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Rizk SS, Moustafa DM, ElBanna SA, Nour El-Din HT, Attia AS. Nanobodies in the fight against infectious diseases: repurposing nature's tiny weapons. World J Microbiol Biotechnol 2024; 40:209. [PMID: 38771414 PMCID: PMC11108896 DOI: 10.1007/s11274-024-03990-4] [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: 02/20/2024] [Accepted: 04/15/2024] [Indexed: 05/22/2024]
Abstract
Nanobodies are the smallest known antigen-binding molecules to date. Their small size, good tissue penetration, high stability and solubility, ease of expression, refolding ability, and negligible immunogenicity in the human body have granted them excellence over conventional antibodies. Those exceptional attributes of nanobodies make them promising candidates for various applications in biotechnology, medicine, protein engineering, structural biology, food, and agriculture. This review presents an overview of their structure, development methods, advantages, possible challenges, and applications with special emphasis on infectious diseases-related ones. A showcase of how nanobodies can be harnessed for applications including neutralization of viruses and combating antibiotic-resistant bacteria is detailed. Overall, the impact of nanobodies in vaccine design, rapid diagnostics, and targeted therapies, besides exploring their role in deciphering microbial structures and virulence mechanisms are highlighted. Indeed, nanobodies are reshaping the future of infectious disease prevention and treatment.
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Affiliation(s)
- Soha S Rizk
- Microbiology and Immunology Postgraduate Program, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt
| | - Dina M Moustafa
- Department of Medical Sciences, Faculty of Dentistry, The British University in Egypt, El Sherouk City, Cairo, 11837, Egypt
| | - Shahira A ElBanna
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt
| | - Hanzada T Nour El-Din
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt
| | - Ahmed S Attia
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt.
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2
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Islam Z, Vaikath NN, Hmila I, El‐Agnaf OMA, Kolatkar PR. Structural insights into the unique recognition module between α-synuclein peptide and nanobody. Protein Sci 2024; 33:e4875. [PMID: 38105512 PMCID: PMC10807187 DOI: 10.1002/pro.4875] [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: 08/16/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 12/19/2023]
Abstract
Nanobodies are single-domain fragments of antibodies with comparable specificity and affinity to antibodies. They are emerging as versatile tools in biology due to their relatively small size. Here, we report the crystal structure of a specific nanobody Nbα-syn01, bound to a 14 amino acid long peptide of α-synuclein (αSyn), a 140-residue protein whose aggregation is associated with Parkinson's disease. The complex structure exhibits a unique binding pattern where the αSyn peptide replaces the N-terminal region of nanobody. Recognition is mediated principally by extended main chain interaction of the αSyn peptide and specificity of the interaction lies in the central 48-52 region of αSyn peptide. Structure-guided truncation of Nbα-syn01 shows tighter binding to αSyn peptide and improved inhibition of α-synuclein aggregation. The structure of the truncated complex was subsequently determined and was indistinguishable to full length complex as the full-length form had no visible electron density for the N-terminal end. These findings reveal the molecular basis for a previously unobserved binding mode for nanobody recognition of α-synuclein, providing an explanation for the enhanced binding, and potential for an alternate framework for structure-based protein engineering of nanobodies to develop better diagnostic and therapeutic tools.
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Affiliation(s)
- Zeyaul Islam
- Diabetes CenterQatar Biomedical Research Institute, Hamad Bin Khalifa University, Qatar FoundationDohaQatar
| | - Nishant N. Vaikath
- Neurological Disorder Research CenterQatar Biomedical Research Institute, Hamad Bin Khalifa University, Qatar FoundationDohaQatar
| | - Issam Hmila
- Neurological Disorder Research CenterQatar Biomedical Research Institute, Hamad Bin Khalifa University, Qatar FoundationDohaQatar
| | - Omar M. A. El‐Agnaf
- Neurological Disorder Research CenterQatar Biomedical Research Institute, Hamad Bin Khalifa University, Qatar FoundationDohaQatar
| | - Prasanna R. Kolatkar
- Diabetes CenterQatar Biomedical Research Institute, Hamad Bin Khalifa University, Qatar FoundationDohaQatar
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3
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Tawfeeq C, Song J, Khaniya U, Madej T, Wang J, Youkharibache P, Abrol R. Towards a structural and functional analysis of the immunoglobulin-fold proteome. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 138:135-178. [PMID: 38220423 DOI: 10.1016/bs.apcsb.2023.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
The immunoglobulin fold (Ig fold) domain is a super-secondary structural motif consisting of a sandwich with two layers of β-sheets that is present in many proteins with very diverse biological functions covering a wide range of physiological processes. This domain presents a modular architecture built with β strands connected by variable length loops that has a highly conserved structural core of four β-strands and quite variable β-sheet extensions in the two sandwich layers that enable both divergent and convergent evolutionary mechanisms in the known Ig fold proteome. The central role of this Ig fold's structural plasticity in the evolutionary success of antibodies in our immune system is well established. Nature has also utilized this Ig fold in all domains of life in many different physiological contexts that go way beyond the immune system. Here we will present a structural and functional overview of the utilization of the Ig fold in different biological processes and in different cellular contexts to highlight some of the innumerable ways that this structural motif can interact in multidomain proteins to enable their diversity of functions. This includes shareable specific protein structure visualizations behind those functions that serve as starting points for further explorations of the biomolecular interactions spanning the Ig fold proteome. This overview also highlights how this Ig fold is being utilized through natural adaptation, engineering, and even building from scratch for a range of biotechnological applications.
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Affiliation(s)
- Caesar Tawfeeq
- Department of Chemistry and Biochemistry, California State University Northridge, Northridge, United States
| | - James Song
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - Umesh Khaniya
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Thomas Madej
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - Jiyao Wang
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - Philippe Youkharibache
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, United States.
| | - Ravinder Abrol
- Department of Chemistry and Biochemistry, California State University Northridge, Northridge, United States.
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Zehnaker A, Vallet A, Gourdon J, Sarti C, Jugnarain V, Haj Hassan M, Mathias L, Gauthier C, Raynaud P, Boulo T, Beauclair L, Bigot Y, Casarini L, Crépieux P, Poupon A, Piégu B, Jean-Alphonse F, Bruneau G, Reiter É. Combined Multiplexed Phage Display, High-Throughput Sequencing, and Functional Assays as a Platform for Identifying Modulatory VHHs Targeting the FSHR. Int J Mol Sci 2023; 24:15961. [PMID: 37958944 PMCID: PMC10650796 DOI: 10.3390/ijms242115961] [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: 09/25/2023] [Revised: 10/30/2023] [Accepted: 11/02/2023] [Indexed: 11/15/2023] Open
Abstract
Developing modulatory antibodies against G protein-coupled receptors is challenging. In this study, we targeted the follicle-stimulating hormone receptor (FSHR), a significant regulator of reproduction, with variable domains of heavy chain-only antibodies (VHHs). We built two immune VHH libraries and submitted them to multiplexed phage display approaches. We used next-generation sequencing to identify 34 clusters of specifically enriched sequences that were functionally assessed in a primary screen based on a cAMP response element (CRE)-dependent reporter gene assay. In this assay, 23 VHHs displayed negative or positive modulation of FSH-induced responses, suggesting a high success rate of the multiplexed strategy. We then focused on the largest cluster identified (i.e., PRC1) that displayed positive modulation of FSH action. We demonstrated that PRC1 specifically binds to the human FSHR and human FSHR/FSH complex while potentiating FSH-induced cAMP production and Gs recruitment. We conclude that the improved selection strategy reported here is effective for rapidly identifying functionally active VHHs and could be adapted to target other challenging membrane receptors. This study also led to the identification of PRC1, the first potential positive modulator VHH reported for the human FSHR.
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Affiliation(s)
- Anielka Zehnaker
- Physiologie de la Reproduction et des Comportements (PRC), Institut National de Recherche Pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Université de Tours, 37380 Nouzilly, France; (A.Z.); (A.V.); (J.G.); (C.S.); (V.J.); (M.H.H.); (L.M.); (C.G.); (P.R.); (T.B.); (L.B.); (Y.B.); (L.C.); (P.C.); (A.P.); (B.P.); (F.J.-A.)
| | - Amandine Vallet
- Physiologie de la Reproduction et des Comportements (PRC), Institut National de Recherche Pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Université de Tours, 37380 Nouzilly, France; (A.Z.); (A.V.); (J.G.); (C.S.); (V.J.); (M.H.H.); (L.M.); (C.G.); (P.R.); (T.B.); (L.B.); (Y.B.); (L.C.); (P.C.); (A.P.); (B.P.); (F.J.-A.)
| | - Juliette Gourdon
- Physiologie de la Reproduction et des Comportements (PRC), Institut National de Recherche Pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Université de Tours, 37380 Nouzilly, France; (A.Z.); (A.V.); (J.G.); (C.S.); (V.J.); (M.H.H.); (L.M.); (C.G.); (P.R.); (T.B.); (L.B.); (Y.B.); (L.C.); (P.C.); (A.P.); (B.P.); (F.J.-A.)
| | - Caterina Sarti
- Physiologie de la Reproduction et des Comportements (PRC), Institut National de Recherche Pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Université de Tours, 37380 Nouzilly, France; (A.Z.); (A.V.); (J.G.); (C.S.); (V.J.); (M.H.H.); (L.M.); (C.G.); (P.R.); (T.B.); (L.B.); (Y.B.); (L.C.); (P.C.); (A.P.); (B.P.); (F.J.-A.)
| | - Vinesh Jugnarain
- Physiologie de la Reproduction et des Comportements (PRC), Institut National de Recherche Pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Université de Tours, 37380 Nouzilly, France; (A.Z.); (A.V.); (J.G.); (C.S.); (V.J.); (M.H.H.); (L.M.); (C.G.); (P.R.); (T.B.); (L.B.); (Y.B.); (L.C.); (P.C.); (A.P.); (B.P.); (F.J.-A.)
| | - Maya Haj Hassan
- Physiologie de la Reproduction et des Comportements (PRC), Institut National de Recherche Pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Université de Tours, 37380 Nouzilly, France; (A.Z.); (A.V.); (J.G.); (C.S.); (V.J.); (M.H.H.); (L.M.); (C.G.); (P.R.); (T.B.); (L.B.); (Y.B.); (L.C.); (P.C.); (A.P.); (B.P.); (F.J.-A.)
| | - Laetitia Mathias
- Physiologie de la Reproduction et des Comportements (PRC), Institut National de Recherche Pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Université de Tours, 37380 Nouzilly, France; (A.Z.); (A.V.); (J.G.); (C.S.); (V.J.); (M.H.H.); (L.M.); (C.G.); (P.R.); (T.B.); (L.B.); (Y.B.); (L.C.); (P.C.); (A.P.); (B.P.); (F.J.-A.)
| | - Camille Gauthier
- Physiologie de la Reproduction et des Comportements (PRC), Institut National de Recherche Pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Université de Tours, 37380 Nouzilly, France; (A.Z.); (A.V.); (J.G.); (C.S.); (V.J.); (M.H.H.); (L.M.); (C.G.); (P.R.); (T.B.); (L.B.); (Y.B.); (L.C.); (P.C.); (A.P.); (B.P.); (F.J.-A.)
| | - Pauline Raynaud
- Physiologie de la Reproduction et des Comportements (PRC), Institut National de Recherche Pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Université de Tours, 37380 Nouzilly, France; (A.Z.); (A.V.); (J.G.); (C.S.); (V.J.); (M.H.H.); (L.M.); (C.G.); (P.R.); (T.B.); (L.B.); (Y.B.); (L.C.); (P.C.); (A.P.); (B.P.); (F.J.-A.)
| | - Thomas Boulo
- Physiologie de la Reproduction et des Comportements (PRC), Institut National de Recherche Pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Université de Tours, 37380 Nouzilly, France; (A.Z.); (A.V.); (J.G.); (C.S.); (V.J.); (M.H.H.); (L.M.); (C.G.); (P.R.); (T.B.); (L.B.); (Y.B.); (L.C.); (P.C.); (A.P.); (B.P.); (F.J.-A.)
| | - Linda Beauclair
- Physiologie de la Reproduction et des Comportements (PRC), Institut National de Recherche Pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Université de Tours, 37380 Nouzilly, France; (A.Z.); (A.V.); (J.G.); (C.S.); (V.J.); (M.H.H.); (L.M.); (C.G.); (P.R.); (T.B.); (L.B.); (Y.B.); (L.C.); (P.C.); (A.P.); (B.P.); (F.J.-A.)
| | - Yves Bigot
- Physiologie de la Reproduction et des Comportements (PRC), Institut National de Recherche Pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Université de Tours, 37380 Nouzilly, France; (A.Z.); (A.V.); (J.G.); (C.S.); (V.J.); (M.H.H.); (L.M.); (C.G.); (P.R.); (T.B.); (L.B.); (Y.B.); (L.C.); (P.C.); (A.P.); (B.P.); (F.J.-A.)
| | - Livio Casarini
- Physiologie de la Reproduction et des Comportements (PRC), Institut National de Recherche Pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Université de Tours, 37380 Nouzilly, France; (A.Z.); (A.V.); (J.G.); (C.S.); (V.J.); (M.H.H.); (L.M.); (C.G.); (P.R.); (T.B.); (L.B.); (Y.B.); (L.C.); (P.C.); (A.P.); (B.P.); (F.J.-A.)
- Unit of Endocrinology, Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Pascale Crépieux
- Physiologie de la Reproduction et des Comportements (PRC), Institut National de Recherche Pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Université de Tours, 37380 Nouzilly, France; (A.Z.); (A.V.); (J.G.); (C.S.); (V.J.); (M.H.H.); (L.M.); (C.G.); (P.R.); (T.B.); (L.B.); (Y.B.); (L.C.); (P.C.); (A.P.); (B.P.); (F.J.-A.)
- Inria, Inria Saclay-Ile-de-France, 91120 Palaiseau, France
| | - Anne Poupon
- Physiologie de la Reproduction et des Comportements (PRC), Institut National de Recherche Pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Université de Tours, 37380 Nouzilly, France; (A.Z.); (A.V.); (J.G.); (C.S.); (V.J.); (M.H.H.); (L.M.); (C.G.); (P.R.); (T.B.); (L.B.); (Y.B.); (L.C.); (P.C.); (A.P.); (B.P.); (F.J.-A.)
- Inria, Inria Saclay-Ile-de-France, 91120 Palaiseau, France
- MAbSilico, 1 Impasse du Palais, 37000 Tours, France
| | - Benoît Piégu
- Physiologie de la Reproduction et des Comportements (PRC), Institut National de Recherche Pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Université de Tours, 37380 Nouzilly, France; (A.Z.); (A.V.); (J.G.); (C.S.); (V.J.); (M.H.H.); (L.M.); (C.G.); (P.R.); (T.B.); (L.B.); (Y.B.); (L.C.); (P.C.); (A.P.); (B.P.); (F.J.-A.)
| | - Frédéric Jean-Alphonse
- Physiologie de la Reproduction et des Comportements (PRC), Institut National de Recherche Pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Université de Tours, 37380 Nouzilly, France; (A.Z.); (A.V.); (J.G.); (C.S.); (V.J.); (M.H.H.); (L.M.); (C.G.); (P.R.); (T.B.); (L.B.); (Y.B.); (L.C.); (P.C.); (A.P.); (B.P.); (F.J.-A.)
- Inria, Inria Saclay-Ile-de-France, 91120 Palaiseau, France
| | - Gilles Bruneau
- Physiologie de la Reproduction et des Comportements (PRC), Institut National de Recherche Pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Université de Tours, 37380 Nouzilly, France; (A.Z.); (A.V.); (J.G.); (C.S.); (V.J.); (M.H.H.); (L.M.); (C.G.); (P.R.); (T.B.); (L.B.); (Y.B.); (L.C.); (P.C.); (A.P.); (B.P.); (F.J.-A.)
| | - Éric Reiter
- Physiologie de la Reproduction et des Comportements (PRC), Institut National de Recherche Pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Université de Tours, 37380 Nouzilly, France; (A.Z.); (A.V.); (J.G.); (C.S.); (V.J.); (M.H.H.); (L.M.); (C.G.); (P.R.); (T.B.); (L.B.); (Y.B.); (L.C.); (P.C.); (A.P.); (B.P.); (F.J.-A.)
- Inria, Inria Saclay-Ile-de-France, 91120 Palaiseau, France
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Sogues A, Fioravanti A, Jonckheere W, Pardon E, Steyaert J, Remaut H. Structure and function of the EA1 surface layer of Bacillus anthracis. Nat Commun 2023; 14:7051. [PMID: 37923757 PMCID: PMC10624894 DOI: 10.1038/s41467-023-42826-x] [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: 04/24/2023] [Accepted: 10/23/2023] [Indexed: 11/06/2023] Open
Abstract
The Gram-positive spore-forming bacterium Bacillus anthracis is the causative agent of anthrax, a deadly disease mostly affecting wildlife and livestock, as well as representing a bioterrorism threat. Its cell surface is covered by the mutually exclusive S-layers Sap and EA1, found in early and late growth phases, respectively. Here we report the nanobody-based structural characterization of EA1 and its native lattice contacts. The EA1 assembly domain consists of 6 immunoglobulin-like domains, where three calcium-binding sites structure interdomain contacts that allow monomers to adopt their assembly-competent conformation. Nanobody-induced depolymerization of EA1 S-layers results in surface defects, membrane blebbing and cell lysis under hypotonic conditions, indicating that S-layers provide additional mechanical stability to the cell wall. Taken together, we report a complete model of the EA1 S-layer and present a set of nanobodies that may have therapeutic potential against Bacillus anthracis.
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Affiliation(s)
- Adrià Sogues
- Structural and Molecular Microbiology, VIB-VUB Center for Structural Biology, VIB, Pleinlaan 2, 1050, Brussels, Belgium.
- Structural Biology Brussels, Vrije Universiteit Brussel, VUB, Pleinlaan 2, 1050, Brussels, Belgium.
| | - Antonella Fioravanti
- Structural and Molecular Microbiology, VIB-VUB Center for Structural Biology, VIB, Pleinlaan 2, 1050, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, VUB, Pleinlaan 2, 1050, Brussels, Belgium
| | - Wim Jonckheere
- Structural and Molecular Microbiology, VIB-VUB Center for Structural Biology, VIB, Pleinlaan 2, 1050, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, VUB, Pleinlaan 2, 1050, Brussels, Belgium
| | - Els Pardon
- Structural Biology Brussels, Vrije Universiteit Brussel, VUB, Pleinlaan 2, 1050, Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel, VUB, Pleinlaan 2, 1050, Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Han Remaut
- Structural and Molecular Microbiology, VIB-VUB Center for Structural Biology, VIB, Pleinlaan 2, 1050, Brussels, Belgium.
- Structural Biology Brussels, Vrije Universiteit Brussel, VUB, Pleinlaan 2, 1050, Brussels, Belgium.
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6
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Wu C, Xu Y, He Q, Li D, Duan J, Li C, You C, Chen H, Fan W, Jiang Y, Eric Xu H. Ligand-induced activation and G protein coupling of prostaglandin F 2α receptor. Nat Commun 2023; 14:2668. [PMID: 37160891 PMCID: PMC10169810 DOI: 10.1038/s41467-023-38411-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 05/02/2023] [Indexed: 05/11/2023] Open
Abstract
Prostaglandin F2α (PGF2α), an endogenous arachidonic acid metabolite, regulates diverse physiological functions in many tissues and cell types through binding and activation of a G-protein-coupled receptor (GPCR), the PGF2α receptor (FP), which also is the primary therapeutic target for glaucoma and several other diseases. Here, we report cryo-electron microscopy (cryo-EM) structures of the human FP bound to endogenous ligand PGF2α and anti-glaucoma drugs LTPA and TFPA at global resolutions of 2.67 Å, 2.78 Å, and 3.14 Å. These structures reveal distinct features of FP within the lipid receptor family in terms of ligand binding selectivity, its receptor activation, and G protein coupling mechanisms, including activation in the absence of canonical PIF and ERY motifs and Gq coupling through direct interactions with receptor transmembrane helix 1 and intracellular loop 1. Together with mutagenesis and functional studies, our structures reveal mechanisms of ligand recognition, receptor activation, and G protein coupling by FP, which could facilitate rational design of FP-targeting drugs.
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Affiliation(s)
- Canrong Wu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
| | - Youwei Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Qian He
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Dianrong Li
- Sironax (Beijing) Co., Ltd., Beijing, 102206, China
| | - Jia Duan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Changyao Li
- Lingang Laboratory, Shanghai, 200031, China
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Chongzhao You
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Han Chen
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian, 350108, China
| | - Weiliang Fan
- Sironax (Beijing) Co., Ltd., Beijing, 102206, China
| | - Yi Jiang
- Lingang Laboratory, Shanghai, 200031, China
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - H Eric Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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7
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Mehrabi P, Schulz EC. Sample Preparation for Time-Resolved Serial Crystallography: Practical Considerations. Methods Mol Biol 2023; 2652:361-379. [PMID: 37093487 DOI: 10.1007/978-1-0716-3147-8_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Time-resolved serial crystallography is an emerging method to elucidate the structure-function relationship of biomolecular systems at up to atomic resolution. However, to make this demanding method a success, a number of experimental requirements have to be met. In this chapter, we summarize general guidelines and protocols towards performing time-resolved crystallography experiments, with a particular emphasis on sample requirements and preparation but also a brief excursion into reaction initiation.
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Affiliation(s)
- Pedram Mehrabi
- Institute for Nanostructure and Solid State Physics, Universität Hamburg, Hamburg, Germany.
- Max Planck Institute for Structure and Dynamics of Matter, Hamburg, Germany.
| | - Eike C Schulz
- Max Planck Institute for Structure and Dynamics of Matter, Hamburg, Germany.
- University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany.
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8
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Qin Q, Liu H, He W, Guo Y, Zhang J, She J, Zheng F, Zhang S, Muyldermans S, Wen Y. Single Domain Antibody application in bacterial infection diagnosis and neutralization. Front Immunol 2022; 13:1014377. [PMID: 36248787 PMCID: PMC9558170 DOI: 10.3389/fimmu.2022.1014377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/15/2022] [Indexed: 11/21/2022] Open
Abstract
Increasing antibiotic resistance to bacterial infections causes a serious threat to human health. Efficient detection and treatment strategies are the keys to preventing and reducing bacterial infections. Due to the high affinity and antigen specificity, antibodies have become an important tool for diagnosis and treatment of various human diseases. In addition to conventional antibodies, a unique class of “heavy-chain-only” antibodies (HCAbs) were found in the serum of camelids and sharks. HCAbs binds to the antigen through only one variable domain Referred to as VHH (variable domain of the heavy chain of HCAbs). The recombinant format of the VHH is also called single domain antibody (sdAb) or nanobody (Nb). Sharks might also have an ancestor HCAb from where SdAbs or V-NAR might be engineered. Compared with traditional Abs, Nbs have several outstanding properties such as small size, high stability, strong antigen-binding affinity, high solubility and low immunogenicity. Furthermore, they are expressed at low cost in microorganisms and amenable to engineering. These superior properties make Nbs a highly desired alternative to conventional antibodies, which are extensively employed in structural biology, unravelling biochemical mechanisms, molecular imaging, diagnosis and treatment of diseases. In this review, we summarized recent progress of nanobody-based approaches in diagnosis and neutralization of bacterial infection and further discussed the challenges of Nbs in these fields.
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Affiliation(s)
- Qian Qin
- Department of General Surgery, Center for Microbiome Research of Med-X Institute, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
- The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Hao Liu
- Center for Biomedical Research, Institute of Future Agriculture, Northwest A&F University, Yangling, China
| | - Wenbo He
- Department of General Surgery, Center for Microbiome Research of Med-X Institute, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Yucheng Guo
- The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Jiaxin Zhang
- The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Junjun She
- Department of General Surgery, Center for Microbiome Research of Med-X Institute, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Fang Zheng
- The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Sicai Zhang
- Center for Biomedical Research, Institute of Future Agriculture, Northwest A&F University, Yangling, China
| | - Serge Muyldermans
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Yurong Wen
- Department of General Surgery, Center for Microbiome Research of Med-X Institute, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
- The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education, Health Science Center, Xi'an Jiaotong University, Xi'an, China
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9
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Abstract
SignificanceThe coronavirus main protease (Mpro) is required for viral replication. Here, we obtained the extended conformation of the native monomer of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Mpro by trapping it with nanobodies and found that the catalytic domain and the helix domain dissociate, revealing allosteric targets. Another monomeric state is termed compact conformation and is similar to one protomer of the dimeric form. We designed a Nanoluc Binary Techonology (NanoBiT)-based high-throughput allosteric inhibitor assay based on structural conformational change. Our results provide insight into the maturation, dimerization, and catalysis of the coronavirus Mpro and pave a way to develop an anticoronaviral drug through targeting the maturation process to inhibit the autocleavage of Mpro.
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10
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Marino M, Zhou L, Rincon MY, Callaerts-Vegh Z, Verhaert J, Wahis J, Creemers E, Yshii L, Wierda K, Saito T, Marneffe C, Voytyuk I, Wouters Y, Dewilde M, Duqué SI, Vincke C, Levites Y, Golde TE, Saido TC, Muyldermans S, Liston A, De Strooper B, Holt MG. AAV-mediated delivery of an anti-BACE1 VHH alleviates pathology in an Alzheimer's disease model. EMBO Mol Med 2022; 14:e09824. [PMID: 35352880 PMCID: PMC8988209 DOI: 10.15252/emmm.201809824] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 01/18/2023] Open
Abstract
Single domain antibodies (VHHs) are potentially disruptive therapeutics, with important biological value for treatment of several diseases, including neurological disorders. However, VHHs have not been widely used in the central nervous system (CNS), largely because of their restricted blood-brain barrier (BBB) penetration. Here, we propose a gene transfer strategy based on BBB-crossing Adeno-associated virus (AAV)-based vectors to deliver VHH directly into the CNS. As a proof-of-concept, we explored the potential of AAV-delivered VHH to inhibit BACE1, a well-characterized target in Alzheimer's disease. First, we generated a panel of VHHs targeting BACE1, one of which, VHH-B9, shows high selectivity for BACE1 and efficacy in lowering BACE1 activity in vitro. We further demonstrate that a single systemic dose of AAV-VHH-B9 produces positive long-term (12 months plus) effects on amyloid load, neuroinflammation, synaptic function, and cognitive performance, in the AppNL-G-F Alzheimer's disease mouse model. These results constitute a novel therapeutic approach forneurodegenerative diseases, which is applicable to a range of CNS disease targets.
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Affiliation(s)
- Marika Marino
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Lujia Zhou
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Melvin Y Rincon
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium
| | | | - Jens Verhaert
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Jérôme Wahis
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Eline Creemers
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium.,Electrophysiology Expertise Unit, VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium
| | - Lidia Yshii
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium.,Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Keimpe Wierda
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium.,Electrophysiology Expertise Unit, VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium
| | - Takashi Saito
- Department of Neurocognitive Science, Institute of Brain Science, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Catherine Marneffe
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Iryna Voytyuk
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Yessica Wouters
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Maarten Dewilde
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Sandra I Duqué
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Cécile Vincke
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Yona Levites
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Todd E Golde
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Takaomi C Saido
- Laboratory for Proteolytic Neuroscience, RIKEN Brain Science Institute, Wako-shi, Japan
| | - Serge Muyldermans
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Adrian Liston
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium.,Immunology Programme, The Babraham Institute, Cambridge, UK
| | - Bart De Strooper
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium.,UK Dementia Research institute at UCL, London, UK.,Leuven Brain Institute, Leuven, Belgium
| | - Matthew G Holt
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium.,Leuven Brain Institute, Leuven, Belgium.,Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
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11
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Endomembrane-Based Signaling by GPCRs and G-Proteins. Cells 2022; 11:cells11030528. [PMID: 35159337 PMCID: PMC8834376 DOI: 10.3390/cells11030528] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/26/2022] [Accepted: 01/28/2022] [Indexed: 12/14/2022] Open
Abstract
G-protein-coupled receptors (GPCRs) and G-proteins have a range of roles in many physiological and pathological processes and are among the most studied signaling proteins. A plethora of extracellular stimuli can activate the GPCR and can elicit distinct intracellular responses through the activation of specific transduction pathways. For many years, biologists thought that GPCR signaling occurred entirely on the plasma membrane. However, in recent decades, many lines of evidence have proved that the GPCRs and G-proteins may reside on endomembranes and can start or propagate signaling pathways through the organelles that form the secretory route. How these alternative intracellular signaling pathways of the GPCR and G-proteins influence the physiological and pathological function of the endomembranes is still under investigation. Here, we review the general role and classification of GPCRs and G-proteins with a focus on their signaling pathways in the membrane transport apparatus.
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12
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Chandler B, Todd L, Smith SO. Magic angle spinning NMR of G protein-coupled receptors. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 128:25-43. [PMID: 35282868 PMCID: PMC10718405 DOI: 10.1016/j.pnmrs.2021.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 06/14/2023]
Abstract
G protein-coupled receptors (GPCRs) have a simple seven transmembrane helix architecture which has evolved to recognize a diverse number of chemical signals. The more than 800 GPCRs encoded in the human genome function as receptors for vision, smell and taste, and mediate key physiological processes. Consequently, these receptors are a major target for pharmaceuticals. Protein crystallography and electron cryo-microscopy have provided high resolution structures of many GPCRs in both active and inactive conformations. However, these structures have not sparked a surge in rational drug design, in part because GPCRs are inherently dynamic and the structural changes induced by ligand or drug binding to stabilize inactive or active conformations are often subtle rearrangements in packing or hydrogen-bonding interactions. NMR spectroscopy provides a sensitive probe of local structure and dynamics at specific sites within these receptors as well as global changes in receptor structure and dynamics. These methods can also capture intermediate states and conformations with low populations that provide insights into the activation pathways. We review the use of solid-state magic angle spinning NMR to address the structure and activation mechanisms of GPCRs. The focus is on the large and diverse class A family of receptors. We highlight three specific class A GPCRs in order to illustrate how solid-state, as well as solution-state, NMR spectroscopy can answer questions in the field involving how different GPCR classes and subfamilies are activated by their associated ligands, and how small molecule drugs can modulate GPCR activation.
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Affiliation(s)
- Bianca Chandler
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, United States.
| | - Lauren Todd
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, United States.
| | - Steven O Smith
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, United States.
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13
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Cai J, Romão E, Wu G, Li J, Li L, Wang Z, Li Y, Yang J, Shen Y, Xu Z, Muyldermans S, Wang H. Nanobodies as binding-chaperones stabilize the recombinant Bombyx mori acetylcholinesterase and protect the enzyme activity in pesticide detection. Enzyme Microb Technol 2022; 155:109992. [DOI: 10.1016/j.enzmictec.2022.109992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 01/02/2022] [Accepted: 01/05/2022] [Indexed: 11/03/2022]
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14
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Dingus JG, Tang JCY, Amamoto R, Wallick GK, Cepko CL. A general approach for stabilizing nanobodies for intracellular expression. eLife 2022; 11:68253. [PMID: 36416528 PMCID: PMC9683787 DOI: 10.7554/elife.68253] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 11/08/2022] [Indexed: 11/24/2022] Open
Abstract
Conventional antibodies and their derived fragments are difficult to deploy against intracellular targets in live cells, due to their bulk and structural complexity. Nanobodies provide an alternative modality, with well-documented examples of intracellular expression. Despite their promise as intracellular reagents, there has not been a systematic study of nanobody intracellular expression. Here, we examined intracellular expression of 75 nanobodies from the Protein Data Bank. Surprisingly, a majority of these nanobodies were unstable in cells, illustrated by aggregation and clearance. Using comparative analysis and framework mutagenesis, we developed a general approach that stabilized a great majority of nanobodies that were originally unstable intracellularly, without significantly compromising target binding. This approach led to the identification of distinct sequence features that impacted the intracellular stability of tested nanobodies. Mutationally stabilized nanobody expression was found to extend to in vivo contexts, in the murine retina and in E. coli. These data provide for improvements in nanobody engineering for intracellular applications, potentiating a growing field of intracellular interrogation and intervention.
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Affiliation(s)
- John G Dingus
- Howard Hughes Medical Institute, Blavatnik Institute, Harvard Medical SchoolBostonUnited States
| | - Jonathan CY Tang
- Howard Hughes Medical Institute, Blavatnik Institute, Harvard Medical SchoolBostonUnited States
| | - Ryoji Amamoto
- Howard Hughes Medical Institute, Blavatnik Institute, Harvard Medical SchoolBostonUnited States
| | - Grace K Wallick
- Howard Hughes Medical Institute, Blavatnik Institute, Harvard Medical SchoolBostonUnited States
| | - Constance L Cepko
- Howard Hughes Medical Institute, Blavatnik Institute, Harvard Medical SchoolBostonUnited States
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15
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Mannes M, Martin C, Triest S, Pia Dimmito M, Mollica A, Laeremans T, Menet CJ, Ballet S. Development of Generic G Protein Peptidomimetics Able to Stabilize Active State G s Protein-Coupled Receptors for Application in Drug Discovery. Angew Chem Int Ed Engl 2021; 60:10247-10254. [PMID: 33596327 DOI: 10.1002/anie.202100180] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/05/2021] [Indexed: 11/06/2022]
Abstract
G protein-coupled receptors (GPCRs) represent an important group of membrane proteins that play a central role in modern medicine. Unfortunately, conformational promiscuity hampers full therapeutic exploitation of GPCRs, since the largest population of the receptor will adopt a basal conformation, which subsequently challenges screens for agonist drug discovery programs. Herein, we describe a set of peptidomimetics able to mimic the ability of G proteins in stabilizing the active state of the β2 adrenergic receptor (β2 AR) and the dopamine 1 receptor (D1R). During fragment-based screening efforts, these (un)constrained peptide analogues of the α5 helix in Gs proteins, were able to identify agonism pre-imprinted fragments for the examined GPCRs, and as such, they behave as a generic tool, enabling an engagement in agonist earmarked discovery programs.
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Affiliation(s)
- Morgane Mannes
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Charlotte Martin
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Sarah Triest
- Confo Therapeutics N.V., Technologiepark-Zwijnaarde 94, 9052, Ghent, Belgium
| | - Marilisa Pia Dimmito
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.,Department of Pharmacy, University "G. d'Annunzio" of Chieti-Pescara, Via dei Vestini 31, 66100, Chieti, Italy
| | - Adriano Mollica
- Department of Pharmacy, University "G. d'Annunzio" of Chieti-Pescara, Via dei Vestini 31, 66100, Chieti, Italy
| | - Toon Laeremans
- Confo Therapeutics N.V., Technologiepark-Zwijnaarde 94, 9052, Ghent, Belgium
| | - Christel J Menet
- Confo Therapeutics N.V., Technologiepark-Zwijnaarde 94, 9052, Ghent, Belgium
| | - Steven Ballet
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
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16
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Mannes M, Martin C, Triest S, Pia Dimmito M, Mollica A, Laeremans T, Menet CJ, Ballet S. Development of Generic G Protein Peptidomimetics Able to Stabilize Active State G
s
Protein‐Coupled Receptors for Application in Drug Discovery. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202100180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Morgane Mannes
- Research Group of Organic Chemistry Vrije Universiteit Brussel Pleinlaan 2 1050 Brussels Belgium
| | - Charlotte Martin
- Research Group of Organic Chemistry Vrije Universiteit Brussel Pleinlaan 2 1050 Brussels Belgium
| | - Sarah Triest
- Confo Therapeutics N.V. Technologiepark-Zwijnaarde 94 9052 Ghent Belgium
| | - Marilisa Pia Dimmito
- Research Group of Organic Chemistry Vrije Universiteit Brussel Pleinlaan 2 1050 Brussels Belgium
- Department of Pharmacy University “G. d'Annunzio” of Chieti-Pescara Via dei Vestini 31 66100 Chieti Italy
| | - Adriano Mollica
- Department of Pharmacy University “G. d'Annunzio” of Chieti-Pescara Via dei Vestini 31 66100 Chieti Italy
| | - Toon Laeremans
- Confo Therapeutics N.V. Technologiepark-Zwijnaarde 94 9052 Ghent Belgium
| | - Christel J. Menet
- Confo Therapeutics N.V. Technologiepark-Zwijnaarde 94 9052 Ghent Belgium
| | - Steven Ballet
- Research Group of Organic Chemistry Vrije Universiteit Brussel Pleinlaan 2 1050 Brussels Belgium
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17
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Zhuang Y, Xu P, Mao C, Wang L, Krumm B, Zhou XE, Huang S, Liu H, Cheng X, Huang XP, Shen DD, Xu T, Liu YF, Wang Y, Guo J, Jiang Y, Jiang H, Melcher K, Roth BL, Zhang Y, Zhang C, Xu HE. Structural insights into the human D1 and D2 dopamine receptor signaling complexes. Cell 2021; 184:931-942.e18. [PMID: 33571431 PMCID: PMC8215686 DOI: 10.1016/j.cell.2021.01.027] [Citation(s) in RCA: 127] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 12/02/2020] [Accepted: 01/15/2021] [Indexed: 12/26/2022]
Abstract
The D1- and D2-dopamine receptors (D1R and D2R), which signal through Gs and Gi, respectively, represent the principal stimulatory and inhibitory dopamine receptors in the central nervous system. D1R and D2R also represent the main therapeutic targets for Parkinson's disease, schizophrenia, and many other neuropsychiatric disorders, and insight into their signaling is essential for understanding both therapeutic and side effects of dopaminergic drugs. Here, we report four cryoelectron microscopy (cryo-EM) structures of D1R-Gs and D2R-Gi signaling complexes with selective and non-selective dopamine agonists, including two currently used anti-Parkinson's disease drugs, apomorphine and bromocriptine. These structures, together with mutagenesis studies, reveal the conserved binding mode of dopamine agonists, the unique pocket topology underlying ligand selectivity, the conformational changes in receptor activation, and potential structural determinants for G protein-coupling selectivity. These results provide both a molecular understanding of dopamine signaling and multiple structural templates for drug design targeting the dopaminergic system.
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MESH Headings
- 2,3,4,5-Tetrahydro-7,8-dihydroxy-1-phenyl-1H-3-benzazepine/analogs & derivatives
- 2,3,4,5-Tetrahydro-7,8-dihydroxy-1-phenyl-1H-3-benzazepine/pharmacology
- Amino Acid Sequence
- Conserved Sequence
- Cryoelectron Microscopy
- Cyclic AMP/metabolism
- GTP-Binding Proteins/metabolism
- HEK293 Cells
- Humans
- Ligands
- Models, Molecular
- Mutant Proteins/chemistry
- Mutant Proteins/metabolism
- Receptors, Adrenergic, beta-2/metabolism
- Receptors, Dopamine D1/chemistry
- Receptors, Dopamine D1/metabolism
- Receptors, Dopamine D1/ultrastructure
- Receptors, Dopamine D2/chemistry
- Receptors, Dopamine D2/metabolism
- Receptors, Dopamine D2/ultrastructure
- Signal Transduction
- Structural Homology, Protein
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Affiliation(s)
- Youwen Zhuang
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peiyu Xu
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China; Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Chunyou Mao
- Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Zhejiang Laboratory for Systems and Precison Medicine, Zhejiang University Medical Center, Hangzhou 311121, China; MOE Frontier Science Center for Brain Research and Brain-Machine Integration, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Lei Wang
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Brian Krumm
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7365, USA
| | - X Edward Zhou
- Center for Cancer and Cell Biology, Program for Structural Biology, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Sijie Huang
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Heng Liu
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Xi Cheng
- State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xi-Ping Huang
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7365, USA
| | - Dan-Dan Shen
- Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Zhejiang Laboratory for Systems and Precison Medicine, Zhejiang University Medical Center, Hangzhou 311121, China; MOE Frontier Science Center for Brain Research and Brain-Machine Integration, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Tinghai Xu
- Center for Cancer and Cell Biology, Program for Structural Biology, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Yong-Feng Liu
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7365, USA
| | - Yue Wang
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jia Guo
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Jiang
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hualiang Jiang
- State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Karsten Melcher
- Center for Cancer and Cell Biology, Program for Structural Biology, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Bryan L Roth
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7365, USA.
| | - Yan Zhang
- Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Zhejiang Laboratory for Systems and Precison Medicine, Zhejiang University Medical Center, Hangzhou 311121, China; MOE Frontier Science Center for Brain Research and Brain-Machine Integration, Zhejiang University School of Medicine, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Immunity and Inflammatory Diseases, Hangzhou 310058, China.
| | - Cheng Zhang
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA.
| | - H Eric Xu
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
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18
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Expression, Purification and Crystallization of Asrij, A Novel Scaffold Transmembrane Protein. J Membr Biol 2021; 254:65-74. [PMID: 33433647 DOI: 10.1007/s00232-020-00166-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 12/17/2020] [Indexed: 10/22/2022]
Abstract
Asrij/OCIAD1 is a scaffold transmembrane protein belonging to the Ovarian Carcinoma Immunoreactive Antigen Domain containing protein family. In Drosophila and mouse models, Asrij localizes at the endosomal and mitochondrial membrane and is shown to regulate the stemness of hematopoietic stem cells. Interaction of Asrij with ADP Ribosylation Factor 1 (Arf1) is shown to be crucial for hematopoietic niche function and prohemocyte maintenance. Here, we report the heterologous expression, standardization of detergents and purification methodologies for crystallization of Asrij/OCIAD1. To probe the activity of bacterially expressed Asrij, we developed a protein complementation assay and conclusively show that Asrij and Arf1 physically interact. Further, we find that sophorolipids improve the solubility and monodispersibility of Asrij. Hence, we propose that sophorolipids could be novel additives for stabilization of membrane proteins. To our knowledge, this is the first study detailing methodology for the production and crystallization of a heterologously expressed scaffold membrane protein and will be widely applicable to understand membrane protein structure and function.
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Miles JA, Hobor F, Trinh CH, Taylor J, Tiede C, Rowell PR, Jackson BR, Nadat FA, Ramsahye P, Kyle HF, Wicky BIM, Clarke J, Tomlinson DC, Wilson AJ, Edwards TA. Selective Affimers Recognise the BCL-2 Family Proteins BCL-x L and MCL-1 through Noncanonical Structural Motifs*. Chembiochem 2021; 22:232-240. [PMID: 32961017 PMCID: PMC7821230 DOI: 10.1002/cbic.202000585] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/17/2020] [Indexed: 12/26/2022]
Abstract
The BCL-2 family is a challenging group of proteins to target selectively due to sequence and structural homologies across the family. Selective ligands for the BCL-2 family regulators of apoptosis are useful as probes to understand cell biology and apoptotic signalling pathways, and as starting points for inhibitor design. We have used phage display to isolate Affimer reagents (non-antibody-binding proteins based on a conserved scaffold) to identify ligands for MCL-1, BCL-xL , BCL-2, BAK and BAX, then used multiple biophysical characterisation methods to probe the interactions. We established that purified Affimers elicit selective recognition of their target BCL-2 protein. For anti-apoptotic targets BCL-xL and MCL-1, competitive inhibition of their canonical protein-protein interactions is demonstrated. Co-crystal structures reveal an unprecedented mode of molecular recognition; where a BH3 helix is normally bound, flexible loops from the Affimer dock into the BH3 binding cleft. Moreover, the Affimers induce a change in the target proteins towards a desirable drug-bound-like conformation. These proof-of-concept studies indicate that Affimers could be used as alternative templates to inspire the design of selective BCL-2 family modulators and more generally other protein-protein interaction inhibitors.
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Affiliation(s)
- Jennifer A. Miles
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Fruzsina Hobor
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Chi H. Trinh
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - James Taylor
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Christian Tiede
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Philip R. Rowell
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Brian R. Jackson
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Protein Production FacilityUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Fatima A. Nadat
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Protein Production FacilityUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Pallavi Ramsahye
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Hannah F. Kyle
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Basile I. M. Wicky
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Jane Clarke
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Darren C. Tomlinson
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Andrew J. Wilson
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Thomas A. Edwards
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
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Abstract
Recombinant antibodies in single-domain format (VHHs) have been recently used for stabilizing antigens during their purification and crystallization. VHHs are also known for their structural stability and a significant part of them share the characteristic of remaining functionally folded also in the absence of the internal disulfide bond. Therefore, they can be expressed as intrabodies in the cell cytoplasm as well as in the bacterial periplasm. This evidence means that, in theory, VHHs can be co-expressed with their antigens independently on the redox constrains. It has also suggested the idea of using co-expression and co-purification of antigen-antibody complexes for maximizing the stabilizing effect of the antibody on its antigen during all the production steps for both cytoplasmic and periplasmic expression strategies.
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21
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GPCR Activation States Induced by Nanobodies and Mini-G Proteins Compared by NMR Spectroscopy. MOLECULES (BASEL, SWITZERLAND) 2020; 25:molecules25245984. [PMID: 33348734 PMCID: PMC7767065 DOI: 10.3390/molecules25245984] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/04/2020] [Accepted: 12/14/2020] [Indexed: 12/12/2022]
Abstract
In this work, we examine methyl nuclear magnetic resonance (NMR) spectra of the methionine ε-[13CH3] labelled thermostabilized β1 adrenergic receptor from turkey in association with a variety of different effectors, including mini-Gs and nanobody 60 (Nb60), which have not been previously studied in complex with β1 adrenergic receptor (β1AR) by NMR. Complexes with pindolol and Nb60 induce highly similar inactive states of the receptor, closely resembling the resting state conformational ensemble. We show that, upon binding of mini-Gs or nanobody 80 (Nb80), large allosteric changes throughout the receptor take place. The conformation of tβ1AR stabilized by the native-like mini-Gs protein is highly similar to the conformation induced by the currently used surrogate Nb80. Interestingly, in both cases residual dynamics are present, which were not observed in the resting states. Finally, we reproduce a pharmaceutically relevant situation, where an antagonist abolishes the interaction of the receptor with the mini-G protein in a competitive manner, validating the functional integrity of our preparation. The presented system is therefore well suited for reproducing the individual steps of the activation cycle of a G protein-coupled receptor (GPCR) in vitro and serves as a basis for functional and pharmacological characterizations of more native-like systems in the future.
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Abstract
Unique, functional, homodimeric heavy chain-only antibodies, devoid of light chains, are circulating in the blood of Camelidae. These antibodies recognize their cognate antigen via one single domain, known as VHH or Nanobody. This serendipitous discovery made three decades ago has stimulated a growing number of researchers to generate highly specific Nanobodies against a myriad of targets. The small size, strict monomeric state, robustness, and easy tailoring of these Nanobodies have inspired many groups to design innovative Nanobody-based multi-domain constructs to explore novel applications. As such, Nanobodies have been employed as an exquisite research tool in structural, cell, and developmental biology. Furthermore, Nanobodies have demonstrated their benefit for more sensitive diagnostic tests. Finally, several Nanobody-based constructs have been designed to develop new therapeutic products.
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Affiliation(s)
- Serge Muyldermans
- Cellular and Molecular Immunology, Vrije Universiteit Brussel, 1050 Brussels, Belgium; .,Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian 116023, Liaoning, People's Republic of China
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23
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Allosteric modulation of the GTPase activity of a bacterial LRRK2 homolog by conformation-specific Nanobodies. Biochem J 2020; 477:1203-1218. [PMID: 32167135 PMCID: PMC7135905 DOI: 10.1042/bcj20190843] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 03/09/2020] [Accepted: 03/13/2020] [Indexed: 01/02/2023]
Abstract
Mutations in the Parkinson's disease (PD)-associated protein leucine-rich repeat kinase 2 (LRRK2) commonly lead to a reduction of GTPase activity and increase in kinase activity. Therefore, strategies for drug development have mainly been focusing on the design of LRRK2 kinase inhibitors. We recently showed that the central RocCOR domains (Roc: Ras of complex proteins; COR: C-terminal of Roc) of a bacterial LRRK2 homolog cycle between a dimeric and monomeric form concomitant with GTP binding and hydrolysis. PD-associated mutations can slow down GTP hydrolysis by stabilizing the protein in its dimeric form. Here, we report the identification of two Nanobodies (NbRoco1 and NbRoco2) that bind the bacterial Roco protein (CtRoco) in a conformation-specific way, with a preference for the GTP-bound state. NbRoco1 considerably increases the GTP turnover rate of CtRoco and reverts the decrease in GTPase activity caused by a PD-analogous mutation. We show that NbRoco1 exerts its effect by allosterically interfering with the CtRoco dimer–monomer cycle through the destabilization of the dimeric form. Hence, we provide the first proof of principle that allosteric modulation of the RocCOR dimer–monomer cycle can alter its GTPase activity, which might present a potential novel strategy to overcome the effect of LRRK2 PD mutations.
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Mohammad Nezhady MA, Rivera JC, Chemtob S. Location Bias as Emerging Paradigm in GPCR Biology and Drug Discovery. iScience 2020; 23:101643. [PMID: 33103080 PMCID: PMC7569339 DOI: 10.1016/j.isci.2020.101643] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
GPCRs are the largest receptor family that are involved in virtually all biological processes. Pharmacologically, they are highly druggable targets, as they cover more than 40% of all drugs in the market. Our knowledge of biased signaling provided insight into pharmacology vastly improving drug design to avoid unwanted effects and achieve higher efficacy and selectivity. However, yet another feature of GPCR biology is left largely unexplored, location bias. Recent developments in this field show promising avenues for evolution of new class of pharmaceuticals with greater potential for higher level of precision medicine. Further consideration and understanding of this phenomenon with deep biochemical and molecular insights would pave the road to success. In this review, we critically analyze this perspective and discuss new avenues of investigation.
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Affiliation(s)
- Mohammad Ali Mohammad Nezhady
- Programmes en Biologie Moléculaire, Faculté de Médecine, Université de Montréal, Montreal, QC, Canada
- Centre de Recherche du CHU Sainte-Justine, Montreal, QC H3T 1C5, Canada
- Corresponding author
| | | | - Sylvain Chemtob
- Programmes en Biologie Moléculaire, Faculté de Médecine, Université de Montréal, Montreal, QC, Canada
- Centre de Recherche du CHU Sainte-Justine, Montreal, QC H3T 1C5, Canada
- Maisonneuve-Rosemont Hospital Research Centre, Montreal, QC, Canada
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25
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Norman RA, Ambrosetti F, Bonvin AMJJ, Colwell LJ, Kelm S, Kumar S, Krawczyk K. Computational approaches to therapeutic antibody design: established methods and emerging trends. Brief Bioinform 2020; 21:1549-1567. [PMID: 31626279 PMCID: PMC7947987 DOI: 10.1093/bib/bbz095] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/07/2019] [Accepted: 07/05/2019] [Indexed: 12/31/2022] Open
Abstract
Antibodies are proteins that recognize the molecular surfaces of potentially noxious molecules to mount an adaptive immune response or, in the case of autoimmune diseases, molecules that are part of healthy cells and tissues. Due to their binding versatility, antibodies are currently the largest class of biotherapeutics, with five monoclonal antibodies ranked in the top 10 blockbuster drugs. Computational advances in protein modelling and design can have a tangible impact on antibody-based therapeutic development. Antibody-specific computational protocols currently benefit from an increasing volume of data provided by next generation sequencing and application to related drug modalities based on traditional antibodies, such as nanobodies. Here we present a structured overview of available databases, methods and emerging trends in computational antibody analysis and contextualize them towards the engineering of candidate antibody therapeutics.
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Ji Y, Li X, Lu Y, Guo P, Zhang G, Wang Y, Zhang Y, Zhu W, Pan J, Wang J. Nanobodies Based on a Sandwich Immunoassay for the Detection of Staphylococcal Enterotoxin B Free from Interference by Protein A. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:5959-5968. [PMID: 32374597 DOI: 10.1021/acs.jafc.0c00422] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
As one of the leading causes of food poisoning, staphylococcal enterotoxins (SEs) secreted by Staphylococcus aureus pose a serious threat to human health. The immunoassay has become the dominant tool used for the rapid detection of harmful bacteria and toxins as a result of its excellent specificity. However, with regard to SEs, staphylococcal protein A (SpA) is likely to bind with the fragment crystallizable (Fc) terminal of the traditional antibody and result in a false positive, limiting the practical application of this method. Therefore, to eliminate the bottleneck problem, the sandwich immunoassay was development by replacing the traditional antibody with a nanobody (Nb) that lacked a Fc terminal. Using 0.5 × 107 colony-forming units, the Nb library was constructed using Bactrian camels immunized with staphylococcal enterotoxin B (SEB) to obtain a paired Nb against SEB with good affinity. A sandwich enzyme-linked immunosorbent assay (ELISA) was developed using one Nb as the capture antibody and a phage-displayed Nb with signal-amplifying properties as the detection antibody. In optimal conditions, the current immunoassay displayed a broad quantitative range from 1 to 512 ng/mL and a 0.3 ng/mL limit of detection. The recovery of spiked milk, milk powder, cheese, and beef ranged from 87.66 to 114.2%. The Nbs-ELISA was not influenced by SpA during the detection of SEB in S. aureus food poisoning. Therefore, the Nb developed here presented the perfect candidates for immunoassay application during SE determination as a result of the complete absence of SpA interference.
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Affiliation(s)
- Yanwei Ji
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Xiang Li
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Yunlong Lu
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Pengli Guo
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Ganwei Zhang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Yanru Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Yi Zhang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Wenxin Zhu
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Jiachuan Pan
- Guangdong Provincial Key Laboratory of Emergency Test for Dangerous Chemicals, Guangdong Institute of Analysis, Guangzhou, Guangdong 510070, People's Republic of China
| | - Jianlong Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
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Diversity in kinetics correlated with structure in nano body-stabilized LacY. PLoS One 2020; 15:e0232846. [PMID: 32380514 PMCID: PMC7205474 DOI: 10.1371/journal.pone.0232846] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 04/22/2020] [Indexed: 12/04/2022] Open
Abstract
The structure of lactose permease, stabilized in a periplasmic open conformation by two Gly to Trp replacements (LacYww) and complexed with a nanobody directed against this conformation, provides the highest resolution structure of the symporter. The nanobody binds in a different manner than two other nanobodies made against the same mutant, which also bind to the same general region on the periplasmic side. This region of the protein may represent an immune hotspot. The CDR3 loop of the nanobody is held by hydrogen bonds in a conformation that partially blocks access to the substrate-binding site. As a result, kon and koff for galactoside binding to either LacY or the double mutant complexed with the nanobody are lower than for the other two LacY/nanobody complexes though the Kd values are similar, reflecting the fact that the nanobodies rigidify structures along the pathway. While the wild-type LacY/nanobody complex clearly stabilizes a similar ‘extracellular open’ conformation in solution, judged by binding kinetics, the complex with wild-type LacY did not yet crystallize, suggesting the nanobody does not bind strongly enough to shift the equilibrium to stabilize a periplasmic side-open conformation suitable for crystallization. However, the similarity of the galactoside binding kinetics for the nanobody-bound complexes with wild type LacY and with LacYWW indicates that they have similar structures, showing that the reported co-structures reliably show nanobody interactions with LacY.
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28
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Ghali GZ, Ghali MGZ. β adrenergic receptor modulated signaling in glioma models: promoting β adrenergic receptor-β arrestin scaffold-mediated activation of extracellular-regulated kinase 1/2 may prove to be a panacea in the treatment of intracranial and spinal malignancy and extra-neuraxial carcinoma. Mol Biol Rep 2020; 47:4631-4650. [PMID: 32303958 PMCID: PMC7165076 DOI: 10.1007/s11033-020-05427-1] [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: 02/25/2020] [Accepted: 04/03/2020] [Indexed: 12/03/2022]
Abstract
Neoplastically transformed astrocytes express functionally active cell surface β adrenergic receptors (βARs). Treatment of glioma models in vitro and in vivo with β adrenergic agonists variably amplifies or attenuates cellular proliferation. In the majority of in vivo models, β adrenergic agonists generally reduce cellular proliferation. However, treatment with β adrenergic agonists consistently reduces tumor cell invasive potential, angiogenesis, and metastasis. β adrenergic agonists induced decreases of invasive potential are chiefly mediated through reductions in the expression of matrix metalloproteinases types 2 and 9. Treatment with β adrenergic agonists also clearly reduce tumoral neoangiogenesis, which may represent a putatively useful mechanism to adjuvantly amplify the effects of bevacizumab. Bevacizumab is a monoclonal antibody targeting the vascular endothelial growth factor receptor. We may accordingly designate βagonists to represent an enhancer of bevacizumab. The antiangiogenic effects of β adrenergic agonists may thus effectively render an otherwise borderline effective therapy to generate significant enhancement in clinical outcomes. β adrenergic agonists upregulate expression of the major histocompatibility class II DR alpha gene, effectively potentiating the immunogenicity of tumor cells to tumor surveillance mechanisms. Authors have also demonstrated crossmodal modulation of signaling events downstream from the β adrenergic cell surface receptor and microtubular polymerization and depolymerization. Complex effects and desensitization mechanisms of the β adrenergic signaling may putatively represent promising therapeutic targets. Constant stimulation of the β adrenergic receptor induces its phosphorylation by β adrenergic receptor kinase (βARK), rendering it a suitable substrate for alternate binding by β arrestins 1 or 2. The binding of a β arrestin to βARK phosphorylated βAR promotes receptor mediated internalization and downregulation of cell surface receptor and contemporaneously generates a cell surface scaffold at the βAR. The scaffold mediated activation of extracellular regulated kinase 1/2, compared with protein kinase A mediated activation, preferentially favors cytosolic retention of ERK1/2 and blunting of nuclear translocation and ensuant pro-transcriptional activity. Thus, βAR desensitization and consequent scaffold assembly effectively retains the cytosolic homeostatic functions of ERK1/2 while inhibiting its pro-proliferative effects. We suggest these mechanisms specifically will prove quite promising in developing primary and adjuvant therapies mitigating glioma growth, angiogenesis, invasive potential, and angiogenesis. We suggest generating compounds and targeted mutations of the β adrenergic receptor favoring β arrestin binding and scaffold facilitated activation of ERK1/2 may hold potential promise and therapeutic benefit in adjuvantly treating most or all cancers. We hope our discussion will generate fruitful research endeavors seeking to exploit these mechanisms.
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Affiliation(s)
- George Zaki Ghali
- United States Environmental Protection Agency, Arlington, VA, USA.,Emeritus Professor, Department of Toxicology, Purdue University, West Lafayette, IN, USA
| | - Michael George Zaki Ghali
- Department of Neurological Surgery, University of California, San Francisco, 505 Parnassus Avenue, Box-0112, San Francisco, CA, 94143, USA. .,Department of Neurological Surgery, Karolinska Institutet, Nobels väg 6, Solna and Alfred Nobels Allé 8, Huddinge, SE-171 77, Stockholm, Sweden.
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29
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Conformational plasticity of ligand-bound and ternary GPCR complexes studied by 19F NMR of the β 1-adrenergic receptor. Nat Commun 2020; 11:669. [PMID: 32015348 PMCID: PMC6997182 DOI: 10.1038/s41467-020-14526-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 01/10/2020] [Indexed: 01/14/2023] Open
Abstract
G-protein-coupled receptors (GPCRs) are allosteric signaling proteins that transmit an extracellular stimulus across the cell membrane. Using 19F NMR and site-specific labelling, we investigate the response of the cytoplasmic region of transmembrane helices 6 and 7 of the β1-adrenergic receptor to agonist stimulation and coupling to a Gs-protein-mimetic nanobody. Agonist binding shows the receptor in equilibrium between two inactive states and a pre-active form, increasingly populated with higher ligand efficacy. Nanobody coupling leads to a fully active ternary receptor complex present in amounts correlating directly with agonist efficacy, consistent with partial agonism. While for different agonists the helix 6 environment in the active-state ternary complexes resides in a well-defined conformation, showing little conformational mobility, the environment of the highly conserved NPxxY motif on helix 7 remains dynamic adopting diverse, agonist-specific conformations, implying a further role of this region in receptor function. An inactive nanobody-coupled ternary receptor form is also observed.
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30
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Uchański T, Pardon E, Steyaert J. Nanobodies to study protein conformational states. Curr Opin Struct Biol 2020; 60:117-123. [DOI: 10.1016/j.sbi.2020.01.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/08/2020] [Accepted: 01/09/2020] [Indexed: 01/07/2023]
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31
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Tsai YCI, Johansson H, Dixon D, Martin S, Chung CW, Clarkson J, House D, Rittinger K. Single-Domain Antibodies as Crystallization Chaperones to Enable Structure-Based Inhibitor Development for RBR E3 Ubiquitin Ligases. Cell Chem Biol 2020; 27:83-93.e9. [PMID: 31813847 PMCID: PMC6963773 DOI: 10.1016/j.chembiol.2019.11.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 10/15/2019] [Accepted: 11/14/2019] [Indexed: 01/14/2023]
Abstract
Protein ubiquitination plays a key role in the regulation of cellular processes, and misregulation of the ubiquitin system is linked to many diseases. So far, development of tool compounds that target enzymes of the ubiquitin system has been slow and only a few specific inhibitors are available. Here, we report the selection of single-domain antibodies (single-dAbs) based on a human scaffold that recognize the catalytic domain of HOIP, a subunit of the multi-component E3 LUBAC and member of the RBR family of E3 ligases. Some of these dAbs affect ligase activity and provide mechanistic insight into the ubiquitin transfer mechanism of different E2-conjugating enzymes. Furthermore, we show that the co-crystal structure of a HOIP RBR/dAb complex serves as a robust platform for soaking of ligands that target the active site cysteine of HOIP, thereby providing easy access to structure-based ligand design for this important class of E3 ligases.
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Affiliation(s)
- Yi-Chun Isabella Tsai
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Henrik Johansson
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Crick-GSK Biomedical LinkLabs, GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - David Dixon
- R&D Medicinal Science & Technology, GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Stephen Martin
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Chun-Wa Chung
- Crick-GSK Biomedical LinkLabs, GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK; R&D Medicinal Science & Technology, GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Jane Clarkson
- R&D Medicinal Science & Technology, GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - David House
- Crick-GSK Biomedical LinkLabs, GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Katrin Rittinger
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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32
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Abstract
The selective immobilization of proteins represents an essential step in the selection of binding proteins such as antibodies. The immobilization strategy determines how the target protein is presented to the binders and thereby directly affects the experimental outcome. This poses specific challenges for membrane proteins due to their inherent lack of stability and limited exposed hydrophilic surfaces. Here we detail methodologies for the selective immobilization of membrane proteins based on the strong biotin-avidin interaction and with a specific focus on its application for the selection of nanobodies and sybodies. We discuss the challenges in generating and benefits of obtaining an equimolar biotin to target-protein ratio.
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33
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Molecular Basis of Opioid Action: From Structures to New Leads. Biol Psychiatry 2020; 87:6-14. [PMID: 31653480 PMCID: PMC6898784 DOI: 10.1016/j.biopsych.2019.08.028] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 08/30/2019] [Accepted: 08/31/2019] [Indexed: 02/06/2023]
Abstract
Since the isolation of morphine from the opium poppy over 200 years ago, the molecular basis of opioid action has remained the subject of intense inquiry. The identification of specific receptors responsible for opioid function and the discovery of many chemically diverse molecules with unique opioid-like efficacies have provided glimpses into the molecular logic of opioid action. Recent revolutions in the structural biology of transmembrane proteins have, for the first time, yielded high-resolution views into the 3-dimensional shapes of all 4 opioid receptors. These studies have begun to decode the chemical logic that enables opioids to specifically bind and activate their receptor targets. A combination of spectroscopic experiments and computational simulations has provided a view into the molecular movements of the opioid receptors, which itself gives rise to the complex opioid pharmacology observed at the cellular and behavioral levels. Further diversity in opioid receptor structure is driven by both genetic variation and receptor oligomerization. These insights have enabled computational drug discovery efforts, with some evidence of success in the design of completely novel opioids with unique efficacies. The combined progress over the past few years provides hope for new, efficacious opioids devoid of the side effects that have made them the scourge of humanity for millennia.
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Chiu ML, Goulet DR, Teplyakov A, Gilliland GL. Antibody Structure and Function: The Basis for Engineering Therapeutics. Antibodies (Basel) 2019; 8:antib8040055. [PMID: 31816964 PMCID: PMC6963682 DOI: 10.3390/antib8040055] [Citation(s) in RCA: 207] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/25/2019] [Accepted: 11/28/2019] [Indexed: 12/11/2022] Open
Abstract
Antibodies and antibody-derived macromolecules have established themselves as the mainstay in protein-based therapeutic molecules (biologics). Our knowledge of the structure–function relationships of antibodies provides a platform for protein engineering that has been exploited to generate a wide range of biologics for a host of therapeutic indications. In this review, our basic understanding of the antibody structure is described along with how that knowledge has leveraged the engineering of antibody and antibody-related therapeutics having the appropriate antigen affinity, effector function, and biophysical properties. The platforms examined include the development of antibodies, antibody fragments, bispecific antibody, and antibody fusion products, whose efficacy and manufacturability can be improved via humanization, affinity modulation, and stability enhancement. We also review the design and selection of binding arms, and avidity modulation. Different strategies of preparing bispecific and multispecific molecules for an array of therapeutic applications are included.
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Affiliation(s)
- Mark L. Chiu
- Drug Product Development Science, Janssen Research & Development, LLC, Malvern, PA 19355, USA
- Correspondence:
| | - Dennis R. Goulet
- Department of Medicinal Chemistry, University of Washington, P.O. Box 357610, Seattle, WA 98195-7610, USA;
| | - Alexey Teplyakov
- Biologics Research, Janssen Research & Development, LLC, Spring House, PA 19477, USA; (A.T.); (G.L.G.)
| | - Gary L. Gilliland
- Biologics Research, Janssen Research & Development, LLC, Spring House, PA 19477, USA; (A.T.); (G.L.G.)
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Sencanski M, Glisic S, Šnajder M, Veljkovic N, Poklar Ulrih N, Mavri J, Vrecl M. Computational design and characterization of nanobody-derived peptides that stabilize the active conformation of the β 2-adrenergic receptor (β 2-AR). Sci Rep 2019; 9:16555. [PMID: 31719570 PMCID: PMC6851183 DOI: 10.1038/s41598-019-52934-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 10/26/2019] [Indexed: 12/15/2022] Open
Abstract
This study aimed to design and functionally characterize peptide mimetics of the nanobody (Nb) related to the β2-adrenergic receptor (β2-AR) (nanobody-derived peptide, NDP). We postulated that the computationally derived and optimized complementarity-determining region 3 (CDR3) of Nb is sufficient for its interaction with receptor. Sequence-related Nb-families preferring the agonist-bound active conformation of β2-AR were analysed using the informational spectrum method (ISM) and β2-AR:NDP complexes studied using protein-peptide docking and molecular dynamics (MD) simulations in conjunction with metadynamics calculations of free energy binding. The selected NDP of Nb71, designated P3, was 17 amino acids long and included CDR3. Metadynamics calculations yielded a binding free energy for the β2-AR:P3 complex of ΔG = (-7.23 ± 0.04) kcal/mol, or a Kd of (7.9 ± 0.5) μM, for T = 310 K. In vitro circular dichroism (CD) spectropolarimetry and microscale thermophoresis (MST) data provided additional evidence for P3 interaction with agonist-activated β2-AR, which displayed ~10-fold higher affinity for P3 than the unstimulated receptor (MST-derived EC50 of 3.57 µM vs. 58.22 µM), while its ability to inhibit the agonist-induced interaction of β2-AR with β-arrestin 2 was less evident. In summary, theoretical and experimental evidence indicated that P3 preferentially binds agonist-activated β2-AR.
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Affiliation(s)
- Milan Sencanski
- Center for Multidisciplinary Research, Institute of Nuclear Sciences VINCA, University of Belgrade, Belgrade, Serbia
| | - Sanja Glisic
- Center for Multidisciplinary Research, Institute of Nuclear Sciences VINCA, University of Belgrade, Belgrade, Serbia
| | - Marko Šnajder
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Nevena Veljkovic
- Center for Multidisciplinary Research, Institute of Nuclear Sciences VINCA, University of Belgrade, Belgrade, Serbia
| | | | - Janez Mavri
- Laboratory of Computational Biochemistry and Drug Design, National Institute of Chemistry, Ljubljana, Slovenia
| | - Milka Vrecl
- Institute of Preclinical Sciences, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia.
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Jana S, Ghosh S, Muk S, Levy B, Vaidehi N. Prediction of Conformation Specific Thermostabilizing Mutations for Class A G Protein-Coupled Receptors. J Chem Inf Model 2019; 59:3744-3754. [PMID: 31408606 DOI: 10.1021/acs.jcim.9b00175] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
G protein-coupled receptors (GPCRs) are highly flexible and prone to denaturation during protein extraction in detergents and purification. This poses a huge challenge to purify a conformationally homogeneous solution of GPCRs. Thermostabilizing mutations have been used widely to purify and obtain crystal structures of several GPCRs. However, identifying thermostabilizing mutations for GPCRs remains a tedious and expensive task as they are not transferable even among closely related GPCRs. Additionally, the mutations stabilizing one conformational state of a GPCR do not always stabilize other conformational state(s) of the same GPCR. Previously we developed a computational method, LiticonDesign, for rapid prediction of thermostabilizing mutations for a specific GPCR conformation. In this study, we have used LiticonDesign to predict thermostabilizing mutations for the agonist bound active-intermediate state of the human adenosine receptor (A2AR) using the structure of the inactive state of the same GPCR and vice versa. Our study shows that the thermostable mutation predictions using LiticonDesign, for an active-intermediate state of a GPCR (A2AR in our case), requires a homology model that is derived from an active/active-intermediate state GPCR structure as a template. Similarly, the homology models derived from inactive state GPCR conformations are better in predicting the thermostable mutations for the inactive state of A2AR. Overall, LiticonDesign method is not only efficient in predicting thermostabilizing mutations for a given GPCR sequence but also can recover conformation specific mutations for a state of interest, if a suitable starting structure of desired conformation is chosen.
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Affiliation(s)
- Suvamay Jana
- Department of Computation and Quantitative Medicine , Beckman Research Institute of the City of Hope , 1500 E. Duarte Road , Duarte , California 91010 , United States
| | - Soumadwip Ghosh
- Department of Computation and Quantitative Medicine , Beckman Research Institute of the City of Hope , 1500 E. Duarte Road , Duarte , California 91010 , United States
| | - Sanychen Muk
- Department of Computation and Quantitative Medicine , Beckman Research Institute of the City of Hope , 1500 E. Duarte Road , Duarte , California 91010 , United States
| | - Benjamin Levy
- Department of Computation and Quantitative Medicine , Beckman Research Institute of the City of Hope , 1500 E. Duarte Road , Duarte , California 91010 , United States
| | - Nagarajan Vaidehi
- Department of Computation and Quantitative Medicine , Beckman Research Institute of the City of Hope , 1500 E. Duarte Road , Duarte , California 91010 , United States
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Conformational Plasticity of Human Protease-Activated Receptor 1 upon Antagonist- and Agonist-Binding. Structure 2019; 27:1517-1526.e3. [PMID: 31422910 DOI: 10.1016/j.str.2019.07.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/07/2019] [Accepted: 07/23/2019] [Indexed: 01/14/2023]
Abstract
G protein-coupled receptors (GPCRs) show complex relationships between functional states and conformational plasticity that can be qualitatively and quantitatively described by contouring their free energy landscape. However, how ligands modulate the free energy landscape to direct conformation and function of GPCRs is not entirely understood. Here, we employ single-molecule force spectroscopy to parametrize the free energy landscape of the human protease-activated receptor 1 (PAR1), and delineate the mechanical, kinetic, and energetic properties of PAR1 being set into different functional states. Whereas in the inactive unliganded state PAR1 adopts mechanically rigid and stiff conformations, upon agonist or antagonist binding the receptor mechanically softens, while increasing its conformational flexibility, and kinetic and energetic stability. By mapping the free energy landscape to the PAR1 structure, we observe key structural regions putting this conformational plasticity into effect. Our insight, complemented with previously acquired knowledge on other GPCRs, outlines a more general framework to understand how GPCRs stabilize certain functional states.
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Ruprecht JJ, Kunji ER. Structural changes in the transport cycle of the mitochondrial ADP/ATP carrier. Curr Opin Struct Biol 2019; 57:135-144. [PMID: 31039524 PMCID: PMC6700394 DOI: 10.1016/j.sbi.2019.03.029] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 03/15/2019] [Accepted: 03/20/2019] [Indexed: 11/27/2022]
Abstract
The mitochondrial ADP/ATP carrier, also called adenine nucleotide translocase, accomplishes one of the most important transport activities in eukaryotic cells, importing ADP into the mitochondrial matrix for ATP synthesis, and exporting ATP to fuel cellular activities. In the transport cycle, the carrier changes between a cytoplasmic and matrix state, in which the central substrate binding site is alternately accessible to these compartments. A structure of a cytoplasmic state was known, but recently, a structure of a matrix-state in complex with bongkrekic acid was solved. Comparison of the two states explains the function of highly conserved sequence features and reveals that the transport mechanism is unique, involving the coordinated movement of six dynamic elements around a central translocation pathway.
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Affiliation(s)
- Jonathan J Ruprecht
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XY, UK.
| | - Edmund Rs Kunji
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XY, UK.
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Abstract
G protein-coupled receptors (GPCRs) mediate the majority of cellular responses to external stimuli. Upon activation by a ligand, the receptor binds to a partner heterotrimeric G protein and promotes exchange of GTP for GDP, leading to dissociation of the G protein into α and βγ subunits that mediate downstream signals. GPCRs can also activate distinct signaling pathways through arrestins. Active states of GPCRs form by small rearrangements of the ligand-binding, or orthosteric, site that are amplified into larger conformational changes. Molecular understanding of the allosteric coupling between ligand binding and G protein or arrestin interaction is emerging from structures of several GPCRs crystallized in inactive and active states, spectroscopic data, and computer simulations. The coupling is loose, rather than concerted, and agonist binding does not fully stabilize the receptor in an active conformation. Distinct intermediates whose populations are shifted by ligands of different efficacies underlie the complex pharmacology of GPCRs.
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Affiliation(s)
- William I Weis
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, USA; .,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305, USA;
| | - Brian K Kobilka
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305, USA;
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Engineering of Nanobodies Recognizing the Human Chemokine Receptor CCR7. Int J Mol Sci 2019; 20:ijms20102597. [PMID: 31137829 PMCID: PMC6566259 DOI: 10.3390/ijms20102597] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 05/20/2019] [Accepted: 05/24/2019] [Indexed: 01/12/2023] Open
Abstract
The chemokine receptor CCR7 plays a pivotal role in health and disease. In particular, CCR7 controls homing of antigen-bearing dendritic cells and T cells to lymph nodes, where adaptive immune responses are initiated. However, CCR7 also guides T cells to inflamed synovium and thereby contributes to rheumatoid arthritis and promotes cancer cell migration and metastasis formation. Nanobodies have recently emerged as versatile tools to study G-protein-coupled receptor functions and are being tested in diagnostics and therapeutics. In this study, we designed a strategy to engineer novel nanobodies recognizing human CCR7. We generated a nanobody library based on a solved crystal structure of the nanobody Nb80 recognizing the β2-adrenergic receptor (β2AR) and by specifically randomizing two segments within complementarity determining region 1 (CDR1) and CDR3 of Nb80 known to interact with β2AR. We fused the nanobody library to one half of split-YFP in order to identify individual nanobody clones interacting with CCR7 fused to the other half of split-YFP using bimolecular fluorescence complementation. We present three novel nanobodies, termed Nb1, Nb5, and Nb38, that recognize human CCR7 without interfering with G-protein-coupling and downstream signaling. Moreover, we were able to follow CCR7 trafficking upon CCL19 triggering using Nb1, Nb5, and Nb38.
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García-Nafría J, Tate CG. Cryo-EM structures of GPCRs coupled to G s, G i and G o. Mol Cell Endocrinol 2019; 488:1-13. [PMID: 30930094 DOI: 10.1016/j.mce.2019.02.006] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 02/07/2019] [Accepted: 02/08/2019] [Indexed: 01/14/2023]
Abstract
Advances in electron cryo-microscopy (cryo-EM) now permit the structure determination of G protein-coupled receptors (GPCRs) coupled to heterotrimeric G proteins by single-particle imaging. A combination of G protein engineering and the development of antibodies that stabilise the heterotrimeric G protein facilitate the formation of stable GPCR-G protein complexes suitable for structural biology. Structures have been determined of GPCRs coupled to either heterotrimeric G proteins (Gs, Gi or Go) or mini-G proteins (mini-Gs or mini-Go) by single-particle cryo-EM and X-ray crystallography, respectively. This review describes the technical breakthroughs allowing their structure determination and compares the different techniques. In addition, we compare the structures of GPCRs coupled either to Gs, Gi or Go and analyse the contributions of amino acid residues to the GPCR-G protein interface. There is no unique set of interactions that specifies coupling either to Gs, Gi or Go. Instead, there is a common core of interactions between the C-terminal α-helix of the G protein α-subunit and helices H3, H5 and H6 of the receptor. In addition, there are varying degrees of interaction between all the other GPCR helices and intracellular loops to five regions of the α-subunit and four regions of the β-subunit. These data support the contention that there is not a simple linear barcode that defines the specificity of G protein coupling and thus how a G protein couples to a GPCR cannot currently be determined from simply analysing amino acid sequences. Although the overall architecture of GPCR-G protein complexes is conserved, there are significant differences in the molecular details. The number and type of molecular interactions between amino acid residues at the interfaces varies, resulting in subtly different orientation and position of the G protein with respect to the GPCR. This in turn affects the interface surface area that varies between 845 Å2 and 1490 Å2, which could impact upon the lifetime of signalling complexes in the cell.
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Affiliation(s)
- Javier García-Nafría
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Christopher G Tate
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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42
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Ibrahim P, Clark T. Metadynamics simulations of ligand binding to GPCRs. Curr Opin Struct Biol 2019; 55:129-137. [PMID: 31100549 DOI: 10.1016/j.sbi.2019.04.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 03/28/2019] [Accepted: 04/05/2019] [Indexed: 11/17/2022]
Abstract
Recent developments in metadynamics simulation techniques for ligand binding to Class A GPCRs are described and the results obtained elucidated. The computational protocol makes good use of modern massively parallel hardware, making simulations of the binding/unbinding process routine. The simulations reveal unprecedented details of the ligand-binding pathways, including multiple binding sites in many cases. Free energies of binding are reproduced very well and the simulations allow prediction of the efficacy (agonist, antagonist etc.) of ligands.
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Affiliation(s)
- Passainte Ibrahim
- Computer-Chemistry Center, Department of Chemistry and Pharmacy, Friedrich-Alexander-University Erlangen-Nürnberg, Nägelsbachstr. 25, 91052 Erlangen, Germany
| | - Timothy Clark
- Computer-Chemistry Center, Department of Chemistry and Pharmacy, Friedrich-Alexander-University Erlangen-Nürnberg, Nägelsbachstr. 25, 91052 Erlangen, Germany.
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Kilpatrick LE, Alcobia DC, White CW, Peach CJ, Glenn JR, Zimmerman K, Kondrashov A, Pfleger KDG, Ohana RF, Robers MB, Wood KV, Sloan EK, Woolard J, Hill SJ. Complex Formation between VEGFR2 and the β 2-Adrenoceptor. Cell Chem Biol 2019; 26:830-841.e9. [PMID: 30956148 PMCID: PMC6593180 DOI: 10.1016/j.chembiol.2019.02.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 12/30/2018] [Accepted: 02/24/2019] [Indexed: 12/26/2022]
Abstract
Vascular endothelial growth factor (VEGF) is an important mediator of endothelial cell proliferation and angiogenesis via its receptor VEGFR2. A common tumor associated with elevated VEGFR2 signaling is infantile hemangioma that is caused by a rapid proliferation of vascular endothelial cells. The current first-line treatment for infantile hemangioma is the β-adrenoceptor antagonist, propranolol, although its mechanism of action is not understood. Here we have used bioluminescence resonance energy transfer and VEGFR2 genetically tagged with NanoLuc luciferase to demonstrate that oligomeric complexes involving VEGFR2 and the β2-adrenoceptor can be generated in both cell membranes and intracellular endosomes. These complexes are induced by agonist treatment and retain their ability to couple to intracellular signaling proteins. Furthermore, coupling of β2-adrenoceptor to β-arrestin2 is prolonged by VEGFR2 activation. These data suggest that protein-protein interactions between VEGFR2, the β2-adrenoceptor, and β-arrestin2 may provide insight into their roles in health and disease.
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Affiliation(s)
- Laura E Kilpatrick
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK; Centre of Membrane Proteins and Receptors, University of Birmingham and University of Nottingham, The Midlands, UK
| | - Diana C Alcobia
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK; Centre of Membrane Proteins and Receptors, University of Birmingham and University of Nottingham, The Midlands, UK; Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Melbourne, VIC 3052, Australia
| | - Carl W White
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK; Centre of Membrane Proteins and Receptors, University of Birmingham and University of Nottingham, The Midlands, UK; Harry Perkins Institute of Medical Research and Centre for Medical Research, The University of Western Australia, Nedlands, Perth, WA 6009, Australia
| | - Chloe J Peach
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK; Centre of Membrane Proteins and Receptors, University of Birmingham and University of Nottingham, The Midlands, UK
| | - Jackie R Glenn
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK; Centre of Membrane Proteins and Receptors, University of Birmingham and University of Nottingham, The Midlands, UK
| | | | - Alexander Kondrashov
- Wolfson Centre for Stem Cells, Tissue Engineering & Modelling (STEM), Centre for Biomolecular Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Kevin D G Pfleger
- Harry Perkins Institute of Medical Research and Centre for Medical Research, The University of Western Australia, Nedlands, Perth, WA 6009, Australia; Dimerix Limited, Nedlands, Perth, WA 6009, Australia
| | | | | | | | - Erica K Sloan
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Melbourne, VIC 3052, Australia; Cousins Center for Neuroimmunology, Semel Institute for Neuroscience and Human Behavior, Jonsson Comprehensive Cancer Center, UCLA AIDS Institute, University of California, Los Angeles, CA 90095, USA; Division of Surgical Oncology, Peter MacCallum Cancer Centre, Victorian Comprehensive Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia
| | - Jeanette Woolard
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK; Centre of Membrane Proteins and Receptors, University of Birmingham and University of Nottingham, The Midlands, UK.
| | - Stephen J Hill
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK; Centre of Membrane Proteins and Receptors, University of Birmingham and University of Nottingham, The Midlands, UK.
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Heukers R, De Groof TW, Smit MJ. Nanobodies detecting and modulating GPCRs outside in and inside out. Curr Opin Cell Biol 2019; 57:115-122. [DOI: 10.1016/j.ceb.2019.01.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/29/2019] [Accepted: 01/31/2019] [Indexed: 12/19/2022]
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Alzogaray V, Urrutia M, Berguer P, Rossi A, Zylberman V, Pardo R, Bonomi HR, Goldbaum FA. Characterization of folding-sensitive nanobodies as tools to study the expression and quality of protein particle immunogens. J Biotechnol 2019; 293:17-23. [PMID: 30690101 DOI: 10.1016/j.jbiotec.2019.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 12/04/2018] [Accepted: 01/07/2019] [Indexed: 01/05/2023]
Abstract
Vaccination is as one of the most beneficial biopharmaceutical interventions against pathogens due to its ability to induce adaptive immunity through targeted activation of the immune system. Each vaccine needs a tailor-made set of tests in order to monitor its quality throughout the development and manufacturing. The analysis of the conformational state of protein nanoparticles is one of the key steps in vaccine quality control. The enzyme lumazine synthase from Brucella spp. (BLS) acts as a potent oral and systemic immunogen. BLS has been used as a carrier of foreign peptides, protein domains and whole proteins, serving as a versatile platform for vaccine engineering purposes. Here, we show the generation and characterization of four families of nanobodies (Nbs) which only recognize BLS in its native conformational state and that bind to its active site. The present results support the use of conformation-sensitive Nbs as molecular probes during the development and production of vaccines based on the BLS platform. Finally, we propose Nbs as useful molecular tools targeting other protein scaffolds with potential applications in nano-and biotechnology.
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Affiliation(s)
- Vanina Alzogaray
- Fundación Instituto Leloir, IIBBA-CONICET, Avenida Patricias Argentinas 435 (C1405BWE), Ciudad de Buenos Aires, Argentina
| | - Mariela Urrutia
- Fundación Instituto Leloir, IIBBA-CONICET, Avenida Patricias Argentinas 435 (C1405BWE), Ciudad de Buenos Aires, Argentina
| | - Paula Berguer
- Fundación Instituto Leloir, IIBBA-CONICET, Avenida Patricias Argentinas 435 (C1405BWE), Ciudad de Buenos Aires, Argentina
| | - Andrés Rossi
- Fundación Instituto Leloir, IIBBA-CONICET, Avenida Patricias Argentinas 435 (C1405BWE), Ciudad de Buenos Aires, Argentina
| | - Vanesa Zylberman
- INMUNOVA, 25 de Mayo 1021 (B1650HMI), San Martin, Buenos Aires, Argentina
| | - Romina Pardo
- INMUNOVA, 25 de Mayo 1021 (B1650HMI), San Martin, Buenos Aires, Argentina
| | - Hernán R Bonomi
- Fundación Instituto Leloir, IIBBA-CONICET, Avenida Patricias Argentinas 435 (C1405BWE), Ciudad de Buenos Aires, Argentina
| | - Fernando A Goldbaum
- Fundación Instituto Leloir, IIBBA-CONICET, Avenida Patricias Argentinas 435 (C1405BWE), Ciudad de Buenos Aires, Argentina.
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Ali A, Baby B, Vijayan R. From Desert to Medicine: A Review of Camel Genomics and Therapeutic Products. Front Genet 2019; 10:17. [PMID: 30838017 PMCID: PMC6389616 DOI: 10.3389/fgene.2019.00017] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 01/14/2019] [Indexed: 12/11/2022] Open
Abstract
Camels have an important role in the lives of human beings, especially in arid regions, due to their multipurpose role and unique ability to adapt to harsh conditions. In spite of its enormous economic, cultural, and biological importance, the camel genome has not been widely studied. The size of camel genome is roughly 2.38 GB, containing over 20,000 genes. The unusual genetic makeup of the camel is the main reason behind its ability to survive under extreme environmental conditions. The camel genome harbors several unique variations which are being investigated for the treatment of several disorders. Various natural products from camels have also been tested and prescribed as adjunct therapy to control the progression of ailments. Interestingly, the camel employs unique immunological and molecular mechanisms against pathogenic agents and pathological conditions. Here, we broadly review camel classification, distribution and breed as well as recent progress in the determination of the camel genome, its size, genetic distribution, response to various physiological conditions, immunogenetics and the medicinal potential of camel gene products.
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Affiliation(s)
| | | | - Ranjit Vijayan
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates
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47
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Wright SC, Kozielewicz P, Kowalski-Jahn M, Petersen J, Bowin CF, Slodkowicz G, Marti-Solano M, Rodríguez D, Hot B, Okashah N, Strakova K, Valnohova J, Babu MM, Lambert NA, Carlsson J, Schulte G. A conserved molecular switch in Class F receptors regulates receptor activation and pathway selection. Nat Commun 2019; 10:667. [PMID: 30737406 PMCID: PMC6368630 DOI: 10.1038/s41467-019-08630-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 01/22/2019] [Indexed: 12/21/2022] Open
Abstract
Class F receptors are considered valuable therapeutic targets due to their role in human disease, but structural changes accompanying receptor activation remain unexplored. Employing population and cancer genomics data, structural analyses, molecular dynamics simulations, resonance energy transfer-based approaches and mutagenesis, we identify a conserved basic amino acid in TM6 in Class F receptors that acts as a molecular switch to mediate receptor activation. Across all tested Class F receptors (FZD4,5,6,7, SMO), mutation of the molecular switch confers an increased potency of agonists by stabilizing an active conformation as assessed by engineered mini G proteins as conformational sensors. Disruption of the switch abrogates the functional interaction between FZDs and the phosphoprotein Dishevelled, supporting conformational selection as a prerequisite for functional selectivity. Our studies reveal the molecular basis of a common activation mechanism conserved in all Class F receptors, which facilitates assay development and future discovery of Class F receptor-targeting drugs. Class F receptors are therapeutic targets in human disease and understanding their structural changes during receptor activation may provide important pharmacological insight. Here, the authors combine computational and experimental methods to identify a molecular switch in TM6/7 of Class F receptors that mediates receptor activation.
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Affiliation(s)
- Shane C Wright
- Section of Receptor Biology & Signaling, Dept. Physiology & Pharmacology, Karolinska Institutet, S17165, Stockholm, Sweden
| | - Paweł Kozielewicz
- Section of Receptor Biology & Signaling, Dept. Physiology & Pharmacology, Karolinska Institutet, S17165, Stockholm, Sweden
| | - Maria Kowalski-Jahn
- Section of Receptor Biology & Signaling, Dept. Physiology & Pharmacology, Karolinska Institutet, S17165, Stockholm, Sweden
| | - Julian Petersen
- Section of Receptor Biology & Signaling, Dept. Physiology & Pharmacology, Karolinska Institutet, S17165, Stockholm, Sweden
| | - Carl-Fredrik Bowin
- Section of Receptor Biology & Signaling, Dept. Physiology & Pharmacology, Karolinska Institutet, S17165, Stockholm, Sweden
| | - Greg Slodkowicz
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, United Kingdom
| | - Maria Marti-Solano
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, United Kingdom
| | - David Rodríguez
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, P.O. Box 596, SE-751 24, Uppsala, Sweden
| | - Belma Hot
- Section of Receptor Biology & Signaling, Dept. Physiology & Pharmacology, Karolinska Institutet, S17165, Stockholm, Sweden
| | - Najeah Okashah
- Department of Pharmacology and Toxicology, Medical College of Georgia at Augusta University, Augusta, Georgia, 30912, USA
| | - Katerina Strakova
- Section of Receptor Biology & Signaling, Dept. Physiology & Pharmacology, Karolinska Institutet, S17165, Stockholm, Sweden
| | - Jana Valnohova
- Section of Receptor Biology & Signaling, Dept. Physiology & Pharmacology, Karolinska Institutet, S17165, Stockholm, Sweden
| | - M Madan Babu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, United Kingdom
| | - Nevin A Lambert
- Department of Pharmacology and Toxicology, Medical College of Georgia at Augusta University, Augusta, Georgia, 30912, USA
| | - Jens Carlsson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, P.O. Box 596, SE-751 24, Uppsala, Sweden
| | - Gunnar Schulte
- Section of Receptor Biology & Signaling, Dept. Physiology & Pharmacology, Karolinska Institutet, S17165, Stockholm, Sweden.
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48
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Vass M, Podlewska S, de Esch IJP, Bojarski AJ, Leurs R, Kooistra AJ, de Graaf C. Aminergic GPCR-Ligand Interactions: A Chemical and Structural Map of Receptor Mutation Data. J Med Chem 2018; 62:3784-3839. [PMID: 30351004 DOI: 10.1021/acs.jmedchem.8b00836] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The aminergic family of G protein-coupled receptors (GPCRs) plays an important role in various diseases and represents a major drug discovery target class. Structure determination of all major aminergic subfamilies has enabled structure-based ligand design for these receptors. Site-directed mutagenesis data provides an invaluable complementary source of information for elucidating the structural determinants of binding of different ligand chemotypes. The current study provides a comparative analysis of 6692 mutation data points on 34 aminergic GPCR subtypes, covering the chemical space of 540 unique ligands from mutagenesis experiments and information from experimentally determined structures of 52 distinct aminergic receptor-ligand complexes. The integrated analysis enables detailed investigation of structural receptor-ligand interactions and assessment of the transferability of combined binding mode and mutation data across ligand chemotypes and receptor subtypes. An overview is provided of the possibilities and limitations of using mutation data to guide the design of novel aminergic receptor ligands.
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Affiliation(s)
- Márton Vass
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS) , VU University Amsterdam , 1081HZ Amsterdam , The Netherlands
| | - Sabina Podlewska
- Department of Medicinal Chemistry, Institute of Pharmacology , Polish Academy of Sciences , Smętna 12 , PL31-343 Kraków , Poland
| | - Iwan J P de Esch
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS) , VU University Amsterdam , 1081HZ Amsterdam , The Netherlands
| | - Andrzej J Bojarski
- Department of Medicinal Chemistry, Institute of Pharmacology , Polish Academy of Sciences , Smętna 12 , PL31-343 Kraków , Poland
| | - Rob Leurs
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS) , VU University Amsterdam , 1081HZ Amsterdam , The Netherlands
| | - Albert J Kooistra
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS) , VU University Amsterdam , 1081HZ Amsterdam , The Netherlands.,Department of Drug Design and Pharmacology , University of Copenhagen , Universitetsparken 2 , 2100 Copenhagen , Denmark
| | - Chris de Graaf
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS) , VU University Amsterdam , 1081HZ Amsterdam , The Netherlands.,Sosei Heptares , Steinmetz Building, Granta Park, Great Abington , Cambridge CB21 6DG , U.K
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49
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Yun JH, Li X, Park JH, Wang Y, Ohki M, Jin Z, Lee W, Park SY, Hu H, Li C, Zatsepin N, Hunter MS, Sierra RG, Koralek J, Yoon CH, Cho HS, Weierstall U, Tang L, Liu H, Lee W. Non-cryogenic structure of a chloride pump provides crucial clues to temperature-dependent channel transport efficiency. J Biol Chem 2018; 294:794-804. [PMID: 30455349 DOI: 10.1074/jbc.ra118.004038] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 11/12/2018] [Indexed: 11/06/2022] Open
Abstract
Non-cryogenic protein structures determined at ambient temperature may disclose significant information about protein activity. Chloride-pumping rhodopsin (ClR) exhibits a trend to hyperactivity induced by a change in the photoreaction rate because of a gradual decrease in temperature. Here, to track the structural changes that explain the differences in CIR activity resulting from these temperature changes, we used serial femtosecond crystallography (SFX) with an X-ray free electron laser (XFEL) to determine the non-cryogenic structure of ClR at a resolution of 1.85 Å, and compared this structure with a cryogenic ClR structure obtained with synchrotron X-ray crystallography. The XFEL-derived ClR structure revealed that the all-trans retinal (ATR) region and positions of two coordinated chloride ions slightly differed from those of the synchrotron-derived structure. Moreover, the XFEL structure enabled identification of one additional water molecule forming a hydrogen bond network with a chloride ion. Analysis of the channel cavity and a difference distance matrix plot (DDMP) clearly revealed additional structural differences. B-factor information obtained from the non-cryogenic structure supported a motility change on the residual main and side chains as well as of chloride and water molecules because of temperature effects. Our results indicate that non-cryogenic structures and time-resolved XFEL experiments could contribute to a better understanding of the chloride-pumping mechanism of ClR and other ion pumps.
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Affiliation(s)
- Ji-Hye Yun
- From the Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, South Korea
| | - Xuanxuan Li
- Complex Systems Division, Beijing Computational Science Research Center, 10 East Xibeiwang Road, Haidian District, Beijing 100193, China.,Department of Engineering Physics, Tsinghua University, Beijing 100086, China
| | - Jae-Hyun Park
- From the Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, South Korea
| | - Yang Wang
- Complex Systems Division, Beijing Computational Science Research Center, 10 East Xibeiwang Road, Haidian District, Beijing 100193, China
| | - Mio Ohki
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan
| | - Zeyu Jin
- From the Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, South Korea
| | - Wonbin Lee
- From the Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, South Korea
| | - Sam-Yong Park
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan
| | - Hao Hu
- Physics Department, and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona 85287
| | - Chufeng Li
- Physics Department, and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona 85287
| | - Nadia Zatsepin
- Physics Department, and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona 85287
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, and
| | - Raymond G Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, and
| | - Jake Koralek
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, and
| | - Chun Hong Yoon
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, and
| | - Hyun-Soo Cho
- Department of Systems Biology and Division of Life Sciences, Yonsei University, Seoul 03722, South Korea
| | - Uwe Weierstall
- Physics Department, and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona 85287
| | - Leihan Tang
- Complex Systems Division, Beijing Computational Science Research Center, 10 East Xibeiwang Road, Haidian District, Beijing 100193, China
| | - Haiguang Liu
- Complex Systems Division, Beijing Computational Science Research Center, 10 East Xibeiwang Road, Haidian District, Beijing 100193, China,
| | - Weontae Lee
- From the Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, South Korea,
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50
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GPCR drug discovery: integrating solution NMR data with crystal and cryo-EM structures. Nat Rev Drug Discov 2018; 18:59-82. [PMID: 30410121 DOI: 10.1038/nrd.2018.180] [Citation(s) in RCA: 154] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The 826 G protein-coupled receptors (GPCRs) in the human proteome regulate key physiological processes and thus have long been attractive drug targets. With the crystal structures of more than 50 different human GPCRs determined over the past decade, an initial platform for structure-based rational design has been established for drugs that target GPCRs, which is currently being augmented with cryo-electron microscopy (cryo-EM) structures of higher-order GPCR complexes. Nuclear magnetic resonance (NMR) spectroscopy in solution is one of the key approaches for expanding this platform with dynamic features, which can be accessed at physiological temperature and with minimal modification of the wild-type GPCR covalent structures. Here, we review strategies for the use of advanced biochemistry and NMR techniques with GPCRs, survey projects in which crystal or cryo-EM structures have been complemented with NMR investigations and discuss the impact of this integrative approach on GPCR biology and drug discovery.
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