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Dilly JJ, Morgan AL, Bedding MJ, Low JKK, Mackay JP, Conibear AC, Bhusal RP, Stone MJ, Franck C, Payne RJ. Tyrosine Sulfation Modulates the Binding Affinity of Chemokine-Targeting Nanobodies. ACS Chem Biol 2024. [PMID: 38941516 DOI: 10.1021/acschembio.4c00230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Chemokines are an important family of small proteins integral to leukocyte recruitment during inflammation. Dysregulation of the chemokine-chemokine receptor axis is implicated in many diseases, and both chemokines and their cognate receptors have been the targets of therapeutic development. Analysis of the antigen-binding regions of chemokine-binding nanobodies revealed a sequence motif suggestive of tyrosine sulfation. Given the well-established importance of post-translational tyrosine sulfation of receptors for chemokine affinity, it was hypothesized that the sulfation of these nanobodies may contribute to chemokine binding and selectivity. Four nanobodies (16C1, 9F1, 11B1, and 11F2) were expressed using amber codon suppression to incorporate tyrosine sulfation. The sulfated variant of 16C1 demonstrated significantly improved chemokine binding compared to the non-sulfated counterpart, while the other nanobodies displayed equipotent or reduced affinity upon sulfation. The ability of tyrosine sulfation to modulate chemokine binding, both positively and negatively, could be leveraged for chemokine-targeted sulfo-nanobody therapeutics in the future.
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Affiliation(s)
- Joshua J Dilly
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Alexandra L Morgan
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
- Cardiovascular Disease Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Max J Bedding
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Jason K K Low
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Joel P Mackay
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Anne C Conibear
- Institute of Applied Synthetic Chemistry, TU Wien, Getreidemarkt 9/163, Wien 1060, Austria
| | - Ram Prasad Bhusal
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
- Cardiovascular Disease Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Martin J Stone
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
- Cardiovascular Disease Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Charlotte Franck
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Richard J Payne
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
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2
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Devkota SR, Aryal P, Wilce MCJ, Payne RJ, Stone MJ, Bhusal RP. Structural basis of chemokine recognition by the class A3 tick evasin EVA-ACA1001. Protein Sci 2024; 33:e4999. [PMID: 38723106 PMCID: PMC11081419 DOI: 10.1002/pro.4999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 05/13/2024]
Abstract
Ticks produce chemokine-binding proteins, known as evasins, in their saliva to subvert the host's immune response. Evasins bind to chemokines and thereby inhibit the activation of their cognate chemokine receptors, thus suppressing leukocyte recruitment and inflammation. We recently described subclass A3 evasins, which, like other class A evasins, exclusively target CC chemokines but appear to use a different binding site architecture to control target selectivity among CC chemokines. We now describe the structural basis of chemokine recognition by the class A3 evasin EVA-ACA1001. EVA-ACA1001 binds to almost all human CC chemokines and inhibits receptor activation. Truncation mutants of EVA-ACA1001 showed that, unlike class A1 evasins, both the N- and C-termini of EVA-ACA1001 play minimal roles in chemokine binding. To understand the structural basis of its broad chemokine recognition, we determined the crystal structure of EVA-ACA1001 in complex with the human chemokine CCL16. EVA-ACA1001 forms backbone-backbone interactions with the CC motif of CCL16, a conserved feature of all class A evasin-chemokine complexes. A hydrophobic pocket in EVA-ACA1001, formed by several aromatic side chains and the unique disulfide bond of class A3 evasins, accommodates the residue immediately following the CC motif (the "CC + 1 residue") of CCL16. This interaction is shared with EVA-AAM1001, the only other class A3 evasins characterized to date, suggesting it may represent a common mechanism that accounts for the broad recognition of CC chemokines by class A3 evasins.
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Affiliation(s)
- Shankar Raj Devkota
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery InstituteMonash UniversityClaytonVICAustralia
| | - Pramod Aryal
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery InstituteMonash UniversityClaytonVICAustralia
| | - Matthew C. J. Wilce
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery InstituteMonash UniversityClaytonVICAustralia
| | - Richard J. Payne
- School of ChemistryThe University of SydneySydneyNSWAustralia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein ScienceThe University of SydneySydneyNSWAustralia
| | - Martin J. Stone
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery InstituteMonash UniversityClaytonVICAustralia
| | - Ram Prasad Bhusal
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery InstituteMonash UniversityClaytonVICAustralia
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Vales S, Kryukova J, Chandra S, Smagurauskaite G, Payne M, Clark CJ, Hafner K, Mburu P, Denisov S, Davies G, Outeiral C, Deane CM, Morris GM, Bhattacharya S. Discovery and pharmacophoric characterization of chemokine network inhibitors using phage-display, saturation mutagenesis and computational modelling. Nat Commun 2023; 14:5763. [PMID: 37717048 PMCID: PMC10505172 DOI: 10.1038/s41467-023-41488-z] [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: 02/09/2023] [Accepted: 09/06/2023] [Indexed: 09/18/2023] Open
Abstract
CC and CXC-chemokines are the primary drivers of chemotaxis in inflammation, but chemokine network redundancy thwarts pharmacological intervention. Tick evasins promiscuously bind CC and CXC-chemokines, overcoming redundancy. Here we show that short peptides that promiscuously bind both chemokine classes can be identified from evasins by phage-display screening performed with multiple chemokines in parallel. We identify two conserved motifs within these peptides and show using saturation-mutagenesis phage-display and chemotaxis studies of an exemplar peptide that an anionic patch in the first motif and hydrophobic, aromatic and cysteine residues in the second are functionally necessary. AlphaFold2-Multimer modelling suggests that the peptide occludes distinct receptor-binding regions in CC and in CXC-chemokines, with the first and second motifs contributing ionic and hydrophobic interactions respectively. Our results indicate that peptides with broad-spectrum anti-chemokine activity and therapeutic potential may be identified from evasins, and the pharmacophore characterised by phage display, saturation mutagenesis and computational modelling.
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Affiliation(s)
- Serena Vales
- Wellcome Centre for Human Genetics and RDM Cardiovascular Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Jhanna Kryukova
- Wellcome Centre for Human Genetics and RDM Cardiovascular Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Soumyanetra Chandra
- Wellcome Centre for Human Genetics and RDM Cardiovascular Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Gintare Smagurauskaite
- Wellcome Centre for Human Genetics and RDM Cardiovascular Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Megan Payne
- Wellcome Centre for Human Genetics and RDM Cardiovascular Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Charlie J Clark
- Wellcome Centre for Human Genetics and RDM Cardiovascular Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Katrin Hafner
- Wellcome Centre for Human Genetics and RDM Cardiovascular Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Philomena Mburu
- Wellcome Centre for Human Genetics and RDM Cardiovascular Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Stepan Denisov
- Wellcome Centre for Human Genetics and RDM Cardiovascular Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Graham Davies
- Wellcome Centre for Human Genetics and RDM Cardiovascular Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Carlos Outeiral
- Department of Statistics, University of Oxford, 24-29 St Giles, Oxford, OX1 3LB, UK
| | - Charlotte M Deane
- Department of Statistics, University of Oxford, 24-29 St Giles, Oxford, OX1 3LB, UK
| | - Garrett M Morris
- Department of Statistics, University of Oxford, 24-29 St Giles, Oxford, OX1 3LB, UK
| | - Shoumo Bhattacharya
- Wellcome Centre for Human Genetics and RDM Cardiovascular Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK.
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Devkota SR, Aryal P, Pokhrel R, Jiao W, Perry A, Panjikar S, Payne RJ, Wilce MCJ, Bhusal RP, Stone MJ. Engineering broad-spectrum inhibitors of inflammatory chemokines from subclass A3 tick evasins. Nat Commun 2023; 14:4204. [PMID: 37452046 PMCID: PMC10349104 DOI: 10.1038/s41467-023-39879-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 07/03/2023] [Indexed: 07/18/2023] Open
Abstract
Chemokines are key regulators of leukocyte trafficking and attractive targets for anti-inflammatory therapy. Evasins are chemokine-binding proteins from tick saliva, whose application as anti-inflammatory therapeutics will require manipulation of their chemokine target selectivity. Here we describe subclass A3 evasins, which are unique to the tick genus Amblyomma and distinguished from "classical" class A1 evasins by an additional disulfide bond near the chemokine recognition interface. The A3 evasin EVA-AAM1001 (EVA-A) bound to CC chemokines and inhibited their receptor activation. Unlike A1 evasins, EVA-A was not highly dependent on N- and C-terminal regions to differentiate chemokine targets. Structures of chemokine-bound EVA-A revealed a deep hydrophobic pocket, unique to A3 evasins, that interacts with the residue immediately following the CC motif of the chemokine. Mutations to this pocket altered the chemokine selectivity of EVA-A. Thus, class A3 evasins provide a suitable platform for engineering proteins with applications in research, diagnosis or anti-inflammatory therapy.
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Affiliation(s)
- Shankar Raj Devkota
- Monash Biomedicine Discovery Institute, and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia
| | - Pramod Aryal
- Monash Biomedicine Discovery Institute, and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia
| | - Rina Pokhrel
- Monash Biomedicine Discovery Institute, and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia
| | - Wanting Jiao
- Ferrier Research Institute, Victoria University of Wellington, Wellington 6140, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, 1142, New Zealand
| | - Andrew Perry
- Monash Bioinformatics Platform, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Santosh Panjikar
- Monash Biomedicine Discovery Institute, and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia
- Australian Synchrotron, ANSTO, Clayton, VIC, 3168, Australia
| | - Richard J Payne
- School of Chemistry, The University of Sydney, Sydney, NSW, 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Matthew C J Wilce
- Monash Biomedicine Discovery Institute, and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia
| | - Ram Prasad Bhusal
- Monash Biomedicine Discovery Institute, and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia.
| | - Martin J Stone
- Monash Biomedicine Discovery Institute, and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia.
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Swapping N-terminal regions among tick evasins reveals cooperative interactions influencing chemokine binding and selectivity. J Biol Chem 2022; 298:102382. [PMID: 35973511 PMCID: PMC9478924 DOI: 10.1016/j.jbc.2022.102382] [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: 06/01/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 11/21/2022] Open
Abstract
Class A tick evasins are natural chemokine-binding proteins that block the signaling of multiple chemokines from the CC subfamily through their cognate receptors, thus suppressing leukocyte recruitment and inflammation. Development of tick evasins as chemokine-targeted anti-inflammatory therapeutics requires an understanding of the factors controlling their chemokine recognition and selectivity. To investigate the role of the evasin N-terminal region for chemokine recognition, we prepared chimeric evasins by interchanging the N-terminal regions of four class A evasins, including a newly identified evasin, EVA-RPU02. We show through chemokine binding analysis of the parental and chimeric evasins that the N-terminal region is critical for chemokine binding affinity and selectivity. Notably, we found some chimeras were unable to bind certain cognate chemokine ligands of both parental evasins. Moreover, unlike any natural evasins characterized to date, some chimeras exhibited specific binding to a single chemokine. These results indicate that the evasin N terminus interacts cooperatively with the “body” of the evasin to enable optimum chemokine recognition. Furthermore, the altered chemokine selectivity of the chimeras validates the approach of engineering the N termini of evasins to yield unique chemokine recognition profiles.
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