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Mpakali A, Georgaki G, Buson A, Findlay AD, Foot JS, Mauvais F, van Endert P, Giastas P, Hamprecht DW, Stratikos E. Stabilization of the open conformation οf insulin-regulated aminopeptidase by a novel substrate-selective small-molecule inhibitor. Protein Sci 2024; 33:e5151. [PMID: 39167040 PMCID: PMC11337929 DOI: 10.1002/pro.5151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 07/30/2024] [Accepted: 08/06/2024] [Indexed: 08/23/2024]
Abstract
Insulin-regulated aminopeptidase (IRAP) is an enzyme with important biological functions and the target of drug-discovery efforts. We combined in silico screening with a medicinal chemistry optimization campaign to discover a nanomolar inhibitor of IRAP based on a pyrazolylpyrimidine scaffold. This compound displays an excellent selectivity profile versus homologous aminopeptidases, and kinetic analysis suggests it utilizes an uncompetitive mechanism of action when inhibiting the cleavage of a typical dipeptidic substrate. Surprisingly, the compound is a poor inhibitor of the processing of the physiological cyclic peptide substrate oxytocin and a 10mer antigenic epitope precursor but displays a biphasic inhibition profile for the trimming of a 9mer antigenic peptide. While the compound reduces IRAP-dependent cross-presentation of an 8mer epitope in a cellular assay, it fails to block in vitro trimming of select epitope precursors. To gain insight into the mechanism and basis of this unusual selectivity for this inhibitor, we solved the crystal structure of its complex with IRAP. The structure indicated direct zinc(II) engagement by the pyrazolylpyrimidine scaffold and revealed that the compound binds to an open conformation of the enzyme in a pose that should block the conformational transition to the enzymatically active closed conformation previously observed for other low-molecular-weight inhibitors. This compound constitutes the first IRAP inhibitor targeting the active site that utilizes a conformation-specific mechanism of action, provides insight into the intricacies of the IRAP catalytic cycle, and highlights a novel approach to regulating IRAP activity by blocking its conformational rearrangements.
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Affiliation(s)
- Anastasia Mpakali
- National Centre for Scientific Research DemokritosAthensGreece
- Laboratory of Biochemistry, Department of ChemistryNational and Kapodistrian University of AthensAthensGreece
| | - Galateia Georgaki
- National Centre for Scientific Research DemokritosAthensGreece
- Laboratory of Biochemistry, Department of ChemistryNational and Kapodistrian University of AthensAthensGreece
| | | | | | | | | | - Peter van Endert
- INSERM, CNRS, Institut Necker Enfants MaladesUniversité Paris CitéParisFrance
| | - Petros Giastas
- Department of Biotechnology, School of Applied Biology & BiotechnologyAgricultural University of AthensAthensGreece
| | | | - Efstratios Stratikos
- National Centre for Scientific Research DemokritosAthensGreece
- Laboratory of Biochemistry, Department of ChemistryNational and Kapodistrian University of AthensAthensGreece
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2
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Vargas-Pinilla P, S Oliveira Fam B, Medina Tavares G, Lima T, Landau L, Paré P, de Cássia Aleixo Tostes R, Pissinatti A, Falótico T, Costa-Neto C, Maestri R, Bortolini MC. From molecular variations to behavioral adaptations: Unveiling adaptive epistasis in primate oxytocin system. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2024; 184:e24947. [PMID: 38783700 DOI: 10.1002/ajpa.24947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 04/12/2024] [Accepted: 04/24/2024] [Indexed: 05/25/2024]
Abstract
OBJECTIVE Our primary objective was to investigate the variability of oxytocin (OT) and the GAMEN binding motif within the LNPEP oxytocinase in primates. MATERIALS AND METHODS We sequenced the LNPEP segment encompassing the GAMEN motif in 34 Platyrrhini species, with 21 of them also sequenced for the OT gene. Our dataset was supplemented with primate sequences of LNPEP, OT, and the oxytocin receptor (OTR) sourced from public databases. Evolutionary analysis and coevolution predictions were made followed by the macroevolution analysis of relevant amino acids associated with phenotypic traits, such as mating systems, parental care, and litter size. To account for phylogenetic structure, we utilized two distinct statistical tests. Additionally, we calculated binding energies focusing on the interaction between Callithtrix jacchus VAMEN and Pro8OT. RESULTS We identified two novel motifs (AAMEN and VAMEN), challenging the current knowledge of motif conservation in placental mammals. Coevolution analysis demonstrated a correlation between GAMEN, AAMEN, and VAMEN and their corresponding OTs and OTRs. Callithrix jacchus exhibited a higher binding energy between VAMEN and Pro8OT than orthologous molecules found in humans (GAMEN and Leu8OT). DISCUSSION The coevolution of AAMEN and VAMEN with their corresponding OTs and OTRs suggests a functional relationship that could have contributed to specific reproductive and adaptive behaviors, including paternal care, social monogamy, and twin births, prominent traits in Cebidae species, such as marmosets and tamarins. Our findings underscore the coevolution of taxon-specific amino acids among the three studied molecules, shedding light on the oxytocinergic system as an adaptive epistatic repertoire in primates.
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Affiliation(s)
- Pedro Vargas-Pinilla
- Laboratory of Human and Molecular Evolution, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Departamento de Farmacologia, Faculdade de Medicina, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Bibiana S Oliveira Fam
- Laboratory of Human and Molecular Evolution, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental (CPE), Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Gustavo Medina Tavares
- Laboratory of Human and Molecular Evolution, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Thaynara Lima
- Laboratory of Human and Molecular Evolution, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Luane Landau
- Laboratory of Human and Molecular Evolution, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, USA
| | - Pâmela Paré
- Laboratory of Human and Molecular Evolution, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | | | - Tiago Falótico
- Escola de Artes, Ciências e Humanidades, Universidade de São Paulo, São Paulo, Brazil
| | - Cláudio Costa-Neto
- Departamento de Bioquímica e Imunologia, Faculdade de Medicina, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Renan Maestri
- Laboratório de Ecomorfologia e Macroevolução, Departamento de Ecologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Maria Cátira Bortolini
- Laboratory of Human and Molecular Evolution, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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3
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Gising J, Honarnejad S, Bras M, Baillie GL, McElroy SP, Jones PS, Morrison A, Beveridge J, Hallberg M, Larhed M. The Discovery of New Inhibitors of Insulin-Regulated Aminopeptidase by a High-Throughput Screening of 400,000 Drug-like Compounds. Int J Mol Sci 2024; 25:4084. [PMID: 38612894 PMCID: PMC11012289 DOI: 10.3390/ijms25074084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 03/25/2024] [Accepted: 04/02/2024] [Indexed: 04/14/2024] Open
Abstract
With the ambition to identify novel chemical starting points that can be further optimized into small drug-like inhibitors of insulin-regulated aminopeptidase (IRAP) and serve as potential future cognitive enhancers in the clinic, we conducted an ultra-high-throughput screening campaign of a chemically diverse compound library of approximately 400,000 drug-like small molecules. Three biochemical and one biophysical assays were developed to enable large-scale screening and hit triaging. The screening funnel, designed to be compatible with high-density microplates, was established with two enzyme inhibition assays employing either fluorescent or absorbance readouts. As IRAP is a zinc-dependent enzyme, the remaining active compounds were further evaluated in the primary assay, albeit with the addition of zinc ions. Rescreening with zinc confirmed the inhibitory activity for most compounds, emphasizing a zinc-independent mechanism of action. Additionally, target engagement was confirmed using a complementary biophysical thermal shift assay where compounds causing positive/negative thermal shifts were considered genuine binders. Triaging based on biochemical activity, target engagement, and drug-likeness resulted in the selection of 50 qualified hits, of which the IC50 of 32 compounds was below 3.5 µM. Despite hydroxamic acid dominance, diverse chemotypes with biochemical activity and target engagement were discovered, including non-hydroxamic acid compounds. The most potent compound (QHL1) was resynthesized with a confirmed inhibitory IC50 of 320 nM. Amongst these compounds, 20 new compound structure classes were identified, providing many new starting points for the development of unique IRAP inhibitors. Detailed characterization and optimization of lead compounds, considering both hydroxamic acids and other diverse structures, are in progress for further exploration.
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Affiliation(s)
- Johan Gising
- The Beijer Laboratory, Science for Life Laboratory, Department of Medicinal Chemistry, Biomedical Centre, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden; (J.B.); (M.L.)
| | - Saman Honarnejad
- Pivot Park Screening Centre, Kloosterstraat 9, 5349 AB Oss, The Netherlands; (S.H.); (M.B.)
| | - Maaike Bras
- Pivot Park Screening Centre, Kloosterstraat 9, 5349 AB Oss, The Netherlands; (S.H.); (M.B.)
| | - Gemma L. Baillie
- BioAscent Discovery Ltd., Bo‘Ness Road, Newhouse, Motherwell ML1 5UH, UK; (G.L.B.); (S.P.M.); (P.S.J.); (A.M.)
| | - Stuart P. McElroy
- BioAscent Discovery Ltd., Bo‘Ness Road, Newhouse, Motherwell ML1 5UH, UK; (G.L.B.); (S.P.M.); (P.S.J.); (A.M.)
| | - Philip S. Jones
- BioAscent Discovery Ltd., Bo‘Ness Road, Newhouse, Motherwell ML1 5UH, UK; (G.L.B.); (S.P.M.); (P.S.J.); (A.M.)
| | - Angus Morrison
- BioAscent Discovery Ltd., Bo‘Ness Road, Newhouse, Motherwell ML1 5UH, UK; (G.L.B.); (S.P.M.); (P.S.J.); (A.M.)
| | - Julia Beveridge
- The Beijer Laboratory, Science for Life Laboratory, Department of Medicinal Chemistry, Biomedical Centre, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden; (J.B.); (M.L.)
| | - Mathias Hallberg
- The Beijer Laboratory, Department of Pharmaceutical Biosciences, Neuropharmacology and Addiction Research, Biomedical Centre, Uppsala University, P.O. Box 591, SE-751 24 Uppsala, Sweden;
| | - Mats Larhed
- The Beijer Laboratory, Science for Life Laboratory, Department of Medicinal Chemistry, Biomedical Centre, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden; (J.B.); (M.L.)
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4
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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] [Abstract] [Key Words] [MESH Headings] [Grants] [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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5
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Pande S, Guo HC. Structure-guided discovery of aminopeptidase ERAP1 variants capable of processing antigens with novel PC anchor specificities. Immunology 2024; 171:131-145. [PMID: 37858978 PMCID: PMC10841542 DOI: 10.1111/imm.13709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 10/06/2023] [Indexed: 10/21/2023] Open
Abstract
Endoplasmic reticulum aminopeptidase 1 (ERAP1) belongs to the oxytocinase subfamily of M1 aminopeptidases (M1APs), which are a diverse family of metalloenzymes involved in a wide range of functions and have been implicated in various chronic and infectious diseases of humans. ERAP1 trims antigenic precursors into correct sizes (8-10 residues long) for Major Histocompatibility Complex (MHC) presentation, by a unique molecular ruler mechanism in which it makes concurrent bindings to substrate N- and C-termini. We have previously determined four crystal structures of ERAP1 C-terminal regulatory domain (termed ERAP1_C domain) in complex with peptide carboxyl (PC)-ends that carry various anchor residues, and identified a specificity subsite for recognizing the PC anchor side chain, denoted as the SC subsite to follow the conventional notations: S1 site for P1, S2 site for P2, and so forth. In this study, we report studies on structure-guided mutational and hydrolysis kinetics, and peptide trimming assays to further examine the functional roles of this SC subsite. Most strikingly, a point mutation V737R results in a change of substrate preference from a hydrophobic to a negatively charged PC anchor residue; the latter is presumed to be a poor substrate for WT ERAP1. These studies validate the crystallographic observations that this SC subsite is directly involved in binding and recognition of the substrate PC anchor and presents a potential target to modulate MHC-restricted immunopeptidomes.
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Affiliation(s)
- Suchita Pande
- Department of Biological Sciences, University of Massachusetts Lowell, 1 University Avenue, Lowell, MA 01854, USA
- Present Address: Molecular Cardiology Research Institute, Tufts Medical Center, 800 Washington Street, Boston, MA 02111, USA
| | - Hwai-Chen Guo
- Department of Biological Sciences, University of Massachusetts Lowell, 1 University Avenue, Lowell, MA 01854, USA
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6
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Madabushi S, Chow KM, Song ES, Goswami A, Hersh LB, Rodgers DW. Structure of puromycin-sensitive aminopeptidase and polyglutamine binding. PLoS One 2023; 18:e0287086. [PMID: 37440518 PMCID: PMC10343166 DOI: 10.1371/journal.pone.0287086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 06/22/2023] [Indexed: 07/15/2023] Open
Abstract
Puromycin-sensitive aminopeptidase (E.C. 3.4.11.14, UniProt P55786), a zinc metallopeptidase belonging to the M1 family, degrades a number of bioactive peptides as well as peptides released from the proteasome, including polyglutamine. We report the crystal structure of PSA at 2.3 Ǻ. Overall, the enzyme adopts a V-shaped architecture with four domains characteristic of the M1 family aminopeptidases, but it is in a less compact conformation compared to most M1 enzymes of known structure. A microtubule binding sequence is present in a C-terminal HEAT repeat domain of the enzyme in a position where it might serve to mediate interaction with tubulin. In the catalytic metallopeptidase domain, an elongated active site groove lined with aromatic and hydrophobic residues and a large S1 subsite may play a role in broad substrate recognition. The structure with bound polyglutamine shows a possible interacting mode of this peptide, which is supported by mutation.
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Affiliation(s)
- Sowmya Madabushi
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, Kentucky, United States of America
| | - K. Martin Chow
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, Kentucky, United States of America
| | - Eun Suk Song
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, Kentucky, United States of America
| | - Anwesha Goswami
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, Kentucky, United States of America
| | - Louis B. Hersh
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, Kentucky, United States of America
| | - David W. Rodgers
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, Kentucky, United States of America
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7
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Rerick MT, Chen J, Weber SG. Electroosmotic Perfusion, External Microdialysis: Simulation and Experiment. ACS Chem Neurosci 2023. [PMID: 37379416 PMCID: PMC10360060 DOI: 10.1021/acschemneuro.3c00057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2023] Open
Abstract
Information about the rates of hydrolysis of neuropeptides by extracellular peptidases can lead to a quantitative understanding of how the steady-state and transient concentrations of neuropeptides are controlled. We have created a small microfluidic device that electroosmotically infuses peptides into, through, and out of the tissue to a microdialysis probe outside the head. The device is created by two-photon polymerization (Nanoscribe). Inferring quantitative estimates of a rate process from the change in concentration of a substrate that has passed through tissue is challenging for two reasons. One is that diffusion is significant, so there is a distribution of peptide substrate residence times in the tissue. This affects the product yield. The other is that there are multiple paths taken by the substrate as it passes through tissue, so there is a distribution of residence times and thus reaction times. Simulation of the process is essential. The simulations presented here imply that a range of first order rate constants of more than 3 orders of magnitude is measurable and that 5-10 min is required to reach a steady state value of product concentration following initiation of substrate infusion. Experiments using a peptidase-resistant d-amino acid pentapeptide, yaGfl, agree with simulations.
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Affiliation(s)
- Michael T Rerick
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Jun Chen
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Stephen G Weber
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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8
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Hydrogen Peroxide Induced Toxicity Is Reversed by the Macrocyclic IRAP-Inhibitor HA08 in Primary Hippocampal Cell Cultures. Curr Issues Mol Biol 2022; 44:5000-5012. [PMID: 36286055 PMCID: PMC9601255 DOI: 10.3390/cimb44100340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/14/2022] [Accepted: 10/16/2022] [Indexed: 11/16/2022] Open
Abstract
Angiotensin IV (Ang IV), a metabolite of Angiotensin II, is a bioactive hexapeptide that inhibits the insulin-regulated aminopeptidase (IRAP). This transmembrane zinc metallopeptidase with many biological functions has in recent years emerged as a new pharmacological target. IRAP is expressed in a variety of tissues and can be found in high density in the hippocampus and neocortex, brain regions associated with cognition. Ang IV is known to improve memory tasks in experimental animals. One of the most potent IRAP inhibitors known today is the macrocyclic compound HA08 that is significantly more stable than the endogenous Ang IV. HA08 combines structural elements from Ang IV and the physiological substrates oxytocin and vasopressin, and binds to the catalytic site of IRAP. In the present study we evaluate whether HA08 can restore cell viability in rat primary cells submitted to hydrogen peroxide damage. After damaging the cells with hydrogen peroxide and subsequently treating them with HA08, the conceivable restoring effects of the IRAP inhibitor were assessed. The cellular viability was determined by measuring mitochondrial activity and lactate dehydrogenase (LDH) release. The mitochondrial activity was significantly higher in primary hippocampal cells, whereas the amount of LDH was unaffected. We conclude that the cell viability can be restored in this cell type by blocking IRAP with the potent macrocyclic inhibitor HA08, although the mechanism by which HA08 exerts its effects remains unclear.
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Liu S, Lu J, Wu J, Feng D, Su X, Cao H. Structural and biochemical insights into the association between ERAP1 polymorphism and autoimmune diseases. Biochem Biophys Res Commun 2022; 632:189-194. [DOI: 10.1016/j.bbrc.2022.09.086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 09/22/2022] [Indexed: 11/02/2022]
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10
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Conformational remodeling enhances activity of lanthipeptide zinc-metallopeptidases. Nat Chem Biol 2022; 18:724-732. [PMID: 35513512 DOI: 10.1038/s41589-022-01018-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 03/23/2022] [Indexed: 02/05/2023]
Abstract
Lanthipeptides are an important group of natural products with diverse biological functions, and their biosynthesis requires the removal of N-terminal leader peptides (LPs) by designated proteases. LanPM1 enzymes, a subgroup of M1 zinc-metallopeptidases, have been recently identified as bifunctional proteases with both endo- and aminopeptidase activities to remove LPs of class III and class IV lanthipeptides. Herein, we report the biochemical and structural characterization of EryP as the LanPM1 enzyme from the biosynthesis of class III lanthipeptide erythreapeptin. We determined X-ray crystal structures of EryP in three conformational states, the open, intermediate and closed states, and identified a unique interdomain Ca2+ binding site as a regulatory element that modulates its domain dynamics and proteolytic activity. Inspired by this regulatory Ca2+ binding, we developed a strategy to engineer LanPM1 enzymes for enhanced catalytic activities by strengthening interdomain associations and driving the conformational equilibrium toward their closed forms.
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Mattorre B, Caristi S, Donato S, Volpe E, Faiella M, Paiardini A, Sorrentino R, Paladini F. A Short ERAP2 That Binds IRAP Is Expressed in Macrophages Independently of Gene Variation. Int J Mol Sci 2022; 23:ijms23094961. [PMID: 35563348 PMCID: PMC9101739 DOI: 10.3390/ijms23094961] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/17/2022] [Accepted: 04/27/2022] [Indexed: 01/19/2023] Open
Abstract
The M1 zinc metalloproteases ERAP1, ERAP2, and IRAP play a role in HLA-I antigen presentation by refining the peptidome either in the ER (ERAP1 and ERAP2) or in the endosomes (IRAP). They have also been entrusted with other, although less defined, functions such as the regulation of the angiotensin system and blood pressure. In humans, ERAP1 and IRAP are commonly expressed. ERAP2 instead has evolved under balancing selection that maintains two haplotypes, one of which undergoing RNA splicing leading to nonsense-mediated decay and loss of protein. Hence, likewise in rodents, wherein the ERAP2 gene is missing, about a quarter of the human population does not express ERAP2. We report here that macrophages, but not monocytes or other mononuclear blood cells, express and secrete an ERAP2 shorter form independent of the haplotype. The generation of this "short" ERAP2 is due to an autocatalytic cleavage within a distinctive structural motif and requires an acidic micro-environment. Remarkably, ERAP2 "short" binds IRAP and the two molecules are co-expressed in the endosomes as well as in the cell membrane. Of note, the same phenomenon could be observed in some cancer cells. These data prompt us to reconsider the role of ERAP2, which might have been maintained in humans due to fulfilling a relevant function in its "short" form.
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Affiliation(s)
- Benedetta Mattorre
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (B.M.); (S.C.); (S.D.); (E.V.); (M.F.)
| | - Silvana Caristi
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (B.M.); (S.C.); (S.D.); (E.V.); (M.F.)
| | - Simona Donato
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (B.M.); (S.C.); (S.D.); (E.V.); (M.F.)
| | - Emilia Volpe
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (B.M.); (S.C.); (S.D.); (E.V.); (M.F.)
| | - Marika Faiella
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (B.M.); (S.C.); (S.D.); (E.V.); (M.F.)
| | - Alessandro Paiardini
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy;
| | - Rosa Sorrentino
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (B.M.); (S.C.); (S.D.); (E.V.); (M.F.)
- Correspondence: (R.S.); (F.P.)
| | - Fabiana Paladini
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (B.M.); (S.C.); (S.D.); (E.V.); (M.F.)
- Correspondence: (R.S.); (F.P.)
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Papakyriakou A, Mpakali A, Stratikos E. Can ERAP1 and ERAP2 Form Functional Heterodimers? A Structural Dynamics Investigation. Front Immunol 2022; 13:863529. [PMID: 35514997 PMCID: PMC9065437 DOI: 10.3389/fimmu.2022.863529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/07/2022] [Indexed: 11/28/2022] Open
Abstract
Endoplasmic reticulum aminopeptidases 1 and 2 (ERAP1 and ERAP2) play important roles in the generation of antigenic peptides presented by Major Histocompatibility Class I (MHCI) molecules and indirectly regulate adaptive immune responses. Although the discrete function of these enzymes has been extensively characterized, recent reports have suggested that they can also form heterodimers with functional consequences. However, lack of structural characterization of a putative ERAP1/ERAP2 dimer has limited our understanding of its biological role and significance. To address this, we employed computational molecular dynamics calculations to explore the topology of interactions between these two, based on experimentally determined homo-dimerization interfaces observed in crystal structures of ERAP2 or homologous enzymes. Our analysis of 8 possible dimerization models, suggested that the most likely ERAP1/ERAP2 heterodimerization topology involves the exon 10 loop, a non-conserved loop previously implicated in interactions between ERAP1 and the disulfide-bond shuffling chaperone ERp44. This dimerization topology allows access to the active site of both enzymes and is consistent with a previously reported construct in which ERAP1 and ERAP2 were linked by Fos/Jun zipper tags. The proposed model constitutes a tentative structural template to help understand the physiological role and significance of ERAP1/ERAP2 molecular interactions.
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Affiliation(s)
- Athanasios Papakyriakou
- Institute of Biosciences and Applications, National Centre for Scientific Research “Demokritos”, Athens, Greece
| | - Anastasia Mpakali
- Institute of Biosciences and Applications, National Centre for Scientific Research “Demokritos”, Athens, Greece
| | - Efstratios Stratikos
- Institute of Biosciences and Applications, National Centre for Scientific Research “Demokritos”, Athens, Greece
- Laboratory of Biochemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
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13
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Maben Z, Arya R, Georgiadis D, Stratikos E, Stern LJ. Conformational dynamics linked to domain closure and substrate binding explain the ERAP1 allosteric regulation mechanism. Nat Commun 2021; 12:5302. [PMID: 34489420 PMCID: PMC8421391 DOI: 10.1038/s41467-021-25564-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 08/10/2021] [Indexed: 11/27/2022] Open
Abstract
The endoplasmic-reticulum aminopeptidase ERAP1 processes antigenic peptides for loading on MHC-I proteins and recognition by CD8 T cells as they survey the body for infection and malignancy. Crystal structures have revealed ERAP1 in either open or closed conformations, but whether these occur in solution and are involved in catalysis is not clear. Here, we assess ERAP1 conformational states in solution in the presence of substrates, allosteric activators, and inhibitors by small-angle X-ray scattering. We also characterize changes in protein conformation by X-ray crystallography, and we localize alternate C-terminal binding sites by chemical crosslinking. Structural and enzymatic data suggest that the structural reconfigurations of ERAP1 active site are physically linked to domain closure and are promoted by binding of long peptide substrates. These results clarify steps required for ERAP1 catalysis, demonstrate the importance of conformational dynamics within the catalytic cycle, and provide a mechanism for the observed allosteric regulation and Lys/Arg528 polymorphism disease association.
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Affiliation(s)
- Zachary Maben
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Richa Arya
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Dimitris Georgiadis
- Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
| | - Efstratios Stratikos
- Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
| | - Lawrence J Stern
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA.
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14
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Tsujimoto M, Aoki K, Goto Y, Ohnishi A. Molecular and functional diversity of the oxytocinase subfamily of M1 aminopeptidases. J Biochem 2021; 169:409-420. [PMID: 33481005 DOI: 10.1093/jb/mvab009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 01/11/2021] [Indexed: 02/04/2023] Open
Abstract
The placental leucine aminopeptidase/insulin-regulated aminopeptidase, endoplasmic reticulum aminopeptidase 1 and endoplasmic reticulum aminopeptidase 2 are part of a distinct subfamily of M1 aminopeptidases termed the 'oxytocinase subfamily'. The subfamily members show molecular diversity due to differential usage of translation initiation sites, alternative splicing and multiple single nucleotide polymorphisms. It is becoming evident that, depending on their intracellular or extracellular location, members of the oxytocinase subfamily play important roles in the maintenance of homeostasis, including the regulation of blood pressure, maintenance of normal pregnancy, retention of memory and trimming of antigenic peptides presented to major histocompatibility complex class I molecules, by acting as either aminopeptidases or binding partners of specific functional proteins in the cells. Based on their molecular diversity and moonlighting protein-like properties, it is conceivable that the subfamily members exert pleiotropic effects during evolution, to become important players in the regulation of homeostasis.
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Affiliation(s)
- Masafumi Tsujimoto
- Faculty of Pharmaceutical Sciences, Teikyo Heisei University, Nakano, Tokyo 164-8530, Japan
| | - Kazuma Aoki
- Faculty of Pharmaceutical Sciences, Teikyo Heisei University, Nakano, Tokyo 164-8530, Japan
| | - Yoshikuni Goto
- Faculty of Pharmaceutical Sciences, Teikyo Heisei University, Nakano, Tokyo 164-8530, Japan
| | - Atsushi Ohnishi
- Faculty of Pharmaceutical Sciences, Teikyo Heisei University, Nakano, Tokyo 164-8530, Japan
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15
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Sui L, Guo HC. Enhanced recombinant expression and purification of human IRAP for biochemical and crystallography studies. Biochem Biophys Rep 2021; 27:101042. [PMID: 34169156 PMCID: PMC8207215 DOI: 10.1016/j.bbrep.2021.101042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 11/25/2022] Open
Abstract
Insulin-regulated aminopeptidase (IRAP) in humans is a membrane bound enzyme that has multiple functions. It was first described as a companion protein of the insulin-responsive glucose transporter, Glut4, in specialized vesicles. The protein has subsequently been shown to be identical to the oxytocinase/aminopeptidase or the angiotensin IV (Ang IV) receptor (AT4 receptor). Some AT4 ligand peptides, such as Ang IV and LVV-hemorphin-7, have been shown to act as IRAP inhibitors that exert memory-enhancing properties. As such IRAP has been a target for developing cognitive enhancers. To facilitate detailed mechanistic studies of IRAP catalysis and inhibition, and to pave the way for biophysical and structural studies of IRAP in complex with peptide inhibitors, we report here an optimized expression and purification system using High Five insect cells. We also report biochemical characterizations of the purified recombinant IRAP with a standard aminopeptidase substrate and an optimized IRAP peptide inhibitor with a Ki of 98 nM.
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Key Words
- AT4, Ang IV receptor
- Ang IV, angiotensin IV
- Cognitive enhancers
- Crystallization
- ERAP, endoplasmic reticulum aminopeptidase
- Expression and purification
- IEX, ion exchange chromatography
- IMAC, immobilized metal ion affinity chromatography
- IRAP, insulin-regulated aminopeptidase
- Insulin-regulated aminopeptidase (IRAP)
- L-AMC, leucine 7-amido-4-methylcoumarin
- LVV-H7, LVV-hemorphin-7
- MHC-I, major histocompatibility complex class I
- Peptide inhibitor
- SEC, size exclusion chromatography
- Substrate affinity
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Affiliation(s)
- Lufei Sui
- Department of Biological Sciences, University of Massachusetts Lowell, 1 University Avenue, Lowell, MA, 01854, USA
| | - Hwai-Chen Guo
- Department of Biological Sciences, University of Massachusetts Lowell, 1 University Avenue, Lowell, MA, 01854, USA
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16
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Vanga SR, Åqvist J, Hallberg A, Gutiérrez-de-Terán H. Structural Basis of Inhibition of Human Insulin-Regulated Aminopeptidase (IRAP) by Benzopyran-Based Inhibitors. Front Mol Biosci 2021; 8:625274. [PMID: 33869280 PMCID: PMC8047434 DOI: 10.3389/fmolb.2021.625274] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 03/10/2021] [Indexed: 12/01/2022] Open
Abstract
Inhibition of the insulin-regulated aminopeptidase (IRAP) improves memory and cognition in animal models. The enzyme has recently been crystallized and several series of inhibitors reported. We herein focused on one series of benzopyran-based inhibitors of IRAP known as the HFI series, with unresolved binding mode to IRAP, and developed a robust computational model to explain the structure-activity relationship (SAR) and potentially guide their further optimization. The binding model here proposed places the benzopyran ring in the catalytic binding site, coordinating the Zn2+ ion through the oxygen in position 3, in contrast to previous hypothesis. The whole series of HFI compounds was then systematically simulated, starting from this binding mode, using molecular dynamics and binding affinity estimated with the linear interaction energy (LIE) method. The agreement with experimental affinities supports the binding mode proposed, which was further challenged by rigorous free energy perturbation (FEP) calculations. Here, we found excellent correlation between experimental and calculated binding affinity differences, both between selected compound pairs and also for recently reported experimental data concerning the site directed mutagenesis of residue Phe544. The computationally derived structure-activity relationship of the HFI series and the understanding of the involvement of Phe544 in the binding of this scaffold provide valuable information for further lead optimization of novel IRAP inhibitors.
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Affiliation(s)
| | - Johan Åqvist
- Department of Cell and Molecular Biology, BMC, Uppsala University, Uppsala, Sweden
| | - Anders Hallberg
- Department of Pharmaceutical Chemistry, BMC, Uppsala University, Uppsala, Sweden
| | - Hugo Gutiérrez-de-Terán
- Department of Cell and Molecular Biology, BMC, Uppsala University, Uppsala, Sweden.,Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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17
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Descamps D, Evnouchidou I, Caillens V, Drajac C, Riffault S, van Endert P, Saveanu L. The Role of Insulin Regulated Aminopeptidase in Endocytic Trafficking and Receptor Signaling in Immune Cells. Front Mol Biosci 2020; 7:583556. [PMID: 33195428 PMCID: PMC7606930 DOI: 10.3389/fmolb.2020.583556] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/25/2020] [Indexed: 12/15/2022] Open
Abstract
Insulin regulated aminopeptidase (IRAP) is a type II transmembrane protein with broad tissue distribution initially identified as a major component of Glut4 storage vesicles (GSV) in adipocytes. Despite its almost ubiquitous expression, IRAP had been extensively studied mainly in insulin responsive cells, such as adipocytes and muscle cells. In these cells, the enzyme displays a complex intracellular trafficking pattern regulated by insulin. Early studies using fusion proteins joining the IRAP cytosolic domain to various reporter proteins, such as GFP or the transferrin receptor (TfR), showed that the complex and regulated trafficking of the protein depends on its cytosolic domain. This domain contains several motifs involved in IRAP trafficking, as demonstrated by mutagenesis studies. Also, proteomic studies and yeast two-hybrid experiments showed that the IRAP cytosolic domain engages in multiple protein interactions with cytoskeleton components and vesicular trafficking adaptors. These findings led to the hypothesis that IRAP is not only a cargo of GSV but might be a part of the sorting machinery that controls GSV dynamics. Recent work in adipocytes, immune cells, and neurons confirmed this hypothesis and demonstrated that IRAP has a dual function. Its carboxy-terminal domain located inside endosomes is responsible for the aminopeptidase activity of the enzyme, while its amino-terminal domain located in the cytosol functions as an endosomal trafficking adaptor. In this review, we recapitulate the published protein interactions of IRAP and summarize the increasing body of evidence indicating that IRAP plays a role in intracellular trafficking of several proteins. We describe the impact of IRAP deletion or depletion on endocytic trafficking and the consequences on immune cell functions. These include the ability of dendritic cells to cross-present antigens and prime adaptive immune responses, as well as the control of innate and adaptive immune receptor signaling and modulation of inflammatory responses.
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Affiliation(s)
| | - Irini Evnouchidou
- Université de Paris, Centre de recherche sur l'inflammation, INSERM U1149, CNRS ERL8252, Paris, France.,Inovarion, Paris, France
| | - Vivien Caillens
- Université de Paris, Centre de recherche sur l'inflammation, INSERM U1149, CNRS ERL8252, Paris, France
| | - Carole Drajac
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jou-en-Josas, France
| | - Sabine Riffault
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jou-en-Josas, France
| | - Peter van Endert
- Université de Paris, Centre de recherche sur l'inflammation, INSERM U1149, CNRS ERL8252, Paris, France.,Université de Paris, INSERM Unité 1151, CNRS UMR 8253, Paris, France.,Service d'immunologie biologique, AP-HP, Hôpital Necker, Paris, France
| | - Loredana Saveanu
- Université de Paris, Centre de recherche sur l'inflammation, INSERM U1149, CNRS ERL8252, Paris, France
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18
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Hallberg M, Larhed M. From Angiotensin IV to Small Peptidemimetics Inhibiting Insulin-Regulated Aminopeptidase. Front Pharmacol 2020; 11:590855. [PMID: 33178027 PMCID: PMC7593869 DOI: 10.3389/fphar.2020.590855] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 09/18/2020] [Indexed: 12/26/2022] Open
Abstract
It was reported three decades ago that intracerebroventricular injection of angiotensin IV (Ang IV, Val-Tyr-Ile-His-Pro-Phe) improved memory and learning in the rat. There are several explanations for these positive effects of the hexapeptide and related analogues on cognition available in the literature. In 2001, it was proposed that the insulin-regulated aminopeptidase (IRAP) is a main target for Ang IV and that Ang IV serves as an inhibitor of the enzyme. The focus of this review is the efforts to stepwise transform the hexapeptide into more drug-like Ang IV peptidemimetics serving as IRAP inhibitors. Moreover, the discovery of IRAP inhibitors by virtual and substance library screening and direct design applying knowledge of the structure of IRAP and of related enzymes is briefly presented.
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Affiliation(s)
- Mathias Hallberg
- The Beijer Laboratory, Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, BMC, Uppsala University, Uppsala, Sweden
| | - Mats Larhed
- Department of Medicinal Chemistry, Science for Life Laboratory, BMC, Uppsala University, Uppsala, Sweden
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19
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Todorov P, Peneva P, Tchekalarova J, Georgieva S, Rangelov M, Todorova N. Structure-activity relationship study on new hemorphin-4 analogues containing steric restricted amino acids moiety for evaluation of their anticonvulsant activity. Amino Acids 2020; 52:1375-1390. [PMID: 33011823 DOI: 10.1007/s00726-020-02898-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/28/2020] [Indexed: 12/31/2022]
Abstract
In the present study, several new analogues of hemorphin-4, modified with unnatural conformationally restricted amino acids followed the structure Aaa-Tyr-Xxx-Trp-Thr-NH2, where Aaa is the low-molecular-weight lipophilic adamantyl building block, and Xxx is Ac5c (1-aminocyclopentanecarboxylic acid) or Ac6c (1-aminocyclohexane carboxylic acid) was synthesized, characterized and investigated for anticonvulsant activity in three seizure tests, the maximal electroshock test (MES), 6-Hz psychomotor seizure test and timed intravenous pentylenetetrazole infusion (ivPTZ) test. The acute neurological toxicity was determined using the rota-rod test. The new synthetic neuropeptide analogues were prepared by solid-phase peptide synthesis-Fmoc chemistry and were evaluated in three doses of 1, 3 and 5 µg, respectively, administered intracerebroventricularly in male ICR mice. The physicochemical properties of these peptide analogues were evaluated as pKa and pI values were calculated using potentiometry. The IR spectrum of the compounds was recorded and the characteristic lines of both adamantane moiety and the peptide backbone were registered in the wavelength range from 4000 to 400 cm-1. The hexapeptide Ang IV was used as a positive control. From the six synthesized peptide analogues, the P4-5 was the most active at doses of 1 and 3 µg in the three seizure tests. The order of potency of other peptides was as follows: P4 > P4-3 = P4-4 > P4-2 > Ang IV in MES, P4-4 ≥ P4-1 > P4-3 > P4-2 > P4 > Ang IV in 6-Hz test and P4-4 = P4-3 > P4-2 = P4 > Ang IV in ivPTZ test. None of the peptides displayed neurotoxicity in the rota-rod test. Docking study results suggest that direct H-bonding and ionic interactions between our synthetic ligands and residues, responsible for coordination of Zn2+ along with hydrophobic interactions between our ligands and IRAP active site are the most important for the ligand binding. The results propose that incorporation of adamantane and cycloalkane building blocks in the peptide chain of the hemorphin-4 scaffold is important for the potential high biological activity.
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Affiliation(s)
- Petar Todorov
- Department of Organic Chemistry, University of Chemical Technology and Metallurgy, 1756, Sofia, Bulgaria.
| | - Petia Peneva
- Department of Organic Chemistry, University of Chemical Technology and Metallurgy, 1756, Sofia, Bulgaria
| | - Jana Tchekalarova
- Institute of Neurobiology, Bulgarian Academy of Sciences, 1113, Sofia, Bulgaria
| | - Stela Georgieva
- Department of Analytical Chemistry, University of Chemical Technology and Metallurgy, 1756, Sofia, Bulgaria
| | - Miroslav Rangelov
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, 1113, Sofia, Bulgaria
| | - Nadezhda Todorova
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1113, Sofia, Bulgaria
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20
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Vear A, Gaspari T, Thompson P, Chai SY. Is There an Interplay Between the Functional Domains of IRAP? Front Cell Dev Biol 2020; 8:585237. [PMID: 33134302 PMCID: PMC7550531 DOI: 10.3389/fcell.2020.585237] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/08/2020] [Indexed: 01/16/2023] Open
Abstract
As a member of the M1 family of aminopeptidases, insulin regulated aminopeptidase (IRAP) is characterized by distinct binding motifs at the active site in the C-terminal domain that mediate the catalysis of peptide substrates. However, what makes IRAP unique in this family of enzymes is that it also possesses trafficking motifs at the N-terminal domain which regulate the movement of IRAP within different intracellular compartments. Research on the role of IRAP has focused predominantly on the C-terminus catalytic domain in different physiological and pathophysiological states ranging from pregnancy to memory loss. Many of these studies have utilized IRAP inhibitors, that bind competitively to the active site of IRAP, to explore the functional significance of its catalytic activity. However, it is unknown whether these inhibitors are able to access intracellular sites where IRAP is predominantly located in a basal state as the enzyme may need to be at the cell surface for the inhibitors to mediate their effects. This property of IRAP has often been overlooked. Interestingly, in some pathophysiological states, the distribution of IRAP is altered. This, together with the fact that IRAP possesses trafficking motifs, suggest the localization of IRAP may play an important role in defining its physiological or pathological functions and provide insights into the interplay between the two functional domains of the protein.
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Affiliation(s)
- Anika Vear
- Department of Physiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Tracey Gaspari
- Department of Pharmacology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Philip Thompson
- Department of Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Siew Yeen Chai
- Department of Physiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
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21
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Barlow N, Thompson PE. IRAP Inhibitors: M1-Aminopeptidase Family Inspiration. Front Pharmacol 2020; 11:585930. [PMID: 33101040 PMCID: PMC7546331 DOI: 10.3389/fphar.2020.585930] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 09/04/2020] [Indexed: 11/24/2022] Open
Abstract
The insulin regulated aminopeptidase (IRAP) has been proposed as an important therapeutic target for indications including Alzheimer’s disease and immune disorders. To date, a number of IRAP inhibitor designs have been investigated but the total number of molecules investigated remains quite small. As a member the M1 aminopeptidase family, IRAP shares numerous structural features with the other M1 aminopeptidases. The study of those enzymes and the development of inhibitors provide key learnings and new approaches and are potential sources of inspiration for future IRAP inhibitors.
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Affiliation(s)
- Nicholas Barlow
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Philip E Thompson
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
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22
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Georgiadis D, Ziotopoulou A, Kaloumenou E, Lelis A, Papasava A. The Discovery of Insulin-Regulated Aminopeptidase (IRAP) Inhibitors: A Literature Review. Front Pharmacol 2020; 11:585838. [PMID: 33071797 PMCID: PMC7538644 DOI: 10.3389/fphar.2020.585838] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 08/24/2020] [Indexed: 12/15/2022] Open
Abstract
Insulin-Regulated Aminopeptidase (IRAP, EC 3.4.11.3) is a multi-tasking member of the M1 family of zinc aminopeptidases. Among its diverse biological functions, IRAP is a regulator of oxytocin levels during late stages of pregnancy, it affects cellular glucose uptake by trafficking of the glucose transporter type 4 and it mediates antigen cross-presentation by dendritic cells. Accumulating evidence show that pharmacological inhibition of IRAP may hold promise as a valid approach for the treatment of several pathological states such as memory disorders, neurodegenerative diseases, etc. Aiming to the investigation of physiological roles of IRAP and therapeutic potential of its regulation, intense research efforts have been dedicated to the discovery of small-molecule inhibitors. Moreover, reliable structure-activity relationships have been largely facilitated by recent crystal structures of IRAP and detailed computational studies. This review aims to summarize efforts of medicinal chemists toward the design and development of IRAP inhibitors, with special emphasis to factors affecting inhibitor selectivity.
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Affiliation(s)
- Dimitris Georgiadis
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
| | - Angeliki Ziotopoulou
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
| | - Eleni Kaloumenou
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
| | - Angelos Lelis
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
| | - Antonia Papasava
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
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23
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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] [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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24
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Engen K, Vanga SR, Lundbäck T, Agalo F, Konda V, Jensen AJ, Åqvist J, Gutiérrez‐de‐Terán H, Hallberg M, Larhed M, Rosenström U. Synthesis, Evaluation and Proposed Binding Pose of Substituted Spiro-Oxindole Dihydroquinazolinones as IRAP Inhibitors. ChemistryOpen 2020; 9:325-337. [PMID: 32154052 PMCID: PMC7050655 DOI: 10.1002/open.201900344] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/23/2020] [Indexed: 12/13/2022] Open
Abstract
Insulin-regulated aminopeptidase (IRAP) is a new potential macromolecular target for drugs aimed for treatment of cognitive disorders. Inhibition of IRAP by angiotensin IV (Ang IV) improves the memory and learning in rats. The majority of the known IRAP inhibitors are peptidic in character and suffer from poor pharmacokinetic properties. Herein, we present a series of small non-peptide IRAP inhibitors derived from a spiro-oxindole dihydroquinazolinone screening hit (pIC50 5.8). The compounds were synthesized either by a simple microwave (MW)-promoted three-component reaction, or by a two-step one-pot procedure. For decoration of the oxindole ring system, rapid MW-assisted Suzuki-Miyaura cross-couplings (1 min) were performed. A small improvement of potency (pIC50 6.6 for the most potent compound) and an increased solubility could be achieved. As deduced from computational modelling and MD simulations it is proposed that the S-configuration of the spiro-oxindole dihydroquinazolinones accounts for the inhibition of IRAP.
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Affiliation(s)
- Karin Engen
- Department of Medicinal ChemistryUppsala UniversitySE-751 23UppsalaSWEDEN
| | | | - Thomas Lundbäck
- Chemical Biology Consortium Sweden, Science for Life Laboratory, Department of Medical Biochemistry and BiophysicsKarolinska InstitutetSE-171 65SolnaSWEDEN
- Mechanistic Biology & Profiling, Discovery Sciences, R&DAstraZenecaSE-431 83GöteborgSWEDEN
| | - Faith Agalo
- Department of Medicinal ChemistryUppsala UniversitySE-751 23UppsalaSWEDEN
| | - Vivek Konda
- Department of Medicinal ChemistryUppsala UniversitySE-751 23UppsalaSWEDEN
| | - Annika Jenmalm Jensen
- Chemical Biology Consortium Sweden, Science for Life Laboratory, Department of Medical Biochemistry and BiophysicsKarolinska InstitutetSE-171 65SolnaSWEDEN
| | - Johan Åqvist
- Department of Cell and Molecular BiologyUppsala UniversitySE-751 23UppsalaSWEDEN
| | - Hugo Gutiérrez‐de‐Terán
- Science for Life Laboratory, Department of Cell and Molecular BiologyUppsala UniversitySE-751 23UppsalaSWEDEN
| | - Mathias Hallberg
- The Beijer Laboratory, Department of Pharmaceutical BiosciencesUppsala UniversitySE-751 23UppsalaSWEDEN
| | - Mats Larhed
- Science for Life Laboratory, Department of Medicinal ChemistryUppsala UniversitySE-751 23UppsalaSWEDEN
| | - Ulrika Rosenström
- Department of Medicinal ChemistryUppsala UniversitySE-751 23UppsalaSWEDEN
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25
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Barlow N, Vanga SR, Sävmarker J, Sandström A, Burns P, Hallberg A, Åqvist J, Gutiérrez-de-Terán H, Hallberg M, Larhed M, Chai SY, Thompson PE. Macrocyclic peptidomimetics as inhibitors of insulin-regulated aminopeptidase (IRAP). RSC Med Chem 2020; 11:234-244. [PMID: 33479630 DOI: 10.1039/c9md00485h] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 11/21/2019] [Indexed: 12/25/2022] Open
Abstract
Macrocyclic analogues of the linear hexapeptide, angiotensin IV (AngIV) have proved to be potent inhibitors of insulin-regulated aminopeptidase (IRAP, oxytocinase, EC 3.4.11.3). Along with higher affinity, macrocycles may also offer better metabolic stability, membrane permeability and selectivity, however predicting the outcome of particular cycle modifications is challenging. Here we describe the development of a series of macrocyclic IRAP inhibitors with either disulphide, olefin metathesis or lactam bridges and variations of ring size and other functionality. The binding mode of these compounds is proposed based on molecular dynamics analysis. Estimation of binding affinities (ΔG) and relative binding free energies (ΔΔG) with the linear interaction energy (LIE) method and free energy perturbation (FEP) method showed good general agreement with the observed inhibitory potency. Experimental and calculated data highlight the cumulative importance of an intact N-terminal peptide, the specific nature of the macrocycle, the phenolic oxygen and the C-terminal functionality.
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Affiliation(s)
- Nicholas Barlow
- Department of Medicinal Chemistry , BMC , Uppsala University , P.O. Box 574 , SE-751 23 Uppsala , Sweden.,Medicinal Chemistry , Monash Institute of Pharmaceutical Sciences , Parkville , Victoria 3052 , Australia .
| | - Sudarsana Reddy Vanga
- Department of Cell and Molecular Biology , BMC , Uppsala University , Box 596 , SE-751 24 Uppsala , Sweden
| | - Jonas Sävmarker
- The Beijer Laboratory , Department of Medicinal Chemistry , BMC , Uppsala University , P.O. Box 574 , SE-751 23 Uppsala , Sweden
| | - Anja Sandström
- The Beijer Laboratory , Department of Medicinal Chemistry , BMC , Uppsala University , P.O. Box 574 , SE-751 23 Uppsala , Sweden
| | - Peta Burns
- Biomedicine Discovery Institute , Department of Physiology , Monash University , Clayton , Victoria 3800 , Australia
| | - Anders Hallberg
- Department of Medicinal Chemistry , BMC , Uppsala University , P.O. Box 574 , SE-751 23 Uppsala , Sweden
| | - Johan Åqvist
- Department of Cell and Molecular Biology , BMC , Uppsala University , Box 596 , SE-751 24 Uppsala , Sweden
| | - Hugo Gutiérrez-de-Terán
- Department of Cell and Molecular Biology , BMC , Uppsala University , Box 596 , SE-751 24 Uppsala , Sweden
| | - Mathias Hallberg
- The Beijer Laboratory , Department of Pharmaceutical Biosciences , Division of Biological Research on Drug Dependence , BMC , Uppsala University , P.O. Box 591 , SE-751 24 Uppsala , Sweden
| | - Mats Larhed
- Department of Medicinal Chemistry , BMC , Uppsala University , P.O. Box 574 , SE-751 23 Uppsala , Sweden.,Science for Life Laboratory , Department of Medicinal Chemistry , BMC , Uppsala University , SE-751 24 Uppsala , Sweden
| | - Siew Yeen Chai
- Biomedicine Discovery Institute , Department of Physiology , Monash University , Clayton , Victoria 3800 , Australia
| | - Philip E Thompson
- Medicinal Chemistry , Monash Institute of Pharmaceutical Sciences , Parkville , Victoria 3052 , Australia .
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26
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Hanson AL, Morton CJ, Parker MW, Bessette D, Kenna TJ. The genetics, structure and function of the M1 aminopeptidase oxytocinase subfamily and their therapeutic potential in immune-mediated disease. Hum Immunol 2019; 80:281-289. [DOI: 10.1016/j.humimm.2018.11.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 10/16/2018] [Accepted: 11/05/2018] [Indexed: 12/31/2022]
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27
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Homogentisate 1,2-dioxygenase (HGD) gene variants, their analysis and genotype-phenotype correlations in the largest cohort of patients with AKU. Eur J Hum Genet 2019; 27:888-902. [PMID: 30737480 DOI: 10.1038/s41431-019-0354-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 01/12/2019] [Accepted: 01/24/2019] [Indexed: 11/08/2022] Open
Abstract
Alkaptonuria (AKU) is a rare metabolic disorder caused by a deficient enzyme in the tyrosine degradation pathway, homogentisate 1,2-dioxygenase (HGD). In 172 AKU patients from 39 countries, we identified 28 novel variants of the HGD gene, which include three larger genomic deletions within this gene discovered via self-designed multiplex ligation-dependent probe amplification (MLPA) probes. In addition, using a reporter minigene assay, we provide evidence that three of eight tested variants potentially affecting splicing cause exon skipping or cryptic splice-site activation. Extensive bioinformatics analysis of novel missense variants, and of the entire HGD monomer, confirmed mCSM as an effective computational tool for evaluating possible enzyme inactivation mechanisms. For the first time for AKU, a genotype-phenotype correlation study was performed for the three most frequent HGD variants identified in the Suitability Of Nitisinone in Alkaptonuria 2 (SONIA2) study. We found a small but statistically significant difference in urinary homogentisic acid (HGA) excretion, corrected for dietary protein intake, between variants leading to 1% or >30% residual HGD activity. There was, interestingly, no difference in serum levels or absolute urinary excretion of HGA, or clinical symptoms, indicating that protein intake is more important than differences in HGD variants for the amounts of HGA that accumulate in the body of AKU patients.
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28
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Wang F, Hu X, Zhou B. Structural characterization of plasmodial aminopeptidase: a combined molecular docking and QSAR-based in silico approaches. Mol Divers 2019; 23:965-984. [DOI: 10.1007/s11030-019-09921-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 01/18/2019] [Indexed: 11/24/2022]
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29
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Salomon E, Schmitt M, Marapaka AK, Stamogiannos A, Revelant G, Schmitt C, Alavi S, Florent I, Addlagatta A, Stratikos E, Tarnus C, Albrecht S. Aminobenzosuberone Scaffold as a Modular Chemical Tool for the Inhibition of Therapeutically Relevant M1 Aminopeptidases. Molecules 2018; 23:molecules23102607. [PMID: 30314342 PMCID: PMC6222927 DOI: 10.3390/molecules23102607] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 10/08/2018] [Accepted: 10/10/2018] [Indexed: 01/22/2023] Open
Abstract
The synthesis of racemic substituted 7-amino-5,7,8,9-tetrahydrobenzocyclohepten-6-one hydrochlorides was optimized to enhance reproducibility and increase the overall yield. In order to investigate their specificity, series of enzyme inhibition assays were carried out against a diversity of proteases, covering representative members of aspartic, cysteine, metallo and serine endopeptidases and including eight members of the monometallic M1 family of aminopeptidases as well as two members of the bimetallic M17 and M28 aminopeptidase families. This aminobenzosuberone scaffold indeed demonstrated selective inhibition of M1 aminopeptidases to the exclusion of other tested protease families; it was particularly potent against mammalian APN and its bacterial/parasitic orthologues EcPepN and PfAM1.
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Affiliation(s)
- Emmanuel Salomon
- Laboratoire d'Innovation Moléculaire et Applications, Université de Haute-Alsace, Université de Strasbourg, CNRS, 68093 Mulhouse, France.
| | - Marjorie Schmitt
- Laboratoire d'Innovation Moléculaire et Applications, Université de Haute-Alsace, Université de Strasbourg, CNRS, 68093 Mulhouse, France.
| | - Anil Kumar Marapaka
- Centre for Chemical Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, Telangana, India.
- Academy of Scientific and Innovative Research (AcSIR), Rafi Marg, New Dehli 110001, India.
| | - Athanasios Stamogiannos
- Protein Chemistry Laboratory, INRASTES, National Centre for Scientific Research Demokritos, Agia Paraskevi, 15310 Athens, Greece.
| | - Germain Revelant
- Laboratoire d'Innovation Moléculaire et Applications, Université de Haute-Alsace, Université de Strasbourg, CNRS, 68093 Mulhouse, France.
| | - Céline Schmitt
- Laboratoire d'Innovation Moléculaire et Applications, Université de Haute-Alsace, Université de Strasbourg, CNRS, 68093 Mulhouse, France.
| | - Sarah Alavi
- Laboratoire d'Innovation Moléculaire et Applications, Université de Haute-Alsace, Université de Strasbourg, CNRS, 68093 Mulhouse, France.
| | - Isabelle Florent
- Molécules de Communication et Adaptation des Micro-organismes, Muséum National d'Histoire Naturelle, CNRS, 75231 Paris, France.
| | - Anthony Addlagatta
- Centre for Chemical Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, Telangana, India.
- Academy of Scientific and Innovative Research (AcSIR), Rafi Marg, New Dehli 110001, India.
| | - Efstratios Stratikos
- Protein Chemistry Laboratory, INRASTES, National Centre for Scientific Research Demokritos, Agia Paraskevi, 15310 Athens, Greece.
| | - Céline Tarnus
- Laboratoire d'Innovation Moléculaire et Applications, Université de Haute-Alsace, Université de Strasbourg, CNRS, 68093 Mulhouse, France.
| | - Sébastien Albrecht
- Laboratoire d'Innovation Moléculaire et Applications, Université de Haute-Alsace, Université de Strasbourg, CNRS, 68093 Mulhouse, France.
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30
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Marapaka AK, Pillalamarri V, Gumpena R, Haque N, Bala SC, Jangam A, Addlagatta A. Discovery, Structural and Biochemical Studies of a rare Glu/Asp Specific M1 Class Aminopeptidase from Legionella pneumophila. Int J Biol Macromol 2018; 120:1111-1118. [PMID: 30172821 DOI: 10.1016/j.ijbiomac.2018.08.172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 08/24/2018] [Accepted: 08/28/2018] [Indexed: 10/28/2022]
Abstract
Aminopeptidases catalyze the hydrolysis of amino acids from the N-terminus of protein or peptide substrates. M1 family aminopeptidases are important for the pathogenicity of bacteria and play critical role in many physiological processes such as protein maturation, regulation of peptide hormone levels in humans. Most of the M1 family aminopeptidases reported till date display broad substrates specificity, mostly specific to basic and hydrophobic residues. In the current study we report the discovery of a novel M1 class aminopeptidase from Legionella pneumophila (LePepA), which cleaves only acidic residues. Biochemical and structural studies reveal that the S1 pocket is polar and positively charged. Bioinformatic analysis suggests that such active site is unique to only Legionella species and probably evolved for special needs of the microbe. Given its specific activity, LePepA could be useful in specific biotechnological applications.
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Affiliation(s)
- Anil Kumar Marapaka
- Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500 007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Rafi Marg, New Delhi 110001, India
| | - Vijaykumar Pillalamarri
- Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500 007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Rafi Marg, New Delhi 110001, India
| | - Rajesh Gumpena
- Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500 007, Telangana, India
| | - Neshatul Haque
- Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500 007, Telangana, India
| | - Sandeep Chowdary Bala
- Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500 007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Rafi Marg, New Delhi 110001, India
| | - Aruna Jangam
- Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500 007, Telangana, India
| | - Anthony Addlagatta
- Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500 007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Rafi Marg, New Delhi 110001, India.
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31
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Vanga SR, Sävmarker J, Ng L, Larhed M, Hallberg M, Åqvist J, Hallberg A, Chai SY, Gutiérrez-de-Terán H. Structural Basis of Inhibition of Human Insulin-Regulated Aminopeptidase (IRAP) by Aryl Sulfonamides. ACS OMEGA 2018; 3:4509-4521. [PMID: 30023895 PMCID: PMC6045421 DOI: 10.1021/acsomega.8b00595] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 04/16/2018] [Indexed: 05/07/2023]
Abstract
The insulin-regulated aminopeptidase (IRAP) is a membrane-bound zinc metallopeptidase with many important regulatory functions. It has been demonstrated that inhibition of IRAP by angiotensin IV (Ang IV) and other peptides, as well as more druglike inhibitors, improves cognition in several rodent models. We recently reported a series of aryl sulfonamides as small-molecule IRAP inhibitors and a promising scaffold for pharmacological intervention. We have now expanded with a number of derivatives, report their stability in liver microsomes, and characterize the activity of the whole series in a new assay performed on recombinant human IRAP. Several compounds, such as the new fluorinated derivative 29, present submicromolar affinity and high metabolic stability. Starting from the two binding modes previously proposed for the sulfonamide scaffold, we systematically performed molecular dynamics simulations and binding affinity estimation with the linear interaction energy method for the full compound series. The significant agreement with experimental affinities suggests one of the binding modes, which was further confirmed by the excellent correlation for binding affinity differences between the selected pair of compounds obtained by rigorous free energy perturbation calculations. The new experimental data and the computationally derived structure-activity relationship of the sulfonamide series provide valuable information for further lead optimization of novel IRAP inhibitors.
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Affiliation(s)
- Sudarsana Reddy Vanga
- Department
of Cell and Molecular Biology, BMC, Box 596, Uppsala University, SE-751
24 Uppsala, Sweden
| | - Jonas Sävmarker
- Department of Medicinal Chemistry and Science for Life Laboratory, Department
of Medicinal Chemistry, Uppsala University,
BMC, SE-751 24 Uppsala, Sweden
| | - Leelee Ng
- Biomedicine
Discovery Institute, Department of Physiology, Monash University, Clayton, Victoria 3800, Australia
| | - Mats Larhed
- Department of Medicinal Chemistry and Science for Life Laboratory, Department
of Medicinal Chemistry, Uppsala University,
BMC, SE-751 24 Uppsala, Sweden
| | - Mathias Hallberg
- The
Beijer Laboratory, Department of Pharmaceutical Biosciences, Division
of Biological Research on Drug Dependence, Uppsala University, BMC, SE-751 23 Uppsala, Sweden
| | - Johan Åqvist
- Department
of Cell and Molecular Biology, BMC, Box 596, Uppsala University, SE-751
24 Uppsala, Sweden
| | - Anders Hallberg
- Department of Medicinal Chemistry and Science for Life Laboratory, Department
of Medicinal Chemistry, Uppsala University,
BMC, SE-751 24 Uppsala, Sweden
| | - Siew Yeen Chai
- Biomedicine
Discovery Institute, Department of Physiology, Monash University, Clayton, Victoria 3800, Australia
- E-mail: . Phone: +61 3 990 52515. Fax: +61 3 990 52547 (S.Y.C.)
| | - Hugo Gutiérrez-de-Terán
- Department
of Cell and Molecular Biology, BMC, Box 596, Uppsala University, SE-751
24 Uppsala, Sweden
- E-mail: . Phone: +46 18 471 5056. Fax: +46 18 53 69 71 (H.G.-d.-T.)
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32
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Mpakali A, Maben Z, Stern LJ, Stratikos E. Molecular pathways for antigenic peptide generation by ER aminopeptidase 1. Mol Immunol 2018; 113:50-57. [PMID: 29678301 DOI: 10.1016/j.molimm.2018.03.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 01/11/2018] [Accepted: 03/29/2018] [Indexed: 10/17/2022]
Abstract
Endoplasmic Reticulum aminopeptidase 1 (ERAP1) is an intracellular enzyme that can generate or destroy potential peptide ligands for MHC class I molecules. ERAP1 activity influences the cell-surface immunopeptidome and epitope immunodominance patterns but in complex and poorly understood manners. Two main distinct pathways have been proposed to account for ERAP1's effects on the nature and quantity of MHCI-bound peptides: i) ERAP1 trims peptides in solution, generating the correct length for binding to MHCI or overtrimming peptides so that they are too short to bind, and ii) ERAP1 trims peptides while they are partially bound onto MHCI in manner that leaves the peptide amino terminus accessible. For both pathways, once an appropriate length peptide is generated it could bind conventionally to MHCI, competing with further trimming by ERAP1. The two pathways, although not necessarily mutually exclusive, provide distinct vantage points for understanding of the rules behind the generation of the immunopeptidome. Resolution of the mechanistic details of ERAP1-mediated antigenic peptide generation can have important consequences for pharmacological efforts to regulate the immunopeptidome for therapeutic applications, and for understanding association of ERAP1 alleles with susceptibility to autoimmune disease and cancer. We review current evidence in support of these two pathways and discuss their relative importance and potential complementarity.
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Affiliation(s)
| | - Zachary Maben
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Lawrence J Stern
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA.
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33
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Pires DEV, Kaminskas LM, Ascher DB. Prediction and Optimization of Pharmacokinetic and Toxicity Properties of the Ligand. Methods Mol Biol 2018; 1762:271-284. [PMID: 29594777 DOI: 10.1007/978-1-4939-7756-7_14] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A crucial factor for the approval and success of any drug is how it behaves in the body. Many drugs, however, do not reach the market due to poor efficacy or unacceptable side effects. It is therefore important to take these into consideration early in the drug development process, both in the prioritization of potential hits, and optimization of lead compounds. In silico approaches offer a cost and time-effective approach to rapidly screen and optimize pharmacokinetic and toxicity properties. Here we demonstrate the use of the comprehensive analysis system pkCSM, to allow early identification of potential problems, prioritization of hits, and optimization of leads.
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Affiliation(s)
| | - Lisa M Kaminskas
- School of Biomedical Sciences, University of Queensland, St. Lucia, QLD, Australia
| | - David B Ascher
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC, Australia.
- Department of Biochemistry, University of Cambridge, Cambridge, UK.
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34
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Elkins EA, Walti KA, Newberry KE, Lema SC. Identification of an oxytocinase/vasopressinase-like leucyl-cystinyl aminopeptidase (LNPEP) in teleost fish and evidence for hypothalamic mRNA expression linked to behavioral social status. Gen Comp Endocrinol 2017; 250:58-69. [PMID: 28596078 DOI: 10.1016/j.ygcen.2017.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 06/03/2017] [Accepted: 06/04/2017] [Indexed: 02/06/2023]
Abstract
The vasotocin/vasopressin and isotocin/mesotocin/oxytocin family of nonapeptides regulate social behaviors and physiological functions associated with reproductive physiology and osmotic balance. While experimental and correlative studies provide evidence for these nonapeptides as modulators of behavior across all classes of vertebrates, mechanisms for nonapeptide inactivation in regulating these functions have been largely overlooked. Leucyl-cystinyl aminopeptidase (LNPEP) - also known as vasopressinase, oxytocinase, placental leucine aminopeptidase (P-LAP), and insulin-regulated aminopeptidase (IRAP) - is a membrane-bound zinc-dependent metalloexopeptidase enzyme that inactivates vasopressin, oxytocin, and select other cyclic polypeptides. In humans, LNPEP plays a key role in the clearance of oxytocin during pregnancy. However, the evolutionary diversity, expression distribution, and functional roles of LNPEP remain unresolved for other vertebrates. Here, we isolated and sequenced a full-length cDNA encoding a LNPEP-like polypeptide of 1033 amino acids from the ovarian tissue of Amargosa pupfish, Cyprinodon nevadensis. This deduced polypeptide exhibited high amino acid identity to human LNPEP both in the protein's active domain that includes the peptide binding site and zinc cofactor binding motif (53.1% identity), and in an intracellular region that distinguishes LNPEP from other aminopeptidases (70.3% identity). Transcripts encoding this LNPEP enzyme (lnpep) were detected at highest relative abundance in the gonads, hypothalamus, forebrain, optic tectum, gill and skeletal muscle of adult pupfish. Further evaluation of lnpep transcript abundance in the brain of sexually-mature pupfish revealed that lnpep mRNAs were elevated in the hypothalamus of socially subordinate females and males, and at lower abundance in the telencephalon of socially dominant males compared to dominant females. These findings provide evidence of an association between behavioral social status and hypothalamic lnpep transcript abundance and suggest that variation in the rate of VT/IT peptide inactivation by LNPEP may be a contributing component in the mechanism whereby nonapeptides regulate social behavior.
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Affiliation(s)
- Emma A Elkins
- Biological Sciences Department, Center for Coastal Marine Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Kayla A Walti
- Biological Sciences Department, Center for Coastal Marine Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Kathryn E Newberry
- Biological Sciences Department, Center for Coastal Marine Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Sean C Lema
- Biological Sciences Department, Center for Coastal Marine Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA.
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35
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Mutations at protein-protein interfaces: Small changes over big surfaces have large impacts on human health. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017; 128:3-13. [DOI: 10.1016/j.pbiomolbio.2016.10.002] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 10/15/2016] [Accepted: 10/19/2016] [Indexed: 12/22/2022]
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36
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Yang W, Riley BT, Lei X, Porebski BT, Kass I, Buckle AM, McGowan S. Generation of AMBER force field parameters for zinc centres of M1 and M17 family aminopeptidases. J Biomol Struct Dyn 2017; 36:2595-2604. [DOI: 10.1080/07391102.2017.1364669] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Wei Yang
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Blake T. Riley
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Xiangyun Lei
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive N.W., Atlanta, GA, 30332-0100, USA
| | - Benjamin T. Porebski
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Itamar Kass
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
- Victorian Life Sciences Computation Centre, Monash University, Clayton 3800, Victoria, Australia
| | - Ashley M. Buckle
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Sheena McGowan
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
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37
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Papakyriakou A, Stratikos E. The Role of Conformational Dynamics in Antigen Trimming by Intracellular Aminopeptidases. Front Immunol 2017; 8:946. [PMID: 28824657 PMCID: PMC5545687 DOI: 10.3389/fimmu.2017.00946] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 07/24/2017] [Indexed: 11/13/2022] Open
Abstract
Antigenic peptides presented by the major histocompatibility complex class I (MHC-I) molecules for recognition by cytotoxic T-lymphocytes are processed by members of the oxytocinase sub-family of M1 aminopeptidases ERAP1, ERAP2, and IRAP. These three homologous zinc metallopeptidases trim N-terminally extended precursor antigenic peptides down to the correct length for loading onto the MHC-I but can also destroy some antigenic peptides by over-trimming, therefore, influencing the antigenic peptide repertoire and immunodominance hierarchy. Polymorphic variation has been found to affect their trimming function and predispose to human disease in complex and poorly understood patterns. Structural and biochemical analysis have pointed toward a complicated trimming mechanism that involves a major conformational transition during each catalytic cycle. Here, we provide an overview of current knowledge on the structure and mechanism of action of those enzymes with a focus on the proposed key role of conformational dynamics in their function.
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Affiliation(s)
- Athanasios Papakyriakou
- Centre for Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Southampton, United Kingdom.,National Centre for Scientific Research "Demokritos", Athens, Greece
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38
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Albanaz ATS, Rodrigues CHM, Pires DEV, Ascher DB. Combating mutations in genetic disease and drug resistance: understanding molecular mechanisms to guide drug design. Expert Opin Drug Discov 2017; 12:553-563. [PMID: 28490289 DOI: 10.1080/17460441.2017.1322579] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Mutations introduce diversity into genomes, leading to selective changes and driving evolution. These changes have contributed to the emergence of many of the current major health concerns of the 21st century, from the development of genetic diseases and cancers to the rise and spread of drug resistance. The experimental systematic testing of all mutations in a system of interest is impractical and not cost-effective, which has created interest in the development of computational tools to understand the molecular consequences of mutations to aid and guide rational experimentation. Areas covered: Here, the authors discuss the recent development of computational methods to understand the effects of coding mutations to protein function and interactions, particularly in the context of the 3D structure of the protein. Expert opinion: While significant progress has been made in terms of innovative tools to understand and quantify the different range of effects in which a mutation or a set of mutations can give rise to a phenotype, a great gap still exists when integrating these predictions and drawing causality conclusions linking variants. This often requires a detailed understanding of the system being perturbed. However, as part of the drug development process it can be used preemptively in a similar fashion to pharmacokinetics predictions, to guide development of therapeutics to help guide the design and analysis of clinical trials, patient treatment and public health policy strategies.
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Affiliation(s)
- Amanda T S Albanaz
- a Centro de Pesquisas René Rachou, FIOCRUZ , Belo Horizonte , MG , Brazil.,b Department of Biochemistry and Immunology , Universidade Federal de Minas Gerais , Belo Horizonte , Minas Gerais , Brazil
| | - Carlos H M Rodrigues
- a Centro de Pesquisas René Rachou, FIOCRUZ , Belo Horizonte , MG , Brazil.,b Department of Biochemistry and Immunology , Universidade Federal de Minas Gerais , Belo Horizonte , Minas Gerais , Brazil
| | - Douglas E V Pires
- a Centro de Pesquisas René Rachou, FIOCRUZ , Belo Horizonte , MG , Brazil
| | - David B Ascher
- a Centro de Pesquisas René Rachou, FIOCRUZ , Belo Horizonte , MG , Brazil.,c Department of Biochemistry , University of Cambridge , Cambridge , Cambridgeshire , UK.,d Department of Biochemistry and Molecular Biology , University of Melbourne , Melbourne , Victoria , Australia
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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] [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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Drinkwater N, Lee J, Yang W, Malcolm TR, McGowan S. M1 aminopeptidases as drug targets: broad applications or therapeutic niche? FEBS J 2017; 284:1473-1488. [PMID: 28075056 PMCID: PMC7164018 DOI: 10.1111/febs.14009] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 12/12/2016] [Accepted: 01/09/2017] [Indexed: 12/30/2022]
Abstract
M1 aminopeptidase enzymes are a diverse family of metalloenzymes characterized by conserved structure and reaction specificity. Excluding viruses, M1 aminopeptidases are distributed throughout all phyla, and have been implicated in a wide range of functions including cell maintenance, growth and development, and defense. The structure and catalytic mechanism of M1 aminopeptidases are well understood, and make them ideal candidates for the design of small‐molecule inhibitors. As a result, many research groups have assessed their utility as therapeutic targets for both infectious and chronic diseases of humans, and many inhibitors with a range of target specificities and potential therapeutic applications have been developed. Herein, we have aimed to address these studies, to determine whether the family of M1 aminopeptidases does in fact present a universal target for the treatment of a diverse range of human diseases. Our analysis indicates that early validation of M1 aminopeptidases as therapeutic targets is often overlooked, which prevents the enzymes from being confirmed as drug targets. This validation cannot be neglected, and needs to include a thorough characterization of enzymes’ specific roles within complex physiological pathways. Furthermore, any chemical probes used in target validation must be carefully designed to ensure that specificity over the closely related enzymes has been achieved. While many drug discovery programs that target M1 aminopeptidases remain in their infancy, certain inhibitors have shown promise for the treatment of a range of conditions including malaria, hypertension, and cancer.
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Affiliation(s)
- Nyssa Drinkwater
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Melbourne, Vic., Australia
| | - Jisook Lee
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Vic., Australia
| | - Wei Yang
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Melbourne, Vic., Australia
| | - Tess R Malcolm
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Melbourne, Vic., Australia
| | - Sheena McGowan
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Melbourne, Vic., Australia
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Diwakarla S, Nylander E, Grönbladh A, Vanga SR, Shamsudin Y, Gutiérrez-de-Terán H, Sävmarker J, Ng L, Pham V, Lundbäck T, Jenmalm-Jensen A, Svensson R, Artursson P, Zelleroth S, Engen K, Rosenström U, Larhed M, Åqvist J, Chai SY, Hallberg M. Aryl Sulfonamide Inhibitors of Insulin-Regulated Aminopeptidase Enhance Spine Density in Primary Hippocampal Neuron Cultures. ACS Chem Neurosci 2016; 7:1383-1392. [PMID: 27501164 DOI: 10.1021/acschemneuro.6b00146] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The zinc metallopeptidase insulin regulated aminopeptidase (IRAP), which is highly expressed in the hippocampus and other brain regions associated with cognitive function, has been identified as a high-affinity binding site of the hexapeptide angiotensin IV (Ang IV). This hexapeptide is thought to facilitate learning and memory by binding to the catalytic site of IRAP to inhibit its enzymatic activity. In support of this hypothesis, low molecular weight, nonpeptide specific inhibitors of IRAP have been shown to enhance memory in rodent models. Recently, it was demonstrated that linear and macrocyclic Ang IV-derived peptides can alter the shape and increase the number of dendritic spines in hippocampal cultures, properties associated with enhanced cognitive performance. After screening a library of 10 500 drug-like substances for their ability to inhibit IRAP, we identified a series of low molecular weight aryl sulfonamides, which exhibit no structural similarity to Ang IV, as moderately potent IRAP inhibitors. A structural and biological characterization of three of these aryl sulfonamides was performed. Their binding modes to human IRAP were explored by docking calculations combined with molecular dynamics simulations and binding affinity estimations using the linear interaction energy method. Two alternative binding modes emerged from this analysis, both of which correctly rank the ligands according to their experimental binding affinities for this series of compounds. Finally, we show that two of these drug-like IRAP inhibitors can alter dendritic spine morphology and increase spine density in primary cultures of hippocampal neurons.
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Affiliation(s)
| | | | | | | | | | | | | | - Leelee Ng
- Biomedicine Discovery Institute, Department of Physiology, Monash University , Clayton, Victoria 3800, Australia
| | - Vi Pham
- Biomedicine Discovery Institute, Department of Physiology, Monash University , Clayton, Victoria 3800, Australia
| | - Thomas Lundbäck
- Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medicinal Biochemistry and Biophysics, Karolinska Institute , 171 77 Solna, Sweden
| | - Annika Jenmalm-Jensen
- Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medicinal Biochemistry and Biophysics, Karolinska Institute , 171 77 Solna, Sweden
| | | | | | | | | | | | | | | | - Siew Yeen Chai
- Biomedicine Discovery Institute, Department of Physiology, Monash University , Clayton, Victoria 3800, Australia
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Pacitto A, Ascher DB, Wong LH, Blaszczyk BK, Nookala RK, Zhang N, Dokudovskaya S, Levine TP, Blundell TL. Lst4, the yeast Fnip1/2 orthologue, is a DENN-family protein. Open Biol 2016; 5:150174. [PMID: 26631379 PMCID: PMC4703059 DOI: 10.1098/rsob.150174] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The folliculin/Fnip complex has been demonstrated to play a crucial role in the mechanisms underlying Birt–Hogg–Dubé (BHD) syndrome, a rare inherited cancer syndrome. Lst4 has been previously proposed to be the Fnip1/2 orthologue in yeast and therefore a member of the DENN family. In order to confirm this, we solved the crystal structure of the N-terminal region of Lst4 from Kluyveromyces lactis and show it contains a longin domain, the first domain of the full DENN module. Furthermore, we demonstrate that Lst4 through its DENN domain interacts with Lst7, the yeast folliculin orthologue. Like its human counterpart, the Lst7/Lst4 complex relocates to the vacuolar membrane in response to nutrient starvation, most notably in carbon starvation. Finally, we express and purify the recombinant Lst7/Lst4 complex and show that it exists as a 1 : 1 heterodimer in solution. This work confirms the membership of Lst4 and the Fnip proteins in the DENN family, and provides a basis for using the Lst7/Lst4 complex to understand the molecular function of folliculin and its role in the pathogenesis of BHD syndrome.
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Affiliation(s)
- Angela Pacitto
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - David B Ascher
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Louise H Wong
- Department of Cell Biology, UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
| | - Beata K Blaszczyk
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Ravi K Nookala
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Nianshu Zhang
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Svetlana Dokudovskaya
- CNRS UMR 8126, Université Paris-Sud 11, Institut Gustave Roussy, 114, rue Edouard Vaillant, Villejuif 94805, France
| | - Tim P Levine
- Department of Cell Biology, UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
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Pires DEV, Ascher DB. CSM-lig: a web server for assessing and comparing protein-small molecule affinities. Nucleic Acids Res 2016; 44:W557-61. [PMID: 27151202 PMCID: PMC4987933 DOI: 10.1093/nar/gkw390] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Accepted: 04/28/2016] [Indexed: 12/21/2022] Open
Abstract
Determining the affinity of a ligand for a given protein is a crucial component of drug development and understanding their biological effects. Predicting binding affinities is a challenging and difficult task, and despite being regarded as poorly predictive, scoring functions play an important role in the analysis of molecular docking results. Here, we present CSM-Lig (http://structure.bioc.cam.ac.uk/csm_lig), a web server tailored to predict the binding affinity of a protein-small molecule complex, encompassing both protein and small-molecule complementarity in terms of shape and chemistry via graph-based structural signatures. CSM-Lig was trained and evaluated on different releases of the PDBbind databases, achieving a correlation of up to 0.86 on 10-fold cross validation and 0.80 in blind tests, performing as well as or better than other widely used methods. The web server allows users to rapidly and automatically predict binding affinities of collections of structures and assess the interactions made. We believe CSM-lig would be an invaluable tool for helping assess docking poses, the effects of multiple mutations, including insertions, deletions and alternative splicing events, in protein-small molecule affinity, unraveling important aspects that drive protein–compound recognition.
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Affiliation(s)
- Douglas E V Pires
- Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, 30190-002, Brazil
| | - David B Ascher
- Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, 30190-002, Brazil Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK Department of Biochemistry, University of Melbourne, Victoria 3010, Australia
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Diwakarla S, Nylander E, Grönbladh A, Vanga SR, Khan YS, Gutiérrez-de-Terán H, Ng L, Pham V, Sävmarker J, Lundbäck T, Jenmalm-Jensen A, Andersson H, Engen K, Rosenström U, Larhed M, Åqvist J, Chai SY, Hallberg M. Binding to and Inhibition of Insulin-Regulated Aminopeptidase by Macrocyclic Disulfides Enhances Spine Density. Mol Pharmacol 2016; 89:413-24. [PMID: 26769413 DOI: 10.1124/mol.115.102533] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 01/13/2016] [Indexed: 01/28/2023] Open
Abstract
Angiotensin IV (Ang IV) and related peptide analogs, as well as nonpeptide inhibitors of insulin-regulated aminopeptidase (IRAP), have previously been shown to enhance memory and cognition in animal models. Furthermore, the endogenous IRAP substrates oxytocin and vasopressin are known to facilitate learning and memory. In this study, the two recently synthesized 13-membered macrocyclic competitive IRAP inhibitors HA08 and HA09, which were designed to mimic the N terminus of oxytocin and vasopressin, were assessed and compared based on their ability to bind to the IRAP active site, and alter dendritic spine density in rat hippocampal primary cultures. The binding modes of the IRAP inhibitors HA08, HA09, and of Ang IV in either the extended or γ-turn conformation at the C terminus to human IRAP were predicted by docking and molecular dynamics simulations. The binding free energies calculated with the linear interaction energy method, which are in excellent agreement with experimental data and simulations, have been used to explain the differences in activities of the IRAP inhibitors, both of which are structurally very similar, but differ only with regard to one stereogenic center. In addition, we show that HA08, which is 100-fold more potent than the epimer HA09, can enhance dendritic spine number and alter morphology, a process associated with memory facilitation. Therefore, HA08, one of the most potent IRAP inhibitors known today, may serve as a suitable starting point for medicinal chemistry programs aided by MD simulations aimed at discovering more drug-like cognitive enhancers acting via augmenting synaptic plasticity.
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Affiliation(s)
- Shanti Diwakarla
- The Beijer Laboratory, Department of Pharmaceutical Biosciences, Division of Biological Research on Drug Dependence (S.D., E.N., A.G., M.H.), Department of Cell and Molecular Biology (S.R.V., Y.S.K., H.G.T., J.A.), The Beijer Laboratory, Department of Medicinal Chemistry (J.S.), Department of Medicinal Chemistry (H.A., K.E., U.R.), Science for Life Laboratory, Department of Medicinal Chemistry (M.L.), BMC, Uppsala University, Uppsala, Sweden; Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medicinal Biochemistry and Biophysics (T.L., A.J.), Karolinska Institute, Sweden; and Biomedicine Discovery Institute, Department of Physiology (L.N., V.P., S.Y.C.), Monash University, Melbourne, Australia
| | - Erik Nylander
- The Beijer Laboratory, Department of Pharmaceutical Biosciences, Division of Biological Research on Drug Dependence (S.D., E.N., A.G., M.H.), Department of Cell and Molecular Biology (S.R.V., Y.S.K., H.G.T., J.A.), The Beijer Laboratory, Department of Medicinal Chemistry (J.S.), Department of Medicinal Chemistry (H.A., K.E., U.R.), Science for Life Laboratory, Department of Medicinal Chemistry (M.L.), BMC, Uppsala University, Uppsala, Sweden; Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medicinal Biochemistry and Biophysics (T.L., A.J.), Karolinska Institute, Sweden; and Biomedicine Discovery Institute, Department of Physiology (L.N., V.P., S.Y.C.), Monash University, Melbourne, Australia
| | - Alfhild Grönbladh
- The Beijer Laboratory, Department of Pharmaceutical Biosciences, Division of Biological Research on Drug Dependence (S.D., E.N., A.G., M.H.), Department of Cell and Molecular Biology (S.R.V., Y.S.K., H.G.T., J.A.), The Beijer Laboratory, Department of Medicinal Chemistry (J.S.), Department of Medicinal Chemistry (H.A., K.E., U.R.), Science for Life Laboratory, Department of Medicinal Chemistry (M.L.), BMC, Uppsala University, Uppsala, Sweden; Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medicinal Biochemistry and Biophysics (T.L., A.J.), Karolinska Institute, Sweden; and Biomedicine Discovery Institute, Department of Physiology (L.N., V.P., S.Y.C.), Monash University, Melbourne, Australia
| | - Sudarsana Reddy Vanga
- The Beijer Laboratory, Department of Pharmaceutical Biosciences, Division of Biological Research on Drug Dependence (S.D., E.N., A.G., M.H.), Department of Cell and Molecular Biology (S.R.V., Y.S.K., H.G.T., J.A.), The Beijer Laboratory, Department of Medicinal Chemistry (J.S.), Department of Medicinal Chemistry (H.A., K.E., U.R.), Science for Life Laboratory, Department of Medicinal Chemistry (M.L.), BMC, Uppsala University, Uppsala, Sweden; Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medicinal Biochemistry and Biophysics (T.L., A.J.), Karolinska Institute, Sweden; and Biomedicine Discovery Institute, Department of Physiology (L.N., V.P., S.Y.C.), Monash University, Melbourne, Australia
| | - Yasmin Shamsudin Khan
- The Beijer Laboratory, Department of Pharmaceutical Biosciences, Division of Biological Research on Drug Dependence (S.D., E.N., A.G., M.H.), Department of Cell and Molecular Biology (S.R.V., Y.S.K., H.G.T., J.A.), The Beijer Laboratory, Department of Medicinal Chemistry (J.S.), Department of Medicinal Chemistry (H.A., K.E., U.R.), Science for Life Laboratory, Department of Medicinal Chemistry (M.L.), BMC, Uppsala University, Uppsala, Sweden; Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medicinal Biochemistry and Biophysics (T.L., A.J.), Karolinska Institute, Sweden; and Biomedicine Discovery Institute, Department of Physiology (L.N., V.P., S.Y.C.), Monash University, Melbourne, Australia
| | - Hugo Gutiérrez-de-Terán
- The Beijer Laboratory, Department of Pharmaceutical Biosciences, Division of Biological Research on Drug Dependence (S.D., E.N., A.G., M.H.), Department of Cell and Molecular Biology (S.R.V., Y.S.K., H.G.T., J.A.), The Beijer Laboratory, Department of Medicinal Chemistry (J.S.), Department of Medicinal Chemistry (H.A., K.E., U.R.), Science for Life Laboratory, Department of Medicinal Chemistry (M.L.), BMC, Uppsala University, Uppsala, Sweden; Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medicinal Biochemistry and Biophysics (T.L., A.J.), Karolinska Institute, Sweden; and Biomedicine Discovery Institute, Department of Physiology (L.N., V.P., S.Y.C.), Monash University, Melbourne, Australia
| | - Leelee Ng
- The Beijer Laboratory, Department of Pharmaceutical Biosciences, Division of Biological Research on Drug Dependence (S.D., E.N., A.G., M.H.), Department of Cell and Molecular Biology (S.R.V., Y.S.K., H.G.T., J.A.), The Beijer Laboratory, Department of Medicinal Chemistry (J.S.), Department of Medicinal Chemistry (H.A., K.E., U.R.), Science for Life Laboratory, Department of Medicinal Chemistry (M.L.), BMC, Uppsala University, Uppsala, Sweden; Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medicinal Biochemistry and Biophysics (T.L., A.J.), Karolinska Institute, Sweden; and Biomedicine Discovery Institute, Department of Physiology (L.N., V.P., S.Y.C.), Monash University, Melbourne, Australia
| | - Vi Pham
- The Beijer Laboratory, Department of Pharmaceutical Biosciences, Division of Biological Research on Drug Dependence (S.D., E.N., A.G., M.H.), Department of Cell and Molecular Biology (S.R.V., Y.S.K., H.G.T., J.A.), The Beijer Laboratory, Department of Medicinal Chemistry (J.S.), Department of Medicinal Chemistry (H.A., K.E., U.R.), Science for Life Laboratory, Department of Medicinal Chemistry (M.L.), BMC, Uppsala University, Uppsala, Sweden; Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medicinal Biochemistry and Biophysics (T.L., A.J.), Karolinska Institute, Sweden; and Biomedicine Discovery Institute, Department of Physiology (L.N., V.P., S.Y.C.), Monash University, Melbourne, Australia
| | - Jonas Sävmarker
- The Beijer Laboratory, Department of Pharmaceutical Biosciences, Division of Biological Research on Drug Dependence (S.D., E.N., A.G., M.H.), Department of Cell and Molecular Biology (S.R.V., Y.S.K., H.G.T., J.A.), The Beijer Laboratory, Department of Medicinal Chemistry (J.S.), Department of Medicinal Chemistry (H.A., K.E., U.R.), Science for Life Laboratory, Department of Medicinal Chemistry (M.L.), BMC, Uppsala University, Uppsala, Sweden; Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medicinal Biochemistry and Biophysics (T.L., A.J.), Karolinska Institute, Sweden; and Biomedicine Discovery Institute, Department of Physiology (L.N., V.P., S.Y.C.), Monash University, Melbourne, Australia
| | - Thomas Lundbäck
- The Beijer Laboratory, Department of Pharmaceutical Biosciences, Division of Biological Research on Drug Dependence (S.D., E.N., A.G., M.H.), Department of Cell and Molecular Biology (S.R.V., Y.S.K., H.G.T., J.A.), The Beijer Laboratory, Department of Medicinal Chemistry (J.S.), Department of Medicinal Chemistry (H.A., K.E., U.R.), Science for Life Laboratory, Department of Medicinal Chemistry (M.L.), BMC, Uppsala University, Uppsala, Sweden; Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medicinal Biochemistry and Biophysics (T.L., A.J.), Karolinska Institute, Sweden; and Biomedicine Discovery Institute, Department of Physiology (L.N., V.P., S.Y.C.), Monash University, Melbourne, Australia
| | - Annika Jenmalm-Jensen
- The Beijer Laboratory, Department of Pharmaceutical Biosciences, Division of Biological Research on Drug Dependence (S.D., E.N., A.G., M.H.), Department of Cell and Molecular Biology (S.R.V., Y.S.K., H.G.T., J.A.), The Beijer Laboratory, Department of Medicinal Chemistry (J.S.), Department of Medicinal Chemistry (H.A., K.E., U.R.), Science for Life Laboratory, Department of Medicinal Chemistry (M.L.), BMC, Uppsala University, Uppsala, Sweden; Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medicinal Biochemistry and Biophysics (T.L., A.J.), Karolinska Institute, Sweden; and Biomedicine Discovery Institute, Department of Physiology (L.N., V.P., S.Y.C.), Monash University, Melbourne, Australia
| | - Hanna Andersson
- The Beijer Laboratory, Department of Pharmaceutical Biosciences, Division of Biological Research on Drug Dependence (S.D., E.N., A.G., M.H.), Department of Cell and Molecular Biology (S.R.V., Y.S.K., H.G.T., J.A.), The Beijer Laboratory, Department of Medicinal Chemistry (J.S.), Department of Medicinal Chemistry (H.A., K.E., U.R.), Science for Life Laboratory, Department of Medicinal Chemistry (M.L.), BMC, Uppsala University, Uppsala, Sweden; Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medicinal Biochemistry and Biophysics (T.L., A.J.), Karolinska Institute, Sweden; and Biomedicine Discovery Institute, Department of Physiology (L.N., V.P., S.Y.C.), Monash University, Melbourne, Australia
| | - Karin Engen
- The Beijer Laboratory, Department of Pharmaceutical Biosciences, Division of Biological Research on Drug Dependence (S.D., E.N., A.G., M.H.), Department of Cell and Molecular Biology (S.R.V., Y.S.K., H.G.T., J.A.), The Beijer Laboratory, Department of Medicinal Chemistry (J.S.), Department of Medicinal Chemistry (H.A., K.E., U.R.), Science for Life Laboratory, Department of Medicinal Chemistry (M.L.), BMC, Uppsala University, Uppsala, Sweden; Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medicinal Biochemistry and Biophysics (T.L., A.J.), Karolinska Institute, Sweden; and Biomedicine Discovery Institute, Department of Physiology (L.N., V.P., S.Y.C.), Monash University, Melbourne, Australia
| | - Ulrika Rosenström
- The Beijer Laboratory, Department of Pharmaceutical Biosciences, Division of Biological Research on Drug Dependence (S.D., E.N., A.G., M.H.), Department of Cell and Molecular Biology (S.R.V., Y.S.K., H.G.T., J.A.), The Beijer Laboratory, Department of Medicinal Chemistry (J.S.), Department of Medicinal Chemistry (H.A., K.E., U.R.), Science for Life Laboratory, Department of Medicinal Chemistry (M.L.), BMC, Uppsala University, Uppsala, Sweden; Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medicinal Biochemistry and Biophysics (T.L., A.J.), Karolinska Institute, Sweden; and Biomedicine Discovery Institute, Department of Physiology (L.N., V.P., S.Y.C.), Monash University, Melbourne, Australia
| | - Mats Larhed
- The Beijer Laboratory, Department of Pharmaceutical Biosciences, Division of Biological Research on Drug Dependence (S.D., E.N., A.G., M.H.), Department of Cell and Molecular Biology (S.R.V., Y.S.K., H.G.T., J.A.), The Beijer Laboratory, Department of Medicinal Chemistry (J.S.), Department of Medicinal Chemistry (H.A., K.E., U.R.), Science for Life Laboratory, Department of Medicinal Chemistry (M.L.), BMC, Uppsala University, Uppsala, Sweden; Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medicinal Biochemistry and Biophysics (T.L., A.J.), Karolinska Institute, Sweden; and Biomedicine Discovery Institute, Department of Physiology (L.N., V.P., S.Y.C.), Monash University, Melbourne, Australia
| | - Johan Åqvist
- The Beijer Laboratory, Department of Pharmaceutical Biosciences, Division of Biological Research on Drug Dependence (S.D., E.N., A.G., M.H.), Department of Cell and Molecular Biology (S.R.V., Y.S.K., H.G.T., J.A.), The Beijer Laboratory, Department of Medicinal Chemistry (J.S.), Department of Medicinal Chemistry (H.A., K.E., U.R.), Science for Life Laboratory, Department of Medicinal Chemistry (M.L.), BMC, Uppsala University, Uppsala, Sweden; Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medicinal Biochemistry and Biophysics (T.L., A.J.), Karolinska Institute, Sweden; and Biomedicine Discovery Institute, Department of Physiology (L.N., V.P., S.Y.C.), Monash University, Melbourne, Australia
| | - Siew Yeen Chai
- The Beijer Laboratory, Department of Pharmaceutical Biosciences, Division of Biological Research on Drug Dependence (S.D., E.N., A.G., M.H.), Department of Cell and Molecular Biology (S.R.V., Y.S.K., H.G.T., J.A.), The Beijer Laboratory, Department of Medicinal Chemistry (J.S.), Department of Medicinal Chemistry (H.A., K.E., U.R.), Science for Life Laboratory, Department of Medicinal Chemistry (M.L.), BMC, Uppsala University, Uppsala, Sweden; Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medicinal Biochemistry and Biophysics (T.L., A.J.), Karolinska Institute, Sweden; and Biomedicine Discovery Institute, Department of Physiology (L.N., V.P., S.Y.C.), Monash University, Melbourne, Australia
| | - Mathias Hallberg
- The Beijer Laboratory, Department of Pharmaceutical Biosciences, Division of Biological Research on Drug Dependence (S.D., E.N., A.G., M.H.), Department of Cell and Molecular Biology (S.R.V., Y.S.K., H.G.T., J.A.), The Beijer Laboratory, Department of Medicinal Chemistry (J.S.), Department of Medicinal Chemistry (H.A., K.E., U.R.), Science for Life Laboratory, Department of Medicinal Chemistry (M.L.), BMC, Uppsala University, Uppsala, Sweden; Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medicinal Biochemistry and Biophysics (T.L., A.J.), Karolinska Institute, Sweden; and Biomedicine Discovery Institute, Department of Physiology (L.N., V.P., S.Y.C.), Monash University, Melbourne, Australia
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45
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Ohnishi A, Watanabe J, Ogawa Y, Goto Y, Hattori A, Tsujimoto M. Involvement of Phenylalanine 297 in the Construction of the Substrate Pocket of Human Aminopeptidase B. Biochemistry 2016; 54:6062-70. [PMID: 26352190 DOI: 10.1021/acs.biochem.5b00964] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Aminopeptidase B (APB, EC 3.4.11.6) preferentially hydrolyzes the N-terminal basic amino acids of synthetic and peptide substrates and requires a physiological concentration of NaCl for optimal activity. In this study, we used site-directed mutagenesis and molecular modeling to search for an amino acid residue that is critical for the enzymatic properties of human APB. Substitution of Phe297 with Tyr caused a significant decrease in hydrolytic activity toward synthetic and peptide substrates as well as chloride anion sensitivity. Molecular modeling suggests that Phe297 contributes to the construction of the substrate pocket of APB, which is wide enough to hold a chloride anion and allow the interaction of Gln169 with the N-terminal Arg residue of the substrate through bridging with the chloride anion. These results indicate that Phe297 is crucial for the optimal enzymatic activity and chloride anion sensitivity of APB via formation of the optimal structure of the catalytic pocket.
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Affiliation(s)
- Atsushi Ohnishi
- Faculty of Pharmaceutical Sciences, Teikyo Heisei University , Nakano, Tokyo 164-8530, Japan
| | - Jobu Watanabe
- Faculty of Pharmaceutical Sciences, Teikyo Heisei University , Nakano, Tokyo 164-8530, Japan
| | - Yuko Ogawa
- Faculty of Pharmaceutical Sciences, Teikyo Heisei University , Nakano, Tokyo 164-8530, Japan
| | - Yoshikuni Goto
- Faculty of Pharmaceutical Sciences, Teikyo Heisei University , Nakano, Tokyo 164-8530, Japan
| | - Akira Hattori
- Department of System Chemotherapy and Molecular Sciences, Graduate School of Pharmaceutical Sciences, Kyoto University , Kyoto 606-8501, Japan
| | - Masafumi Tsujimoto
- Faculty of Pharmaceutical Sciences, Teikyo Heisei University , Nakano, Tokyo 164-8530, Japan
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46
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Svensson F, Engen K, Lundbäck T, Larhed M, Sköld C. Virtual Screening for Transition State Analogue Inhibitors of IRAP Based on Quantum Mechanically Derived Reaction Coordinates. J Chem Inf Model 2015; 55:1984-93. [DOI: 10.1021/acs.jcim.5b00359] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Fredrik Svensson
- Organic
Pharmaceutical Chemistry, Department of Medicinal Chemistry, BMC, Uppsala University, P.O.
Box 574, SE-751 23 Uppsala, Sweden
| | - Karin Engen
- Organic
Pharmaceutical Chemistry, Department of Medicinal Chemistry, BMC, Uppsala University, P.O.
Box 574, SE-751 23 Uppsala, Sweden
| | - Thomas Lundbäck
- Chemical
Biology Consortium Sweden, Science for Life Laboratory, Division of
Translational Medicine and Chemical Biology, Department of Medical
Biochemistry and Biophysics, Karolinska Institutet, Tomtebodavägen
23A, SE-171 65 Solna, Sweden
| | - Mats Larhed
- Science
for Life Laboratory, Department of Medicinal Chemistry, BMC, Uppsala University, P.O.
Box 574, SE-751 23 Uppsala, Sweden
| | - Christian Sköld
- Organic
Pharmaceutical Chemistry, Department of Medicinal Chemistry, BMC, Uppsala University, P.O.
Box 574, SE-751 23 Uppsala, Sweden
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47
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Mpakali A, Saridakis E, Harlos K, Zhao Y, Papakyriakou A, Kokkala P, Georgiadis D, Stratikos E. Crystal Structure of Insulin-Regulated Aminopeptidase with Bound Substrate Analogue Provides Insight on Antigenic Epitope Precursor Recognition and Processing. THE JOURNAL OF IMMUNOLOGY 2015; 195:2842-51. [PMID: 26259583 DOI: 10.4049/jimmunol.1501103] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 07/13/2015] [Indexed: 12/12/2022]
Abstract
Aminopeptidases that generate antigenic peptides influence immunodominance and adaptive cytotoxic immune responses. The mechanisms that allow these enzymes to efficiently process a vast number of different long peptide substrates are poorly understood. In this work, we report the structure of insulin-regulated aminopeptidase, an enzyme that prepares antigenic epitopes for cross-presentation in dendritic cells, in complex with an antigenic peptide precursor analog. Insulin-regulated aminopeptidase is found in a semiclosed conformation with an extended internal cavity with limited access to the solvent. The N-terminal moiety of the peptide is located at the active site, positioned optimally for catalysis, whereas the C-terminal moiety of the peptide is stabilized along the extended internal cavity lodged between domains II and IV. Hydrophobic interactions and shape complementarity enhance peptide affinity beyond the catalytic site and support a limited selectivity model for antigenic peptide selection that may underlie the generation of complex immunopeptidomes.
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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; and
| | - Yuguang Zhao
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Oxford University, Oxford OX3 7BN, United Kingdom; and
| | | | - Paraskevi Kokkala
- National Center for Scientific Research Demokritos, Agia Paraskevi, Athens 15310, Greece; Department of Chemistry, University of Athens, Athens 15771, Greece
| | | | - Efstratios Stratikos
- National Center for Scientific Research Demokritos, Agia Paraskevi, Athens 15310, Greece;
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48
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Papakyriakou A, Zervoudi E, Tsoukalidou S, Mauvais FX, Sfyroera G, Mastellos DC, van Endert P, Theodorakis EA, Vourloumis D, Stratikos E. 3,4-diaminobenzoic acid derivatives as inhibitors of the oxytocinase subfamily of M1 aminopeptidases with immune-regulating properties. J Med Chem 2015; 58:1524-43. [PMID: 25635706 DOI: 10.1021/jm501867s] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Members of the oxytocinase subfamily of M1 aminopeptidases (ERAP1, ERAP2, and IRAP) play important roles in both the adaptive and innate human immune responses. Their enzymatic activity can contribute to the pathogenesis of several major human diseases ranging from viral and parasitic infections to autoimmunity and cancer. We have previously demonstrated that diaminobenzoic acid derivatives show promise as selective inhibitors for this group of aminopeptidases. In this study, we have thoroughly explored a series of 3,4-diaminobenzoic acid derivatives as inhibitors of this class of enzymes, achieving submicromolar inhibitors for ERAP2 (IC50 = 237 nM) and IRAP (IC50 = 105 nM). Cell-based analysis indicated that the lead compounds can be effective in downregulating macrophage activation induced by lipopolysaccharide and interferon-γ as well as cross-presentation by bone marrow-derived dendritic cells. Our results indicate that this class of inhibitors may be useful for the targeted downregulation of immune responses.
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Affiliation(s)
- Athanasios Papakyriakou
- National Center for Scientific Research "Demokritos" , Aghia Paraskevi, 15310 Athens, Greece
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