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Affimer Proteins Inhibit Immune Complex Binding to Fcγriiia with High Specificity Through Competitive and Allosteric Modes of Action

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Affimer Proteins Inhibit Immune Complex Binding to Fcγriiia with High Specificity Through Competitive and Allosteric Modes of Action Affimer proteins inhibit immune complex binding to FcγRIIIa with high specificity through competitive and allosteric modes of action James I. Robinsona,b, Euan W. Baxtera,b,1, Robin L. Owenc,1, Maren Thomsend,1, Darren C. Tomlinsond,e,1, Mark P. Waterhousea,b,1, Stephanie J. Wina,b, Joanne E. Nettleshipf,g, Christian Tiedee, Richard J. Fosterd,h, Raymond J. Owensf,g, Colin W. G. Fishwickd,h, Sarah A. Harrisd,i, Adrian Goldmane,j, Michael J. McPhersond,e,2, and Ann W. Morgana,b,2 aLeeds Institute of Rheumatic and Musculoskeletal Medicine, School of Medicine, University of Leeds, Leeds LS9 7TF, United Kingdom; bNational Institute of Health Research-Leeds Biomedical Research Centre, Chapel Allerton Hospital, Leeds LS7 4SA, United Kingdom; cDiamond Light Source, Didcot OX11 0DE, United Kingdom; dAstbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom; eBioScreening Technology Group, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom; fOxford Protein Production Facility-United Kingdom Research Complex at Harwell, Rutherford Appleton Laboratory, Oxford OX11 0FA, United Kingdom; gDivision of Structural Biology, Wellcome Trust Centre for Genomic Medicine, Nuffield Department of Medicine, Oxford University, Oxford OX3 7BN, United Kingdom; hSchool of Chemistry, University of Leeds, Leeds LS2 9JT, United Kingdom; iSchool of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, United Kingdom; and jFaculty of Biological and Environmental Sciences, University of Helsinki, FIN-0014 Helsinki, Finland Edited by Lawrence Steinman, Stanford University School of Medicine, Stanford, CA, and approved November 17, 2017 (received for review May 15, 2017) Protein–protein interactions are essential for the control of cellular domains and chains, poor stability, high production costs, and functions and are critical for regulation of the immune system. batch-to-batch variation, some of which may be due to glycosyl- One example is the binding of Fc regions of IgG to the Fc gamma ation heterogeneity (5). Artificial binding reagents (protein, RNA, receptors (FcγRs). High sequence identity (98%) between the and DNA aptamers) are relatively small and make attractive genes encoding FcγRIIIa (expressed on macrophages and natural alternatives to antibodies. We have recently established a scaf- killer cells) and FcγRIIIb (expressed on neutrophils) has prevented fold consensus protein based on plant cystatins, called “Affimer,” the development of monospecific agents against these therapeutic also known as “Adhiron” (12 kDa), which provides a highly stable targets. We now report the identification of FcγRIIIa-specific arti- scaffold (melting temperature = 101 °C) for presenting one to ficial binding proteins called “Affimer” that block IgG binding and three variable amino acid sequence regions for molecular recog- abrogate FcγRIIIa-mediated downstream effector functions in mac- nition (6). These variable regions (VRs) form a binding interface rophages, namely TNF release and phagocytosis. Cocrystal structures analogous to that presented by the complementarity-determining and molecular dynamics simulations have revealed the structural basis of this specificity for two Affimer proteins: One binds directly Significance to the Fc binding site, whereas the other acts allosterically. Autoimmune disease pathogenesis is driven by inflammation, Fc gamma receptor IIIa | specific inhibitor | Affimer | allosteric | competitive induced partly by IgG autoantibody-containing immune com- plexes binding to Fc gamma receptors (FcγRs). These receptors are valid therapeutic targets in the treatment of autoimmunity. mproved understanding of genetic, genomic, and cellular pro- FcγRIIIa is one of a family of highly homologous receptors for Icesses underpinning human disease has led to the identifica- IgG antibodies; previous attempts at therapeutic blockade have – tion of a multitude of protein protein interactions that represent resulted in off-target effects involving cells that express the potentially important therapeutic targets, frequently for multiple almost identical protein FcγRIIIb. Here we report the identifica- diseases. Drug discovery has traditionally focused on classical tion of functionally specific protein-based inhibitors (Affimer enzyme pockets, and chemical libraries are screened to identify proteins) of FcγRIIIa and the structural/functional basis of their – inhibitors using biochemical and biophysical assays. Protein selectivity. As molecular research tools FcγRIIIa-specific Affimer protein interactions are notoriously difficult to target by this approach, proteins provide the ability to block IgG interaction with a single since the interfaces frequently comprise large contact surfaces, which receptor. Our findings suggest that highly selective protein- generally lack the deep pockets required for traditional medici- based blocking agents that may have therapeutic applications nal chemistry approaches. In recent years, alternative strategies can be readily produced. have emerged including fragment-based approaches to explore the chemical space or the use of peptide-based recognition molecules, Author contributions: J.I.R., E.W.B., D.C.T., R.J.F., R.J.O., S.A.H., M.J.M., and A.W.M. de- such as hydrocarbon-stapled peptides, alpha mimetics, nonanti- signed research; J.I.R., E.W.B., M.P.W., S.J.W., J.E.N., and C.T. performed research; D.C.T., body protein scaffolds, and antibody-aided technologies (reviewed C.T., C.W.G.F., and S.A.H. contributed new reagents/analytic tools; J.I.R., E.W.B., R.L.O., M.T., M.P.W., S.J.W., J.E.N., C.W.G.F., S.A.H., and A.G. analyzed data; and J.I.R., E.W.B., in ref. 1). Proteomimetic molecules have inherently greater po- M.T., D.C.T., M.P.W., S.A.H., A.G., M.J.M., and A.W.M. wrote the paper. tential to bind to critical interaction interfaces and sterically block – Conflict of interest statement: The University of Leeds has filed a patent application on protein protein interactions. Traditional computational-based Adhiron (referred to here as Affimer protein) that is licensed to Avacta Life Sciences Ltd. design tools have tended to focus on orthosteric inhibitors that di- This article is a PNAS Direct Submission. rectly target the interaction site, such as the receptor ligand-binding Published under the PNAS license. domain or active site of an enzyme. Approaches for therapeutic Data deposition: Coordinates and structure factors have been deposited in the Protein development include stabilization of protein complexes and iden- Data Bank under the accession codes 5ML9 and 5MN2. Molecular dynamics simulation set- tification of allosteric modulators that bind at sites distant to the up files and compressed trajectories are available at https://doi.org/10.5518/258. interacting proteins (2, 3). 1E.W.B., R.L.O., M.T., D.C.T., and M.P.W. contributed equally to this work. Currently, antibodies are the best-studied group of protein- 2To whom correspondence may be addressed. Email: [email protected] or based inhibitors with a wide range of therapeutic humanized [email protected]. monoclonal antibodies already in clinical use (4). However, anti- This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. bodies are not always ideal as molecular tools due to their multiple 1073/pnas.1707856115/-/DCSupplemental. E72–E81 | PNAS | Published online December 15, 2017 www.pnas.org/cgi/doi/10.1073/pnas.1707856115 Downloaded by guest on September 26, 2021 regions of an antibody. Affimer proteins are selected from tion. Molecular dynamics (MD) simulations based on the X-ray PNAS PLUS phage display libraries (>3 × 1010), allowing rapid identifica- crystallographic models supported the molecular basis of Affimer tion of highly specific reagents that selectively bind to a target protein’s mode of action and selectivity for FcγRIIIa. One and often act as competitive or allosteric inhibitors (7–9). Non- Affimer protein [Protein Data Bank (PDB) ID code 5ML9] antibody–binding proteins tend to recognize binding hot spots, bound close to the Fc-binding domain, acting as a steric in- which are small groups of amino acids on the target protein that hibitor, whereas the other (PDB ID code 5MN2) recognized an contribute the majority of the interaction free energy (10). We allosteric site and bound in the interdomain hinge region. propose that Affimer proteins can be used to study protein function Our results demonstrate the feasibility of generating highly and to disrupt protein–ligand interactions. This unbiased approach specific inhibitors of protein–ligand interactions that bind un- may also increase the potential for introducing selectivity where explored sites and illustrate the utility of Affimer proteins in the multiple receptors bind to a single ligand or, conversely, where study of protein function at both a molecular and cellular level. multiple ligands bind to a single receptor. We have explored the potential utility of this approach using human Fc gamma receptors Results (FcγRs)asamodelsystem. Identification and Characterization of FcγRIIIa-Specific Affimer Human FcγR–ligand interactions constitute a biological system in Proteins. The extent of the challenge faced when developing spe- which multiple layers of complexity facilitate the fine-tuning of im- cific agents against FcγRIIIa is illustrated by the structural align- mune responses to infections. IgG is the major ligand and mediates ment of FcγR crystal structures,
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