1
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Lopez-Morales J, Vanella R, Kovacevic G, Santos MS, Nash MA. Titrating Avidity of Yeast-Displayed Proteins Using a Transcriptional Regulator. ACS Synth Biol 2023; 12:419-431. [PMID: 36728831 PMCID: PMC9942200 DOI: 10.1021/acssynbio.2c00351] [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] [Indexed: 02/03/2023]
Abstract
Yeast surface display is a valuable tool for protein engineering and directed evolution; however, significant variability in the copy number (i.e., avidity) of displayed variants on the yeast cell wall complicates screening and selection campaigns. Here, we report an engineered titratable display platform that modulates the avidity of Aga2-fusion proteins on the yeast cell wall dependent on the concentration of the anhydrotetracycline (aTc) inducer. Our design is based on a genomic Aga1 gene copy and an episomal Aga2-fusion construct both under the control of an aTc-dependent transcriptional regulator that enables stoichiometric and titratable expression, secretion, and display of Aga2-fusion proteins. We demonstrate tunable display levels over 2-3 orders of magnitude for various model proteins, including glucose oxidase enzyme variants, mechanostable dockerin-binding domains, and anti-PDL1 affibody domains. By regulating the copy number of displayed proteins, we demonstrate the effects of titratable avidity levels on several specific phenotypic activities, including enzyme activity and cell adhesion to surfaces under shear flow. Finally, we show that titrating down the display level allows yeast-based binding affinity measurements to be performed in a regime that avoids ligand depletion effects while maintaining small sample volumes, avoiding a well-known artifact in yeast-based binding assays. The ability to titrate the multivalency of proteins on the yeast cell wall through simple inducer control will benefit protein engineering and directed evolution methodology relying on yeast display for broad classes of therapeutic and diagnostic proteins of interest.
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Affiliation(s)
- Joanan Lopez-Morales
- Department
of Chemistry, University of Basel, Basel 4058, Switzerland,Swiss
Nanoscience Institute, University of Basel, Basel 4056, Switzerland,Department
of Biosystems Science and Engineering, ETH
Zurich, Basel 4058, Switzerland
| | - Rosario Vanella
- Department
of Chemistry, University of Basel, Basel 4058, Switzerland,Department
of Biosystems Science and Engineering, ETH
Zurich, Basel 4058, Switzerland
| | - Gordana Kovacevic
- Department
of Chemistry, University of Basel, Basel 4058, Switzerland,Department
of Biosystems Science and Engineering, ETH
Zurich, Basel 4058, Switzerland
| | - Mariana Sá Santos
- Department
of Chemistry, University of Basel, Basel 4058, Switzerland,Department
of Biosystems Science and Engineering, ETH
Zurich, Basel 4058, Switzerland
| | - Michael A. Nash
- Department
of Chemistry, University of Basel, Basel 4058, Switzerland,Swiss
Nanoscience Institute, University of Basel, Basel 4056, Switzerland,Department
of Biosystems Science and Engineering, ETH
Zurich, Basel 4058, Switzerland,
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2
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Advances of research of Fc-fusion protein that activate NK cells for tumor immunotherapy. Int Immunopharmacol 2022; 109:108783. [PMID: 35561479 DOI: 10.1016/j.intimp.2022.108783] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/02/2022] [Accepted: 04/14/2022] [Indexed: 12/21/2022]
Abstract
The rapid development of bioengineering technology has introduced Fc-fusion proteins, representing a novel kind of recombinant protein, as promising biopharmaceutical products in tumor therapy. Numerous related anti-tumor Fc-fusion proteins have been investigated and are in different stages of development. Fc-fusion proteins are constructed by fusing the Fc-region of the antibody with functional proteins or peptides. They retain the bioactivity of the latter and partial properties of the former. This structural and functional advantage makes Fc-fusion proteins an effective tool in tumor immunotherapy, especially for the recruitment and activation of natural killer (NK) cells, which play a critical role in tumor immunotherapy. Even though tumor cells have developed mechanisms to circumvent the cytotoxic effect of NK cells or induce defective NK cells, Fc-fusion proteins have been proven to effectively activate NK cells to kill tumor cells in different ways, such as antibody-dependent cell-mediated cytotoxicity (ADCC), activate NK cells in different ways in order to promote killing of tumor cells. In this review, we focus on NK cell-based immunity for cancers and current research progress of the Fc-fusion proteins for anti-tumor therapy by activating NK cells.
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3
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Yang X, Miao H, Xiao R, Wang L, Zhao Y, Wu Q, Ji Y, Du J, Qin H, Xuan W. Diverse protein manipulations with genetically encoded glutamic acid benzyl ester. Chem Sci 2021; 12:9778-9785. [PMID: 34349951 PMCID: PMC8299518 DOI: 10.1039/d1sc01882e] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 06/16/2021] [Indexed: 01/01/2023] Open
Abstract
Site-specific modification of proteins has significantly advanced the use of proteins in biological research and therapeutics development. Among various strategies aimed at this end, genetic code expansion (GCE) allows structurally and functionally distinct non-canonical amino acids (ncAAs) to be incorporated into specific sites of a protein. Herein, we genetically encode an esterified glutamic acid analogue (BnE) into proteins, and demonstrate that BnE can be applied in different types of site-specific protein modifications, including N-terminal pyroglutamation, caging Glu in the active site of a toxic protein, and endowing proteins with metal chelator hydroxamic acid and versatile reactive handle acyl hydrazide. Importantly, novel epigenetic mark Gln methylation is generated on histones via the derived acyl hydrazide handle. This work provides useful and unique tools to modify proteins at specific Glu or Gln residues, and complements the toolbox of GCE.
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Affiliation(s)
- Xiaochen Yang
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University Tianjin 300071 China
| | - Hui Miao
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University Tianjin 300071 China
| | - Ruotong Xiao
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University Tianjin 300071 China
| | - Luyao Wang
- School of Pharmaceutical Sciences, Tsinghua University 30 Shuangqing Rd. Beijing China
| | - Yan Zhao
- School of Pharmaceutical Sciences, Tsinghua University 30 Shuangqing Rd. Beijing China
| | - Qifan Wu
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University Tianjin 300071 China
| | - Yanli Ji
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University Tianjin 300071 China
| | - Juanjuan Du
- School of Pharmaceutical Sciences, Tsinghua University 30 Shuangqing Rd. Beijing China
| | - Hongqiang Qin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS) Dalian, 116023 China
| | - Weimin Xuan
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University Tianjin 300071 China
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4
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Longwell CK, Hanna S, Hartrampf N, Sperberg RAP, Huang PS, Pentelute BL, Cochran JR. Identification of N-Terminally Diversified GLP-1R Agonists Using Saturation Mutagenesis and Chemical Design. ACS Chem Biol 2021; 16:58-66. [PMID: 33307682 DOI: 10.1021/acschembio.0c00722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The glucagon-like peptide 1 receptor (GLP-1R) is a class B G-protein coupled receptor (GPCR) and diabetes drug target expressed mainly in pancreatic β-cells that, when activated by its agonist glucagon-like peptide 1 (GLP-1) after a meal, stimulates insulin secretion and β-cell survival and proliferation. The N-terminal region of GLP-1 interacts with membrane-proximal residues of GLP-1R, stabilizing its active conformation to trigger intracellular signaling. The best-studied agonist peptides, GLP-1 and exendin-4, share sequence homology at their N-terminal region; however, modifications that can be tolerated here are not fully understood. In this work, a functional screen of GLP-1 variants with randomized N-terminal domains reveals new GLP-1R agonists and uncovers a pattern whereby a negative charge is preferred at the third position in various sequence contexts. We further tested this sequence-structure-activity principle by synthesizing peptide analogues where this position was mutated to both canonical and noncanonical amino acids. We discovered a highly active GLP-1 analogue in which the native glutamate residue three positions from the N-terminus was replaced with the sulfo-containing amino acid cysteic acid (GLP-1-CYA). The receptor binding and downstream signaling properties elicited by GLP-1-CYA were similar to the wild type GLP-1 peptide. Computational modeling identified a likely mode of interaction of the negatively charged side chain in GLP-1-CYA with an arginine on GLP-1R. This work highlights a strategy of combinatorial peptide screening coupled with chemical exploration that could be used to generate novel agonists for other receptors with peptide ligands.
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Affiliation(s)
- Chelsea K. Longwell
- Department of Chemical and Systems Biology, Stanford University, 269 Campus Drive, Stanford, California 94305, United States
| | - Stephanie Hanna
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Nina Hartrampf
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - R. Andres Parra Sperberg
- Department of Bioengineering, Stanford University, Shriram Center, 443 Via Ortega, Stanford, California 94305, United States
| | - Po-Ssu Huang
- Department of Bioengineering, Stanford University, Shriram Center, 443 Via Ortega, Stanford, California 94305, United States
| | - Bradley L. Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, Massachusetts 02142, United States
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Jennifer R. Cochran
- Department of Bioengineering, Stanford University, Shriram Center, 443 Via Ortega, Stanford, California 94305, United States
- Department of Chemical Engineering, Stanford University, Shriram Center, 443 Via Ortega, Stanford, California 94305, United States
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5
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Zhang B, Li J, He L, Huang H, Weng J. Bio-surface coated titanium scaffolds with cancellous bone-like biomimetic structure for enhanced bone tissue regeneration. Acta Biomater 2020; 114:431-448. [PMID: 32682055 DOI: 10.1016/j.actbio.2020.07.024] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 07/08/2020] [Accepted: 07/09/2020] [Indexed: 02/07/2023]
Abstract
In view of the fact that titanium (Ti)-based implants still face the problem of loosening and failure of the implants caused by the slow biological response, the low osseointegration rate and the implant bacterial infection in clinical application, we designed a cancellous bone-like biomimetic Ti scaffold using the template accumulated by sugar spheres as a pore-forming agent. And based on a modified surface mineralization process and mussel-like adhesion mechanism, a silicon-doped calcium phosphate composite coating (Van-pBNPs/pep@pSiCaP) with Vancomycin (Van)-loaded polydopamine (pDA)-modified albumin nanoparticles (Van-pBNPs) and cell adhesion peptides (GFOGER) was constructed on the surface of Ti scaffold for mimicking the extracellular matrix (ECM) microenvironment of natural bone matrix to induce greater tissue regeneration. The in vitro study demonstrated that this porous Ti scaffold with functional bio-surface could distinctly facilitate cell early adhesion and spreading, and activate the expression of α2β1 integrin receptor on the cell membrane through promoting the formation of focal adhesions (FAs) in bone marrow stromal cells (BMSCs), thus mediating greater osteogenic cell differentiation. And it could also effectively inhibit the adhesion and growth of Staphylococcus epidermidis, exhibiting good antibacterial properties. Moreover, the Van-pBNPs/pep@pSiCaP-Ti scaffolds showed enhanced in vivo bone-forming ability due to the contributions of bioactive chemical components and the natural cancellous bone-like macrostructure. This work offers a promising structural and functional bio-inspired strategy for designing metal implants with desirable ability of osteoinduction synergistically with antibacterial efficacy for promoting bone regeneration and infection prevention simultaneously. STATEMENT OF SIGNIFICANCE: This manuscript describes a new method for making porous Ti scaffolds with a natural cancellous bone-like structure. Besides, a functional bio-surface was constructed on the bionic structure, mimicking some of the functions of the collagen-rich organic matrix and inorganic CaP nanocrystallites of native ECM of bone in chemical components and biological activities. This interconnected inter-pore opening structure encouraged the migration of cells among open macro-pores within the scaffold. In addition, the functionalized surface not only improved early cell adhesion, spreading, stimulated greater osteogenic differentiation of bone-forming cells, but also endowed the scaffold with excellent antibacterial effect. The biomimetic metal implant with multiple biomedical functions designed in this study has a great clinical application potential. This study represents a feasible method for the preparation of biomimetic structure of metal implants and the improvement of their surface biological activity.
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Affiliation(s)
- Bingjun Zhang
- Key Laboratory of Advanced Technologies of Materials (Ministry of Education), School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, 610031, P. R. China; State Key Laboratory of High Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai, 200050, P. R. China
| | - Jia Li
- Key Laboratory of Advanced Technologies of Materials (Ministry of Education), School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, 610031, P. R. China
| | - Lei He
- Key Laboratory of Advanced Technologies of Materials (Ministry of Education), School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, 610031, P. R. China
| | - Hao Huang
- Key Laboratory of Advanced Technologies of Materials (Ministry of Education), School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, 610031, P. R. China
| | - Jie Weng
- Key Laboratory of Advanced Technologies of Materials (Ministry of Education), School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, 610031, P. R. China.
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6
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Kim JS, Sirois AR, Cegla AJV, Jumai’an E, Murata N, Buck ME, Moore SJ. Protein-Polymer Conjugates Synthesized Using Water-Soluble Azlactone-Functionalized Polymers Enable Receptor-Specific Cellular Uptake toward Targeted Drug Delivery. Bioconjug Chem 2019; 30:1220-1231. [PMID: 30920802 PMCID: PMC6608588 DOI: 10.1021/acs.bioconjchem.9b00155] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Conjugation of proteins to drug-loaded polymeric structures is an attractive strategy for facilitating target-specific drug delivery for a variety of clinical needs. Polymers currently available for conjugation to proteins generally have limited chemical versatility for subsequent drug loading. Many polymers that do have chemical functionality useful for drug loading are often insoluble in water, making it difficult to synthesize functional protein-polymer conjugates for targeted drug delivery. In this work, we demonstrate that reactive, azlactone-functionalized polymers can be grafted to proteins, conjugated to a small-molecule fluorophore, and subsequently internalized into cells in a receptor-specific manner. Poly(2-vinyl-4,4-dimethylazlactone), synthesized using reversible addition-fragmentation chain transfer polymerization, was modified post-polymerization with substoichiometric equivalents of triethylene glycol monomethyl ether to yield reactive water-soluble, azlactone-functionalized copolymers. These reactive polymers were then conjugated to proteins holo-transferrin and ovotransferrin. Protein gel analysis verified successful conjugation of proteins to polymer, and protein-polymer conjugates were subsequently purified from unreacted proteins and polymers using size exclusion chromatography. Internalization experiments using a breast cancer cell line that overexpresses the transferrin receptor on its surface showed that the holo-transferrin-polymer conjugate was successfully internalized by cells in a mechanism consistent with receptor-mediated endocytosis. Internalization of protein-polymer conjugate demonstrated that the protein ligand maintained its overall structure and function following conjugation to polymer. Our approach to protein-polymer conjugate synthesis offers a simple, tailorable strategy for preparing bioconjugates of interest for a broad range of biomedical applications.
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Affiliation(s)
- Julia S. Kim
- Biochemistry Program, Smith College, Northampton, Massachusetts 01063, United States
| | - Allison R. Sirois
- Picker Engineering Program, Smith College, Northampton, Massachusetts 01063, United States
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | | | - Eugenie Jumai’an
- Picker Engineering Program, Smith College, Northampton, Massachusetts 01063, United States
| | - Naomi Murata
- Neuroscience Program, Smith College, Northampton, Massachusetts 01063, United States
| | - Maren E. Buck
- Department of Chemistry, Smith College, Northampton, Massachusetts 01063, United States
| | - Sarah J. Moore
- Picker Engineering Program, Smith College, Northampton, Massachusetts 01063, United States
- Department of Biological Sciences, Smith College, Northampton, Massachusetts 01063, United States
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7
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Ryu Y, Kang JA, Kim D, Kim SR, Kim S, Park SJ, Kwon SH, Kim KN, Lee DE, Lee JJ, Kim HS. Programed Assembly of Nucleoprotein Nanoparticles Using DNA and Zinc Fingers for Targeted Protein Delivery. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1802618. [PMID: 30398698 DOI: 10.1002/smll.201802618] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 09/29/2018] [Indexed: 06/08/2023]
Abstract
With a growing number of intracellular drug targets and the high efficacy of protein therapeutics, the targeted delivery of active proteins with negligible toxicity is a challenging issue in the field of precision medicine. Herein, a programed assembly of nucleoprotein nanoparticles (NNPs) using DNA and zinc fingers (ZnFs) for targeted protein delivery is presented. Two types of ZnFs with different sequence specificities are genetically fused to a targeting moiety and a protein cargo, respectively. Double-stranded DNA with multiple ZnF-binding sequences is grafted onto inorganic nanoparticles, followed by conjugation with the ZnF-fused proteins, generating the assembly of NNPs with a uniform size distribution and high stability. The approach enables controlled loading of a protein cargo on the NNPs, offering a high cytosolic delivery efficiency and target specificity. The utility and potential of the assembly as a versatile protein delivery vehicle is demonstrated based on their remarkable antitumor activity and target specificity with negligible toxicity in a xenograft mice model.
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Affiliation(s)
- Yiseul Ryu
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea
| | - Jung Ae Kang
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute (KAERI), Jeongup, 56212, South Korea
| | - Dasom Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea
| | - Song-Rae Kim
- Division of Bio-Imaging, Korea Basic Science Institute (KBSI), Chuncheon, 24341, South Korea
| | - Seungmin Kim
- Department of Biochemistry, Kangwon National University, Chuncheon, 24341, South Korea
| | - Seong Ji Park
- Department of Biochemistry, Kangwon National University, Chuncheon, 24341, South Korea
| | - Seung-Hae Kwon
- Division of Bio-Imaging, Korea Basic Science Institute (KBSI), Chuncheon, 24341, South Korea
| | - Kil-Nam Kim
- Division of Bio-Imaging, Korea Basic Science Institute (KBSI), Chuncheon, 24341, South Korea
| | - Dong-Eun Lee
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute (KAERI), Jeongup, 56212, South Korea
| | - Joong-Jae Lee
- Department of Biochemistry, Kangwon National University, Chuncheon, 24341, South Korea
- Institute of Life Sciences (ILS), Kangwon National University, Chuncheon, 24341, South Korea
| | - Hak-Sung Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea
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8
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Shingarova LN, Petrovskaya LE, Zlobinov AV, Gapizov SS, Kryukova EA, Birikh KR, Boldyreva EF, Yakimov SA, Dolgikh DA, Kirpichnikov MP. Construction of Artificial TNF-Binding Proteins Based on the 10th Human Fibronectin Type III Domain Using Bacterial Display. BIOCHEMISTRY (MOSCOW) 2018; 83:708-716. [PMID: 30195327 DOI: 10.1134/s0006297918060081] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Construction of antibody mimetics on the base of alternative scaffold proteins is a promising strategy for obtaining new products for medicine and biotechnology. The aim of our work was to optimize the cell display system for the 10th human fibronectin type III domain (10Fn3) scaffold protein based on the AT877 autotransporter from Psychrobacter cryohalolentis K5T and to construct new artificial TNF-binding proteins. We obtained a 10Fn3 gene combinatorial library and screened it using the bacterial display method. After expression of the selected 10Fn3 variants in Escherichia coli cells and analysis of their TNF-binding activity, we identified proteins that display high affinity for TNF and characterized their properties.
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Affiliation(s)
- L N Shingarova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | - L E Petrovskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - A V Zlobinov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.,Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234, Russia
| | - S Sh Gapizov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.,Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234, Russia
| | - E A Kryukova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - K R Birikh
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - E F Boldyreva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - S A Yakimov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - D A Dolgikh
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.,Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234, Russia
| | - M P Kirpichnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.,Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234, Russia
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9
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Mason DM, Weber CR, Parola C, Meng SM, Greiff V, Kelton WJ, Reddy ST. High-throughput antibody engineering in mammalian cells by CRISPR/Cas9-mediated homology-directed mutagenesis. Nucleic Acids Res 2018; 46:7436-7449. [PMID: 29931269 PMCID: PMC6101513 DOI: 10.1093/nar/gky550] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 06/04/2018] [Accepted: 06/06/2018] [Indexed: 12/26/2022] Open
Abstract
Antibody engineering is often performed to improve therapeutic properties by directed evolution, usually by high-throughput screening of phage or yeast display libraries. Engineering antibodies in mammalian cells offer advantages associated with expression in their final therapeutic format (full-length glycosylated IgG); however, the inability to express large and diverse libraries severely limits their potential throughput. To address this limitation, we have developed homology-directed mutagenesis (HDM), a novel method which extends the concept of CRISPR/Cas9-mediated homology-directed repair (HDR). HDM leverages oligonucleotides with degenerate codons to generate site-directed mutagenesis libraries in mammalian cells. By improving HDR to a robust efficiency of 15-35% and combining mammalian display screening with next-generation sequencing, we validated this approach can be used for key applications in antibody engineering at high-throughput: rational library construction, novel variant discovery, affinity maturation and deep mutational scanning (DMS). We anticipate that HDM will be a valuable tool for engineering and optimizing antibodies in mammalian cells, and eventually enable directed evolution of other complex proteins and cellular therapeutics.
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Affiliation(s)
- Derek M Mason
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
| | - Cédric R Weber
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
| | - Cristina Parola
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
- Life Science Graduate School, Systems Biology, ETH Zürich, University of Zurich, Zurich 8057, Switzerland
| | - Simon M Meng
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
| | - Victor Greiff
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
| | - William J Kelton
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
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10
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Cyclic peptide natural products chart the frontier of oral bioavailability in the pursuit of undruggable targets. Curr Opin Chem Biol 2017; 38:141-147. [DOI: 10.1016/j.cbpa.2017.04.012] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 04/13/2017] [Accepted: 04/18/2017] [Indexed: 01/23/2023]
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11
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Levin I, Zaretsky M, Aharoni A. Directed evolution of a soluble human DR3 receptor for the inhibition of TL1A induced cytokine secretion. PLoS One 2017; 12:e0173460. [PMID: 28278297 PMCID: PMC5344418 DOI: 10.1371/journal.pone.0173460] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 02/22/2017] [Indexed: 01/14/2023] Open
Abstract
TNF-like 1A (TL1A) is a cytokine belonging to the TNF superfamily that promotes inflammation in autoimmune diseases. Inhibiting the interaction of TL1A with the endogenous death-domain receptor 3 (DR3) offers a therapeutic approach for treating TL1A-induced autoimmune diseases. Here, we generated improved DR3 variants showing increased TL1A binding affinity and stability using a directed evolution approach. Given the high cysteine content and post-translational modification of DR3, we employed yeast surface display and expression in mammalian cell lines for screening, expression and characterization of improved DR3 variants. A cell-based assay performed with the human TF-1 cell line and CD4+ T cells showed that two improved DR3 mutants efficiently inhibited TL1A-induced cell death and secretion of IFN-γ, respectively. These DR3 mutants can be used as drug candidates for the treatment of inflammatory bowel diseases and for other autoimmune diseases, including rheumatic arthritis and asthma.
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Affiliation(s)
- Itay Levin
- The National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, Be’er Sheva, Israel
| | - Marianna Zaretsky
- The National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, Be’er Sheva, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Be’er Sheva, Israel
| | - Amir Aharoni
- The National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, Be’er Sheva, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Be’er Sheva, Israel
- * E-mail:
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12
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Kapur S, Silverman AP, Ye AZ, Papo N, Jindal D, Blumenkranz MS, Cochran JR. Engineered ligand-based VEGFR antagonists with increased receptor binding affinity more effectively inhibit angiogenesis. Bioeng Transl Med 2017; 2:81-91. [PMID: 28516164 PMCID: PMC5412928 DOI: 10.1002/btm2.10051] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Revised: 12/04/2016] [Accepted: 12/11/2016] [Indexed: 12/22/2022] Open
Abstract
Pathologic angiogenesis is mediated by the coordinated action of the vascular endothelial growth factor (VEGF)/vascular endothelial growth factor receptor 2 (VEGFR2) signaling axis, along with crosstalk contributed by other receptors, notably αvβ3 integrin. We build on earlier work demonstrating that point mutations can be introduced into the homodimeric VEGF ligand to convert it into an antagonist through disruption of binding to one copy of VEGFR2. This inhibitor has limited potency, however, due to loss of avidity effects from bivalent VEGFR2 binding. Here, we used yeast surface display to engineer a variant with VEGFR2 binding affinity approximately 40‐fold higher than the parental antagonist, and 14‐fold higher than the natural bivalent VEGF ligand. Increased VEGFR2 binding affinity correlated with the ability to more effectively inhibit VEGF‐mediated signaling, both in vitro and in vivo, as measured using VEGFR2 phosphorylation and Matrigel implantation assays. High affinity mutations found in this variant were then incorporated into a dual‐specific antagonist that we previously designed to simultaneously bind to and inhibit VEGFR2 and αvβ3 integrin. The resulting dual‐specific protein bound to human and murine endothelial cells with relative affinities of 120 ± 10 pM and 360 ± 50 pM, respectively, which is at least 30‐fold tighter than wild‐type VEGF (3.8 ± 0.5 nM). Finally, we demonstrated that this engineered high‐affinity dual‐specific protein could inhibit angiogenesis in a murine corneal neovascularization model. Taken together, these data indicate that protein engineering strategies can be combined to generate unique antiangiogenic candidates for further clinical development.
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Affiliation(s)
- Shiven Kapur
- Dept. of Bioengineering Stanford University Stanford CA 94303
| | | | - Anne Z Ye
- Dept. of Bioengineering Stanford University Stanford CA 94303
| | - Niv Papo
- Dept. of Bioengineering Stanford University Stanford CA 94303
| | - Darren Jindal
- Dept. of Bioengineering Stanford University Stanford CA 94303
| | - Mark S Blumenkranz
- Dept. of Ophthalmology Byers Eye Institute, Stanford University Stanford CA 94303
| | - Jennifer R Cochran
- Dept. of Bioengineering Stanford University Stanford CA 94303.,Dept. of Chemical Engineering Stanford University Stanford CA 94303.,Stanford Cancer Institute Stanford University Stanford CA 94303
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13
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Determination of equilibrium dissociation constants for recombinant antibodies by high-throughput affinity electrophoresis. Sci Rep 2016; 6:39774. [PMID: 28008969 PMCID: PMC5180089 DOI: 10.1038/srep39774] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 11/28/2016] [Indexed: 12/19/2022] Open
Abstract
High-quality immunoreagents enhance the performance and reproducibility of immunoassays and, in turn, the quality of both biological and clinical measurements. High quality recombinant immunoreagents are generated using antibody-phage display. One metric of antibody quality – the binding affinity – is quantified through the dissociation constant (KD) of each recombinant antibody and the target antigen. To characterize the KD of recombinant antibodies and target antigen, we introduce affinity electrophoretic mobility shift assays (EMSAs) in a high-throughput format suitable for small volume samples. A microfluidic card comprised of free-standing polyacrylamide gel (fsPAG) separation lanes supports 384 concurrent EMSAs in 30 s using a single power source. Sample is dispensed onto the microfluidic EMSA card by acoustic droplet ejection (ADE), which reduces EMSA variability compared to sample dispensing using manual or pin tools. The KD for each of a six-member fragment antigen-binding fragment library is reported using ~25-fold less sample mass and ~5-fold less time than conventional heterogeneous assays. Given the form factor and performance of this micro- and mesofluidic workflow, we have developed a sample-sparing, high-throughput, solution-phase alternative for biomolecular affinity characterization.
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14
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Kintzing JR, Filsinger Interrante MV, Cochran JR. Emerging Strategies for Developing Next-Generation Protein Therapeutics for Cancer Treatment. Trends Pharmacol Sci 2016; 37:993-1008. [PMID: 27836202 PMCID: PMC6238641 DOI: 10.1016/j.tips.2016.10.005] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 10/11/2016] [Accepted: 10/11/2016] [Indexed: 12/12/2022]
Abstract
Protein-based therapeutics have been revolutionizing the oncology space since they first appeared in the clinic two decades ago. Unlike traditional small-molecule chemotherapeutics, protein biologics promote active targeting of cancer cells by binding to cell-surface receptors and other markers specifically associated with or overexpressed on tumors versus healthy tissue. While the first approved cancer biologics were monoclonal antibodies, the burgeoning field of protein engineering is spawning research on an expanded range of protein formats and modifications that allow tuning of properties such as target-binding affinity, serum half-life, stability, and immunogenicity. In this review we highlight some of these strategies and provide examples of modified and engineered proteins under development as preclinical and clinical-stage drug candidates for the treatment of cancer.
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Affiliation(s)
- James R Kintzing
- Department of Bioengineering, Stanford University, Stanford, CA, USA; Stanford Cancer Institute, Stanford, CA, USA
| | - Maria V Filsinger Interrante
- Department of Bioengineering, Stanford University, Stanford, CA, USA; Stanford Cancer Institute, Stanford, CA, USA
| | - Jennifer R Cochran
- Department of Bioengineering, Stanford University, Stanford, CA, USA; Stanford Cancer Institute, Stanford, CA, USA; Department of Chemical Engineering, Stanford University, Stanford, CA, USA.
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15
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Kariolis MS, Miao YR, Diep A, Nash SE, Olcina MM, Jiang D, Jones DS, Kapur S, Mathews II, Koong AC, Rankin EB, Cochran JR, Giaccia AJ. Inhibition of the GAS6/AXL pathway augments the efficacy of chemotherapies. J Clin Invest 2016; 127:183-198. [PMID: 27893463 DOI: 10.1172/jci85610] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 10/18/2016] [Indexed: 12/22/2022] Open
Abstract
The AXL receptor and its activating ligand, growth arrest-specific 6 (GAS6), are important drivers of metastasis and therapeutic resistance in human cancers. Given the critical roles that GAS6 and AXL play in refractory disease, this signaling axis represents an attractive target for therapeutic intervention. However, the strong picomolar binding affinity between GAS6 and AXL and the promiscuity of small molecule inhibitors represent important challenges faced by current anti-AXL therapeutics. Here, we have addressed these obstacles by engineering a second-generation, high-affinity AXL decoy receptor with an apparent affinity of 93 femtomolar to GAS6. Our decoy receptor, MYD1-72, profoundly inhibited disease progression in aggressive preclinical models of human cancers and induced cell killing in leukemia cells. When directly compared with the most advanced anti-AXL small molecules in the clinic, MYD1-72 achieved superior antitumor efficacy while displaying no toxicity. Moreover, we uncovered a relationship between AXL and the cellular response to DNA damage whereby abrogation of AXL signaling leads to accumulation of the DNA-damage markers γH2AX, 53BP1, and RAD51. MYD1-72 exploited this relationship, leading to improvements upon the therapeutic index of current standard-of-care chemotherapies in preclinical models of advanced pancreatic and ovarian cancer.
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16
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Immunogenomic engineering of a plug-and-(dis)play hybridoma platform. Nat Commun 2016; 7:12535. [PMID: 27531490 PMCID: PMC4992066 DOI: 10.1038/ncomms12535] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 07/11/2016] [Indexed: 12/22/2022] Open
Abstract
Hybridomas, fusions of primary mouse B cells and myelomas, are stable, rapidly-proliferating cell lines widely utilized for antibody screening and production. Antibody specificity of a hybridoma clone is determined by the immunoglobulin sequence of the primary B cell. Here we report a platform for rapid reprogramming of hybridoma antibody specificity by immunogenomic engineering. Here we use CRISPR-Cas9 to generate double-stranded breaks in immunoglobulin loci, enabling deletion of the native variable light chain and replacement of the endogenous variable heavy chain with a fluorescent reporter protein (mRuby). New antibody genes are introduced by Cas9-targeting of mRuby for replacement with a donor construct encoding a light chain and a variable heavy chain, resulting in full-length antibody expression. Since hybridomas surface express and secrete antibodies, reprogrammed cells are isolated using flow cytometry and cell culture supernatant is used for antibody production. Plug-and-(dis)play hybridomas can be reprogrammed with only a single transfection and screening step.
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17
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Modell AE, Blosser SL, Arora PS. Systematic Targeting of Protein-Protein Interactions. Trends Pharmacol Sci 2016; 37:702-713. [PMID: 27267699 DOI: 10.1016/j.tips.2016.05.008] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 05/14/2016] [Accepted: 05/16/2016] [Indexed: 12/22/2022]
Abstract
Over the past decade, protein-protein interactions (PPIs) have gone from being neglected as 'undruggable' to being considered attractive targets for the development of therapeutics. Recent advances in computational analysis, fragment-based screening, and molecular design have revealed promising strategies to address the basic molecular recognition challenge: how to target large protein surfaces with specificity. Several systematic and complementary workflows have been developed to yield successful inhibitors of PPIs. Here we review the major contemporary approaches utilized for the discovery of inhibitors and focus on a structure-based workflow, from the selection of a biological target to design.
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Affiliation(s)
- Ashley E Modell
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Sarah L Blosser
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Paramjit S Arora
- Department of Chemistry, New York University, New York, NY 10003, USA
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18
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Rosenfeld L, Heyne M, Shifman JM, Papo N. Protein Engineering by Combined Computational and In Vitro Evolution Approaches. Trends Biochem Sci 2016; 41:421-433. [PMID: 27061494 DOI: 10.1016/j.tibs.2016.03.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 02/29/2016] [Accepted: 03/09/2016] [Indexed: 12/30/2022]
Abstract
Two alternative strategies are commonly used to study protein-protein interactions (PPIs) and to engineer protein-based inhibitors. In one approach, binders are selected experimentally from combinatorial libraries of protein mutants that are displayed on a cell surface. In the other approach, computational modeling is used to explore an astronomically large number of protein sequences to select a small number of sequences for experimental testing. While both approaches have some limitations, their combination produces superior results in various protein engineering applications. Such applications include the design of novel binders and inhibitors, the enhancement of affinity and specificity, and the mapping of binding epitopes. The combination of these approaches also aids in the understanding of the specificity profiles of various PPIs.
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Affiliation(s)
- Lior Rosenfeld
- Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Michael Heyne
- Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel; Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Julia M Shifman
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Niv Papo
- Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
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19
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Kapil MA, Pan Y, Duncombe TA, Herr AE. Kinetic Rate Determination via Electrophoresis along a Varying Cross-Section Microchannel. Anal Chem 2016; 88:3669-76. [PMID: 26963604 DOI: 10.1021/acs.analchem.5b04445] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
High throughput, efficient, and readily adoptable analytical tools for the validation and selection of reliable antibody reagents would impact the life sciences, clinical chemistry, and clinical medicine. To directly quantify antibody-antigen association and dissociation rate constants, kon and koff, in a single experiment, we introduce a microfluidic free-standing kinetic polyacrylamide gel electrophoresis (fsKPAGE) assay. Here, an antibody is immobilized in zones along the length of a single freestanding polyacrylamide gel lane of varying cross-sectional width. Fluorescently labeled antigen is electrophoresed through each immobilized antibody zone, with local cross-sectional area determining the local electric field strength and, thus, the local interaction time between immobilized antibody and electromigrating antigen. Upon crossing, the interaction yields immobilized immunocomplex. The kon is quantified by assessing the amount of immunocomplex formed at each interaction time. To quantify koff, immobilized zones of fluorescently labeled immunocomplex are subjected to a buffer dilution and monitored over time. We determine kon and koff for prostate-specific antigen (PSA) and make a comparison to gold-standard values. The fsKPAGE assay determines kon and koff in a single experiment of less than 20 min, using 45 ng of often limited antibody material and standard laboratory equipment. We see the fsKPAGE assay as forming the basis for rapid, quantitative antibody-screening tools.
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Affiliation(s)
- Monica A Kapil
- Bioengineering, University of California , Berkeley, California 94706, United States
| | - Yuchen Pan
- Bioengineering, University of California , Berkeley, California 94706, United States
| | - Todd A Duncombe
- Bioengineering, University of California , Berkeley, California 94706, United States
| | - Amy E Herr
- Bioengineering, University of California , Berkeley, California 94706, United States
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20
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Agarwal R, García AJ. Biomaterial strategies for engineering implants for enhanced osseointegration and bone repair. Adv Drug Deliv Rev 2015; 94:53-62. [PMID: 25861724 DOI: 10.1016/j.addr.2015.03.013] [Citation(s) in RCA: 409] [Impact Index Per Article: 45.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 02/08/2015] [Accepted: 03/17/2015] [Indexed: 12/11/2022]
Abstract
Bone tissue has a remarkable ability to regenerate and heal itself. However, large bone defects and complex fractures still present a significant challenge to the medical community. Current treatments center on metal implants for structural and mechanical support and auto- or allo-grafts to substitute long bone defects. Metal implants are associated with several complications such as implant loosening and infections. Bone grafts suffer from donor site morbidity, reduced bioactivity, and risk of pathogen transmission. Surgical implants can be modified to provide vital biological cues, growth factors and cells in order to improve osseointegration and repair of bone defects. Here we review strategies and technologies to engineer metal surfaces to promote osseointegration with the host tissue. We also discuss strategies for modifying implants for cell adhesion and bone growth via integrin signaling and growth factor and cytokine delivery for bone defect repair.
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21
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Pacelli S, Manoharan V, Desalvo A, Lomis N, Jodha KS, Prakash S, Paul A. Tailoring biomaterial surface properties to modulate host-implant interactions: implication in cardiovascular and bone therapy. J Mater Chem B 2015; 4:1586-1599. [PMID: 27630769 PMCID: PMC5019489 DOI: 10.1039/c5tb01686j] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Host body response to a foreign medical device plays a critical role in defining its fate post implantation. It is thus important to control host-material interactions by designing innovative implant surfaces. In the recent years, biochemical and topographical features have been explored as main target to produce this new type of bioinert or bioresponsive implants. The review discusses specific biofunctional materials and strategies to achieve a precise control over implant surface properties and presents possible solutions to develop next generation of implants, particularly in the fields of bone and cardiovascular therapy.
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Affiliation(s)
- Settimio Pacelli
- BioIntel Research Laboratory, Department of Chemical and Petroleum Engineering, Bioengineering Graduate Program, School of Engineering, University of Kansas, Lawrence, KS, USA
| | - Vijayan Manoharan
- BioIntel Research Laboratory, Department of Chemical and Petroleum Engineering, Bioengineering Graduate Program, School of Engineering, University of Kansas, Lawrence, KS, USA
| | - Anna Desalvo
- University of Southampton, School of Medicine, University Road, Southampton SO17 1BJ, United Kingdom
| | - Nikita Lomis
- Biomedical Technology and Cell Therapy Research Laboratory, Department of Biomedical Engineering, Faculty of Medicine, Duff Medical Building, 3775 University Street, McGill University, QC, Canada H3A 2B4
| | - Kartikeya Singh Jodha
- BioIntel Research Laboratory, Department of Chemical and Petroleum Engineering, Bioengineering Graduate Program, School of Engineering, University of Kansas, Lawrence, KS, USA
| | - Satya Prakash
- Biomedical Technology and Cell Therapy Research Laboratory, Department of Biomedical Engineering, Faculty of Medicine, Duff Medical Building, 3775 University Street, McGill University, QC, Canada H3A 2B4
| | - Arghya Paul
- BioIntel Research Laboratory, Department of Chemical and Petroleum Engineering, Bioengineering Graduate Program, School of Engineering, University of Kansas, Lawrence, KS, USA
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22
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Watkins A, Wuo MG, Arora PS. Protein-Protein Interactions Mediated by Helical Tertiary Structure Motifs. J Am Chem Soc 2015; 137:11622-30. [PMID: 26302018 PMCID: PMC4577960 DOI: 10.1021/jacs.5b05527] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Indexed: 12/26/2022]
Abstract
The modulation of protein-protein interactions (PPIs) by means of creating or stabilizing secondary structure conformations is a rapidly growing area of research. Recent success in the inhibition of difficult PPIs by secondary structure mimetics also points to potential limitations, because often, specific cases require tertiary structure mimetics. To streamline protein structure-based inhibitor design, we have previously described the examination of protein complexes in the Protein Data Bank where α-helices or β-strands form critical contacts. Here, we examined coiled coils and helix bundles that mediate complex formation to create a platform for the discovery of potential tertiary structure mimetics. Though there has been extensive analysis of coiled coil motifs, the interactions between pre-formed coiled coils and globular proteins have not been systematically analyzed. This article identifies critical features of these helical interfaces with respect to coiled coil and other helical PPIs. We expect the analysis to prove useful for the rational design of modulators of this fundamental class of protein assemblies.
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Affiliation(s)
- Andrew
M. Watkins
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Michael G. Wuo
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Paramjit S. Arora
- Department of Chemistry, New York University, New York, New York 10003, United States
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23
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Shah DK. Pharmacokinetic and pharmacodynamic considerations for the next generation protein therapeutics. J Pharmacokinet Pharmacodyn 2015; 42:553-71. [PMID: 26373957 DOI: 10.1007/s10928-015-9447-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 09/10/2015] [Indexed: 12/27/2022]
Abstract
Increasingly sophisticated protein engineering efforts have been undertaken lately to generate protein therapeutics with desired properties. This has resulted in the discovery of the next generation of protein therapeutics, which include: engineered antibodies, immunoconjugates, bi/multi-specific proteins, antibody mimetic novel scaffolds, and engineered ligands/receptors. These novel protein therapeutics possess unique physicochemical properties and act via a unique mechanism-of-action, which collectively makes their pharmacokinetics (PK) and pharmacodynamics (PD) different than other established biological molecules. Consequently, in order to support the discovery and development of these next generation molecules, it becomes important to understand the determinants controlling their PK/PD. This review discusses the determinants that a PK/PD scientist should consider during the design and development of next generation protein therapeutics. In addition, the role of systems PK/PD models in enabling rational development of the next generation protein therapeutics is emphasized.
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Affiliation(s)
- Dhaval K Shah
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, The State University of New York at Buffalo, 455 Kapoor Hall, Buffalo, NY, 14214-8033, USA.
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24
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O’Shea TM, Webber MJ, Aimetti AA, Langer R. Covalent Incorporation of Trehalose within Hydrogels for Enhanced Long-Term Functional Stability and Controlled Release of Biomacromolecules. Adv Healthc Mater 2015; 4:1802-12. [PMID: 26088467 PMCID: PMC4825875 DOI: 10.1002/adhm.201500334] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 05/20/2015] [Indexed: 11/06/2022]
Abstract
Hydrogels with covalently incorporated trehalose are synthesized using thiol-ene Michael addition. Trehalose hydrogels afford prolonged stabilization and -controlled release of model enzymes in vitro and in vivo as well as preservation of protein stability under heat and -lyophilization stressors. Strong and -ordered hydrogen bonding interactions within covalently incorporated trehalose hydrogels represent a possible mechanism for protein stabilization.
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Affiliation(s)
- Timothy M. O’Shea
- Harvard–Massachusetts Institute of Technology Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Matthew J. Webber
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Anesthesiology, Children’s Hospital Boston, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Alex A. Aimetti
- InVivo Therapeutics Corporation, One Kendall Square Building 1400 East, Floor 4, Cambridge, MA 02139, USA
| | - Robert Langer
- Harvard–Massachusetts Institute of Technology Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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25
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Hoinka J, Berezhnoy A, Dao P, Sauna ZE, Gilboa E, Przytycka TM. Large scale analysis of the mutational landscape in HT-SELEX improves aptamer discovery. Nucleic Acids Res 2015; 43:5699-707. [PMID: 25870409 PMCID: PMC4499121 DOI: 10.1093/nar/gkv308] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 03/27/2015] [Indexed: 12/12/2022] Open
Abstract
High-Throughput (HT) SELEX combines SELEX (Systematic Evolution of Ligands by EXponential Enrichment), a method for aptamer discovery, with massively parallel sequencing technologies. This emerging technology provides data for a global analysis of the selection process and for simultaneous discovery of a large number of candidates but currently lacks dedicated computational approaches for their analysis. To close this gap, we developed novel in-silico methods to analyze HT-SELEX data and utilized them to study the emergence of polymerase errors during HT-SELEX. Rather than considering these errors as a nuisance, we demonstrated their utility for guiding aptamer discovery. Our approach builds on two main advancements in aptamer analysis: AptaMut—a novel technique allowing for the identification of polymerase errors conferring an improved binding affinity relative to the ‘parent’ sequence and AptaCluster—an aptamer clustering algorithm which is to our best knowledge, the only currently available tool capable of efficiently clustering entire aptamer pools. We applied these methods to an HT-SELEX experiment developing aptamers against Interleukin 10 receptor alpha chain (IL-10RA) and experimentally confirmed our predictions thus validating our computational methods.
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Affiliation(s)
- Jan Hoinka
- National Center of Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894, USA
| | - Alexey Berezhnoy
- Department of Microbiology & Immunology, University of Miami Miller School of Medicine, Miami, FL 33101, USA
| | - Phuong Dao
- National Center of Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894, USA
| | - Zuben E Sauna
- Laboratory of Hemostasis, Division of Hematology, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Eli Gilboa
- Department of Microbiology & Immunology, University of Miami Miller School of Medicine, Miami, FL 33101, USA
| | - Teresa M Przytycka
- National Center of Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894, USA
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26
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Targeting diverse protein-protein interaction interfaces with α/β-peptides derived from the Z-domain scaffold. Proc Natl Acad Sci U S A 2015; 112:4552-7. [PMID: 25825775 DOI: 10.1073/pnas.1420380112] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Peptide-based agents derived from well-defined scaffolds offer an alternative to antibodies for selective and high-affinity recognition of large and topologically complex protein surfaces. Here, we describe a strategy for designing oligomers containing both α- and β-amino acid residues ("α/β-peptides") that mimic several peptides derived from the three-helix bundle "Z-domain" scaffold. We show that α/β-peptides derived from a Z-domain peptide targeting vascular endothelial growth factor (VEGF) can structurally and functionally mimic the binding surface of the parent peptide while exhibiting significantly decreased susceptibility to proteolysis. The tightest VEGF-binding α/β-peptide inhibits the VEGF165-induced proliferation of human umbilical vein endothelial cells. We demonstrate the versatility of this strategy by showing how principles underlying VEGF signaling inhibitors can be rapidly extended to produce Z-domain-mimetic α/β-peptides that bind to two other protein partners, IgG and tumor necrosis factor-α. Because well-established selection techniques can identify high-affinity Z-domain derivatives from large DNA-encoded libraries, our findings should enable the design of biostable α/β-peptides that bind tightly and specifically to diverse targets of biomedical interest. Such reagents would be useful for diagnostic and therapeutic applications.
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27
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Ng DYW, Wu Y, Kuan SL, Weil T. Programming supramolecular biohybrids as precision therapeutics. Acc Chem Res 2014; 47:3471-80. [PMID: 25357135 DOI: 10.1021/ar5002445] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
CONSPECTUS: Chemical programming of macromolecular structures to instill a set of defined chemical properties designed to behave in a sequential and precise manner is a characteristic vision for creating next generation nanomaterials. In this context, biopolymers such as proteins and nucleic acids provide an attractive platform for the integration of complex chemical design due to their sequence specificity and geometric definition, which allows accurate translation of chemical functionalities to biological activity. Coupled with the advent of amino acid specific modification techniques, "programmable" areas of a protein chain become exclusively available for any synthetic customization. We envision that chemically reprogrammed hybrid proteins will bridge the vital link to overcome the limitations of synthetic and biological materials, providing a unique strategy for tailoring precision therapeutics. In this Account, we present our work toward the chemical design of protein- derived hybrid polymers and their supramolecular responsiveness, while summarizing their impact and the advancement in biomedicine. Proteins, in their native form, represent the central framework of all biological processes and are an unrivaled class of macromolecular drugs with immense specificity. Nonetheless, the route of administration of protein therapeutics is often vastly different from Nature's biosynthesis. Therefore, it is imperative to chemically reprogram these biopolymers to direct their entry and activity toward the designated target. As a consequence of the innate structural regularity of proteins, we show that supramolecular interactions facilitated by stimulus responsive chemistry can be intricately designed as a powerful tool to customize their functions, stability, activity profiles, and transportation capabilities. From another perspective, a protein in its denatured, unfolded form serves as a monodispersed, biodegradable polymer scaffold decorated with functional side chains available for grafting with molecules of interest. Additionally, we are equipped with analytical tools to map the fingerprint of the protein chain, directly elucidating the structure at the molecular level. Contrary to conventional polymers, these biopolymers facilitate a more systematic avenue to investigate engineered macromolecules, with greater detail and accuracy. In this regard, we focus on denaturing serum albumin, an abundant blood protein, and exploit its peptidic array of functionalities to program supramolecular architectures for bioimaging, drug and gene delivery. Ultimately, we seek to assimilate the evolutionary advantage of these protein based biopolymers with the limitless versatility of synthetic chemistry to merge the best of both worlds.
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Affiliation(s)
- David Yuen Wah Ng
- Institute of Organic Chemistry
III, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Yuzhou Wu
- Institute of Organic Chemistry
III, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Seah Ling Kuan
- Institute of Organic Chemistry
III, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Tanja Weil
- Institute of Organic Chemistry
III, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
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28
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Levin D, Golding B, Strome SE, Sauna ZE. Fc fusion as a platform technology: potential for modulating immunogenicity. Trends Biotechnol 2014; 33:27-34. [PMID: 25488117 DOI: 10.1016/j.tibtech.2014.11.001] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 10/31/2014] [Accepted: 11/03/2014] [Indexed: 12/18/2022]
Abstract
The platform technology of fragment crystallizable (Fc) fusion, in which the Fc region of an antibody is genetically linked to an active protein drug, is among the most successful of a new generation of bioengineering strategies. Immunogenicity is a critical safety concern in the development of any protein therapeutic. While the therapeutic goal of generating Fc-fusion proteins has been to extend half-life, there is a critical mass of literature from immunology indicating that appropriate design of the Fc component has the potential to engage the immune system for product-specific outcomes. In the context of Fc-fusion therapeutics, a review of progress in understanding Fc biology suggests the prospect of engineering products that have an extended half-life and are able to modulate the immune system.
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Affiliation(s)
- Ditza Levin
- Laboratory of Hemostasis, Division of Hematology Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Basil Golding
- Plasma Derivatives, Division of Hematology Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Scott E Strome
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland School of Medicine, 16 South Eutaw Street Suite 500, Baltimore, MD 21201, USA
| | - Zuben E Sauna
- Laboratory of Hemostasis, Division of Hematology Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA.
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29
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An engineered Axl 'decoy receptor' effectively silences the Gas6-Axl signaling axis. Nat Chem Biol 2014; 10:977-83. [PMID: 25242553 DOI: 10.1038/nchembio.1636] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 08/14/2014] [Indexed: 12/24/2022]
Abstract
Aberrant signaling through the Axl receptor tyrosine kinase has been associated with a myriad of human diseases, most notably metastatic cancer, identifying Axl and its ligand Gas6 as important therapeutic targets. Using rational and combinatorial approaches, we engineered an Axl 'decoy receptor' that binds Gas6 with high affinity and inhibits its function, offering an alternative approach from drug discovery efforts that directly target Axl. Four mutations within this high-affinity Axl variant caused structural alterations in side chains across the Gas6-Axl binding interface, stabilizing a conformational change on Gas6. When reformatted as an Fc fusion, the engineered decoy receptor bound Gas6 with femtomolar affinity, an 80-fold improvement compared to binding of the wild-type Axl receptor, allowing effective sequestration of Gas6 and specific abrogation of Axl signaling. Moreover, increased Gas6 binding affinity was critical and correlative with the ability of decoy receptors to potently inhibit metastasis and disease progression in vivo.
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30
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Zhou L, Xu N, Sun Y, Liu XM. Targeted biopharmaceuticals for cancer treatment. Cancer Lett 2014; 352:145-51. [PMID: 25016064 DOI: 10.1016/j.canlet.2014.06.020] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Revised: 06/21/2014] [Accepted: 06/29/2014] [Indexed: 01/02/2023]
Abstract
Cancer is a complex invasive genetic disease that causes significant mortality rate worldwide. Protein-based biopharmaceuticals have significantly extended the lives of millions of cancer patients. This article reviews the biological function and application of targeted anticancer biopharmaceuticals. We first discuss the specific antigens and core pathways that are used in the development of targeted cancer therapy. The innovative monoclonal antibodies, non-antibody proteins, and small molecules targeting these antigens or pathways are then reviewed. Finally, the current challenges in anticancer biopharmaceuticals development and the potential solutions to address these challenges are discussed.
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Affiliation(s)
- Lufang Zhou
- Departments of Medicine and Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Ningning Xu
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, AL, USA
| | - Yan Sun
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China; Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Xiaoguang Margaret Liu
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, AL, USA; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China.
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