1
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Fougiaxis V, He B, Khan T, Vatinel R, Koutroumpa NM, Afantitis A, Lesire L, Sierocki P, Deprez B, Deprez-Poulain R. ERAP Inhibitors in Autoimmunity and Immuno-Oncology: Medicinal Chemistry Insights. J Med Chem 2024; 67:11597-11621. [PMID: 39011823 DOI: 10.1021/acs.jmedchem.4c00840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Endoplasmic reticulum aminopeptidases ERAP1 and 2 are intracellular aminopeptidases that trim antigenic precursors and generate antigens presented by major histocompatibility complex class I (MHC-I) molecules. They thus modulate the antigenic repertoire and drive the adaptive immune response. ERAPs are considered as emerging targets for precision immuno-oncology or for the treatment of autoimmune diseases, in particular MHC-I-opathies. This perspective covers the structural and biological characterization of ERAP, their relevance to these diseases and the ongoing research on small-molecule inhibitors. We describe the chemical and pharmacological space explored by medicinal chemists to exploit the potential of these targets given their localization, biological functions, and family depth. Specific emphasis is put on the binding mode, potency, selectivity, and physchem properties of inhibitors featuring diverse scaffolds. The discussion provides valuable insights for the future development of ERAP inhibitors and analysis of persisting challenges for the translation for clinical applications.
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Affiliation(s)
- Vasileios Fougiaxis
- U1177 - Drugs and Molecules for Living Systems, Univ. Lille, Inserm, Institut Pasteur de Lille, F-59000 Lille, France
| | - Ben He
- U1177 - Drugs and Molecules for Living Systems, Univ. Lille, Inserm, Institut Pasteur de Lille, F-59000 Lille, France
| | - Tuhina Khan
- U1177 - Drugs and Molecules for Living Systems, Univ. Lille, Inserm, Institut Pasteur de Lille, F-59000 Lille, France
- European Genomic Institute for Diabetes, EGID, University of Lille, F-59000 Lille, France
| | - Rodolphe Vatinel
- U1177 - Drugs and Molecules for Living Systems, Univ. Lille, Inserm, Institut Pasteur de Lille, F-59000 Lille, France
| | | | | | - Laetitia Lesire
- U1177 - Drugs and Molecules for Living Systems, Univ. Lille, Inserm, Institut Pasteur de Lille, F-59000 Lille, France
- European Genomic Institute for Diabetes, EGID, University of Lille, F-59000 Lille, France
| | - Pierre Sierocki
- U1177 - Drugs and Molecules for Living Systems, Univ. Lille, Inserm, Institut Pasteur de Lille, F-59000 Lille, France
- European Genomic Institute for Diabetes, EGID, University of Lille, F-59000 Lille, France
| | - Benoit Deprez
- U1177 - Drugs and Molecules for Living Systems, Univ. Lille, Inserm, Institut Pasteur de Lille, F-59000 Lille, France
- European Genomic Institute for Diabetes, EGID, University of Lille, F-59000 Lille, France
| | - Rebecca Deprez-Poulain
- U1177 - Drugs and Molecules for Living Systems, Univ. Lille, Inserm, Institut Pasteur de Lille, F-59000 Lille, France
- European Genomic Institute for Diabetes, EGID, University of Lille, F-59000 Lille, France
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2
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Wu J, Li Z, Liu X, Feng D, Liang R, Su X, Li D, Hua H, Cao H. Carnosic Acid: A Novel Selective Inhibitor of ERAP1 by Direct Binding and Its Modulation of Antigen Processing and Presentation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 39024058 DOI: 10.1021/acs.jafc.4c00957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
ERAP1 is an emerging target for a large subclass of severe autoimmune diseases known as "MHC-I-opathy", together with tumor immunity. Nevertheless, effective inhibitors targeting ERAP1 remain a challenge. In this study, a novel food-derived natural product ERAP1-targeting inhibitor, carnosic acid, was identified, and to our knowledge, it is one of the best active compounds among the highly selective inhibitors targeting the orthosteric site of ERAP1. The results reveal that carnosic acid could bind strongly, like a key to the ERAP1 active site in the biased S1' pocket, which is different from the binding mode of the existing orthosteric site inhibitors. HLA-B27-mediated cell modeling validated that carnosic acid has the activity to reverse the AS-associated cellular phenotype brought on by ERAP1 through inhibition. Our findings provide insights into the design of potent inhibitors against the ERAP1 orthosteric site and the discovery of a key direct target of carnosic acid.
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Affiliation(s)
- Jiaqi Wu
- School of Life Science and Biopharmaceutics and Key Laboratory of Microbial Pharmaceutics, Liaoning Province, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang 110016, P. R. China
| | - Zhao Li
- Central Laboratory, Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing 210000, P. R. China
| | - Xiaofan Liu
- School of Life Science and Biopharmaceutics and Key Laboratory of Microbial Pharmaceutics, Liaoning Province, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang 110016, P. R. China
| | - Dongyan Feng
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, and School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang 110016, P. R. China
| | - Ruichao Liang
- School of Life Science and Biopharmaceutics and Key Laboratory of Microbial Pharmaceutics, Liaoning Province, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang 110016, P. R. China
| | - Xin Su
- School of Life Science and Biopharmaceutics and Key Laboratory of Microbial Pharmaceutics, Liaoning Province, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang 110016, P. R. China
| | - Dahong Li
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, and School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang 110016, P. R. China
| | - Huiming Hua
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, and School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang 110016, P. R. China
| | - Hao Cao
- School of Life Science and Biopharmaceutics and Key Laboratory of Microbial Pharmaceutics, Liaoning Province, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang 110016, P. R. China
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3
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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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4
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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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5
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Temponeras I, Samiotaki M, Koumantou D, Nikopaschou M, Kuiper JJW, Panayotou G, Stratikos E. Distinct modulation of cellular immunopeptidome by the allosteric regulatory site of ER aminopeptidase 1. Eur J Immunol 2023; 53:e2350449. [PMID: 37134263 DOI: 10.1002/eji.202350449] [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: 02/22/2023] [Revised: 04/22/2023] [Accepted: 05/02/2023] [Indexed: 05/05/2023]
Abstract
ER aminopeptidase 1 (ERAP1) is an ER-resident aminopeptidase that excises N-terminal residues of peptides that then bind onto Major Histocompatibility Complex I molecules (MHC-I) and indirectly modulates adaptive immune responses. ERAP1 contains an allosteric regulatory site that accommodates the C-terminus of at least some peptide substrates, raising questions about its exact influence on antigen presentation and the potential of allosteric inhibition for cancer immunotherapy. We used an inhibitor that targets this regulatory site to study its effect on the immunopeptidome of a human cancer cell line. The immunopeptidomes of allosterically inhibited and ERAP1 KO cells contain high-affinity peptides with sequence motifs consistent with the cellular HLA class I haplotypes but are strikingly different in peptide composition. Compared to KO cells, allosteric inhibition did not affect the length distribution of peptides and skewed the peptide repertoire both in terms of sequence motifs and HLA allele utilization, indicating significant mechanistic differences between the two ways of disrupting ERAP1 function. These findings suggest that the regulatory site of ERAP1 plays distinct roles in antigenic peptide selection, which should be taken into consideration when designing therapeutic interventions targeting the cancer immunopeptidome.
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Affiliation(s)
- Ioannis Temponeras
- National Centre for Scientific Research Demokritos, Agia Paraskevi, Greece
- Department of Pharmacy, University of Patras, Patra, Greece
| | - Martina Samiotaki
- Biomedical Sciences Research Center "Alexander Fleming,", Institute for Bioinnovation, Vari, Greece
| | - Despoina Koumantou
- National Centre for Scientific Research Demokritos, Agia Paraskevi, Greece
| | - Martha Nikopaschou
- National Centre for Scientific Research Demokritos, Agia Paraskevi, Greece
- Department of Chemistry, National and Kapodistrian University of Athens, Zografou, Greece
| | - Jonas J W Kuiper
- Department of Ophthalmology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - George Panayotou
- Biomedical Sciences Research Center "Alexander Fleming,", Institute for Bioinnovation, Vari, Greece
| | - Efstratios Stratikos
- National Centre for Scientific Research Demokritos, Agia Paraskevi, Greece
- Department of Chemistry, National and Kapodistrian University of Athens, Zografou, Greece
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6
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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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7
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Dueñas ME, Peltier‐Heap RE, Leveridge M, Annan RS, Büttner FH, Trost M. Advances in high-throughput mass spectrometry in drug discovery. EMBO Mol Med 2022; 15:e14850. [PMID: 36515561 PMCID: PMC9832828 DOI: 10.15252/emmm.202114850] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 10/03/2022] [Accepted: 10/07/2022] [Indexed: 12/15/2022] Open
Abstract
High-throughput (HT) screening drug discovery, during which thousands or millions of compounds are screened, remains the key methodology for identifying active chemical matter in early drug discovery pipelines. Recent technological developments in mass spectrometry (MS) and automation have revolutionized the application of MS for use in HT screens. These methods allow the targeting of unlabelled biomolecules in HT assays, thereby expanding the breadth of targets for which HT assays can be developed compared to traditional approaches. Moreover, these label-free MS assays are often cheaper, faster, and more physiologically relevant than competing assay technologies. In this review, we will describe current MS techniques used in drug discovery and explain their advantages and disadvantages. We will highlight the power of mass spectrometry in label-free in vitro assays, and its application for setting up multiplexed cellular phenotypic assays, providing an exciting new tool for screening compounds in cell lines, and even primary cells. Finally, we will give an outlook on how technological advances will increase the future use and the capabilities of mass spectrometry in drug discovery.
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Affiliation(s)
- Maria Emilia Dueñas
- Laboratory for Biomedical Mass Spectrometry, Biosciences InstituteNewcastle UniversityNewcastle‐upon‐TyneUK
| | - Rachel E Peltier‐Heap
- Discovery Analytical, Screening Profiling and Mechanistic Biology, GSK R&DStevenageUK
| | - Melanie Leveridge
- Discovery Analytical, Screening Profiling and Mechanistic Biology, GSK R&DStevenageUK
| | - Roland S Annan
- Discovery Analytical, Screening Profiling and Mechanistic Biology, GSK R&DStevenageUK
| | - Frank H Büttner
- Drug Discovery Sciences, High Throughput BiologyBoehringer Ingelheim Pharma GmbH&CoKGBiberachGermany
| | - Matthias Trost
- Laboratory for Biomedical Mass Spectrometry, Biosciences InstituteNewcastle UniversityNewcastle‐upon‐TyneUK
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8
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Georgiadis D, Skoulikas N, Papakyriakou A, Stratikos E. Phosphinic Peptides as Tool Compounds for the Study of Pharmacologically Relevant Zn-Metalloproteases. ACS Pharmacol Transl Sci 2022; 5:1228-1253. [PMID: 36524013 PMCID: PMC9745897 DOI: 10.1021/acsptsci.2c00183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Indexed: 11/29/2022]
Abstract
Phosphinic peptides constitute an important class of bioactive compounds that have found a wide range of applications in the field of biology and pharmacology of Zn-metalloproteases, the largest family of proteases in humans. They are designed to mimic the structure of natural substrates during their proteolysis, thus acting as mechanism-based, transition state analogue inhibitors. A combination of electrostatic interactions between the phosphinic acid group and the Zn cation as well as optimal noncovalent enzyme-ligand interactions can result in both high binding affinity for the desired target and selectivity against other proteases. Due to these unique properties, phosphinic peptides have been mainly employed as tool compounds for (a) the purposes of rational drug design by serving as ligands in X-ray crystal structures of target enzymes and allowing the identification of crucial interactions that govern optimal molecular recognition, and (b) the delineation of biological pathways where Zn-metalloproteases are key regulators. For the latter objective, inhibitors of the phosphinopeptidic type have been used either unmodified or after being transformed to probes of various types, thus expanding the arsenal of functional tools available to researchers. The aim of this review is to summarize all recent research achievements in which phosphinic peptides have played a central role as tool compounds in the understanding of the mechanism and biological functions of Zn-metalloproteases in both health and disease.
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Affiliation(s)
- Dimitris Georgiadis
- Department
of Chemistry, National and Kapodistrian
University of Athens, GR-15784 Athens, Greece
| | - Nikolaos Skoulikas
- Department
of Chemistry, National and Kapodistrian
University of Athens, GR-15784 Athens, Greece
| | - Athanasios Papakyriakou
- National
Centre for Scientific Research “Demokritos”, Agia Paraskevi GR-15341 Athens, Greece
| | - Efstratios Stratikos
- Department
of Chemistry, National and Kapodistrian
University of Athens, GR-15784 Athens, Greece
- National
Centre for Scientific Research “Demokritos”, Agia Paraskevi GR-15341 Athens, Greece
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9
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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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Vourloumis D, Mavridis I, Athanasoulis A, Temponeras I, Koumantou D, Giastas P, Mpakali A, Magrioti V, Leib J, van Endert P, Stratikos E, Papakyriakou A. Discovery of Selective Nanomolar Inhibitors for Insulin-Regulated Aminopeptidase Based on α-Hydroxy-β-amino Acid Derivatives of Bestatin. J Med Chem 2022; 65:10098-10117. [PMID: 35833347 DOI: 10.1021/acs.jmedchem.2c00904] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The oxytocinase subfamily of M1 zinc aminopeptidases comprises emerging drug targets, including the ER-resident aminopeptidases 1 and 2 (ERAP1 and ERAP2) and insulin-regulated aminopeptidase (IRAP); however, reports on clinically relevant inhibitors are limited. Here we report a new synthetic approach of high diastereo- and regioselectivity for functionalization of the α-hydroxy-β-amino acid scaffold of bestatin. Stereochemistry and mechanism of inhibition were investigated by a high-resolution X-ray crystal structure of ERAP1 in complex with a micromolar inhibitor. By exploring the P1 side-chain functionalities, we achieve significant potency and selectivity, and we report a cell-active, low-nanomolar inhibitor of IRAP with >120-fold selectivity over homologous enzymes. X-ray crystallographic analysis of IRAP in complex with this inhibitor suggest that interactions with the GAMEN loop is an unappreciated key determinant for potency and selectivity. Overall, our results suggest that α-hydroxy-β-amino acid derivatives may constitute useful chemical tools and drug leads for this group of aminopeptidases.
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Affiliation(s)
- Dionisios Vourloumis
- National Centre for Scientific Research "Demokritos", Ag. Paraskevi, GR-15341 Athens, Greece
| | - Ioannis Mavridis
- National Centre for Scientific Research "Demokritos", Ag. Paraskevi, GR-15341 Athens, Greece
| | - Alexandros Athanasoulis
- National Centre for Scientific Research "Demokritos", Ag. Paraskevi, GR-15341 Athens, Greece
| | - Ioannis Temponeras
- National Centre for Scientific Research "Demokritos", Ag. Paraskevi, GR-15341 Athens, Greece.,Department of Pharmacy, University of Patras, 26504 Patra, Greece
| | - Despoina Koumantou
- National Centre for Scientific Research "Demokritos", Ag. Paraskevi, GR-15341 Athens, Greece
| | - Petros Giastas
- Department of Biotechnology, Agricultural University of Athens, GR-11855 Athens, Greece
| | - Anastasia Mpakali
- National Centre for Scientific Research "Demokritos", Ag. Paraskevi, GR-15341 Athens, Greece.,Department of Chemistry, National and Kapodistrian University of Athens, GR-15784 Athens, Greece
| | - Victoria Magrioti
- Department of Chemistry, National and Kapodistrian University of Athens, GR-15784 Athens, Greece
| | - Jacqueline Leib
- Université Paris Cité, INSERM, CNRS, Institut Necker Enfants Malades, F-75015 Paris, France
| | - Peter van Endert
- Université Paris Cité, INSERM, CNRS, Institut Necker Enfants Malades, F-75015 Paris, France.,Service Immunologie Biologique, AP-HP, Hôpital Universitaire Necker-Enfants Malades, F-75015 Paris, France
| | - Efstratios Stratikos
- National Centre for Scientific Research "Demokritos", Ag. Paraskevi, GR-15341 Athens, Greece.,Department of Chemistry, National and Kapodistrian University of Athens, GR-15784 Athens, Greece
| | - Athanasios Papakyriakou
- National Centre for Scientific Research "Demokritos", Ag. Paraskevi, GR-15341 Athens, Greece
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11
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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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12
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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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13
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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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14
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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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15
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Mavridis G, Mpakali A, Zoidakis J, Makridakis M, Vlahou A, Kaloumenou E, Ziotopoulou A, Georgiadis D, Papakyriakou A, Stratikos E. The ERAP1 active site cannot productively access the N-terminus of antigenic peptide precursors stably bound onto MHC class I. Sci Rep 2021; 11:16475. [PMID: 34389743 PMCID: PMC8363620 DOI: 10.1038/s41598-021-95786-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 07/22/2021] [Indexed: 12/01/2022] Open
Abstract
Processing of N-terminally elongated antigenic peptide precursors by Endoplasmic Reticulum Aminopeptidase 1 (ERAP1) is a key step in antigen presentation and the adaptive immune response. Although ERAP1 can efficiently process long peptides in solution, it has been proposed that it can also process peptides bound onto Major Histocompatibility Complex I molecules (MHCI). In a previous study, we suggested that the occasionally observed “ontο MHCI” trimming by ERAP1 is likely due to fast peptide dissociation followed by solution trimming, rather than direct action of ERAP1 onto the MHCI complex. However, other groups have proposed that ERAP1 can trim peptides covalently bound onto MHCI, which would preclude peptide dissociation. To explore this interaction, we constructed disulfide-linked MHCI-peptide complexes using HLA-B*08 and a 12mer kinetically labile peptide, or a 16mer carrying a phosphinic transition-state analogue N-terminus with high-affinity for ERAP1. Kinetic and biochemical analyses suggested that while both peptides could access the ERAP1 active site when free in solution, they were unable to do so when tethered in the MHCI binding groove. Our results suggest that MHCI binding protects, rather than promotes, antigenic peptide precursor trimming by ERAP1 and thus solution trimming is the more likely model of antigenic peptide processing.
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Affiliation(s)
- George Mavridis
- Protein Chemistry Laboratory, National Centre for Scientific Research Demokritos, 15341, Agia Paraskevi, Greece
| | - Anastasia Mpakali
- Protein Chemistry Laboratory, National Centre for Scientific Research Demokritos, 15341, Agia Paraskevi, Greece
| | - Jerome Zoidakis
- Centre of Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527, Athens, Greece
| | - Manousos Makridakis
- Centre of Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527, Athens, Greece
| | - Antonia Vlahou
- Centre of Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527, Athens, Greece
| | - Eleni Kaloumenou
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15784, Panepistimiopolis Zografou, Greece
| | - Angeliki Ziotopoulou
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15784, Panepistimiopolis Zografou, Greece
| | - Dimitris Georgiadis
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15784, Panepistimiopolis Zografou, Greece
| | - Athanasios Papakyriakou
- Protein Chemistry Laboratory, National Centre for Scientific Research Demokritos, 15341, Agia Paraskevi, Greece
| | - Efstratios Stratikos
- Protein Chemistry Laboratory, National Centre for Scientific Research Demokritos, 15341, Agia Paraskevi, Greece. .,Biochemistry Laboratory, National and Kapodistrian University of Athens, 15784, Panepistimiopolis Zografou, Greece.
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16
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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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17
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Discovery of Selective Inhibitor Leads by Targeting an Allosteric Site in Insulin-Regulated Aminopeptidase. Pharmaceuticals (Basel) 2021; 14:ph14060584. [PMID: 34207179 PMCID: PMC8233869 DOI: 10.3390/ph14060584] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 12/23/2022] Open
Abstract
Insulin-Regulated aminopeptidase (IRAP) is a zinc-dependent aminopeptidase with several important biological functions and is an emerging pharmaceutical target for cognitive enhancement and immune system regulation. Aiming to discover lead-like IRAP inhibitors with enhanced selectivity versus homologous enzymes, we targeted an allosteric site at the C-terminal domain pocket of IRAP. We compiled a library of 2.5 million commercially available compounds from the ZINC database, and performed molecular docking at the target pocket of IRAP and the corresponding pocket of the homologous endoplasmic reticulum aminopeptidase 1 (ERAP1). Of the top compounds that showed high selectivity, 305 were further analyzed by molecular dynamics simulations and free energy calculations, leading to the selection of 33 compounds for in vitro evaluation. Two orthogonal functional assays were employed: one using a small fluorogenic substrate and one following the degradation of oxytocin, a natural peptidic substrate of IRAP. In vitro evaluation suggested that several of the compounds tested can inhibit IRAP, but the inhibition profile was dependent on substrate size, consistent with the allosteric nature of the targeted site. Overall, our results describe several novel leads as IRAP inhibitors and suggest that the C-terminal domain pocket of IRAP is a promising target for developing highly selective IRAP inhibitors.
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18
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Wilding B, Pasqua AE, E A Chessum N, Pierrat OA, Hahner T, Tomlin K, Shehu E, Burke R, Richards GM, Whitton B, Arwert EN, Thapaliya A, Salimraj R, van Montfort R, Skawinska A, Hayes A, Raynaud F, Chopra R, Jones K, Newton G, Cheeseman MD. Investigating the phosphinic acid tripeptide mimetic DG013A as a tool compound inhibitor of the M1-aminopeptidase ERAP1. Bioorg Med Chem Lett 2021; 42:128050. [PMID: 33887439 PMCID: PMC8188423 DOI: 10.1016/j.bmcl.2021.128050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/26/2021] [Accepted: 04/13/2021] [Indexed: 11/15/2022]
Abstract
ERAP1 is a zinc-dependent M1-aminopeptidase that trims lipophilic amino acids from the N-terminus of peptides. Owing to its importance in the processing of antigens and regulation of the adaptive immune response, dysregulation of the highly polymorphic ERAP1 has been implicated in autoimmune disease and cancer. To test this hypothesis and establish the role of ERAP1 in these disease areas, high affinity, cell permeable and selective chemical probes are essential. DG013A 1, is a phosphinic acid tripeptide mimetic inhibitor with reported low nanomolar affinity for ERAP1. However, this chemotype is a privileged structure for binding to various metal-dependent peptidases and contains a highly charged phosphinic acid moiety, so it was unclear whether it would display the high selectivity and passive permeability required for a chemical probe. Therefore, we designed a new stereoselective route to synthesize a library of DG013A 1 analogues to determine the suitability of this compound as a cellular chemical probe to validate ERAP1 as a drug discovery target.
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Affiliation(s)
- Birgit Wilding
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SW7 3RP, UK
| | - A Elisa Pasqua
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SW7 3RP, UK
| | - Nicola E A Chessum
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SW7 3RP, UK
| | - Olivier A Pierrat
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SW7 3RP, UK
| | - Tamas Hahner
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SW7 3RP, UK
| | - Kathy Tomlin
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SW7 3RP, UK
| | - Erald Shehu
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SW7 3RP, UK
| | - Rosemary Burke
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SW7 3RP, UK
| | - G Meirion Richards
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SW7 3RP, UK
| | - Bradleigh Whitton
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SW7 3RP, UK
| | - Esther N Arwert
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SW7 3RP, UK
| | - Arjun Thapaliya
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SW7 3RP, UK; Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Ramya Salimraj
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SW7 3RP, UK; Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Rob van Montfort
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SW7 3RP, UK; Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Agi Skawinska
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SW7 3RP, UK
| | - Angela Hayes
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SW7 3RP, UK
| | - Florence Raynaud
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SW7 3RP, UK
| | - Rajesh Chopra
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SW7 3RP, UK
| | - Keith Jones
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SW7 3RP, UK
| | - Gary Newton
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SW7 3RP, UK
| | - Matthew D Cheeseman
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SW7 3RP, UK.
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19
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Hutchinson JP, Temponeras I, Kuiper J, Cortes A, Korczynska J, Kitchen S, Stratikos E. Common allotypes of ER aminopeptidase 1 have substrate-dependent and highly variable enzymatic properties. J Biol Chem 2021; 296:100443. [PMID: 33617882 PMCID: PMC8024916 DOI: 10.1016/j.jbc.2021.100443] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/11/2021] [Accepted: 02/17/2021] [Indexed: 02/06/2023] Open
Abstract
Polymorphic variation of immune system proteins can drive variability of individual immune responses. Endoplasmic reticulum aminopeptidase 1 (ERAP1) generates antigenic peptides for presentation by major histocompatibility complex class I molecules. Coding SNPs in ERAP1 have been associated with predisposition to inflammatory rheumatic disease and shown to affect functional properties of the enzyme, but the interplay between combinations of these SNPs as they exist in allotypes has not been thoroughly explored. We used phased genotype data to estimate ERAP1 allotype frequency in 2504 individuals across five major human populations, generated highly pure recombinant enzymes corresponding to the ten most common ERAP1 allotypes, and systematically characterized their in vitro enzymatic properties. We find that ERAP1 allotypes possess a wide range of enzymatic activities, up to 60-fold, whose ranking is substrate dependent. Strikingly, allotype 10, previously associated with Behçet’s disease, is consistently a low-activity outlier, suggesting that a significant percentage of individuals carry a subactive ERAP1 gene. Enzymatic analysis revealed that ERAP1 allotypes can differ in both catalytic efficiency and substrate affinity, differences that can change intermediate accumulation in multistep trimming reactions. Alterations in efficacy of an allosteric inhibitor that targets the regulatory site suggest that allotypic variation influences the communication between the regulatory and the active site. Our work defines the wide landscape of ERAP1 activity in human populations and demonstrates how common allotypes can induce substrate-dependent variability in antigen processing, thus contributing, in synergy with major histocompatibility complex haplotypes, to immune response variability and predisposition to chronic inflammatory conditions.
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Affiliation(s)
| | - Ioannis Temponeras
- Protein Chemistry Laboratory, National Centre for Scientific Research "Demokritos", Athens, Greece
| | - Jonas Kuiper
- Department of Ophthalmology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands; Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Adrian Cortes
- Human Genetics, GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | - Justyna Korczynska
- Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | - Semra Kitchen
- Adaptive Immunity Research Unit, GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | - Efstratios Stratikos
- Protein Chemistry Laboratory, National Centre for Scientific Research "Demokritos", Athens, Greece; Laboratory of Biochemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, Athens, Greece.
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20
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Mpakali A, Stratikos E. The Role of Antigen Processing and Presentation in Cancer and the Efficacy of Immune Checkpoint Inhibitor Immunotherapy. Cancers (Basel) 2021; 13:E134. [PMID: 33406696 PMCID: PMC7796214 DOI: 10.3390/cancers13010134] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 12/28/2020] [Accepted: 12/30/2020] [Indexed: 02/07/2023] Open
Abstract
Recent clinical successes of cancer immunotherapy using immune checkpoint inhibitors (ICIs) are rapidly changing the landscape of cancer treatment. Regardless of initial impressive clinical results though, the therapeutic benefit of ICIs appears to be limited to a subset of patients and tumor types. Recent analyses have revealed that the potency of ICI therapies depends on the efficient presentation of tumor-specific antigens by cancer cells and professional antigen presenting cells. Here, we review current knowledge on the role of antigen presentation in cancer. We focus on intracellular antigen processing and presentation by Major Histocompatibility class I (MHCI) molecules and how it can affect cancer immune evasion. Finally, we discuss the pharmacological tractability of manipulating intracellular antigen processing as a complementary approach to enhance tumor immunogenicity and the effectiveness of ICI immunotherapy.
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Affiliation(s)
- Anastasia Mpakali
- National Centre for Scientific Research Demokritos, Agia Paraskevi, 15341 Athens, Greece
| | - Efstratios Stratikos
- National Centre for Scientific Research Demokritos, Agia Paraskevi, 15341 Athens, Greece
- Laboratory of Biochemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zographou, 15784 Athens, Greece
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21
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Modulators of hERAP2 discovered by high-throughput screening. Eur J Med Chem 2020; 211:113053. [PMID: 33359953 DOI: 10.1016/j.ejmech.2020.113053] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 11/21/2020] [Accepted: 11/23/2020] [Indexed: 01/17/2023]
Abstract
Endoplasmic reticulum aminopeptidase 2, ERAP2, is an emerging pharmacological target in cancer immunotherapy and control of autoinflammatory diseases, as it is involved in antigen processing. It has been linked to the risk of development of spondyloarthritis, and it associates with the immune infiltration of tumours and strongly predicts the overall survival for patients receiving check-point inhibitor therapy. While some selective inhibitors of its homolog ERAP1 are available, no selective modulator of ERAP2 has been disclosed so far. In order to identify such compounds, we screened an in-house focused library of 1920 compounds designed to target metalloenzymes. Structure-Activity Relationships and docking around two hits led to the discovery of selective inhibitors of ERAP2. Amid those, some bind to yet untapped amino-acids in the S1 pocket. Importantly, we disclose also the first activator of small substrates hydrolysis by ERAP2. Inhibitors and activators identified in this study could serve as useful starting points for optimization.
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22
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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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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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