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Zhu N, Smallwood PM, Rattner A, Chang TH, Williams J, Wang Y, Nathans J. Utility of protein-protein binding surfaces composed of anti-parallel alpha-helices and beta-sheets selected by phage display. J Biol Chem 2024; 300:107283. [PMID: 38608728 PMCID: PMC11107207 DOI: 10.1016/j.jbc.2024.107283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 04/14/2024] Open
Abstract
Over the past 3 decades, a diverse collection of small protein domains have been used as scaffolds to generate general purpose protein-binding reagents using a variety of protein display and enrichment technologies. To expand the repertoire of scaffolds and protein surfaces that might serve this purpose, we have explored the utility of (i) a pair of anti-parallel alpha-helices in a small highly disulfide-bonded 4-helix bundle, the CC4 domain from reversion-inducing Cysteine-rich Protein with Kazal Motifs and (ii) a concave beta-sheet surface and two adjacent loops in the human FN3 domain, the scaffold for the widely used monobody platform. Using M13 phage display and next generation sequencing, we observe that, in both systems, libraries of ∼30 million variants contain binding proteins with affinities in the low μM range for baits corresponding to the extracellular domains of multiple mammalian proteins. CC4- and FN3-based binding proteins were fused to the N- and/or C-termini of Fc domains and used for immunostaining of transfected cells. Additionally, FN3-based binding proteins were inserted into VP1 of AAV to direct AAV infection to cells expressing a defined surface receptor. Finally, FN3-based binding proteins were inserted into the Pvc13 tail fiber protein of an extracellular contractile injection system particle to direct protein cargo delivery to cells expressing a defined surface receptor. These experiments support the utility of CC4 helices B and C and of FN3 beta-strands C, D, and F together with adjacent loops CD and FG as surfaces for engineering general purpose protein-binding reagents.
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Affiliation(s)
- Ningyu Zhu
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, USA; Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Philip M Smallwood
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, USA; Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Amir Rattner
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, USA; Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Tao-Hsin Chang
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, USA; Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, USA
| | - John Williams
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, USA; Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Yanshu Wang
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, USA; Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Jeremy Nathans
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, USA; Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, USA; Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, USA; Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, USA.
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Velappan N, Nguyen HB, Micheva-Viteva S, Bedinger D, Ye C, Mangadu B, Watts AJ, Meagher R, Bradfute S, Hu B, Waldo GS, Lillo AM. Healthy humans can be a source of antibodies countering COVID-19. Bioengineered 2022; 13:12598-12624. [PMID: 35599623 PMCID: PMC9275966 DOI: 10.1080/21655979.2022.2076390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 04/13/2022] [Accepted: 05/06/2022] [Indexed: 11/05/2022] Open
Abstract
Here, we describe the isolation of 18 unique anti SARS-CoV-2 human single-chain antibodies from an antibody library derived from healthy donors. The selection used a combination of phage and yeast display technologies and included counter-selection strategies meant to direct the selection of the receptor-binding motif (RBM) of SARS-CoV-2 spike protein's receptor binding domain (RBD2). Selected antibodies were characterized in various formats including IgG, using flow cytometry, ELISA, high throughput SPR, and fluorescence microscopy. We report antibodies' RBD2 recognition specificity, binding affinity, and epitope diversity, as well as ability to block RBD2 binding to the human receptor angiotensin-converting enzyme 2 (ACE2) and to neutralize authentic SARS-CoV-2 virus infection in vitro. We present evidence supporting that: 1) most of our antibodies (16 out of 18) selectively recognize RBD2; 2) the best performing 8 antibodies target eight different epitopes of RBD2; 3) one of the pairs tested in sandwich assays detects RBD2 with sub-picomolar sensitivity; and 4) two antibody pairs inhibit SARS-CoV-2 infection at low nanomolar half neutralization titers. Based on these results, we conclude that our antibodies have high potential for therapeutic and diagnostic applications. Importantly, our results indicate that readily available non immune (naïve) antibody libraries obtained from healthy donors can be used to select high-quality monoclonal antibodies, bypassing the need for blood of infected patients, and offering a widely accessible and low-cost alternative to more sophisticated and expensive antibody selection approaches (e.g. single B cell analysis and natural evolution in humanized mice).
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Affiliation(s)
- Nileena Velappan
- Biosciences Division, Los Alamos National Laboratory, Los Alamos, NM87547, USA
| | - Hau B. Nguyen
- Biosciences Division, Los Alamos National Laboratory, Los Alamos, NM87547, USA
| | | | - Daniel Bedinger
- Experimental division, Carterra Inc, Walnut Creek, CA, 94568, USA
| | - Chunyan Ye
- Center for Global Health and Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA
| | - Betty Mangadu
- Biotechnology and Bioengineering Department, Sandia National Laboratories, Livermore, CA, 94551, USA
| | - Austin J. Watts
- Biosciences Division, Los Alamos National Laboratory, Los Alamos, NM87547, USA
- Experimental division, Carterra Inc, Walnut Creek, CA, 94568, USA
- Center for Global Health and Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA
- Biotechnology and Bioengineering Department, Sandia National Laboratories, Livermore, CA, 94551, USA
| | - Robert Meagher
- Biotechnology and Bioengineering Department, Sandia National Laboratories, Livermore, CA, 94551, USA
| | - Steven Bradfute
- Center for Global Health and Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA
| | - Bin Hu
- Biosciences Division, Los Alamos National Laboratory, Los Alamos, NM87547, USA
| | - Geoffrey S. Waldo
- Biosciences Division, Los Alamos National Laboratory, Los Alamos, NM87547, USA
| | - Antonietta M. Lillo
- Biosciences Division, Los Alamos National Laboratory, Los Alamos, NM87547, USA
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3
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Formulation of stabilizer-free, nontoxic PLGA and elastin-PLGA nanoparticle delivery systems. Int J Pharm 2021; 597:120340. [PMID: 33545284 DOI: 10.1016/j.ijpharm.2021.120340] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 01/25/2021] [Accepted: 01/31/2021] [Indexed: 12/18/2022]
Abstract
Biocompatible nanoparticles composed of poly(lactic-co-glycolic acid) (PLGA) are used as drug and vaccine delivery systems because of their tunability in size and sustained release of cargo molecules. While the use of toxic stabilizers such as polyvinyl alcohol (PVA) limit the utility of PLGA, stabilizer-free PLGA nanoparticles are rarely used because they can be challenging to prepare. Here, we developed a tunable, stabilizer-free PLGA nanoparticle formulation capable of encapsulating plasmid DNA and demonstrated the formation of an elastin-like polymer PLGA hybrid nanoparticle with exceptional stability and biocompatibility. A suite of PLGAs were fabricated using solvent evaporation methods and assessed for particle size and stability in water. We find that under physiological conditions (PBS at 37˚C), the most stable PLGA formulation (P4) was found to contain a greater L:G ratio (65:35), lower MW, and carboxyl terminus. Subsequent experiments determined P4 nanoparticles were as stable as those made with PVA, yet significantly less cytotoxic. Variation in particle size was achieved through altering PLGA stoichiometry while maintaining the ability to encapsulate DNA and were modified with elastin-like polymers for increased immune tolerance. Overall, a useful method for tunable, stabilizer-free PLGA nanoparticle formulation was developed for use in drug and vaccine delivery, and immune targeting.
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Lillo AM, Velappan N, Kelliher JM, Watts AJ, Merriman SP, Vuyisich G, Lilley LM, Coombs KE, Mastren T, Teshima M, Stein BW, Wagner GL, Iyer S, Bradbury ARM, Harris JF, Dichosa AE, Kozimor SA. Development of Anti- Yersinia pestis Human Antibodies with Features Required for Diagnostic and Therapeutic Applications. Immunotargets Ther 2020; 9:299-316. [PMID: 33294421 PMCID: PMC7716875 DOI: 10.2147/itt.s267077] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 09/16/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Yersinia pestis is a category A infective agent that causes bubonic, septicemic, and pneumonic plague. Notably, the acquisition of antimicrobial or multidrug resistance through natural or purposed means qualifies Y. pestis as a potential biothreat agent. Therefore, high-quality antibodies designed for accurate and sensitive Y. pestis diagnostics, and therapeutics potentiating or replacing traditional antibiotics are of utmost need for national security and public health preparedness. METHODS Here, we describe a set of human monoclonal immunoglobulins (IgG1s) targeting Y. pestis fraction 1 (F1) antigen, previously derived from in vitro evolution of a phage-display library of single-chain antibodies (scFv). We extensively characterized these antibodies and their effect on bacterial and mammalian cells via: ELISA, flow cytometry, mass spectrometry, spectroscopy, and various metabolic assays. RESULTS Two of our anti-F1 IgG (αF1Ig 2 and αF1Ig 8) stood out for high production yield, specificity, and stability. These two antibodies were additionally attractive in that they displayed picomolar affinity, did not compete when binding Y. pestis, and retained immunoreactivity upon chemical derivatization. Most importantly, these antibodies detected <1,000 Y. pestis cells in sandwich ELISA, did not harm respiratory epithelial cells, induced Y. pestis agglutination at low concentration (350 nM), and caused apparent reduction in cell growth when radiolabeled at a nonagglutinating concentration (34 nM). CONCLUSION These antibodies are amenable to the development of accurate and sensitive diagnostics and immuno/radioimmunotherapeutics.
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Affiliation(s)
- Antonietta M Lillo
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Nileena Velappan
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Julia M Kelliher
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Austin J Watts
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Samuel P Merriman
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Grace Vuyisich
- Chemistry Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Laura M Lilley
- Chemistry Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Kent E Coombs
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Tara Mastren
- Chemistry Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Munehiro Teshima
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Benjamin W Stein
- Chemistry Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Gregory L Wagner
- Chemistry Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Srinivas Iyer
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | | | | | - Armand E Dichosa
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Stosh A Kozimor
- Chemistry Division, Los Alamos National Laboratory, Los Alamos, NM, USA
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McAllister TE, Coleman OD, Roper G, Kawamura A. Structural diversity in
de novo
cyclic peptide ligands from genetically encoded library technologies. Pept Sci (Hoboken) 2020. [DOI: 10.1002/pep2.24204] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Tom E. McAllister
- Chemistry – School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK
| | - Oliver D. Coleman
- Chemistry – School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK
| | - Grace Roper
- Chemistry – School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK
- Chemistry Research Laboratory, Department of Chemistry University of Oxford Oxford UK
| | - Akane Kawamura
- Chemistry – School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK
- Chemistry Research Laboratory, Department of Chemistry University of Oxford Oxford UK
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D'Angelo S, Staquicini FI, Ferrara F, Staquicini DI, Sharma G, Tarleton CA, Nguyen H, Naranjo LA, Sidman RL, Arap W, Bradbury AR, Pasqualini R. Selection of phage-displayed accessible recombinant targeted antibodies (SPARTA): methodology and applications. JCI Insight 2018; 3:98305. [PMID: 29720567 DOI: 10.1172/jci.insight.98305] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 04/05/2018] [Indexed: 11/17/2022] Open
Abstract
We developed a potentially novel and robust antibody discovery methodology, termed selection of phage-displayed accessible recombinant targeted antibodies (SPARTA). This combines an in vitro screening step of a naive human antibody library against known tumor targets, with in vivo selections based on tumor-homing capabilities of a preenriched antibody pool. This unique approach overcomes several rate-limiting challenges to generate human antibodies amenable to rapid translation into medical applications. As a proof of concept, we evaluated SPARTA on 2 well-established tumor cell surface targets, EphA5 and GRP78. We evaluated antibodies that showed tumor-targeting selectivity as a representative panel of antibody-drug conjugates (ADCs) and were highly efficacious. Our results validate a discovery platform to identify and validate monoclonal antibodies with favorable tumor-targeting attributes. This approach may also extend to other diseases with known cell surface targets and affected tissues easily isolated for in vivo selection.
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Affiliation(s)
| | - Fernanda I Staquicini
- Rutgers Cancer Institute of New Jersey at University Hospital and Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | | | - Daniela I Staquicini
- Rutgers Cancer Institute of New Jersey at University Hospital and Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Geetanjali Sharma
- University of New Mexico Comprehensive Cancer Center, University of New Mexico School of Medicine, Albuquerque, New Mexico, USA
| | - Christy A Tarleton
- University of New Mexico Comprehensive Cancer Center, University of New Mexico School of Medicine, Albuquerque, New Mexico, USA
| | - Huynh Nguyen
- University of New Mexico Comprehensive Cancer Center, University of New Mexico School of Medicine, Albuquerque, New Mexico, USA
| | | | - Richard L Sidman
- Department of Neurology, Harvard Medical School, Boston, Massachusetts, USA
| | - Wadih Arap
- Rutgers Cancer Institute of New Jersey at University Hospital and Division of Hematology/Oncology, Department of Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | | | - Renata Pasqualini
- Rutgers Cancer Institute of New Jersey at University Hospital and Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, New Jersey, USA
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Chan SK, Rahumatullah A, Lai JY, Lim TS. Naïve Human Antibody Libraries for Infectious Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1053:35-59. [PMID: 29549634 PMCID: PMC7120739 DOI: 10.1007/978-3-319-72077-7_3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Many countries are facing an uphill battle in combating the spread of infectious diseases. The constant evolution of microorganisms magnifies the problem as it facilitates the re-emergence of old infectious diseases as well as promote the introduction of new and more deadly variants. Evidently, infectious diseases have contributed to an alarming rate of mortality worldwide making it a growing concern. Historically, antibodies have been used successfully to prevent and treat infectious diseases since the nineteenth century using antisera collected from immunized animals. The inherent ability of antibodies to trigger effector mechanisms aids the immune system to fight off pathogens that invades the host. Immune libraries have always been an important source of antibodies for infectious diseases due to the skewed repertoire generated post infection. Even so, the role and ability of naïve antibody libraries should not be underestimated. The naïve repertoire has its own unique advantages in generating antibodies against target antigens. This chapter will highlight the concept, advantages and application of human naïve libraries as a source to isolate antibodies against infectious disease target antigens.
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Affiliation(s)
- Soo Khim Chan
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Anizah Rahumatullah
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Jing Yi Lai
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Minden, Penang, Malaysia.
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Minden, 11800, Penang, Malaysia.
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