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Bhat SY. Drug targeting of aminopeptidases: importance of deploying a right metal cofactor. Biophys Rev 2024; 16:249-256. [PMID: 38737204 PMCID: PMC11078913 DOI: 10.1007/s12551-024-01192-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 05/05/2022] [Indexed: 05/14/2024] Open
Abstract
Aminopeptidases are metal co-factor-dependent hydrolases releasing N-terminal amino acid residues from peptides. Many of these enzymes, particularly the M24 methionine aminopeptidases (MetAPs), are considered valid drug targets in the fight against many parasitic and non-parasitic diseases. Targeting MetAPs has shown promising results against the malarial parasite, Plasmodium, which is regarded as potential anti-cancer targets. While targeting these essential enzymes represents a potentially promising approach, many challenges are often ignored by scientists when designing drugs or inhibitory scaffolds against the MetAPs. One such aspect is the metal co-factor, with inadequate attention paid to its role in catalysis, folding and remodeling of the catalytic site, and its role in inhibitor binding or potency. Knowing that a metal co-factor is essential for aminopeptidase enzyme activity and active site remodeling, it is intriguing that most computational biologists often ignore the metal ion while screening millions of potential inhibitors to find hits. Ironically, a similar trend is followed by biologists who avoid metal promiscuity of these enzymes while screening inhibitor libraries in vitro which may lead to false positives. This review highlights the importance of considering a physiologically relevant metal co-factor during the drug discovery processes targeting metal-dependent aminopeptidases. Graphical abstract
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2
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Mansouri M, Daware K, Webb CT, McGowan S. Understanding the structure and function of Plasmodium aminopeptidases to facilitate drug discovery. Curr Opin Struct Biol 2023; 82:102693. [PMID: 37657352 DOI: 10.1016/j.sbi.2023.102693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 09/03/2023]
Abstract
Malaria continues to be the most widespread parasitic disease affecting humans globally. As parasites develop drug resistance at an alarming pace, it has become crucial to identify novel drug targets. Over the last decade, the metalloaminopeptidases have gained importance as potential targets for new antimalarials. These enzymes are responsible for removing the N-terminal amino acids from proteins and peptides, and their restricted specificities suggest that many perform unique and essential roles within the malaria parasite. This mini-review focuses on the recent progress in structure and functional data relating to the Plasmodium metalloaminopeptidases that have been validated or shown promise as new antimalarial drug targets.
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Affiliation(s)
- Mahta Mansouri
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia; Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, 3800, Australia. https://twitter.com/Mahta__Mansouri
| | - Kajal Daware
- Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, 3800, Australia; Centre to Impact AMR, Monash University, Clayton, 3800, Victoria Australia
| | - Chaille T Webb
- Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, 3800, Australia; Centre to Impact AMR, Monash University, Clayton, 3800, Victoria Australia
| | - Sheena McGowan
- Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, 3800, Australia; Centre to Impact AMR, Monash University, Clayton, 3800, Victoria Australia.
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3
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Xiong N, Lv PJ, Song JW, Shen Q, Xue YP, Zheng YG. Engineering of a nitrilase through consensus sequence analysis and conserved site substitution to improve its thermostability and activity. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Gauto DF, Macek P, Malinverni D, Fraga H, Paloni M, Sučec I, Hessel A, Bustamante JP, Barducci A, Schanda P. Functional control of a 0.5 MDa TET aminopeptidase by a flexible loop revealed by MAS NMR. Nat Commun 2022; 13:1927. [PMID: 35395851 PMCID: PMC8993905 DOI: 10.1038/s41467-022-29423-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 03/14/2022] [Indexed: 02/07/2023] Open
Abstract
Large oligomeric enzymes control a myriad of cellular processes, from protein synthesis and degradation to metabolism. The 0.5 MDa large TET2 aminopeptidase, a prototypical protease important for cellular homeostasis, degrades peptides within a ca. 60 Å wide tetrahedral chamber with four lateral openings. The mechanisms of substrate trafficking and processing remain debated. Here, we integrate magic-angle spinning (MAS) NMR, mutagenesis, co-evolution analysis and molecular dynamics simulations and reveal that a loop in the catalytic chamber is a key element for enzymatic function. The loop is able to stabilize ligands in the active site and may additionally have a direct role in activating the catalytic water molecule whereby a conserved histidine plays a key role. Our data provide a strong case for the functional importance of highly dynamic - and often overlooked - parts of an enzyme, and the potential of MAS NMR to investigate their dynamics at atomic resolution.
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Affiliation(s)
- Diego F Gauto
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, F-38044, Grenoble, France.,ICSN, CNRS UPR2301, Univ. Paris-Saclay, Gif-sur-Yvette, France
| | - Pavel Macek
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, F-38044, Grenoble, France.,Celonic AG, Eulerstrasse 55, 4051, Basel, Switzerland
| | - Duccio Malinverni
- Department of Structural Biology and Center for Data Driven Discovery, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Hugo Fraga
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, F-38044, Grenoble, France.,Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Porto, Portugal.,i3S, Instituto de Investigacao e Inovacao em Saude, Universidade do Porto, Porto, Portugal
| | - Matteo Paloni
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, INSERM, Montpellier, France
| | - Iva Sučec
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, F-38044, Grenoble, France
| | - Audrey Hessel
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, F-38044, Grenoble, France
| | - Juan Pablo Bustamante
- Instituto de Bioingenieria y Bioinformatica, IBB (CONICET-UNER), Oro Verde, Entre Rios, Argentina
| | - Alessandro Barducci
- Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Porto, Portugal.
| | - Paul Schanda
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, F-38044, Grenoble, France. .,Institute of Science and Technology Austria, Am Campus 1, A-3400, Klosterneuburg, Austria.
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Malcolm TR, Belousoff MJ, Venugopal H, Borg NA, Drinkwater N, Atkinson SC, McGowan S. Active site metals mediate an oligomeric equilibrium in Plasmodium M17 aminopeptidases. J Biol Chem 2020; 296:100173. [PMID: 33303633 PMCID: PMC7948507 DOI: 10.1074/jbc.ra120.016313] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/08/2020] [Accepted: 12/10/2020] [Indexed: 01/14/2023] Open
Abstract
M17 leucyl aminopeptidases are metal-dependent exopeptidases that rely on oligomerization to diversify their functional roles. The M17 aminopeptidases from Plasmodium falciparum (PfA-M17) and Plasmodium vivax (Pv-M17) function as catalytically active hexamers to generate free amino acids from human hemoglobin and are drug targets for the design of novel antimalarial agents. However, the molecular basis for oligomeric assembly is not fully understood. In this study, we found that the active site metal ions essential for catalytic activity have a secondary structural role mediating the formation of active hexamers. We found that PfA-M17 and Pv-M17 exist in a metal-dependent dynamic equilibrium between active hexameric species and smaller inactive species that can be controlled by manipulating the identity and concentration of metals available. Mutation of residues involved in metal ion binding impaired catalytic activity and the formation of active hexamers. Structural resolution of Pv-M17 by cryoelectron microscopy and X-ray crystallography together with solution studies revealed that PfA-M17 and Pv-M17 bind metal ions and substrates in a conserved fashion, although Pv-M17 forms the active hexamer more readily and processes substrates faster than PfA-M17. On the basis of these studies, we propose a dynamic equilibrium between monomer ↔ dimer ↔ tetramer ↔ hexamer, which becomes directional toward the large oligomeric states with the addition of metal ions. This sophisticated metal-dependent dynamic equilibrium may apply to other M17 aminopeptidases and underpin the moonlighting capabilities of this enzyme family.
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Affiliation(s)
- Tess R Malcolm
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Matthew J Belousoff
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Hariprasad Venugopal
- Ramacciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, Victoria, Australia
| | - Natalie A Borg
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia; Immunity and Immune Evasion Laboratory, Chronic Infectious and Inflammatory Diseases Research, School of Health and Biomedical Sciences, RMIT University, Bundoora, Victoria, Australia
| | - Nyssa Drinkwater
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Sarah C Atkinson
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia; Immunity and Immune Evasion Laboratory, Chronic Infectious and Inflammatory Diseases Research, School of Health and Biomedical Sciences, RMIT University, Bundoora, Victoria, Australia
| | - Sheena McGowan
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia.
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Dutoit R, Brandt N, Van Gompel T, Van Elder D, Van Dyck J, Sobott F, Droogmans L. M42 aminopeptidase catalytic site: the structural and functional role of a strictly conserved aspartate residue. Proteins 2020; 88:1639-1647. [PMID: 32673419 DOI: 10.1002/prot.25982] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 06/06/2020] [Accepted: 07/02/2020] [Indexed: 11/08/2022]
Abstract
The M42 aminopeptidases are a family of dinuclear aminopeptidases widely distributed in Prokaryotes. They are potentially associated to the proteasome, achieving complete peptide destruction. Their most peculiar characteristic is their quaternary structure, a tetrahedron-shaped particle made of twelve subunits. The catalytic site of M42 aminopeptidases is defined by seven conserved residues. Five of them are involved in metal ion binding which is important to maintain both the activity and the oligomeric state. The sixth conserved residue, a glutamate, is the catalytic base deprotonating the water molecule during peptide bond hydrolysis. The seventh residue is an aspartate whose function remains poorly understood. This aspartate residue, however, must have a critical role as it is strictly conserved in all MH clan enzymes. It forms some kind of catalytic triad with the histidine residue and the metal ion of the M2 binding site. We assess its role in TmPep1050, an M42 aminopeptidase of Thermotoga maritima, through a mutational approach. Asp-62 was substituted with alanine, asparagine, or glutamate residue. The Asp-62 substitutions completely abolished TmPep1050 activity and impeded dodecamer formation. They also interfered with metal ion binding as only one cobalt ion is bound per subunit instead of two. The structure of Asp62Ala variant was solved at 1.5 Å showing how the substitution has an impact on the active site fold. We propose a structural role for Asp-62, helping to stabilize a crucial loop in the active site and to position correctly the catalytic base and a metal ion ligand of the M1 site.
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Affiliation(s)
- Raphaël Dutoit
- Laboratory of Microbiology, Department of Molecular Biology, Université Libre de Bruxelles, Brussels, Belgium.,Labiris Institut de Recherche, Brussels, Belgium
| | | | - Tom Van Gompel
- Biomolecular & Analytical Mass Spectrometry, Department of Chemistry, Universiteit van Antwerpen, Antwerpen, Belgium
| | - Dany Van Elder
- Laboratory of Microbiology, Department of Molecular Biology, Université Libre de Bruxelles, Brussels, Belgium
| | - Jeroen Van Dyck
- Biomolecular & Analytical Mass Spectrometry, Department of Chemistry, Universiteit van Antwerpen, Antwerpen, Belgium
| | - Frank Sobott
- Biomolecular & Analytical Mass Spectrometry, Department of Chemistry, Universiteit van Antwerpen, Antwerpen, Belgium.,Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, UK
| | - Louis Droogmans
- Laboratory of Microbiology, Department of Molecular Biology, Université Libre de Bruxelles, Brussels, Belgium
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Ross J, Lambert T, Piergentili C, He D, Waldron KJ, Mackay CL, Marles-Wright J, Clarke DJ. Mass spectrometry reveals the assembly pathway of encapsulated ferritins and highlights a dynamic ferroxidase interface. Chem Commun (Camb) 2020; 56:3417-3420. [PMID: 32090213 DOI: 10.1039/c9cc08130e] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Encapsulated ferritins (EncFtn) are a recently characterised member of the ferritin superfamily. EncFtn proteins are sequestered within encapsulin nanocompartments and form a unique biological iron storage system. Here, we use native mass spectrometry and hydrogen-deuterium exchange mass spectrometry to elucidate the metal-mediated assembly pathway of EncFtn.
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Affiliation(s)
- Jennifer Ross
- EaStCHEM School of Chemistry, The University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, Scotland, UK.
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