-bound states of human α9 nicotinic receptor extracellular domain. Nat Struct Mol Biol 2014; 21:976-80. [PMID: 25282151 DOI: 10.1038/nsmb.2900] [Citation(s) in RCA: 77] [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] [Received: 10/12/2013] [Accepted: 09/09/2014] [Indexed: 01/06/2023]
Abstract
We determined the X-ray crystal structures of the extracellular domain (ECD) of the monomeric state of human neuronal α9 nicotinic acetylcholine receptor (nAChR) and of its complexes with the antagonists methyllycaconitine and α-bungarotoxin at resolutions of 1.8 Å, 1.7 Å and 2.7 Å, respectively. The structure of the monomeric α9 ECD superimposed well with the structures of homologous proteins in pentameric assemblies, denoting native folding, despite the absence of a complementary subunit and transmembrane domain. The interaction motifs of both antagonists were similar to those in the complexes with homologous pentameric proteins, thus highlighting the major contribution of the principal side of α9 ECD to their binding. The structures revealed a functionally important β7-β10 strand interaction in α9-containing nAChRs, involving their unique Thr147, a hydration pocket similar to that of mouse α1 ECD and a membrane-facing network coordinated by the invariant Arg210.
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Affiliation(s)
- Marios Zouridakis
- Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece
| | - Petros Giastas
- Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece
| | - Eleftherios Zarkadas
- 1] Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece. [2] Department of Pharmacy, University of Patras, Rio, Greece
| | | | - Piotr Bregestovski
- INSERM UMR1106, Brain Dynamics Institute, University Aix-Marseille, Marseille, France
| | - Socrates J Tzartos
- 1] Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece. [2] Department of Pharmacy, University of Patras, Rio, Greece
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Lazaridis K, Zisimopoulou P, Giastas P, Bitzopoulou K, Evangelakou P, Sideri A, Tzartos SJ. Expression of human AChR extracellular domain mutants with improved characteristics. Int J Biol Macromol 2014; 63:210-7. [DOI: 10.1016/j.ijbiomac.2013.11.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 11/07/2013] [Accepted: 11/10/2013] [Indexed: 10/26/2022]
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Grigoropoulos A, Maganas D, Symeonidis D, Giastas P, Cowley AR, Kyritsis P, Pneumatikakis G. Synthesis of Chalcogenidoimidodiphosphinato–Rh
I
Complexes and DFT Investigation of Their Catalytic Activation in Olefin Hydroformylation. Eur J Inorg Chem 2012. [DOI: 10.1002/ejic.201200921] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Alexios Grigoropoulos
- Inorganic Chemistry Laboratory, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis 15771, Athens, Greece, Fax: +30‐210‐7274782, http://www.chem.uoa.gr/
| | - Dimitrios Maganas
- Inorganic Chemistry Laboratory, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis 15771, Athens, Greece, Fax: +30‐210‐7274782, http://www.chem.uoa.gr/
- Max‐Planck Institute for Chemical Energy Conversion, 45470 Mülheim an der Ruhr, Germany
| | - Dimitrios Symeonidis
- Inorganic Chemistry Laboratory, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis 15771, Athens, Greece, Fax: +30‐210‐7274782, http://www.chem.uoa.gr/
| | - Petros Giastas
- Laboratory of Structural and Supramolecular Chemistry, NCSR “Demokritos”, Agia Paraskevi 15310, Athens, Greece
| | - Andrew R. Cowley
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Panayotis Kyritsis
- Inorganic Chemistry Laboratory, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis 15771, Athens, Greece, Fax: +30‐210‐7274782, http://www.chem.uoa.gr/
| | - Georgios Pneumatikakis
- Inorganic Chemistry Laboratory, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis 15771, Athens, Greece, Fax: +30‐210‐7274782, http://www.chem.uoa.gr/
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Evnouchidou I, Birtley J, Seregin S, Papakyriakou A, Zervoudi E, Samiotaki M, Panayotou G, Giastas P, Petrakis O, Georgiadis D, Amalfitano A, Saridakis E, Mavridis IM, Stratikos E. A common single nucleotide polymorphism in endoplasmic reticulum aminopeptidase 2 induces a specificity switch that leads to altered antigen processing. J Immunol 2012; 189:2383-92. [PMID: 22837489 DOI: 10.4049/jimmunol.1200918] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Endoplasmic reticulum aminopeptidases 1 and 2 (ERAP1 and ERAP2) cooperate to trim antigenic peptide precursors for loading onto MHC class I molecules and help regulate the adaptive immune response. Common coding single nucleotide polymorphisms in ERAP1 and ERAP2 have been linked with predisposition to human diseases ranging from viral and bacterial infections to autoimmunity and cancer. It has been hypothesized that altered Ag processing by these enzymes is a causal link to disease etiology, but the molecular mechanisms are obscure. We report in this article that the common ERAP2 single nucleotide polymorphism rs2549782 that codes for amino acid variation N392K leads to alterations in both the activity and the specificity of the enzyme. Specifically, the 392N allele excises hydrophobic N-terminal residues from epitope precursors up to 165-fold faster compared with the 392K allele, although both alleles are very similar in excising positively charged N-terminal amino acids. These effects are primarily due to changes in the catalytic turnover rate (k(cat)) and not in the affinity for the substrate. X-ray crystallographic analysis of the ERAP2 392K allele suggests that the polymorphism interferes with the stabilization of the N terminus of the peptide both directly and indirectly through interactions with key residues participating in catalysis. This specificity switch allows the 392N allele of ERAP2 to supplement ERAP1 activity for the removal of hydrophobic N-terminal residues. Our results provide mechanistic insight to the association of this ERAP2 polymorphism with disease and support the idea that polymorphic variation in Ag processing enzymes constitutes a component of immune response variability in humans.
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Affiliation(s)
- Irini Evnouchidou
- National Center for Scientific Research Demokritos, 15310 Athens, Greece
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Saridakis E, Giastas P, Moulis JM, Kyritsis P, Mavridis IM. Insight into the reduction potentials of Allochromatium vinosum-like ferredoxins. Acta Crystallogr A 2009. [DOI: 10.1107/s0108767309096457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Saridakis E, Giastas P, Efthymiou G, Moulis JM, Kyritsis P, Mavridis IM. Comparison of ferredoxins from Ps. aeruginosa, E. coliand an Al. vinosummutant. Acta Crystallogr A 2007. [DOI: 10.1107/s0108767307096018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Paulidou A, Giastas P, Mourtzis N, Yannakopoulou K, Mavridis IM. Crystal and molecular structure of octakis(6-bromo-6-deoxy)-γ-cyclodextrin. A novel stacking of a distorted macrocycle. Carbohydr Res 2007; 342:1519-24. [PMID: 17555730 DOI: 10.1016/j.carres.2007.05.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 02/06/2007] [Revised: 05/10/2007] [Accepted: 05/11/2007] [Indexed: 10/23/2022]
Abstract
Octakis(6-bromo-6-deoxy)cyclomaltooctaose, perbrominated gamma-cyclodextrin at the primary side, crystallises from methanol in a very unique manner. The macrocycles are quite distorted in contrast to their beta-cyclodextrin analogue, heptakis(6-bromo-6-deoxy)cyclomaltoheptaose. The two monomers, arranged head-to-head, form a completely new kind of dimer by mutually entering into each other, both at the primary and the secondary sides. At the primary, hydrophobic side, they interact by Br...Br interactions and at the secondary, hydrophilic side, by direct H-bonds between hydroxylic groups. The short contacts of the Br atoms contribute to the macrocycle's distortion, which is considerable compared to the few available structures of gamma-CDs persubstituted at the primary side with bulkier and in some occasions charged substituents. Water and methanol molecules are entrapped in the cyclodextrin cavity, mostly in the area of the secondary hydroxylic groups connecting the macrocycles by indirect H-bonds. Thus the solvent molecules strengthen the association of the two monomers and contribute to the stabilisation of the cavity. The monomers stack along the a-axis and form columns that align in parallel lines along the same axis resulting in the formation of alternating hydrophobic and hydrophilic layers perpendicular to the a-axis resembling in this respect, the structure of the analogous perbrominated beta-cyclodextrin.
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Affiliation(s)
- Anastasia Paulidou
- Institute of Physical Chemistry, National Center for Scientific Research 'Demokritos', Aghia Paraskevi 15310, PO Box 60228, Athens, Greece
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Giastas P, Pinotsis N, Efthymiou G, Wilmanns M, Kyritsis P, Moulis JM, Mavridis IM. The structure of the 2[4Fe-4S] ferredoxin from Pseudomonas aeruginosa at 1.32-A resolution: comparison with other high-resolution structures of ferredoxins and contributing structural features to reduction potential values. J Biol Inorg Chem 2006; 11:445-58. [PMID: 16596388 DOI: 10.1007/s00775-006-0094-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [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: 01/04/2006] [Accepted: 02/09/2006] [Indexed: 10/24/2022]
Abstract
The structure of the 2[4Fe-4S] ferredoxin (PaFd) from Pseudomonas aeruginosa, which belongs to the Allochromatium vinosum (Alvin) subfamily, has been determined by X-ray crystallography at 1.32-A resolution, which is the highest up to now for a member of this subfamily of Fds. The main structural features of PaFd are similar to those of AlvinFd. However, the significantly higher resolution of the PaFd structure makes possible a reliable comparison with available high-resolution structures of [4Fe-4S]-containing Fds, in an effort to rationalize the unusual electrochemical properties of Alvin-like Fds. Three major factors contributing to the reduction potential values of [4Fe-4S]2+/+ clusters of Fds, namely, the surface accessibility of the clusters, the N-H...S hydrogen-bonding network, and the volume of the cavities hosting the clusters, are extensively discussed. The volume of the cavities is introduced in the present work for the first time, and can in part explain the very negative potential of cluster I of Alvin-like Fds.
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Affiliation(s)
- Petros Giastas
- Institute of Physical Chemistry, NCSR Demokritos, Aghia Paraskevi, 15310, PO Box 60228, Athens, Greece
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Mavridis IM, Giastas P, Pinotsis N, Efthymiou G, Wilmanns M, Kyritsis P, Moulis JM. Structure of the 2[4Fe-4S] ferredoxin from Pseudomonas aeruginosaat 1.32 Å resolution. Acta Crystallogr A 2005. [DOI: 10.1107/s0108767305090999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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31
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Yoshizawa K, Toyota S, Toda F, Chatziefthimiou S, Giastas P, Mavridis IM, Kato M. Control of Differential Inclusion Complexation in the Solid State by Seed Crystals. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200501364] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Yoshizawa K, Toyota S, Toda F, Chatziefthimiou S, Giastas P, Mavridis IM, Kato M. Control of Differential Inclusion Complexation in the Solid State by Seed Crystals. Angew Chem Int Ed Engl 2005; 44:5097-100. [PMID: 16007722 DOI: 10.1002/anie.200501364] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Kazuhiro Yoshizawa
- Department of Chemistry, Okayama University of Science, Ridaicho 1-1, Okayama 700-0005, Japan
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Tsorteki F, Bethanis K, Pinotsis N, Giastas P, Mentzafos D. Inclusion compounds of plant growth regulators in cyclodextrins. V. 4-Chlorophenoxyacetic acid encapsulated in β-cyclodextrin and heptakis(2,3,6-tri-O-methyl)-β-cyclodextrin. Acta Crystallogr B Struct Sci 2005; 61:207-17. [PMID: 15772454 DOI: 10.1107/s0108768105004106] [Citation(s) in RCA: 13] [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] [Received: 09/14/2004] [Accepted: 02/07/2005] [Indexed: 05/02/2023]
Abstract
The crystal structures of 4-chlorophenoxyacetic acid (4CPA) included in β-cyclodextrin (β-CD) and heptakis(2,3,6-tri-O-methyl)-β-cyclodextrin (TMβCD) have been studied by X-ray diffraction. The 4CPA/β-CD complex crystallizes as a head-to-head dimer in the space group C2 in the Tetrad packing mode. The packing modes of some β-CD dimeric complexes, having unique stackings, are also discussed. The 4CPA/TMβCD inclusion complex crystallizes in the space group P21 and its asymmetric unit contains two crystallographically independent complexes, complex A and complex B, exhibiting different conformations. The host molecule of complex A is significantly distorted, as a glucosidic residue rotated about the O4′—C1 and C4—O4 bonds forms an aperture where the guest molecule is accommodated. The phenyl moiety of the guest molecule of complex B is nearly perpendicular to the mean plane of the O4n atoms. The conformations of the guest molecules of the two complexes are similar. The crystal packing consists of antiparallel columns as in the majority of the TMβCD complexes published so far.
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Affiliation(s)
- Frantzeska Tsorteki
- Physics Laboratory, Agricultural University of Athens, 75 Iera Odos, 118 55 Athens, Greece
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Giastas P, Eliadou K, Plyta ZF, Yannakopoulou K, Mavridis IM. X-ray crystallography and solution NMR spectroscopy characterization of heptakis(2,3-di-O-acetyl-6-bromo-6-deoxy)cyclomaltoheptaose. Carbohydr Res 2004; 339:1189-94. [PMID: 15063210 DOI: 10.1016/j.carres.2004.01.012] [Citation(s) in RCA: 3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2003] [Revised: 01/22/2004] [Accepted: 01/28/2004] [Indexed: 10/26/2022]
Abstract
Heptakis(2,3-di-O-acetyl-6-bromo-6-deoxy)cyclomaltoheptaose has been characterized in aqueous solution by 1D and 2D NMR spectroscopy and in the solid state by X-ray crystallography. In methanol solution, the acetyl groups were found to interact with both inward and outward-pointing protons. This and the strong deshielding of the bridging carbons, relative to the nonacetylated precursor, indicate macrocyclic flexibility. In the crystalline state the macrocycle exists as a methanol complex. It exhibits elliptical distortion, all glucose residues been tilted with their primary side toward the cavity. The existing strain due to the congestion of 14 acetyl groups at the secondary site is relieved by two glucose rings acquiring the rarely observed skew-boat conformation, (0)S(2), by the increased tilting of two glucose residues, as well as by minor variations of the torsion angles of the acetyl groups. The seven bromine atoms are quite accessible to nucleophiles.
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Affiliation(s)
- Petros Giastas
- Institute of Physical Chemistry, National Center for Scientific Research 'Demokritos', Aghia Paraskevi, GRC-15310 Athens, Greece
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Eliadou K, Giastas P, Yannakopoulou K, Mavridis IM. Synthesis of 6-mono-6-deoxy-beta-cyclodextrins substituted with isomeric aminobenzoic acids. Structural characterization, conformational preferences, and self-inclusion as studied by NMR spectroscopy in aqueous solution and by X-ray crystallography in the solid state. J Org Chem 2004; 68:8550-7. [PMID: 14575485 DOI: 10.1021/jo034503+] [Citation(s) in RCA: 17] [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] [Indexed: 11/28/2022]
Abstract
The synthesis, purification, and characterization of mono-6-modified-beta-cyclodextrins bearing N-attached o-, m-, and p-aminobenzoic acids (2, 3, and 4, respectively) are presented. The structures in aqueous solution were investigated using one- and two-dimensional NMR spectroscopy. Detailed assignment of the spectra together with intramolecular NOE correlations revealed the way each of the isomeric appendages is positioned relative to the macrocyclic cavity. No self-inclusion is observed. The o-isomer 2 turns inward over the top of the primary side and interacts with specific protons of the substituted glucopyranose unit A and those of a neighboring unit. The m-isomer 3 displays two conformations, where the substituent resides above the primary side in a tilted manner and interacts either with the previous or the next unit. We propose that the carboxyl groups in both 2 and 3 are localized through H-bonding with one or two, respectively, primary hydroxyl groups of the neighboring glucopyranose units. In a similar positioning of the aromatic ring of the p-isomer 4, the hydrophilic carboxyl end is fully exposed to the aqueous environment. The X-ray structure of 4 shows that the solution conformation has evolved such that in the crystalline state, the aromatic moiety is inserted through its carboxyl part inside another CD where it establishes intermolecular H-bonds with inward-turned primary OH groups. Besides this stabilization, 4 forms parallel and antiparallel supramolecular chains in the crystal that are additionally stabilized by direct H-bonds.
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Affiliation(s)
- Kyriaki Eliadou
- Institute of Physical Chemistry, National Center for Scientific Research Demokritos, Ag. Paraskevi 15310, Athens, Greece
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Giastas P, Yannakopoulou K, Mavridis IM. Molecular structures of the inclusion complexes beta-cyclodextrin-1,2-bis(4-aminophenyl)ethane and beta-cyclodextrin-4,4'-diaminobiphenyl; packing of dimeric beta-cyclodextrin inclusion complexes. Acta Crystallogr B 2003; 59:287-99. [PMID: 12657820 DOI: 10.1107/s010876810300257x] [Citation(s) in RCA: 19] [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] [Subscribe] [Scholar Register] [Received: 11/03/2002] [Accepted: 01/29/2003] [Indexed: 11/10/2022]
Abstract
The present investigation is part of an ongoing study on the influence of the long end-functonalized guest molecules DBA and BNZ in the crystal packing of beta-cyclodextrin (betaCD) dimeric complexes. The title compounds are 2:2 host:guest complexes showing limited host-guest hydrogen bonding at the primary faces of the betaCD dimers. Within the betaCD cavity the guests exhibit mutual pi...pi interactions and between betaCD dimers perpendicular NH...pi interactions. The DBA guest molecule exhibits one extended and two bent conformations in the complex. The BNZ guest molecule is not planar inside betaCD, in contrast to the structure of BNZ itself, which indicates that the cavity isolates the molecules and forbids the pi...pi stacking of the aromatic rings. NMR spectroscopy studies show that in aqueous solution both DBA and BNZ form strong complexes that have 1:1 stoichiometry and structures similar to the solid state ones. The relative packing of the dimers is the same in both complexes. The axes of two adjacent dimers form an angle close to 20 degrees and have a lateral displacement approximately 2.45 A, both of which characterize the screw-channel mode of packing. Although the betaCD/BNZ complex indeed crystallizes in a space group characterizing the latter mode, the betaCD/DBA complex crystallizes in a space group with novel dimensions not resembling any of the packing modes reported so far. The new lattice is attributed to the three conformations exhibited by the guest in the crystals. However, this lattice can be transformed into another, which is isostructural to that of the betaCD/BNZ inclusion complex, if the conformation of the guest is not taken into account.
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Affiliation(s)
- Petros Giastas
- Insitute of Physical Chemistry, National Center for Scientific Research, Athens, Greece
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Toda F, Yagi M, Hirano S, Toyota S, Giastas P, M. Marvidis I. Photoreactions of 2- and 4-Pyridones in Their Inclusion Crystal with a Host Compound. HETEROCYCLES 2003. [DOI: 10.3987/com-02-s85] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Salakhutdinov BA, Dalimov DN, Aripov TF, Tukfatullina II, Ziyatdinova RK, Dzhuraev AZ, Kamaev FG, Izotova LY, Ibragimov BT, Mavridis I, Giastas P. Chem Nat Compd 2002; 38:249-256. [DOI: 10.1023/a:1020479911050] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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