1
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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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2
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Müller L, Burton AK, Tayler CL, Rowedder JE, Hutchinson JP, Peace S, Quayle JM, Leveridge MV, Annan RS, Trost M, Peltier-Heap RE, Dueñas ME. A high-throughput MALDI-TOF MS biochemical screen for small molecule inhibitors of the antigen aminopeptidase ERAP1. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2023; 28:3-11. [PMID: 36414185 DOI: 10.1016/j.slasd.2022.11.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/10/2022] [Accepted: 11/15/2022] [Indexed: 11/21/2022]
Abstract
MALDI-TOF MS is a powerful analytical technique that provides a fast and label-free readout for in vitro assays in the high-throughput screening (HTS) environment. Here, we describe the development of a novel, HTS compatible, MALDI-TOF MS-based drug discovery assay for the endoplasmic reticulum aminopeptidase 1 (ERAP1), an important target in immuno-oncology and auto-immune diseases. A MALDI-TOF MS assay was developed beginning with an already established ERAP1 RapidFire MS (RF MS) assay, where the peptide YTAFTIPSI is trimmed into the product TAFTIPSI. We noted low ionisation efficiency of these peptides in MALDI-TOF MS and hence incorporated arginine residues into the peptide sequences to improve ionisation. The optimal assay conditions were established with these new basic assay peptides on the MALDI-TOF MS platform and validated with known ERAP1 inhibitors. Assay stability, reproducibility and robustness was demonstrated on the MALDI-TOF MS platform. From a set of 699 confirmed ERAP1 binders, identified in a prior affinity selection mass spectrometry (ASMS) screen, active compounds were determined at single concentration and in a dose-response format with the new MALDI-TOF MS setup. Furthermore, to allow for platform performance comparison, the same compound set was tested on the established RF MS setup, as the new basic peptides showed fragmentation in ESI-MS. The two platforms showed a comparable performance, but the MALDI-TOF MS platform had several advantages, such as shorter sample cycle times, reduced reagent consumption, and a lower tight-binding limit.
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Affiliation(s)
- Leonie Müller
- Newcastle University, Faculty of Medical Sciences, Biosciences Institute, Framlington Place, Newcastle Upon Tyne NE2 4HH, United Kingdom
| | - Amy K Burton
- GSK, Discovery Analytical, Gunnels Wood Rd, Stevenage SG1 2NY, United Kingdom
| | - Chloe L Tayler
- GSK, Discovery Analytical, Gunnels Wood Rd, Stevenage SG1 2NY, United Kingdom
| | - James E Rowedder
- GSK, Screening, Profiling and Mechanistic Biology, Gunnels Wood Rd, Stevenage SG1 2NY, United Kingdom
| | - Jonathan P Hutchinson
- GSK, Screening, Profiling and Mechanistic Biology, Gunnels Wood Rd, Stevenage SG1 2NY, United Kingdom
| | - Simon Peace
- GSK, Medicinal Chemistry, Gunnels Wood Rd, Stevenage SG1 2NY, United Kingdom
| | - Julie M Quayle
- GSK, Discovery Analytical, Gunnels Wood Rd, Stevenage SG1 2NY, United Kingdom
| | - Melanie V Leveridge
- GSK, Screening, Profiling and Mechanistic Biology, Gunnels Wood Rd, Stevenage SG1 2NY, United Kingdom
| | - Roland S Annan
- GSK, Discovery Analytical, Gunnels Wood Rd, Stevenage SG1 2NY, United Kingdom
| | - Matthias Trost
- Newcastle University, Faculty of Medical Sciences, Biosciences Institute, Framlington Place, Newcastle Upon Tyne NE2 4HH, United Kingdom.
| | | | - Maria Emilia Dueñas
- Newcastle University, Faculty of Medical Sciences, Biosciences Institute, Framlington Place, Newcastle Upon Tyne NE2 4HH, United Kingdom.
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3
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Arya R, Maben Z, Rane D, Ali A, Stern LJ. Phenylsulfamoyl Benzoic Acid Inhibitor of ERAP2 with a Novel Mode of Inhibition. ACS Chem Biol 2022; 17:1756-1768. [PMID: 35767698 DOI: 10.1021/acschembio.2c00093] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
ERAP1 and ERAP2 are endoplasmic reticulum zinc-binding aminopeptidases that play crucial roles in processing peptides for loading onto class I major histocompatibility complex proteins. These enzymes are therapeutic targets in cancer and autoimmune disorders. The discovery of inhibitors specific to ERAP1 or ERAP2 has been challenging due to the similarity in their active site residues and domain architectures. Here, we identify 4-methoxy-3-{[2-piperidin-1-yl-4-(trifluoromethyl) phenyl] sulfamoyl} benzoic acid (compound 61) as a novel inhibitor of ERAP2 and determine the crystal structure of ERAP2 bound to compound 61. Compound 61 binds near the catalytic center of ERAP2, at a distinct site from previously known peptidomimetic inhibitors, and inhibits by an uncompetitive mechanism. Surprisingly, for ERAP1, compound 61 was found to activate model substrate hydrolysis, similarly to the previously characterized 5-trifluoromethyl regioisomer of compound 61, known as compound 3. We characterized the specificity determinants of ERAP1 and ERAP2 that control the binding of compounds 3 and 61. At the active site of ERAP1, Lys380 in the S1' pocket is a key determinant for the binding of both compounds 3 and 61. At the allosteric site, ERAP1 binds either compound, leading to the activation of model substrate hydrolysis. Although ERAP2 substrate hydrolysis is not activated by either compound, the mutation of His904 to alanine reveals a cryptic allosteric site that allows for the activation by compound 3. Thus, we have identified selectivity determinants in the active and allosteric sites of ERAP2 that govern the binding of two similar compounds, which potentially could be exploited to develop more potent and specific inhibitors.
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Affiliation(s)
- Richa Arya
- Department of Pathology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01655, United States
| | - Zachary Maben
- Department of Pathology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01655, United States
| | - Digamber Rane
- Kansas University Specialized Chemistry Center, Lawrence, Kansas 66047, United States
| | - Akbar Ali
- Department of Biochemistry & Molecular Pharmacology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01655, United States
| | - Lawrence J Stern
- Department of Pathology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01655, United States.,Department of Biochemistry & Molecular Pharmacology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01655, United States
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4
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Law ME, Yaaghubi E, Ghilardi AF, Davis BJ, Ferreira RB, Koh J, Chen S, DePeter SF, Schilson CM, Chiang CW, Heldermon CD, Nørgaard P, Castellano RK, Law BK. Inhibitors of ERp44, PDIA1, and AGR2 induce disulfide-mediated oligomerization of Death Receptors 4 and 5 and cancer cell death. Cancer Lett 2022; 534:215604. [PMID: 35247515 DOI: 10.1016/j.canlet.2022.215604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/27/2022] [Accepted: 02/21/2022] [Indexed: 01/08/2023]
Abstract
Breast cancer mortality remains unacceptably high, indicating a need for safer and more effective therapeutic agents. Disulfide bond Disrupting Agents (DDAs) were previously identified as a novel class of anticancer compounds that selectively kill cancers that overexpress the Epidermal Growth Factor Receptor (EGFR) or its family member HER2. DDAs kill EGFR+ and HER2+ cancer cells via the parallel downregulation of EGFR, HER2, and HER3 and activation/oligomerization of Death Receptors 4 and 5 (DR4/5). However, the mechanisms by which DDAs mediate these effects are unknown. Affinity purification analyses employing biotinylated-DDAs reveal that the Protein Disulfide Isomerase (PDI) family members AGR2, PDIA1, and ERp44 are DDA target proteins. Further analyses demonstrate that shRNA-mediated knockdown of AGR2 and ERp44, or expression of ERp44 mutants, enhance basal DR5 oligomerization. DDA treatment of breast cancer cells disrupts PDIA1 and ERp44 mixed disulfide bonds with their client proteins. Together, the results herein reveal DDAs as the first small molecule, active site inhibitors of AGR2 and ERp44, and demonstrate roles for AGR2 and ERp44 in regulating the activity, stability, and localization of DR4 and DR5, and activation of Caspase 8.
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Affiliation(s)
- Mary E Law
- Department of Pharmacology & Therapeutics, University of Florida, Gainesville, FL, 32610, USA
| | - Elham Yaaghubi
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA
| | - Amanda F Ghilardi
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA
| | - Bradley J Davis
- Department of Pharmacology & Therapeutics, University of Florida, Gainesville, FL, 32610, USA
| | - Renan B Ferreira
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA
| | - Jin Koh
- Proteomics and Mass Spectrometry Facility, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, 32610, USA
| | - Sixue Chen
- Proteomics and Mass Spectrometry Facility, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, 32610, USA; Department of Biology, Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Sadie F DePeter
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA
| | | | - Chi-Wu Chiang
- Institute of Molecular Medicine, College of Medicine and Center for Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan
| | - Coy D Heldermon
- Department of Medicine, University of Florida, Gainesville, FL, 32610, USA; UF-Health Cancer Center, University of Florida, Gainesville, FL, 32610, USA
| | - Peter Nørgaard
- Department of Pathology, Copenhagen University Hospital Herlev, DK, 2730, Herlev, Denmark
| | - Ronald K Castellano
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA; UF-Health Cancer Center, University of Florida, Gainesville, FL, 32610, USA.
| | - Brian K Law
- Department of Pharmacology & Therapeutics, University of Florida, Gainesville, FL, 32610, USA; UF-Health Cancer Center, University of Florida, Gainesville, FL, 32610, USA.
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5
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D'Amico S, D'Alicandro V, Compagnone M, Tempora P, Guida G, Romania P, Lucarini V, Melaiu O, Falco M, Algeri M, Pende D, Cifaldi L, Fruci D. ERAP1 Controls the Interaction of the Inhibitory Receptor KIR3DL1 With HLA-B51:01 by Affecting Natural Killer Cell Function. Front Immunol 2021; 12:778103. [PMID: 34917091 PMCID: PMC8669763 DOI: 10.3389/fimmu.2021.778103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/15/2021] [Indexed: 12/21/2022] Open
Abstract
The endoplasmic reticulum aminopeptidase ERAP1 regulates innate and adaptive immune responses by trimming peptides for presentation by major histocompatibility complex (MHC) class I molecules. Previously, we have shown that genetic or pharmacological inhibition of ERAP1 on murine and human tumor cell lines perturbs the engagement of NK cell inhibitory receptors Ly49C/I and Killer-cell Immunoglobulin-like receptors (KIRs), respectively, by their specific ligands (MHC class I molecules), thus leading to NK cell killing. However, the effect of ERAP1 inhibition in tumor cells was highly variable, suggesting that its efficacy may depend on several factors, including MHC class I typing. To identify MHC class I alleles and KIRs that are more sensitive to ERAP1 depletion, we stably silenced ERAP1 expression in human HLA class I-negative B lymphoblastoid cell line 721.221 (referred to as 221) transfected with a panel of KIR ligands (i.e. HLA-B*51:01, -Cw3, -Cw4 and -Cw7), or HLA-A2 which does not bind any KIR, and tested their ability to induce NK cell degranulation and cytotoxicity. No change in HLA class I surface expression was detected in all 221 transfectant cells after ERAP1 depletion. In contrast, CD107a expression levels were significantly increased on NK cells stimulated with 221-B*51:01 cells lacking ERAP1, particularly in the KIR3DL1-positive NK cell subset. Consistently, genetic or pharmacological inhibition of ERAP1 impaired the recognition of HLA-B*51:01 by the YTS NK cell overexpressing KIR3DL1*001, suggesting that ERAP1 inhibition renders HLA-B*51:01 molecules less eligible for binding to KIR3DL1. Overall, these results identify HLA-B*51:01/KIR3DL1 as one of the most susceptible combinations for ERAP1 inhibition, suggesting that individuals carrying HLA-B*51:01-like antigens may be candidates for immunotherapy based on pharmacological inhibition of ERAP1.
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Affiliation(s)
- Silvia D'Amico
- Department of Paediatric Haematology/Oncology and of Cell and Gene Therapy, Bambino Gesù Children Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Valerio D'Alicandro
- Department of Paediatric Haematology/Oncology and of Cell and Gene Therapy, Bambino Gesù Children Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Mirco Compagnone
- Department of Paediatric Haematology/Oncology and of Cell and Gene Therapy, Bambino Gesù Children Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Patrizia Tempora
- Department of Paediatric Haematology/Oncology and of Cell and Gene Therapy, Bambino Gesù Children Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Giusy Guida
- Department of Paediatric Haematology/Oncology and of Cell and Gene Therapy, Bambino Gesù Children Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Paolo Romania
- Department of Paediatric Haematology/Oncology and of Cell and Gene Therapy, Bambino Gesù Children Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Valeria Lucarini
- Department of Paediatric Haematology/Oncology and of Cell and Gene Therapy, Bambino Gesù Children Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Ombretta Melaiu
- Department of Paediatric Haematology/Oncology and of Cell and Gene Therapy, Bambino Gesù Children Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Michela Falco
- Laboratory of Clinical and Experimental Immunology, Integrated Department of Services and Laboratories, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Giannina Gaslini, Genoa, Italy
| | - Mattia Algeri
- Department of Paediatric Haematology/Oncology and of Cell and Gene Therapy, Bambino Gesù Children Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Daniela Pende
- Laboratory of Immunology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ospedale Policlinico San Martino, Genoa, Italy
| | - Loredana Cifaldi
- Academic Department of Pediatrics (DPUO), Bambino Gesù Children Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy.,Department of Clinical Sciences and Translational Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Doriana Fruci
- Department of Paediatric Haematology/Oncology and of Cell and Gene Therapy, Bambino Gesù Children Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
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6
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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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7
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Sui L, Guo HC. ERAP1 binds peptide C-termini of different sequences and/or lengths by a common recognition mechanism. Immunobiology 2021; 226:152112. [PMID: 34247019 DOI: 10.1016/j.imbio.2021.152112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 05/24/2021] [Accepted: 06/03/2021] [Indexed: 01/25/2023]
Abstract
Endoplasmic reticulum aminopeptidase 1 (ERAP1) plays a key role in controlling the immunopeptidomes available for presentation by MHC (major histocompatibility complex) molecules, thus influences immunodominance and cell-mediated immunity. It carries out this critical function by a unique molecular ruler mechanism that trims antigenic precursors in a peptide-length and sequence dependent manner. Acting as a molecular ruler, ERAP1 is capable of concurrently binding antigen peptide N- and C-termini by its N-terminal catalytic and C-terminal regulatory domains, respectively. As such ERAP1 can not only monitor substrate's lengths, but also exhibit a degree of sequence specificity at substrates' N- and C-termini. On the other hand, it also allows certain sequence and length flexibility in the middle part of peptide substrates that is critical for shaping MHC restricted immunopeptidomes. Here we report structural and biochemical studies to understand the molecular details on how ERAP1 can accommodate side chains of different anchoring residues at the substrate's C-terminus. We also examine how ERAP1 can accommodate antigen peptide precursors with length flexibility. Based on two newly determined complex structures, we find that ERAP1 binds the C-termini of peptides similarly even with different substrate sequences and/or lengths, by utilizing the same hydrophobic specificity pocket to accommodate peptides with either a Phe or Leu as the C-terminal anchor residue. In addition, SPR (surface plasmon resonance) binding analyses in solution further confirm the biological significance of these peptide-ERAP1 interactions. Similar to the binding mode of MHC-I molecules, ERAP1 accommodates for antigenic peptide length difference by allowing the peptide middle part to kink or bulge at the middle of its substrate binding cleft. This explains how SNP coded variants located at the middle of ERAP1 substrate binding cleft would influence the antigen pool and an individual's susceptibility to diseases.
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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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8
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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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9
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Jiménez KM, Morel A, Parada-Niño L, Alejandra González-Rodriguez M, Flórez S, Bolívar-Salazar D, Becerra-Bayona S, Aguirre-García A, Gómez-Murcia T, Fernanda Castillo L, Carlosama C, Ardila J, Vaiman D, Serrano N, Laissue P. Identifying new potential genetic biomarkers for HELLP syndrome using massive parallel sequencing. Pregnancy Hypertens 2020; 22:181-190. [PMID: 33059327 DOI: 10.1016/j.preghy.2020.09.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 07/20/2020] [Accepted: 09/05/2020] [Indexed: 12/19/2022]
Abstract
BACKGROUND Preeclampsia (PE) is a frequently occurring multisystemic disease affecting ~5% of pregnancies. PE patients may develop HELLP syndrome (haemolysis, elevated liver enzymes, and low platelet), a mother and foetus life-threatening condition. Research into HELLP's genetic origin has been relatively unsuccessful, mainly because normal placental function and blood pressure regulation involve the fine-regulation of hundreds of genes. OBJECTIVE To identify new genes and mutations constituting potential biomarkers for HELLP syndrome. STUDY DESIGN The present case-control study involved whole-exome sequencing of 79 unrelated HELLP women. Candidate variants were screened in a control population constituted by 176 individuals. Stringent bioinformatics filters were used for selecting potentially etiological sequence variants in a subset of 487 genes. We used robust in silico mutation modelling for predicting the potential effect on protein structure. RESULTS We identified numerous sequence variants in genes related to angiogenesis/coagulation/blood pressure regulation, cell differentiation/communication/adhesion, cell cycle and transcriptional gene regulation, extracellular matrix biology, lipid metabolism and immunological response. Five sequence variants generated premature stop codons in genes playing an essential role in placental physiology (STOX1, PDGFD, IGF2, MMP1 and DNAH11). Six variants (ERAP1- p.Ile915Thr, ERAP2- p.Leu837Ser, COMT-p.His192Gln, CSAD-p.Pro418Ser, CDH1- p.Ala298Thr and CCR2-p.Met249Lys) led to destabilisation of protein structure as they had significant energy and residue interaction-related changes. We identified at least two mutations in 57% of patients, arguing in favour of a polygenic origin for the HELLP syndrome. CONCLUSION Our results provide novel evidence regarding PE/HELLP's genetic origin, leading to new biomarkers, having potential clinical usefulness, being proposed.
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Affiliation(s)
- Karen Marcela Jiménez
- Center For Research in Genetics and Genomics-CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Adrien Morel
- Center For Research in Genetics and Genomics-CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Laura Parada-Niño
- Center For Research in Genetics and Genomics-CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - María Alejandra González-Rodriguez
- Center For Research in Genetics and Genomics-CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Stephanie Flórez
- Hospital Universitario Mayor Méderi, Universidad del Rosario, Bogotá, Colombia
| | - David Bolívar-Salazar
- Center For Research in Genetics and Genomics-CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | | | - Angel Aguirre-García
- Center For Research in Genetics and Genomics-CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia; Hospital Universitario Mayor Méderi, Universidad del Rosario, Bogotá, Colombia
| | - Tatiana Gómez-Murcia
- Center For Research in Genetics and Genomics-CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia; Hospital Universitario Mayor Méderi, Universidad del Rosario, Bogotá, Colombia
| | - Luisa Fernanda Castillo
- Center For Research in Genetics and Genomics-CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Carolina Carlosama
- Center For Research in Genetics and Genomics-CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Javier Ardila
- Hospital Universitario Mayor Méderi, Universidad del Rosario, Bogotá, Colombia
| | - Daniel Vaiman
- Inserm U1016, CNRS UMR8104, Institut Cochin, équipe FGTB, 24, rue du faubourg Saint-Jacques, 75014 Paris, France
| | - Norma Serrano
- Research Centre, Fundación Cardiovascular de Colombia (FCV), Bucaramanga, Colombia
| | - Paul Laissue
- Center For Research in Genetics and Genomics-CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia; Inserm U1016, CNRS UMR8104, Institut Cochin, équipe FGTB, 24, rue du faubourg Saint-Jacques, 75014 Paris, France; Orphan Diseases Group, Biopas Laboratoires, Bogotá, Colombia.
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10
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Mavridis G, Arya R, Domnick A, Zoidakis J, Makridakis M, Vlahou A, Mpakali A, Lelis A, Georgiadis D, Tampé R, Papakyriakou A, Stern LJ, Stratikos E. A systematic re-examination of processing of MHCI-bound antigenic peptide precursors by endoplasmic reticulum aminopeptidase 1. J Biol Chem 2020; 295:7193-7210. [PMID: 32184355 PMCID: PMC7247305 DOI: 10.1074/jbc.ra120.012976] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 03/09/2020] [Indexed: 11/06/2022] Open
Abstract
Endoplasmic reticulum aminopeptidase 1 (ERAP1) trims antigenic peptide precursors to generate mature antigenic peptides for presentation by major histocompatibility complex class I (MHCI) molecules and regulates adaptive immune responses. ERAP1 has been proposed to trim peptide precursors both in solution and in preformed MHCI-peptide complexes, but which mode is more relevant to its biological function remains controversial. Here, we compared ERAP1-mediated trimming of antigenic peptide precursors in solution or when bound to three MHCI alleles, HLA-B*58, HLA-B*08, and HLA-A*02. For all MHCI-peptide combinations, peptide binding onto MHCI protected against ERAP1-mediated trimming. In only a single MHCI-peptide combination, trimming of an HLA-B*08-bound 12-mer progressed at a considerable rate, albeit still slower than in solution. Results from thermodynamic, kinetic, and computational analyses suggested that this 12-mer is highly labile and that apparent on-MHC trimming rates are always slower than that of MHCI-peptide dissociation. Both ERAP2 and leucine aminopeptidase, an enzyme unrelated to antigen processing, could trim this labile peptide from preformed MHCI complexes as efficiently as ERAP1. A pseudopeptide analogue with high affinity for both HLA-B*08 and the ERAP1 active site could not promote the formation of a ternary ERAP1/MHCI/peptide complex. Similarly, no interactions between ERAP1 and purified peptide-loading complex were detected in the absence or presence of a pseudopeptide trap. We conclude that MHCI binding protects peptides from ERAP1 degradation and that trimming in solution along with the dynamic nature of peptide binding to MHCI are sufficient to explain ERAP1 processing of antigenic peptide precursors.
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Affiliation(s)
- George Mavridis
- National Centre for Scientific Research Demokritos, Agia Paraskevi 15341, Greece
| | - Richa Arya
- University of Massachusetts Medical School, Worcester, Massachusetts 01655
| | - Alexander Domnick
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Strasse 9, D-60438 Frankfurt/Main, Germany
| | - Jerome Zoidakis
- Centre of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens 11527, Greece
| | - Manousos Makridakis
- Centre of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens 11527, Greece
| | - Antonia Vlahou
- Centre of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens 11527, Greece
| | - Anastasia Mpakali
- National Centre for Scientific Research Demokritos, Agia Paraskevi 15341, Greece
| | - Angelos Lelis
- Laboratory of Organic Chemistry, Chemistry Department, University of Athens, Athens 15772, Greece
| | - Dimitris Georgiadis
- Laboratory of Organic Chemistry, Chemistry Department, University of Athens, Athens 15772, Greece
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Strasse 9, D-60438 Frankfurt/Main, Germany
| | | | - Lawrence J Stern
- University of Massachusetts Medical School, Worcester, Massachusetts 01655
| | - Efstratios Stratikos
- National Centre for Scientific Research Demokritos, Agia Paraskevi 15341, Greece.
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11
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Reeves E, Islam Y, James E. ERAP1: a potential therapeutic target for a myriad of diseases. Expert Opin Ther Targets 2020; 24:535-544. [PMID: 32249641 DOI: 10.1080/14728222.2020.1751821] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Introduction: Endoplasmic Reticulum Aminopeptidase 1 (ERAP1) is a key regulator of the peptide repertoire displayed by Major Histocompatibility Complex I (MHC I) to circulating CD8 + T cells and NK cells. Studies have highlighted the essential requirement for the generation of stable peptide MHC I in regulating both innate and adaptive immune responses in health and disease.Areas covered: We review the role of ERAP1 in peptide trimming of N-terminally extended precursors that enter the ER, before loading on to MHC I, and the consequence of loss or downregulation of this activity. Polymorphisms in ERAP1 form multiple combinations (allotypes) within the population, and we discuss the contribution of this ERAP1 variation, and expression, on disease pathogenesis, including the resulting effect on both innate and adaptive immunity. We consider the current efforts to design inhibitors based on approaches using rational design and small molecule screening, and the potential effect of pharmacological modulation on the treatment of autoimmunity and cancer.Expert opinion: ERAP1 is fundamental for the regulation of immune responses, through generation of the presented peptide repertoire at the cell surface. Modulation of ERAP1 function, through design of inhibitors, may serve as a vital tool for changing immune responses in disease.
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Affiliation(s)
- Emma Reeves
- Centre for Cancer Immunology, Faculty of Medicine, University Hospital Southampton, Southampton, UK.,Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Yasmin Islam
- Centre for Cancer Immunology, Faculty of Medicine, University Hospital Southampton, Southampton, UK
| | - Edward James
- Centre for Cancer Immunology, Faculty of Medicine, University Hospital Southampton, Southampton, UK.,Institute for Life Sciences, University of Southampton, Southampton, UK
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12
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Liddle J, Hutchinson JP, Kitchen S, Rowland P, Neu M, Cecconie T, Holmes DS, Jones E, Korczynska J, Koumantou D, Lea JD, Nickels L, Pemberton M, Phillipou A, Schneck JL, Sheehan H, Tinworth CP, Uings I, Wojno-Picon J, Young RJ, Stratikos E. Targeting the Regulatory Site of ER Aminopeptidase 1 Leads to the Discovery of a Natural Product Modulator of Antigen Presentation. J Med Chem 2020; 63:3348-3358. [PMID: 32109056 DOI: 10.1021/acs.jmedchem.9b02123] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
ER aminopeptidase 1 (ERAP1) is an intracellular enzyme that generates antigenic peptides and is an emerging target for cancer immunotherapy and the control of autoimmunity. ERAP1 inhibitors described previously target the active site and are limited in selectivity, minimizing their clinical potential. To address this, we targeted the regulatory site of ERAP1 using a high-throughput screen and discovered a small molecule hit that is highly selective for ERAP1. (4aR,5S,6R,8S,8aR)-5-(2-(Furan-3-yl)ethyl)-8-hydroxy-5,6,8a-trimethyl-3,4,4a,5,6,7,8,8a-octahydronaphthalene-1-carboxylic acid is a natural product found in Dodonaea viscosa that constitutes a submicromolar, highly selective, and cell-active modulator of ERAP1. Although the compound activates hydrolysis of small model substrates, it is a competitive inhibitor for physiologically relevant longer peptides. Crystallographic analysis confirmed that the compound targets the regulatory site of the enzyme that normally binds the C-terminus of the peptide substrate. Our findings constitute a novel starting point for the development of selective ERAP1 modulators that have potential for further clinical development.
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Affiliation(s)
- John Liddle
- Discovery Partnerships with Academia, GlaxoSmithKline, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Jonathan P Hutchinson
- Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Semra Kitchen
- Discovery Partnerships with Academia, GlaxoSmithKline, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Paul Rowland
- Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Margarete Neu
- Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Ted Cecconie
- Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Duncan S Holmes
- Discovery Partnerships with Academia, GlaxoSmithKline, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Emma Jones
- Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Justyna Korczynska
- Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Despoina Koumantou
- National Centre for Scientific Research "Demokritos", Patriarchou Gregoriou and Neapoleos 27, Agia Paraskevi, Athens 15341, Greece
| | - Jonathan D Lea
- Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Leng Nickels
- Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Michelle Pemberton
- Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Alex Phillipou
- Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Jessica L Schneck
- Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Hester Sheehan
- Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Christopher P Tinworth
- Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Iain Uings
- Discovery Partnerships with Academia, GlaxoSmithKline, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Justyna Wojno-Picon
- Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Robert J Young
- Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Efstratios Stratikos
- National Centre for Scientific Research "Demokritos", Patriarchou Gregoriou and Neapoleos 27, Agia Paraskevi, Athens 15341, Greece
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13
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Maben Z, Arya R, Rane D, An WF, Metkar S, Hickey M, Bender S, Ali A, Nguyen TT, Evnouchidou I, Schilling R, Stratikos E, Golden J, Stern LJ. Discovery of Selective Inhibitors of Endoplasmic Reticulum Aminopeptidase 1. J Med Chem 2019; 63:103-121. [PMID: 31841350 DOI: 10.1021/acs.jmedchem.9b00293] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
ERAP1 is an endoplasmic reticulum-resident zinc aminopeptidase that plays an important role in the immune system by trimming peptides for loading onto major histocompatibility complex proteins. Here, we report discovery of the first inhibitors selective for ERAP1 over its paralogues ERAP2 and IRAP. Compound 1 (N-(N-(2-(1H-indol-3-yl)ethyl)carbamimidoyl)-2,5-difluorobenzenesulfonamide) and compound 2 (1-(1-(4-acetylpiperazine-1-carbonyl)cyclohexyl)-3-(p-tolyl)urea) are competitive inhibitors of ERAP1 aminopeptidase activity. Compound 3 (4-methoxy-3-(N-(2-(piperidin-1-yl)-5-(trifluoromethyl)phenyl)sulfamoyl)benzoic acid) allosterically activates ERAP1's hydrolysis of fluorogenic and chromogenic amino acid substrates but competitively inhibits its activity toward a nonamer peptide representative of physiological substrates. Compounds 2 and 3 inhibit antigen presentation in a cellular assay. Compound 3 displays higher potency for an ERAP1 variant associated with increased risk of autoimmune disease. These inhibitors provide mechanistic insights into the determinants of specificity for ERAP1, ERAP2, and IRAP and offer a new therapeutic approach of specifically inhibiting ERAP1 activity in vivo.
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Affiliation(s)
| | | | - Digamber Rane
- Kansas University Specialized Chemistry Center , Lawrence , Kansas 66047 , United States
| | - W Frank An
- Broad Institute of MIT and Harvard , Cambridge , Massachusetts 02142 , United States
| | - Shailesh Metkar
- Broad Institute of MIT and Harvard , Cambridge , Massachusetts 02142 , United States
| | - Marc Hickey
- Broad Institute of MIT and Harvard , Cambridge , Massachusetts 02142 , United States
| | - Samantha Bender
- Broad Institute of MIT and Harvard , Cambridge , Massachusetts 02142 , United States
| | | | | | - Irini Evnouchidou
- National Centre for Scientific Research Demokritos , Agia Paraskevi, Athens 15341 , Greece
| | - Roger Schilling
- Broad Institute of MIT and Harvard , Cambridge , Massachusetts 02142 , United States
| | - Efstratios Stratikos
- National Centre for Scientific Research Demokritos , Agia Paraskevi, Athens 15341 , Greece
| | - Jennifer Golden
- Kansas University Specialized Chemistry Center , Lawrence , Kansas 66047 , United States
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14
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Mechanism for antigenic peptide selection by endoplasmic reticulum aminopeptidase 1. Proc Natl Acad Sci U S A 2019; 116:26709-26716. [PMID: 31843903 DOI: 10.1073/pnas.1912070116] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Endoplasmic reticulum aminopeptidase 1 (ERAP1) is an intracellular enzyme that optimizes the peptide cargo of major histocompatibility class I (MHC-I) molecules and regulates adaptive immunity. It has unusual substrate selectivity for length and sequence, resulting in poorly understood effects on the cellular immunopeptidome. To understand substrate selection by ERAP1, we solved 2 crystal structures of the enzyme with bound transition-state pseudopeptide analogs at 1.68 Å and 1.72 Å. Both peptides have their N terminus bound at the active site and extend away along a large internal cavity, interacting with shallow pockets that can influence selectivity. The longer peptide is disordered through the central region of the cavity and has its C terminus bound in an allosteric pocket of domain IV that features a carboxypeptidase-like structural motif. These structures, along with enzymatic and computational analyses, explain how ERAP1 can select peptides based on length while retaining the broad sequence-specificity necessary for its biological function.
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15
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Georgiadis D, Mpakali A, Koumantou D, Stratikos E. Inhibitors of ER Aminopeptidase 1 and 2: From Design to Clinical Application. Curr Med Chem 2019; 26:2715-2729. [PMID: 29446724 DOI: 10.2174/0929867325666180214111849] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 01/04/2018] [Accepted: 01/31/2018] [Indexed: 12/19/2022]
Abstract
Endoplasmic Reticulum aminopeptidase 1 and 2 are two homologous enzymes that help generate peptide ligands for presentation by Major Histocompatibility Class I molecules. Their enzymatic activity influences the antigenic peptide repertoire and indirectly controls adaptive immune responses. Accumulating evidence suggests that these two enzymes are tractable targets for the regulation of immune responses with possible applications ranging from cancer immunotherapy to treating inflammatory autoimmune diseases. Here, we review the state-of-the-art in the development of inhibitors of ERAP1 and ERAP2 as well as their potential and limitations for clinical applications.
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Affiliation(s)
- Dimitris Georgiadis
- Department of Chemistry, National and Kapodistrian University of Athens, Zografou, 15771, Athens, Greece
| | - Anastasia Mpakali
- National Center for Scientific Research Demokritos, Agia Paraskevi, 15341, Greece
| | - Despoina Koumantou
- National Center for Scientific Research Demokritos, Agia Paraskevi, 15341, Greece
| | - Efstratios Stratikos
- National Center for Scientific Research Demokritos, Agia Paraskevi, 15341, Greece
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16
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Giastas P, Neu M, Rowland P, Stratikos E. High-Resolution Crystal Structure of Endoplasmic Reticulum Aminopeptidase 1 with Bound Phosphinic Transition-State Analogue Inhibitor. ACS Med Chem Lett 2019; 10:708-713. [PMID: 31097987 PMCID: PMC6511960 DOI: 10.1021/acsmedchemlett.9b00002] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 02/13/2019] [Indexed: 01/25/2023] Open
Abstract
Endoplasmic reticulum aminopeptidase 1 (ERAP1) is an intracellular enzyme that helps generate peptides presented by Major Histocompatibility Complex Class I (MHC class I) molecules and is an emerging target for immunotherapy applications. Despite almost two decades of research on ERAP1, lack of high-resolution crystal structures has hampered drug-development efforts. By optimizing the protein construct, we obtained a high-resolution (1.60 Å) crystal structure of the closed-conformation of ERAP1 with a potent phosphinic pseudopeptide inhibitor bound in its active site. The structure provides key insight on the mechanism of inhibition as well as selectivity toward homologous enzymes and allows detailed mapping of the internal cavity of the enzyme that accommodates peptide-substrates. Bis-tris propane and malic acid molecules, found bound in pockets in the internal cavity, reveal potential druggable secondary binding sites. The ability to obtain high-resolution crystal structures of ERAP1 removes a major bottleneck in the development of compounds that regulate its activity and will greatly accelerate drug-discovery efforts.
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Affiliation(s)
- Petros Giastas
- National Center for Scientific Research Demokritos, Agia
Paraskevi, Athens 15310, Greece
| | - Margarete Neu
- Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Paul Rowland
- Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Efstratios Stratikos
- National Center for Scientific Research Demokritos, Agia
Paraskevi, Athens 15310, Greece
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17
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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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18
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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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