1
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Blanchard PL, Knick BJ, Whelan SA, Hackel BJ. Hyperstable Synthetic Mini-Proteins as Effective Ligand Scaffolds. ACS Synth Biol 2023; 12:3608-3622. [PMID: 38010428 PMCID: PMC10822706 DOI: 10.1021/acssynbio.3c00409] [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] [Indexed: 11/29/2023]
Abstract
Small, single-domain protein scaffolds are compelling sources of molecular binding ligands with the potential for efficient physiological transport, modularity, and manufacturing. Yet, mini-proteins require a balance between biophysical robustness and diversity to enable new functions. We tested the developability and evolvability of millions of variants of 43 designed libraries of synthetic 40-amino acid βαββ proteins with diversified sheet, loop, or helix paratopes. We discovered a scaffold library that yielded hundreds of binders to seven targets while exhibiting high stability and soluble expression. Binder discovery yielded 6-122 nM affinities without affinity maturation and Tms averaging ≥78 °C. Broader βαββ libraries exhibited varied developability and evolvability. Sheet paratopes were the most consistently developable, and framework 1 was the most evolvable. Paratope evolvability was dependent on target, though several libraries were evolvable across many targets while exhibiting high stability and soluble expression. Select βαββ proteins are strong starting points for engineering performant binders.
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Affiliation(s)
- Paul L. Blanchard
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Avenue SE, Minneapolis, MN 55455
| | - Brandon J. Knick
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Avenue SE, Minneapolis, MN 55455
| | - Sarah A. Whelan
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Avenue SE, Minneapolis, MN 55455
| | - Benjamin J. Hackel
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Avenue SE, Minneapolis, MN 55455
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2
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David TI, Pestov NB, Korneenko TV, Barlev NA. Non-Immunoglobulin Synthetic Binding Proteins for Oncology. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1232-1247. [PMID: 37770391 DOI: 10.1134/s0006297923090043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/01/2023] [Accepted: 08/01/2023] [Indexed: 09/30/2023]
Abstract
Extensive application of technologies like phage display in screening peptide and protein combinatorial libraries has not only facilitated creation of new recombinant antibodies but has also significantly enriched repertoire of the protein binders that have polypeptide scaffolds without homology to immunoglobulins. These innovative synthetic binding protein (SBP) platforms have grown in number and now encompass monobodies/adnectins, DARPins, lipocalins/anticalins, and a variety of miniproteins such as affibodies and knottins, among others. They serve as versatile modules for developing complex affinity tools that hold promise in both diagnostic and therapeutic settings. An optimal scaffold typically has low molecular weight, minimal immunogenicity, and demonstrates resistance against various challenging conditions, including proteolysis - making it potentially suitable for peroral administration. Retaining functionality under reducing intracellular milieu is also advantageous. However, paramount to its functionality is the scaffold's ability to tolerate mutations across numerous positions, allowing for the formation of a sufficiently large target binding region. This is achieved through the library construction, screening, and subsequent expression in an appropriate system. Scaffolds that exhibit high thermodynamic stability are especially coveted by the developers of new SBPs. These are steadily making their way into clinical settings, notably as antagonists of oncoproteins in signaling pathways. This review surveys the diverse landscape of SBPs, placing particular emphasis on the inhibitors targeting the oncoprotein KRAS, and highlights groundbreaking opportunities for SBPs in oncology.
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Affiliation(s)
- Temitope I David
- Institute of Biomedical Chemistry, Moscow, 119121, Russia
- Laboratory of Molecular Oncology, Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Nikolay B Pestov
- Institute of Biomedical Chemistry, Moscow, 119121, Russia.
- Laboratory of Tick-Borne Encephalitis and Other Viral Encephalitides, Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products, Russian Academy of Sciences, Moscow, 108819, Russia
- Group of Cross-Linking Enzymes, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
| | - Tatyana V Korneenko
- Group of Cross-Linking Enzymes, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
| | - Nikolai A Barlev
- Institute of Biomedical Chemistry, Moscow, 119121, Russia
- Laboratory of Tick-Borne Encephalitis and Other Viral Encephalitides, Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products, Russian Academy of Sciences, Moscow, 108819, Russia
- Institute of Cytology Russian Academy of Sciences, St.-Petersburg, 194064, Russia
- School of Medicine, Nazarbayev University, Astana, 010000, Kazakhstan
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3
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Islam M, Kehoe HP, Lissoos JB, Huang M, Ghadban CE, Sánchez GB, Lane HZ, Van Deventer JA. Chemical Diversification of Simple Synthetic Antibodies. ACS Chem Biol 2021; 16:344-359. [PMID: 33482061 PMCID: PMC8096149 DOI: 10.1021/acschembio.0c00865] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Antibodies possess properties that make them valuable as therapeutics, diagnostics, and basic research tools. However, antibody chemical reactivity and covalent antigen binding are constrained, or even prevented, by the narrow range of chemistries encoded in canonical amino acids. In this work, we investigate strategies for leveraging an expanded range of chemical functionality using yeast displayed antibodies containing noncanonical amino acids (ncAAs) in or near antibody complementarity determining regions (CDRs). To enable systematic characterization of the effects of ncAA incorporation on antibody function, we first investigated whether diversification of a single antibody loop would support the isolation of binding clones against immunoglobulins from three species. We constructed and screened a billion-member library containing canonical amino acid diversity and loop length diversity only within the third complementarity determining region of the heavy chain (CDR-H3). Isolated clones exhibited moderate affinities (double- to triple-digit nanomolar affinities) and, in several cases, single-species specificity, confirming that antibody specificity can be mediated by a single CDR. This constrained diversity enabled the utilization of additional CDRs for the installation of chemically reactive and photo-cross-linkable ncAAs. Binding studies of ncAA-substituted antibodies revealed that ncAA incorporation is reasonably well tolerated, with observed changes in affinity occurring as a function of ncAA side chain identity, substitution site, and the ncAA incorporation machinery used. Multiple azide-containing ncAAs supported copper-catalyzed azide-alkyne cycloaddition (CuAAC) and strain-promoted azide-alkyne cycloaddition (SPAAC) without the abrogation of binding function. Similarly, several alkyne substitutions facilitated CuAAC without the apparent disruption of binding. Finally, antibodies substituted with a photo-cross-linkable ncAA were evaluated for ultraviolet-mediated cross-linking on the yeast surface. Competition-based assays revealed position-dependent covalent linkages, strongly suggesting successful cross-linking. Key findings regarding CuAAC reactions and photo-cross-linking on the yeast surface were confirmed using soluble forms of ncAA-substituted clones. The consistency of findings on the yeast surface and in solution suggest that chemical diversification can be incorporated into yeast display screening approaches. Taken together, our results highlight the power of integrating the use of yeast display and ncAAs in search of proteins with "chemically augmented" binding functions. This includes strategies for systematically introducing small molecule functionality within binding protein structures and evaluating protein-based covalent target binding. The efficient preparation and chemical diversification of antibodies on the yeast surface open up new possibilities for discovering "drug-like" protein leads in high throughput.
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Affiliation(s)
- Mariha Islam
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - Haixing P. Kehoe
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - Jacob B. Lissoos
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - Manjie Huang
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - Christopher E. Ghadban
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - Greg B. Sánchez
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - Hanan Z. Lane
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - James A. Van Deventer
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
- Biomedical Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
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4
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Remmel JL, Ackerman ME. Rationalizing Random Walks: Replicating Protective Antibody Trajectories. Trends Immunol 2021; 42:186-197. [PMID: 33514459 DOI: 10.1016/j.it.2021.01.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 12/29/2020] [Accepted: 01/04/2021] [Indexed: 12/12/2022]
Abstract
'Reverse vaccinology 2.0' aims to rationally reproduce template antibody responses, such as broadly neutralizing antibodies against human immunodeficiency virus-1. While observations of antibody convergence across individuals support the assumption that responses may be replicated, the diversity of humoral immunity and the process of antibody selection are rooted in stochasticity. Drawing from experience with in vitro antibody engineering by directed evolution, we consider how antibody selection may be driven, as in germline-targeting vaccine approaches to elicit broadly neutralizing antibodies and illustrate the potential consequences of over-defining a template antibody response. We posit that the prospective definition of template antibody responses and the odds of replicating them must be considered within the randomness of humoral immunity.
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Affiliation(s)
- Jennifer L Remmel
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA
| | - Margaret E Ackerman
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA; Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA.
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5
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A conformation-specific ON-switch for controlling CAR T cells with an orally available drug. Proc Natl Acad Sci U S A 2020; 117:14926-14935. [PMID: 32554495 PMCID: PMC7334647 DOI: 10.1073/pnas.1911154117] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Molecular ON-switches in which a chemical compound induces protein-protein interactions can allow cellular function to be controlled with small molecules. ON-switches based on clinically applicable compounds and human proteins would greatly facilitate their therapeutic use. Here, we developed an ON-switch system in which the human retinol binding protein 4 (hRBP4) of the lipocalin family interacts with engineered hRBP4 binders in a small molecule-dependent manner. Two different protein scaffolds were engineered to bind to hRBP4 when loaded with the orally available small molecule A1120. The crystal structure of an assembled ON-switch shows that the engineered binder specifically recognizes the conformational changes induced by A1120 in two loop regions of hRBP4. We demonstrate that this conformation-specific ON-switch is highly dependent on the presence of A1120, as demonstrated by an ∼500-fold increase in affinity upon addition of the small molecule drug. Furthermore, the ON-switch successfully regulated the activity of primary human CAR T cells in vitro. We anticipate that lipocalin-based ON-switches have the potential to be broadly applied for the safe pharmacological control of cellular therapeutics.
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6
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Abstract
Bioconjugation of biologically useful proteins is in great demand (e.g., conjugation to biotins, metal chelators, and drug carriers to target specific tissues for both in vitro and in vivo use). These conjugates provide widespread opportunities for various biological and biomedical applications. Evolving state-of-the-art protein conjugation strategies have led to the development of many affinity ligands, including for cancer imaging and diagnosis. However, to achieve the desirable protein conjugates, there are many challenges that remain to be addressed in order to obtain a reproducible procedure for all proteins and ligands. These include a control over the protein modification and the efficiency of the conjugation while retaining the original biological protein affinity postmodification. Here we present detailed conjugation methods for the human fibronectin tenth type III domain (FN3) protein scaffold for use in preclinical PET imaging. More specifically, this chapter provides detailed methods to produce a FN3 and a FN3-chelator-conjugate, its labeling with the radionuclide 64-Cu, and its use for noninvasive PET imaging in mice.
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Affiliation(s)
- Arutselvan Natarajan
- Department of Radiology, James H. Clark Center, Stanford University, Stanford, CA, USA.
| | - Lotfi Abou-Elkacem
- Department of Radiology, James H. Clark Center, Stanford University, Stanford, CA, USA
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7
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Hantschel O, Biancalana M, Koide S. Monobodies as enabling tools for structural and mechanistic biology. Curr Opin Struct Biol 2020; 60:167-174. [PMID: 32145686 DOI: 10.1016/j.sbi.2020.01.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 01/14/2020] [Accepted: 01/21/2020] [Indexed: 02/06/2023]
Abstract
Monobodies, built with the scaffold of the fibronectin type III domain, are among the most well-established synthetic binding proteins. They promote crystallization of challenging molecular systems. They have strong tendency to bind to functional sites and thus serve as drug-like molecules that perturb the biological functions of their targets. Monobodies lack disulfide bonds and thus they are particularly suited as genetically encoded reagents to be used intracellularly. This article reviews recent monobody-enabled studies that reveal new structures, molecular mechanisms and potential therapeutic opportunities. A systematic analysis of the crystal structures of monobody-target complexes suggests important attributes that make monobodies effective crystallization chaperones.
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Affiliation(s)
- Oliver Hantschel
- Institute of Physiological Chemistry, Faculty of Medicine, Philipps-University of Marburg, Karl-von-Frisch-Straße 1, 35032 Marburg, Germany; Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École polytechnique fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland.
| | - Matthew Biancalana
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, 522 1st Avenue, New York, NY 10016, USA
| | - Shohei Koide
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, 522 1st Avenue, New York, NY 10016, USA; Department of Medicine and Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 522 1st Avenue, New York, NY 10016, USA.
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8
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Toxin Neutralization Using Alternative Binding Proteins. Toxins (Basel) 2019; 11:toxins11010053. [PMID: 30658491 PMCID: PMC6356946 DOI: 10.3390/toxins11010053] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 01/07/2019] [Accepted: 01/12/2019] [Indexed: 12/20/2022] Open
Abstract
Animal toxins present a major threat to human health worldwide, predominantly through snakebite envenomings, which are responsible for over 100,000 deaths each year. To date, the only available treatment against snakebite envenoming is plasma-derived antivenom. However, despite being key to limiting morbidity and mortality among snakebite victims, current antivenoms suffer from several drawbacks, such as immunogenicity and high cost of production. Consequently, avenues for improving envenoming therapy, such as the discovery of toxin-sequestering monoclonal antibodies against medically important target toxins through phage display selection, are being explored. However, alternative binding protein scaffolds that exhibit certain advantages compared to the well-known immunoglobulin G scaffold, including high stability under harsh conditions and low cost of production, may pose as possible low-cost alternatives to antibody-based therapeutics. There is now a plethora of alternative binding protein scaffolds, ranging from antibody derivatives (e.g., nanobodies), through rationally designed derivatives of other human proteins (e.g., DARPins), to derivatives of non-human proteins (e.g., affibodies), all exhibiting different biochemical and pharmacokinetic profiles. Undeniably, the high level of engineerability and potentially low cost of production, associated with many alternative protein scaffolds, present an exciting possibility for the future of snakebite therapeutics and merit thorough investigation. In this review, a comprehensive overview of the different types of binding protein scaffolds is provided together with a discussion on their relevance as potential modalities for use as next-generation antivenoms.
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9
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Kruziki MA, Sarma V, Hackel BJ. Constrained Combinatorial Libraries of Gp2 Proteins Enhance Discovery of PD-L1 Binders. ACS COMBINATORIAL SCIENCE 2018; 20:423-435. [PMID: 29799714 DOI: 10.1021/acscombsci.8b00010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Engineered protein ligands are used for molecular therapy, diagnostics, and industrial biotechnology. The Gp2 domain is a 45-amino acid scaffold that has been evolved for specific, high-affinity binding to multiple targets by diversification of two solvent-exposed loops. Inspired by sitewise enrichment of select amino acids, including cysteine pairs, in earlier Gp2 discovery campaigns, we hypothesized that the breadth and efficiency of de novo Gp2 discovery will be aided by sitewise amino acid constraint within combinatorial library design. We systematically constructed eight libraries and comparatively evaluated their efficacy for binder discovery via yeast display against a panel of targets. Conservation of a cysteine pair at the termini of the first diversified paratope loop increased binder discovery 16-fold ( p < 0.001). Yet two other libraries with conserved cysteine pairs, within the second loop or an interloop pair, did not aid discovery thereby indicating site-specific impact. Via a yeast display protease resistance assay, Gp2 variants from the loop one cysteine pair library were 3.3 ± 2.1-fold ( p = 0.005) more stable than nonconstrained variants. Sitewise constraint of noncysteine residues-guided by previously evolved binders, natural Gp2 homology, computed stability, and structural analysis-did not aid discovery. A panel of binders to programmed death ligand 1 (PD-L1), a key target in cancer immunotherapy, were discovered from the loop 1 cysteine constraint library. Affinity maturation via loop walking resulted in strong, specific cellular PD-L1 affinity ( Kd = 6-9 nM).
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Affiliation(s)
- Max A. Kruziki
- University of Minnesota—Twin Cities, Department of Chemical Engineering and Materials Science, 421 Washington Avenue Southeast, Minneapolis, Minnesota 55455, United States
| | - Vidur Sarma
- University of Minnesota—Twin Cities, Department of Chemical Engineering and Materials Science, 421 Washington Avenue Southeast, Minneapolis, Minnesota 55455, United States
| | - Benjamin J. Hackel
- University of Minnesota—Twin Cities, Department of Chemical Engineering and Materials Science, 421 Washington Avenue Southeast, Minneapolis, Minnesota 55455, United States
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10
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Affiliation(s)
- Nika Kruljec
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
| | - Tomaž Bratkovič
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
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11
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Chan JY, Hackel BJ, Yee D. Targeting Insulin Receptor in Breast Cancer Using Small Engineered Protein Scaffolds. Mol Cancer Ther 2017; 16:1324-1334. [PMID: 28468775 DOI: 10.1158/1535-7163.mct-16-0685] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 02/15/2017] [Accepted: 04/20/2017] [Indexed: 11/16/2022]
Abstract
Insulin receptor (InsR) and the type I insulin-like growth factor (IGF1R) are homologous receptors necessary for signal transduction by their cognate ligands insulin, IGF-I and IGF-II. IGF1R mAbs, intended to inhibit malignant phenotypic signaling, failed to show benefit in patients with endocrine-resistant tumors in phase III clinical trials. Our previous work showed that in tamoxifen-resistant cells, IGF1R expression was lacking, but InsR inhibition effectively blocked growth. In endocrine-sensitive breast cancer cells, insulin was not growth stimulatory, likely due to the presence of hybrid InsR/IGF1R, which has high affinity for IGF-I, but not insulin. Combination inhibition of InsR and IGF1R showed complete suppression of the system in endocrine-sensitive breast cancer cells. To develop InsR-binding agents, we employed a small protein scaffold, T7 phage gene 2 protein (Gp2) with the long-term goal of creating effective InsR inhibitors and diagnostics. Using yeast display and directed evolution, we identified three Gp2 variants (Gp2 #1, #5, and #10) with low nanomolar affinity and specific binding to cell surface InsR. These Gp2 variants inhibited insulin-mediated monolayer proliferation in both endocrine-sensitive and resistant breast cancer, but did not downregulate InsR expression. Gp2 #5 and Gp2 #10 disrupted InsR function by inhibiting ligand-induced receptor activation. In contrast, Gp2 #1 did not block InsR phosphorylation. Notably, Gp2 #1 binding was enhanced by pretreatment of cells with insulin, suggesting a unique receptor-ligand-binding mode. These Gp2 variants are the first nonimmunoglobulin protein scaffolds to target insulin receptor and present compelling opportunity for modulation of InsR signaling. Mol Cancer Ther; 16(7); 1324-34. ©2017 AACR.
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Affiliation(s)
- Jie Ying Chan
- Department of Pharmacology, University of Minnesota, Minneapolis, Minnesota
| | - Benjamin J Hackel
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota
| | - Douglas Yee
- Department of Pharmacology, University of Minnesota, Minneapolis, Minnesota. .,Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota.,Department of Medicine, University of Minnesota, Minneapolis, Minnesota
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12
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Abstract
The crystallizable fragment (Fc) of the immunoglobulin class G (IgG) is a very attractive scaffold for the design of novel therapeutics due to its quality of uniting all essential antibody functions. This article reviews the functionalization of this homodimeric glycoprotein by diversification of structural loops of CH3 domains for the design of Fcabs, i.e. antigen-binding Fc proteins. It reports the design of libraries for the selection of nanomolar binders with wildtype-like in vivo half-life and correlation of Fc receptor binding and ADCC. The in vitro and preclinical biological activity of selected Fcabs is compared with that of clinically approved antibodies. Recently, the great potential of the scaffold for the development of therapeutics for clinical use has been shown when the HER2-binding Fcab FS102 entered clinical phase I. Furthermore, methods for the engineering of biophysical properties of Fcabs applicable to proteins in general are presented as well as the different approaches in the design of heterodimeric Fc-based scaffolds used in the generation of bispecific monoclonal antibodies. Finally, this work critically analyzes and compares the various efforts in the design of highly diverse and functional libraries that have been made in the engineering of IgG1-Fc and structurally similar scaffolds.
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Affiliation(s)
- Elisabeth Lobner
- Christian Doppler Laboratory for Antibody Engineering, Department of Chemistry, Vienna Institute of BioTechnology, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
| | - Michael W Traxlmayr
- Christian Doppler Laboratory for Antibody Engineering, Department of Chemistry, Vienna Institute of BioTechnology, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
| | - Christian Obinger
- Christian Doppler Laboratory for Antibody Engineering, Department of Chemistry, Vienna Institute of BioTechnology, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
| | - Christoph Hasenhindl
- Christian Doppler Laboratory for Antibody Engineering, Department of Chemistry, Vienna Institute of BioTechnology, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
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13
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de Picciotto S, Dickson PM, Traxlmayr MW, Marques BS, Socher E, Zhao S, Cheung S, Kiefer JD, Wand AJ, Griffith LG, Imperiali B, Wittrup KD. Design Principles for SuCESsFul Biosensors: Specific Fluorophore/Analyte Binding and Minimization of Fluorophore/Scaffold Interactions. J Mol Biol 2016; 428:4228-4241. [PMID: 27448945 PMCID: PMC5048519 DOI: 10.1016/j.jmb.2016.07.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 06/30/2016] [Accepted: 07/04/2016] [Indexed: 11/18/2022]
Abstract
Quantifying protein location and concentration is critical for understanding function in situ. Scaffold conjugated to environment-sensitive fluorophore (SuCESsFul) biosensors, in which a reporting fluorophore is conjugated to a binding scaffold, can, in principle, detect analytes of interest with high temporal and spatial resolution. However, their adoption has been limited due to the extensive empirical screening required for their development. We sought to establish design principles for this class of biosensor by characterizing over 400 biosensors based on various protein analytes, binding proteins, and fluorophores. We found that the brightest readouts are attained when a specific binding pocket for the fluorophore is present on the analyte. Also, interaction of the fluorophore with the binding protein it is conjugated to can raise background fluorescence, considerably limiting sensor dynamic range. Exploiting these two concepts, we designed biosensors that attain a 100-fold increase in fluorescence upon binding to analyte, an order of magnitude improvement over the previously best-reported SuCESsFul biosensor. These design principles should facilitate the development of improved SuCESsFul biosensors.
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Affiliation(s)
- Seymour de Picciotto
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Paige M Dickson
- Department of Chemistry, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
| | - Michael W Traxlmayr
- Koch Institute for Integrative Cancer Research, 500 Main Street, Cambridge, MA 02139, USA
| | - Bryan S Marques
- Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Elke Socher
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 01239, USA
| | - Sixing Zhao
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Stephanie Cheung
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 01239, USA
| | - Jonathan D Kiefer
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology, Zurich, 8093, Switzerland
| | - A Joshua Wand
- Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Linda G Griffith
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Barbara Imperiali
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 01239, USA; Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - K Dane Wittrup
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 500 Main Street, Cambridge, MA 02139, USA; Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
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14
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Park SH, Park S, Kim DY, Pyo A, Kimura RH, Sathirachinda A, Choy HE, Min JJ, Gambhir SS, Hong Y. Isolation and Characterization of a Monobody with a Fibronectin Domain III Scaffold That Specifically Binds EphA2. PLoS One 2015; 10:e0132976. [PMID: 26177208 PMCID: PMC4503726 DOI: 10.1371/journal.pone.0132976] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 06/19/2015] [Indexed: 01/21/2023] Open
Abstract
Monobodies are binding scaffold proteins originating from a human fibronectin domain III (Fn3) scaffold that can be easily engineered with specificity and affinity. Human EphA2 (hEphA2) is an early detection marker protein for various tumors including lung, breast, and colon cancer. In this study, we isolated two hEphA2-specific monobodies (E1 and E10) by screening a yeast surface display library. They showed the same amino acid sequence except in the DE loop and had high affinity (~2 nM Kd) against hEphA2. E1 bound only hEphA2 and mEphA2, although it bound hEphA2 with an affinity 2-fold higher than that of mEphA2. However, E10 also bound the mEphA6 and mEphA8 homologs as well as hEphA2 and mEphA2. Thus, E1 but not E10 was highly specific for hEphA2. E1 specifically bound human cells and xenograft tumor tissues expressing hEphA on the cell surface. In vivo optical imaging showed strong targeting of Cy5.5-labeled E1 to mouse tumor tissue induced by PC3 cells, a human prostate cancer cell line that expresses a high level of hEphA2. In conclusion, the highly specific monobody E1 is useful as a hEphA2 probe candidate for in vivo diagnosis and therapy.
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Affiliation(s)
- Seung-Hwan Park
- Department of Nuclear Medicine, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Sukho Park
- Department of Microbiology, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Dong-Yeon Kim
- Department of Nuclear Medicine, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Ayoung Pyo
- Department of Nuclear Medicine, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Richard H. Kimura
- Molecular Imaging Program at Stanford, Department of Radiology, Bio-X Program, Stanford University, Palo Alto, CA, United States of America
| | - Ataya Sathirachinda
- Molecular Imaging Program at Stanford, Department of Radiology, Bio-X Program, Stanford University, Palo Alto, CA, United States of America
| | - Hyon E. Choy
- Department of Microbiology, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Jung-Joon Min
- Department of Nuclear Medicine, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Sanjiv Sam Gambhir
- Molecular Imaging Program at Stanford, Department of Radiology, Bio-X Program, Stanford University, Palo Alto, CA, United States of America
| | - Yeongjin Hong
- Department of Microbiology, Chonnam National University Medical School, Gwangju, Republic of Korea
- * E-mail:
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15
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Kruziki MA, Bhatnagar S, Woldring DR, Duong VT, Hackel BJ. A 45-Amino-Acid Scaffold Mined from the PDB for High-Affinity Ligand Engineering. ACTA ACUST UNITED AC 2015; 22:946-56. [PMID: 26165154 DOI: 10.1016/j.chembiol.2015.06.012] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Revised: 05/08/2015] [Accepted: 06/04/2015] [Indexed: 12/20/2022]
Abstract
Small protein ligands can provide superior physiological distribution compared with antibodies, and improved stability, production, and specific conjugation. Systematic evaluation of the PDB identified a scaffold to push the limits of small size and robust evolution of stable, high-affinity ligands: 45-residue T7 phage gene 2 protein (Gp2) contains an α helix opposite a β sheet with two adjacent loops amenable to mutation. De novo ligand discovery from 10(8) mutants and directed evolution toward four targets yielded target-specific binders with affinities as strong as 200 ± 100 pM, Tms from 65 °C ± 3 °C to 80°C ± 1 °C, and retained activity after thermal denaturation. For cancer targeting, a Gp2 domain for epidermal growth factor receptor was evolved with 18 ± 8 nM affinity, receptor-specific binding, and high thermal stability with refolding. The efficiency of evolving new binding function and the size, affinity, specificity, and stability of evolved domains render Gp2 a uniquely effective ligand scaffold.
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Affiliation(s)
- Max A Kruziki
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA
| | - Sumit Bhatnagar
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA
| | - Daniel R Woldring
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA
| | - Vandon T Duong
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA
| | - Benjamin J Hackel
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA.
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16
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Codon-Precise, Synthetic, Antibody Fragment Libraries Built Using Automated Hexamer Codon Additions and Validated through Next Generation Sequencing. Antibodies (Basel) 2015. [DOI: 10.3390/antib4020088] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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17
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AlDeghaither D, Smaglo BG, Weiner LM. Beyond peptides and mAbs--current status and future perspectives for biotherapeutics with novel constructs. J Clin Pharmacol 2015; 55 Suppl 3:S4-20. [PMID: 25707963 PMCID: PMC4340091 DOI: 10.1002/jcph.407] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 09/29/2014] [Indexed: 12/26/2022]
Abstract
Biotherapeutics are attractive anti-cancer agents due to their high specificity and limited toxicity compared to conventional small molecules. Antibodies are widely used in cancer therapy, either directly or conjugated to a cytotoxic payload. Peptide therapies, though not as prevalent, have been utilized in hormonal therapy and imaging. The limitations associated with unmodified forms of both types of biotherapeutics have led to the design and development of novel structures, which incorporate key features and structures that have improved the molecules' abilities to bind to tumor targets, avoid degradation, and exhibit favorable pharmacokinetics. In this review, we highlight the current status of monoclonal antibodies and peptides, and provide a perspective on the future of biotherapeutics using novel constructs.
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Affiliation(s)
- Dalal AlDeghaither
- Georgetown Lombardi Comprehensive Cancer Center, Department of Oncology, Georgetown University Medical Center, 3970 Reservoir Road NW, Washington DC 20057
| | - Brandon G Smaglo
- Medstar Georgetown University Hospital, Department of Medicine, Division of Hematology/Oncology, 3800 Reservoir Road NW, Washington DC 20007
| | - Louis M. Weiner
- Georgetown Lombardi Comprehensive Cancer Center, Department of Oncology, Georgetown University Medical Center, 3970 Reservoir Road NW, Washington DC 20057
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18
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Artificial affinity proteins as ligands of immunoglobulins. Biomolecules 2015; 5:60-75. [PMID: 25647098 PMCID: PMC4384111 DOI: 10.3390/biom5010060] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 12/17/2014] [Accepted: 01/23/2015] [Indexed: 12/17/2022] Open
Abstract
A number of natural proteins are known to have affinity and specificity for immunoglobulins. Some of them are widely used as reagents for detection or capture applications, such as Protein G and Protein A. However, these natural proteins have a defined spectrum of recognition that may not fit specific needs. With the development of combinatorial protein engineering and selection techniques, it has become possible to design artificial affinity proteins with the desired properties. These proteins, termed alternative scaffold proteins, are most often chosen for their stability, ease of engineering and cost-efficient recombinant production in bacteria. In this review, we focus on alternative scaffold proteins for which immunoglobulin binders have been identified and characterized.
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19
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20
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Ting JM, Navale TS, Bates FS, Reineke TM. Precise Compositional Control and Systematic Preparation of Multimonomeric Statistical Copolymers. ACS Macro Lett 2013; 2:770-774. [PMID: 35606978 DOI: 10.1021/mz4003112] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A comprehensive approach to target exact molecular weights and chemical compositions for multimonomeric statistical copolymers using a new controlled statistics method with reversible addition-fragmentation chain transfer free-radical (RAFT) polymerization is presented. The system chosen to illustrate this procedure is an acrylic quarterpolymer consisting of methyl acrylate, 2-carboxyethyl acrylate, 2-hydroxypropyl acrylate, and 2-propylacetyl acrylate, modeling a well-known macromolecule utilized to deliver poorly water-soluble drugs (hydroxypropyl methylcellulose acetate succinate, HPMCAS). The relative reactivities at 70 °C between monomer pairs were measured and employed to predict the feed ratio necessary for synthesizing well-defined compositions based on the Walling-Briggs model. Application of Skeist's equations addressed compositional drift and anticipated the general monomer incorporation distribution as a function of conversion, which was verified experimentally. This new and simple paradigm combining both predictive models provides complementary synthetic and predictive tools for designing macromolecular chemical architectures with hierarchical control over spatially dependent structure-property relationships for complex applications such as oral drug delivery.
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Affiliation(s)
- Jeffrey M. Ting
- Departments of §Chemistry and ‡Chemical Engineering and Materials
Science, University of Minnesota, Minneapolis, Minnesota 55455-0431,
United States
| | - Tushar S. Navale
- Departments of §Chemistry and ‡Chemical Engineering and Materials
Science, University of Minnesota, Minneapolis, Minnesota 55455-0431,
United States
| | - Frank S. Bates
- Departments of §Chemistry and ‡Chemical Engineering and Materials
Science, University of Minnesota, Minneapolis, Minnesota 55455-0431,
United States
| | - Theresa M. Reineke
- Departments of §Chemistry and ‡Chemical Engineering and Materials
Science, University of Minnesota, Minneapolis, Minnesota 55455-0431,
United States
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21
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Mahon CM, Lambert MA, Glanville J, Wade JM, Fennell BJ, Krebs MR, Armellino D, Yang S, Liu X, O'Sullivan CM, Autin B, Oficjalska K, Bloom L, Paulsen J, Gill D, Damelin M, Cunningham O, Finlay WJJ. Comprehensive interrogation of a minimalist synthetic CDR-H3 library and its ability to generate antibodies with therapeutic potential. J Mol Biol 2013; 425:1712-30. [PMID: 23429058 DOI: 10.1016/j.jmb.2013.02.015] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 01/31/2013] [Accepted: 02/11/2013] [Indexed: 11/17/2022]
Abstract
We have generated large libraries of single-chain Fv antibody fragments (>10(10) transformants) containing unbiased amino acid diversity that is restricted to the central combining site of the stable, well-expressed DP47 and DPK22 germline V-genes. Library WySH2A was constructed to examine the potential for synthetic complementarity-determining region (CDR)-H3 diversity to act as the lone source of binding specificity. Library WySH2B was constructed to assess the necessity for diversification in both the H3 and L3. Both libraries provided diverse, specific antibodies, yielding a total of 243 unique hits against 7 different targets, but WySH2B produced fewer hits than WySH2A when selected in parallel. WySH2A also consistently produced hits of similar quality to WySH2B, demonstrating that the diversification of the CDR-L3 reduces library fitness. Despite the absence of deliberate bias in the library design, CDR length was strongly associated with the number of hits produced, leading to a functional loop length distribution profile that mimics the biases observed in the natural repertoire. A similar trend was also observed for the CDR-L3. After target selections, several key amino acids were enriched in the CDR-H3 (e.g., small and aromatic residues) while others were reduced (e.g., strongly charged residues) in a manner that was specific to position, preferentially occurred in CDR-H3 stem positions, and tended towards residues associated with loop stabilization. As proof of principle for the WySH2 libraries to produce viable lead candidate antibodies, 114 unique hits were produced against Delta-like ligand 4 (DLL4). Leads exhibited nanomolar binding affinities, highly specific staining of DLL4+ cells, and biochemical neutralization of DLL4-NOTCH1 interaction.
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Affiliation(s)
- Ciara M Mahon
- Pfizer, Global Biotherapeutics Technologies, Grange Castle Business Park, Clondalkin, Dublin 22, Ireland
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22
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Abstract
Yeast surface display (YSD) presents proteins on the surface of yeast through interaction of the agglutinin subunits Aga1p and Aga2p. The human 10th type III fibronectin (Fn3) is a small, 10-kDa protein domain that maintains its native fold without disulfide bonds. A YSD library of Fn3s has been engineered with a loop amino acid composition similar to that of human antibody complementarity-determining region heavy chain loop 3 (CDR-H3) and varying loop lengths, which has been shown to improve binding ability. There are many advantages of using these small, stable domains that maintain binding capabilities similar to that of antibodies. Here, we outline a YSD methodology to isolate Fn3 binders to a diverse set of target antigens.
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23
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Finlay WJJ, Almagro JC. Natural and man-made V-gene repertoires for antibody discovery. Front Immunol 2012; 3:342. [PMID: 23162556 PMCID: PMC3498902 DOI: 10.3389/fimmu.2012.00342] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2012] [Accepted: 10/27/2012] [Indexed: 01/15/2023] Open
Abstract
Antibodies are the fastest-growing segment of the biologics market. The success of antibody-based drugs resides in their exquisite specificity, high potency, stability, solubility, safety, and relatively inexpensive manufacturing process in comparison with other biologics. We outline here the structural studies and fundamental principles that define how antibodies interact with diverse targets. We also describe the antibody repertoires and affinity maturation mechanisms of humans, mice, and chickens, plus the use of novel single-domain antibodies in camelids and sharks. These species all utilize diverse evolutionary solutions to generate specific and high affinity antibodies and illustrate the plasticity of natural antibody repertoires. In addition, we discuss the multiple variations of man-made antibody repertoires designed and validated in the last two decades, which have served as tools to explore how the size, diversity, and composition of a repertoire impact the antibody discovery process.
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24
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You C, Percival Zhang YH. Easy preparation of a large-size random gene mutagenesis library in Escherichia coli. Anal Biochem 2012; 428:7-12. [PMID: 22659340 DOI: 10.1016/j.ab.2012.05.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Revised: 05/21/2012] [Accepted: 05/22/2012] [Indexed: 11/17/2022]
Abstract
A simple and fast protocol for the preparation of a large-size mutant library for directed evolution in Escherichia coli was developed based on the DNA multimers generated by prolonged overlap extension polymerase chain reaction (POE-PCR). This protocol comprised the following: (i) a linear DNA mutant library was generated by error-prone PCR or shuffling, and a linear vector backbone was prepared by regular PCR; (ii) the DNA multimers were generated based on these two DNA templates by POE-PCR; and (iii) the one restriction enzyme-digested DNA multimers were ligated to circular plasmids, followed by transformation to E. coli. Because the ligation efficiency of one DNA fragment was several orders of magnitude higher than that of two DNA fragments for typical mutant library construction, it was very easy to generate a mutant library with a size of more than 10(7) protein mutants per 50 μl of the POE-PCR product. Via this method, four new fluorescent protein mutants were obtained based on monomeric cherry fluorescent protein. This new protocol was simple and fast because it did not require labor-intensive optimizations in restriction enzyme digestion and ligation, did not involve special plasmid design, and enabled constructing a large-size mutant library for directed enzyme evolution within 1 day.
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Affiliation(s)
- Chun You
- Biological Systems Engineering Department, Virginia Tech, Blacksburg, VA 24061, USA
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25
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Boder ET, Raeeszadeh-Sarmazdeh M, Price JV. Engineering antibodies by yeast display. Arch Biochem Biophys 2012; 526:99-106. [PMID: 22450168 DOI: 10.1016/j.abb.2012.03.009] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Revised: 03/09/2012] [Accepted: 03/10/2012] [Indexed: 12/19/2022]
Abstract
Since its first application to antibody engineering 15 years ago, yeast display technology has been developed into a highly potent tool for both affinity maturing lead molecules and isolating novel antibodies and antibody-like species. Robust approaches to the creation of diversity, construction of yeast libraries, and library screening or selection have been elaborated, improving the quality of engineered molecules and certainty of success in an antibody engineering campaign and positioning yeast display as one of the premier antibody engineering technologies currently in use. Here, we summarize the history of antibody engineering by yeast surface display, approaches used in its application, and a number of examples highlighting the utility of this method for antibody engineering.
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Affiliation(s)
- Eric T Boder
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996-2200, USA.
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27
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Gera N, Hussain M, Wright RC, Rao BM. Highly stable binding proteins derived from the hyperthermophilic Sso7d scaffold. J Mol Biol 2011; 409:601-16. [PMID: 21515282 DOI: 10.1016/j.jmb.2011.04.020] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Accepted: 04/08/2011] [Indexed: 12/16/2022]
Abstract
We have shown that highly stable binding proteins for a wide spectrum of targets can be generated through mutagenesis of the Sso7d protein from the hyperthermophilic archaeon Sulfolobus solfataricus. Sso7d is a small (~7 kDa, 63 amino acids) DNA-binding protein that lacks cysteine residues and has a melting temperature of nearly 100 °C. We generated a library of 10(8) Sso7d mutants by randomizing 10 amino acid residues on the DNA-binding surface of Sso7d, using yeast surface display. Binding proteins for a diverse set of model targets could be isolated from this library; our chosen targets included a small organic molecule (fluorescein), a 12 amino acid peptide fragment from the C-terminus of β-catenin, the model proteins hen egg lysozyme and streptavidin, and immunoglobulins from chicken and mouse. Without the application of any affinity maturation strategy, the binding proteins isolated had equilibrium dissociation constants in the nanomolar to micromolar range. Further, Sso7d-derived binding proteins could discriminate between closely related immunoglobulins. Mutant proteins based on Sso7d were expressed at high yields in the Escherichia coli cytoplasm. Despite extensive mutagenesis, Sso7d mutants have high thermal stability; five of six mutants analyzed have melting temperatures >89 °C. They are also resistant to chemical denaturation by guanidine hydrochloride and retain their secondary structure after extended incubation at extreme pH values. Because of their favorable properties, such as ease of recombinant expression, and high thermal, chemical and pH stability, Sso7d-derived binding proteins will have wide applicability in several areas of biotechnology and medicine.
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Affiliation(s)
- Nimish Gera
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
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28
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Lipovsek D. Adnectins: engineered target-binding protein therapeutics. Protein Eng Des Sel 2011; 24:3-9. [PMID: 21068165 PMCID: PMC3003446 DOI: 10.1093/protein/gzq097] [Citation(s) in RCA: 179] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Revised: 10/06/2010] [Accepted: 10/12/2010] [Indexed: 11/22/2022] Open
Abstract
Adnectins™ are a new family of therapeutic proteins based on the 10th fibronectin type III domain, and designed to bind with high affinity and specificity to therapeutically relevant targets. Adnectins share with antibody variable domains a beta-sheet sandwich fold with diversified loops, but differ from antibodies in primary sequence and have a simpler, single-domain structure without disulfide bonds. As a consequence, Adnectins bind targets with affinity and specificity as high as those of antibodies, but are easier to manipulate genetically and compatible with bacterial expression systems. Adnectins that bind macromolecular targets with nanomolar and picomolar affinity have been selected using in vitro evolution methods, including mRNA display, phage display and yeast display. CT-322, a PEGylated, anti-angiogenic Adnectin that binds vascular endothelial growth factor (VEGF) receptor 2 and blocks its interaction with VEGF A, C and D, is being evaluated in Phase II clinical trials for efficacy in several oncology indications.
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Affiliation(s)
- D Lipovsek
- Department of Protein Design, Adnexus, Bristol-Myers Squibb R&D Company, Waltham, MA 02453, USA.
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29
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Stability and CDR composition biases enrich binder functionality landscapes. J Mol Biol 2010; 401:84-96. [PMID: 20540948 DOI: 10.1016/j.jmb.2010.06.004] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2009] [Revised: 05/31/2010] [Accepted: 06/01/2010] [Indexed: 11/23/2022]
Abstract
The rugged protein sequence-function landscape complicates efforts, both in nature and in the laboratory, to evolve protein function. Protein library diversification must strike a balance between sufficient variegation to thoroughly sample alternative functionality versus the probability of mutant destabilization below an expressible threshold. In this work, we explore the sequence-function landscape in the context of screening for molecular recognition from an Ig scaffold library. The fibronectin type III domain is used to explore the impact of two sequence diversification strategies: (a) partial wild-type conservation at structurally important positions within the paratope region and (b) tailored amino acid composition mimicking antibody binding-site composition at putative paratope positions. Structurally important positions within the paratope region were identified through stability, structural, and phylogenetic analyses and partially or fully conserved in sequence. To achieve tailored antibody-like diversity, we designed a set of skewed nucleotide mixtures yielding codons approximately matching the distribution observed in antibody complementarity-determining regions without incurring the expense of triphosphoramidite-based construction. These design elements were explored via comparison of three library designs: a random library, a library with wild-type bias in the DE loop only and tyrosine-serine diversity elsewhere, and a library with wild-type bias at 11 positions and the antibody-inspired amino acid distribution. Using pooled libraries for direct competition in a single tube, selection and maturation of binders to seven targets yielded 19 of 21 clones that originated from the structurally biased, tailored-diversity library design. Sequence analysis of the selected clones supports the importance of both tailored compositional diversity and structural bias. In addition, selection of both well and poorly expressed clones from two libraries further elucidated the impact of structural bias.
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