Moderate‐Affinity Affibodies Modulate the Delivery and Bioactivity of Bone Morphogenetic Protein‐2

Uncontrolled bone morphogenetic protein-2 (BMP-2) release can lead to off-target bone growth and other adverse events. To tackle this challenge, we used yeast surface display to identify unique BMP-2-specific protein binders known as affibodies that bound to BMP-2 with different affinities. Biolayer interferometry revealed an equilibrium dissociation constant of 10.7 nM for the interaction between BMP-2 and high-affinity affibody and 34.8 nM for the interaction between BMP-2 and the low-affinity affibody. The low-affinity affibody-BMP-2 interaction also exhibited an off-rate constant that was an order of magnitude higher. Computational modeling of affibody-BMP-2 binding predicted that the high- and low-affinity affibodies bind to two distinct sites on BMP-2 that function as different cell-receptor binding sites. BMP-2 binding to affibodies reduced expression of the osteogenic marker alkaline phosphatase (ALP) in C2C12 myoblasts. Affibody-conjugated polyethylene glycol-maleimide hydrogels increased uptake of BMP-2 compared to affibody-free hydrogels, and high-affinity hydrogels exhibited lower BMP-2 release into serum compared to low-affinity hydrogels and affibody-free hydrogels over four weeks. Loading BMP-2 into affibody-conjugated hydrogels prolonged the ALP activity of C2C12 myoblasts compared to soluble BMP-2. This work demonstrates that affibodies with different affinities can modulate BMP-2 delivery and activity, creating a promising approach for controlling BMP-2 delivery in clinical applications. This article is protected by copyright. All rights reserved.

[1]  M. Shoichet,et al.  Affibody-mediated controlled release of fibroblast growth factor 2. , 2022, Journal of controlled release : official journal of the Controlled Release Society.

[2]  M. Shoichet,et al.  Directed Evolution Enables Simultaneous Controlled Release of Multiple Therapeutic Proteins from Biopolymer‐Based Hydrogels , 2022, Advanced materials.

[3]  B. Liu,et al.  Crystal structures of BMPRII extracellular domain in binary and ternary receptor complexes with BMP10 , 2022, Nature Communications.

[4]  T. Deming,et al.  Poly(dehydroalanine): Synthesis, Properties, and Functional Diversification of a Fluorescent Polypeptide. , 2022, Journal of the American Chemical Society.

[5]  Yi Cao,et al.  Regulating the Homogeneity of Thiol-Maleimide Michael-Type Addition-Based Hydrogels Using Amino Biomolecules , 2021, Gels.

[6]  O. Korsgren,et al.  Discovery, optimization and biodistribution of an Affibody molecule for imaging of CD69 , 2021, Scientific Reports.

[7]  Md. Shahriar Karim,et al.  Heterodimer-heterotetramer formation mediates enhanced sensor activity in a biophysical model for BMP signaling , 2021, PLoS Comput. Biol..

[8]  S. Ovchinnikov,et al.  ColabFold: making protein folding accessible to all , 2022, Nature Methods.

[9]  Oriol Vinyals,et al.  Highly accurate protein structure prediction with AlphaFold , 2021, Nature.

[10]  Jun‐Seok Lee,et al.  Recent advances in protein modifications techniques for the targeting N‐terminal cysteine , 2021, Peptide Science.

[11]  J. Hubbell,et al.  Engineered bridge protein with dual affinity for bone morphogenetic protein-2 and collagen enhances bone regeneration for spinal fusion , 2021, Science Advances.

[12]  G. Duda,et al.  Bone morphogenetic protein 2-induced cellular chemotaxis drives tissue patterning during critical-sized bone defect healing: an in silico study , 2021, Biomechanics and modeling in mechanobiology.

[13]  A. Rodger,et al.  Beginners guide to circular dichroism , 2021, The Biochemist.

[14]  Yong Wang,et al.  Affinity Hydrogels for Protein Delivery. , 2021, Trends in pharmacological sciences.

[15]  G. Corfas,et al.  An injectable PEG hydrogel controlling neurotrophin-3 release by affinity peptides. , 2020, Journal of controlled release : official journal of the Controlled Release Society.

[16]  H. Bunjes,et al.  Bone Morphogenetic Protein 2 (BMP-2) Aggregates Can be Solubilized by Albumin—Investigation of BMP-2 Aggregation by Light Scattering and Electrophoresis , 2020, Pharmaceutics.

[17]  J. Löfblom,et al.  Increasing thermal stability and improving biodistribution of VEGFR2-binding affibody molecules by a combination of in silico and directed evolution approaches , 2020, Scientific Reports.

[18]  G. Doerk,et al.  Controlling Drug Absorption, Release and Erosion of Photopatterned Protein Engineered Hydrogels. , 2020, Biomacromolecules.

[19]  Jack B. Maguire,et al.  Perturbing the energy landscape for improved packing during computational protein design , 2020, Proteins.

[20]  C. Werner,et al.  Tuning the Local Availability of VEGF within Glycosaminoglycan‐Based Hydrogels to Modulate Vascular Endothelial Cell Morphogenesis , 2020, Advanced Functional Materials.

[21]  A. Mohs,et al.  Sulfation modulates the targeting properties of hyaluronic acid to P-selectin and CD44. , 2020, ACS biomaterials science & engineering.

[22]  Guixue Wang,et al.  Covalent immobilization of biomolecules on stent materials through mussel adhesive protein coating to form biofunctional films. , 2020, Materials science & engineering. C, Materials for biological applications.

[23]  R. Guldberg,et al.  Heparin-mediated delivery of bone morphogenetic protein-2 improves spatial localization of bone regeneration , 2020, Science Advances.

[24]  M. Rathinam,et al.  Predicting Drug Release From Degradable Hydrogels Using Fluorescence Correlation Spectroscopy and Mathematical Modeling , 2019, Front. Bioeng. Biotechnol..

[25]  N. Trier,et al.  Peptides, Antibodies, Peptide Antibodies and More , 2019, International journal of molecular sciences.

[26]  Xin Wen,et al.  Selection and screening strategies in directed evolution to improve protein stability , 2019, Bioresources and Bioprocessing.

[27]  U. Rinas,et al.  Stability and Biological Activity of E. coli Derived Soluble and Precipitated Bone Morphogenetic Protein-2 , 2019, Pharmaceutical Research.

[28]  R. Cameron,et al.  Impact of UV- and carbodiimide-based crosslinking on the integrin-binding properties of collagen-based materials: Integrin binding to UV- and carbodiimide-crosslinked collagen. , 2019, Acta biomaterialia.

[29]  J. Kohn,et al.  In Vitro Evaluation of Recombinant Bone Morphogenetic Protein-2 Bioactivity for Regenerative Medicine , 2019, Tissue engineering. Part C, Methods.

[30]  Barry A Badeau,et al.  Logic‐Based Delivery of Site‐Specifically Modified Proteins from Environmentally Responsive Hydrogel Biomaterials , 2019, Advanced materials.

[31]  Shota Yamamoto,et al.  Epidermal growth factor-nanoparticle conjugates change the activity from anti-apoptotic to pro-apoptotic at membrane rafts. , 2019, Acta biomaterialia.

[32]  J. Tsai,et al.  A Rational Approach for Creating Peptides Mimicking Antibody Binding , 2019, Scientific Reports.

[33]  J. Lai,et al.  Effect of Cross-Linking Density on the Structures and Properties of Carbodiimide-Treated Gelatin Matrices as Limbal Stem Cell Niches , 2018, International journal of molecular sciences.

[34]  M Mirdita,et al.  MMseqs2 desktop and local web server app for fast, interactive sequence searches , 2018, bioRxiv.

[35]  D. Saris,et al.  Bioactive Tape With BMP-2 Binding Peptides Captures Endogenous Growth Factors and Accelerates Healing After Anterior Cruciate Ligament Reconstruction , 2018, The American journal of sports medicine.

[36]  S. Peyton,et al.  Control of thiol-maleimide reaction kinetics in PEG hydrogel networks. , 2018, Acta biomaterialia.

[37]  Mohammad Kazemi Ashtiani,et al.  Effect of chemical immobilization of SDF‐1α into muscle‐derived scaffolds on angiogenesis and muscle progenitor recruitment , 2018, Journal of tissue engineering and regenerative medicine.

[38]  R. Guldberg,et al.  Enhanced in vivo retention of low dose BMP-2 via heparin microparticle delivery does not accelerate bone healing in a critically sized femoral defect. , 2017, Acta biomaterialia.

[39]  Ju Wang,et al.  Synergistic effects of fibroblast growth factor-2 and bone morphogenetic protein-2 on bone induction , 2017, Molecular medicine reports.

[40]  R. Guldberg,et al.  Competitive Protein Binding Influences Heparin-Based Modulation of Spatial Growth Factor Delivery for Bone Regeneration. , 2017, Tissue engineering. Part A.

[41]  M. Shoichet,et al.  Designing Peptide and Protein Modified Hydrogels: Selecting the Optimal Conjugation Strategy. , 2017, Journal of the American Chemical Society.

[42]  S. Komarova,et al.  Collagen Type I as a Ligand for Receptor-Mediated Signaling , 2017, Front. Phys..

[43]  C. Wagner,et al.  Titratable Avidity Reduction Enhances Affinity Discrimination in Mammalian Cellular Selections of Yeast-Displayed Ligands. , 2017, ACS combinatorial science.

[44]  B. Hackel,et al.  A Gradient of Sitewise Diversity Promotes Evolutionary Fitness for Binder Discovery in a Three-Helix Bundle Protein Scaffold. , 2017, Biochemistry.

[45]  Fredrik Y Frejd,et al.  Affibody molecules as engineered protein drugs , 2017, Experimental &Molecular Medicine.

[46]  S. Moon,et al.  Effect of BMP-2 Delivery Mode on Osteogenic Differentiation of Stem Cells , 2017, Stem cells international.

[47]  Maria Jesus Martin,et al.  Uniclust databases of clustered and deeply annotated protein sequences and alignments , 2016, Nucleic Acids Res..

[48]  Jia Shen,et al.  A Review of the Clinical Side Effects of Bone Morphogenetic Protein-2. , 2016, Tissue engineering. Part B, Reviews.

[49]  S. Rüdiger,et al.  A script to highlight hydrophobicity and charge on protein surfaces , 2015, Front. Mol. Biosci..

[50]  Jian Sun,et al.  Role of bone morphogenetic protein-2 in osteogenic differentiation of mesenchymal stem cells , 2015, Molecular medicine reports.

[51]  H. M. Jamil,et al.  TGF-β/BMP signaling and other molecular events: regulation of osteoblastogenesis and bone formation , 2015, Bone Research.

[52]  Erik G Marklund,et al.  Bayesian deconvolution of mass and ion mobility spectra: from binary interactions to polydisperse ensembles. , 2015, Analytical chemistry.

[53]  Sara A Abouelmagd,et al.  Release kinetics study of poorly water-soluble drugs from nanoparticles: are we doing it right? , 2015, Molecular pharmaceutics.

[54]  D. Benoit,et al.  Development and in vitro assessment of enzymatically-responsive poly(ethylene glycol) hydrogels for the delivery of therapeutic peptides. , 2014, Biomaterials.

[55]  Todd C McDevitt,et al.  Heparin microparticle effects on presentation and bioactivity of bone morphogenetic protein-2. , 2014, Biomaterials.

[56]  Zhiping Weng,et al.  ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers , 2014, Bioinform..

[57]  P. Knaus,et al.  BMP2-induced chemotaxis requires PI3K p55γ/p110α-dependent phosphatidylinositol (3,4,5)-triphosphate production and LL5β recruitment at the cytocortex , 2014, BMC Biology.

[58]  Sylvie Ricard-Blum,et al.  Heparin-protein interactions: from affinity and kinetics to biological roles. Application to an interaction network regulating angiogenesis. , 2014, Matrix biology : journal of the International Society for Matrix Biology.

[59]  Mikaël M. Martino,et al.  Growth Factors Engineered for Super-Affinity to the Extracellular Matrix Enhance Tissue Healing , 2014, Science.

[60]  D. Baker,et al.  Relaxation of backbone bond geometry improves protein energy landscape modeling , 2014, Protein science : a publication of the Protein Society.

[61]  G. Gstraunthaler,et al.  A plea to reduce or replace fetal bovine serum in cell culture media , 2013, Cytotechnology.

[62]  T. Katagiri,et al.  The unique activity of bone morphogenetic proteins in bone: a critical role of the Smad signaling pathway , 2013, Biological chemistry.

[63]  Brian W. Pogue,et al.  Fluorescent Affibody Peptide Penetration in Glioma Margin Is Superior to Full Antibody , 2013, PloS one.

[64]  David Baker,et al.  A Pareto-Optimal Refinement Method for Protein Design Scaffolds , 2013, PloS one.

[65]  A. Shaughnessy Monoclonal antibodies: magic bullets with a hefty price tag , 2012, BMJ : British Medical Journal.

[66]  Chien-Chi Lin,et al.  Cross-linking and degradation of step-growth hydrogels formed by thiol-ene photoclick chemistry. , 2012, Biomacromolecules.

[67]  I. Shaifali,et al.  Antibiotic Susceptibility Patterns of Urinary Pathogens in Female Outpatients , 2012, North American journal of medical sciences.

[68]  Wim E Hennink,et al.  Hydrogels for protein delivery. , 2012, Chemical reviews.

[69]  Byung-Soo Kim,et al.  Comparison between heparin-conjugated fibrin and collagen sponge as bone morphogenetic protein-2 carriers for bone regeneration , 2012, Experimental & Molecular Medicine.

[70]  Jay C. Sy,et al.  Maleimide Cross‐Linked Bioactive PEG Hydrogel Exhibits Improved Reaction Kinetics and Cross‐Linking for Cell Encapsulation and In Situ Delivery , 2012, Advanced materials.

[71]  David Baker,et al.  Algorithm discovery by protein folding game players , 2011, Proceedings of the National Academy of Sciences.

[72]  J. Winther,et al.  Trisulfides in proteins. , 2011, Antioxidants & redox signaling.

[73]  D. Baker,et al.  Alternate states of proteins revealed by detailed energy landscape mapping. , 2011, Journal of molecular biology.

[74]  S. Zustiak,et al.  Characterization of protein release from hydrolytically degradable poly(ethylene glycol) hydrogels , 2011, Biotechnology and bioengineering.

[75]  Fredrik Y Frejd,et al.  Affibody molecules: Engineered proteins for therapeutic, diagnostic and biotechnological applications , 2010, FEBS letters.

[76]  Kristi S Anseth,et al.  Effects of PEG hydrogel crosslinking density on protein diffusion and encapsulated islet survival and function. , 2009, Journal of biomedical materials research. Part A.

[77]  T. Albert,et al.  Complications associated with single-level transforaminal lumbar interbody fusion. , 2009, The spine journal : official journal of the North American Spine Society.

[78]  M. Lek,et al.  Myoblast sensitivity and fibroblast insensitivity to osteogenic conversion by BMP-2 correlates with the expression of Bmpr-1a , 2009, BMC musculoskeletal disorders.

[79]  Pamela Basto,et al.  HER‐2‐Targeted Nanoparticle–Affibody Bioconjugates for Cancer Therapy , 2008, ChemMedChem.

[80]  A. Kapila,et al.  Picomolar affinity fibronectin domains engineered utilizing loop length diversity, recursive mutagenesis, and loop shuffling. , 2008, Journal of molecular biology.

[81]  K Dane Wittrup,et al.  Isolating and engineering human antibodies using yeast surface display , 2006, Nature Protocols.

[82]  Jennifer A. Craig,et al.  Design of a novel fibronectin-mimetic peptide-amphiphile for functionalized biomaterials. , 2006, Langmuir : the ACS journal of surfaces and colloids.

[83]  M. Davies,et al.  Evidence for the formation of adducts and S-(carboxymethyl)cysteine on reaction of alpha-dicarbonyl compounds with thiol groups on amino acids, peptides, and proteins. , 2005, Chemical research in toxicology.

[84]  W. Sebald,et al.  Molecular recognition of BMP-2 and BMP receptor IA , 2004, Nature Structural &Molecular Biology.

[85]  Hyun D Kim,et al.  Retention and activity of BMP-2 in hyaluronic acid-based scaffolds in vitro. , 2002, Journal of biomedical materials research.

[86]  H. Ohgushi,et al.  Recombinant human bone morphogenetic protein-2 potentiates the in vivo osteogenic ability of marrow/hydroxyapatite composites. , 2001, Artificial organs.

[87]  T. Kirsch,et al.  BMP‐2 antagonists emerge from alterations in the low‐affinity binding epitope for receptor BMPR‐II , 2000, The EMBO journal.

[88]  W. B. Upholt,et al.  Regulation of alkaline phosphatase and alpha 2(I) procollagen synthesis during early intramembranous bone formation in the rat mandible. , 1990, Differentiation; research in biological diversity.

[89]  Nicholas A. Peppas,et al.  A simple equation for description of solute release II. Fickian and anomalous release from swellable devices , 1987 .

[90]  J. Siepmann,et al.  In vitro release studies of insulin from lipid implants in solution and in a hydrogel matrix mimicking the subcutis. , 2016, European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences.

[91]  Kohei Miyazono,et al.  Bone morphogenetic protein receptors and signal transduction. , 2010, Journal of biochemistry.

[92]  K. Anseth,et al.  The effect of heparin-functionalized PEG hydrogels on three-dimensional human mesenchymal stem cell osteogenic differentiation. , 2007, Biomaterials.

[93]  N. Greenfield Using circular dichroism spectra to estimate protein secondary structure , 2007, Nature Protocols.

[94]  Christine E Schmidt,et al.  Characterization of protein release from photocrosslinkable hyaluronic acid-polyethylene glycol hydrogel tissue engineering scaffolds. , 2005, Biomaterials.

[95]  A. Metters,et al.  Network formation and degradation behavior of hydrogels formed by Michael-type addition reactions. , 2005, Biomacromolecules.

[96]  C. Bünger,et al.  Bone morphogenetic protein-2 but not bone morphogenetic protein-4 and -6 stimulates chemotactic migration of human osteoblasts, human marrow osteoblasts, and U2-OS cells. , 1996, Bone.