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Ha Y, Ko S, Kim I, Huang Y, Mohanty K, Huh C, Maynard JA. Recent Advances Incorporating Superparamagnetic Nanoparticles into Immunoassays. ACS APPLIED NANO MATERIALS 2018; 1:512-521. [PMID: 29911680 PMCID: PMC5999228 DOI: 10.1021/acsanm.7b00025] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 01/31/2018] [Indexed: 05/09/2023]
Abstract
Superparamagnetic nanoparticles (SPMNPs) have attracted interest for various biomedical applications due to their unique magnetic behavior, excellent biocompatibility, easy surface modification, and low cost. Their unique magnetic properties, superparamagnetism, and magnetophoretic mobility have led to their inclusion in immunoassays to enhance biosensor sensitivity and allow for rapid detection of various analytes. In this review, we describe SPMNP characteristics valuable for incorporation into biosensors, including the use of SPMNPs to increase detection capabilities of surface plasmon resonance and giant magneto-resistive biosensors. The current status of SPMNP-based immunoassays to improve the sensitivity of rapid diagnostic tests is reviewed, and suggested strategies for the successful adoption of SPMNPs for immunoassays are presented.
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Laber JR, Dear BJ, Martins ML, Jackson DE, DiVenere A, Gollihar JD, Ellington AD, Truskett TM, Johnston KP, Maynard JA. Charge Shielding Prevents Aggregation of Supercharged GFP Variants at High Protein Concentration. Mol Pharm 2017; 14:3269-3280. [PMID: 28870080 DOI: 10.1021/acs.molpharmaceut.7b00322] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding protein stability is central to combatting protein aggregation diseases and developing new protein therapeutics. At the high concentrations often present in biological systems, purified proteins can exhibit undesirable high solution viscosities and poor solubilities mediated by short-range electrostatic and hydrophobic protein-protein interactions. The interplay between protein amino acid sequence, protein structure, and solvent conditions to minimize protein-protein interactions is key to designing well-behaved pharmaceutical proteins. However, theoretical approaches have yet to yield a general framework to address these problems. Here, we analyzed the high concentration behavior of superfolder GFP (sfGFP) and two supercharged sfGFP variants engineered to have formal charges of -18 or +15. Under low cosolute conditions, sfGFP and the -18 variant formed a gel or phase separated at ∼10 mg/mL. Under conditions that screen surface charges, including formulations with high histidine or high NaCl concentrations, all three variants attained concentrations up to 250 mg/mL with moderate viscosities. Moreover, all three variants exhibited very similar viscosity-concentration profiles over this range. This effect was not mimicked by high sugar concentrations that exert excluded-volume effects without shielding charge. Collectively, these data demonstrate that charge shielding neutralizes not only long-range electrostatic interactions but also, surprisingly, short-range electrostatic effects due to surface charge anisotropy. This work shows that supercharged sfGFP behavior under high ionic strength is largely determined by particle geometry, a conclusion that is supported by colloid models and may be applicable to pharmaceutically relevant proteins.
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Entzminger KC, Hyun JM, Pantazes RJ, Patterson-Orazem AC, Qerqez AN, Frye ZP, Hughes RA, Ellington AD, Lieberman RL, Maranas CD, Maynard JA. De novo design of antibody complementarity determining regions binding a FLAG tetra-peptide. Sci Rep 2017; 7:10295. [PMID: 28860479 PMCID: PMC5579192 DOI: 10.1038/s41598-017-10737-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 08/14/2017] [Indexed: 12/30/2022] Open
Abstract
Computational antibody engineering efforts to date have focused on improving binding affinities or biophysical characteristics. De novo design of antibodies binding specific epitopes could greatly accelerate discovery of therapeutics as compared to conventional immunization or synthetic library selection strategies. Here, we employed de novo complementarity determining region (CDR) design to engineer targeted antibody-antigen interactions using previously described in silico methods. CDRs predicted to bind the minimal FLAG peptide (Asp-Tyr-Lys-Asp) were grafted onto a single-chain variable fragment (scFv) acceptor framework. Fifty scFvs comprised of designed heavy and light or just heavy chain CDRs were synthesized and screened for peptide binding by phage ELISA. Roughly half of the designs resulted in detectable scFv expression. Four antibodies, designed entirely in silico, bound the minimal FLAG sequence with high specificity and sensitivity. When reformatted as soluble antigen-binding fragments (Fab), these clones expressed well, were predominantly monomeric and retained peptide specificity. In both formats, the antibodies bind the peptide only when present at the amino-terminus of a carrier protein and even conservative peptide amino acid substitutions resulted in a complete loss of binding. These results support in silico CDR design of antibody specificity as an emerging antibody engineering strategy.
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Wang X, Stapleton JA, Klesmith JR, Hewlett EL, Whitehead TA, Maynard JA. Fine Epitope Mapping of Two Antibodies Neutralizing the Bordetella Adenylate Cyclase Toxin. Biochemistry 2017; 56:1324-1336. [PMID: 28177609 DOI: 10.1021/acs.biochem.6b01163] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Adenylate cyclase toxin (ACT) is an important Bordetella pertussis virulence factor that is not included in current acellular pertussis vaccines. We previously demonstrated that immunization with the repeat-in-toxin (RTX) domain of ACT elicits neutralizing antibodies in mice and discovered the first two antibodies to neutralize ACT activities by occluding the receptor-binding site. Here, we fully characterize these antibodies and their epitopes. Both antibodies bind ACT with low nanomolar affinity and cross-react with ACT homologues produced by B. parapertussis and B. bronchiseptica. Antibody M1H5 binds B. pertussis RTX751 ∼100-fold tighter than RTX751 from the other two species, while antibody M2B10 has similar affinity for all three variants. To initially map the antibody epitopes, we generated a series of ACT chimeras and truncation variants, which implicated the repeat blocks II-III. To identify individual epitope residues, we displayed randomly mutated RTX751 libraries on yeast and isolated clones with decreased antibody binding by flow cytometry. Next-generation sequencing identified candidate epitope residues on the basis of enrichment of clones with mutations at specific positions. These epitopes form two adjacent surface patches on a predicted structural model of the RTX751 domain, one for each antibody. Notably, the cellular receptor also binds within blocks II-III and shares at least one residue with the M1H5 epitope. The RTX751 model supports the notion that the antibody and receptor epitopes overlap. These data provide insight into mechanisms of ACT neutralization and guidance for engineering more stable RTX variants that may be more appropriate vaccine antigens.
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Wagner EK, Wang X, Bui A, Maynard JA. Synergistic Neutralization of Pertussis Toxin by a Bispecific Antibody In Vitro and In Vivo. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2016; 23:851-862. [PMID: 27581436 PMCID: PMC5098018 DOI: 10.1128/cvi.00371-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 08/25/2016] [Indexed: 02/08/2023]
Abstract
Bispecific antibodies are a rapidly growing class of therapeutic molecules, originally developed for the treatment of cancer but recently explored for the treatment of autoimmune and infectious diseases. Bordetella pertussis is a reemerging pathogen, and several of the key symptoms of infection are caused by the pertussis toxin (PTx). Two humanized antibodies, hu1B7 and hu11E6, bind distinct epitopes on PTx and, when coadministered, mitigate disease severity in murine and baboon models of infection. Here we describe the generation of a bispecific human IgG1 molecule combining the hu1B7 and hu11E6 binding sites via a knobs-in-holes design. The bispecific antibody showed binding activity equivalent to that of the antibody mixture in a competition enzyme-linked immunosorbent assay (ELISA). A CHO cell neutralization assay provided preliminary evidence for synergy between the two antibodies, while a murine model of PTx-induced leukocytosis definitively showed synergistic neutralization. Notably, the bispecific antibody retained the synergy observed for the antibody mixture, supporting the conclusion that synergy is due to simultaneous blockade of both the catalytic and receptor binding activities of pertussis toxin. These data suggest that a hu1B7/hu11E6 bispecific antibody is a viable alternative to an antibody mixture for pertussis treatment.
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MESH Headings
- Animals
- Antibodies, Bispecific/immunology
- Antibodies, Bispecific/metabolism
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal, Humanized/chemistry
- Antibodies, Monoclonal, Humanized/immunology
- Antibodies, Monoclonal, Humanized/metabolism
- Antibodies, Monoclonal, Humanized/therapeutic use
- Binding Sites, Antibody
- Bordetella pertussis/immunology
- CHO Cells
- Cricetinae
- Cricetulus
- Drug Synergism
- Enzyme-Linked Immunosorbent Assay
- Epitopes/chemistry
- Epitopes/immunology
- Humans
- Immunoglobulin G/chemistry
- Immunoglobulin G/immunology
- Immunoglobulin G/isolation & purification
- Immunoglobulin G/metabolism
- Mice
- Neutralization Tests
- Pertussis Toxin/immunology
- Whooping Cough/immunology
- Whooping Cough/prevention & control
- Whooping Cough/therapy
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Borwankar AU, Dear BJ, Twu A, Hung JJ, Dinin AK, Wilson BK, Yue J, Maynard JA, Truskett TM, Johnston KP. Viscosity Reduction of a Concentrated Monoclonal Antibody with Arginine·HCl and Arginine·Glutamate. Ind Eng Chem Res 2016. [DOI: 10.1021/acs.iecr.6b02042] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Nguyen AW, Wagner EK, Posada L, Liu X, Connelly S, Papin JF, Wolf RF, Kaleko M, Maynard JA. Prior exposure to Bordetella species as an exclusion criterion in the baboon model of pertussis. J Vet Med Sci 2016; 79:60-64. [PMID: 27666464 PMCID: PMC5289237 DOI: 10.1292/jvms.16-0427] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The baboon model of Bordetella pertussis infection is the newest and most clinically accurate model of the human disease to date. However, among the 15 experimentally infected baboons in this study, a subset of baboons did not exhibit the expected high bacterial colonization levels or increase in white blood cell count. Moreover, cultures of nasopharyngeal wash samples from several baboons suggested B. bronchiseptica coinfection. Analysis of serum antibodies recognizing filamentous hemagglutinin, pertussis toxin and B. pertussis lipo-oligosaccharide indicated that several baboons had likely been previously exposed to Bordetella species and that prior exposure correlated with partial protection from B. pertussis infection. Notably, all animals with a baseline Fha titer of 5 IU/ml or below exhibited symptoms typical of the model, suggesting this value can be used as inclusion criteria for animals prior to study enrollment. While B. pertussis infection is endemic to human populations and B. bronchiseptica is common in wild small mammals, this study illustrates that baboons can readily harbor both organisms. Awareness of Bordetella species that share antigens capable of generating protective immune responses and tracking of prior exposure to those species is required for successful use of the baboon model of pertussis.
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Ha Y, Wang X, Liljestrand HM, Maynard JA, Katz LE. Bioavailability of Fullerene under Environmentally Relevant Conditions: Effects of Humic Acid and Fetal Bovine Serum on Accumulation in Lipid Bilayers and Cellular Uptake. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:6717-6727. [PMID: 26943027 DOI: 10.1021/acs.est.5b04964] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Carbon fullerene (C60) has emerged at the forefront of nanoscale research and application due to its unique properties. As the production of this nanoparticle rapidly increases, it can be released into natural aquatic environments and can accumulate in biological systems. This research examined the effects of humic acid and fetal bovine serum (FBS), which are ubiquitous in aquatic environments and representative of blood plasma in living organisms, respectively, on bioavailability of fullerene. Bioavailability was investigated using in vitro methods for lipid membrane accumulation and cellular uptake studies. Humic acid and FBS significantly changed the characteristics of fullerene including its particle size and surface charge. The effects of humic acid on lipid accumulation of fullerene depended on the lipid head charge. FBS also significantly decreased the lipid accumulation when positively charged and zwitterionic head groups were present on the lipids, possibly due to the higher steric repulsion of the protein coated nanoparticles. In addition, both humic acid and FBS protein effectively lowered the amounts of fullerene taken up by Caco-2 cells, which are derived from a human colorectal adenocarcinoma and have similar functions to the small intestinal epithelium. Results of this study suggest that surface modification of fullerene by environmentally relevant matrices can significantly affect the biological transport, as well as the possible toxicity of this nanomaterial.
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Khan TA, Wang X, Maynard JA. Inclusion of an RGD Motif Alters Invasin Integrin-Binding Affinity and Specificity. Biochemistry 2016; 55:2078-90. [DOI: 10.1021/acs.biochem.5b01243] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Wang X, Gray MC, Hewlett EL, Maynard JA. The Bordetella adenylate cyclase repeat-in-toxin (RTX) domain is immunodominant and elicits neutralizing antibodies. J Biol Chem 2015; 290:23025. [PMID: 26386047 DOI: 10.1074/jbc.a114.585281] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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36
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Nguyen AW, Wagner EK, Laber JR, Goodfield LL, Smallridge WE, Harvill ET, Papin JF, Wolf RF, Padlan EA, Bristol A, Kaleko M, Maynard JA. A cocktail of humanized anti-pertussis toxin antibodies limits disease in murine and baboon models of whooping cough. Sci Transl Med 2015; 7:316ra195. [PMID: 26631634 PMCID: PMC5075433 DOI: 10.1126/scitranslmed.aad0966] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Despite widespread vaccination, pertussis rates are rising in industrialized countries and remain high worldwide. With no specific therapeutics to treat disease, pertussis continues to cause considerable infant morbidity and mortality. The pertussis toxin is a major contributor to disease, responsible for local and systemic effects including leukocytosis and immunosuppression. We humanized two murine monoclonal antibodies that neutralize pertussis toxin and expressed them as human immunoglobulin G1 molecules with no loss of affinity or in vitro neutralization activity. When administered prophylactically to mice as a binary cocktail, antibody treatment completely mitigated the Bordetella pertussis-induced rise in white blood cell counts and decreased bacterial colonization. When administered therapeutically to baboons, antibody-treated, but not untreated control animals, experienced a blunted rise in white blood cell counts and accelerated bacterial clearance rates. These preliminary findings support further investigation into the use of these antibodies to treat human neonatal pertussis in conjunction with antibiotics and supportive care.
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Kowalsky CA, Faber MS, Nath A, Dann HE, Kelly VW, Liu L, Shanker P, Wagner EK, Maynard JA, Chan C, Whitehead TA. Rapid fine conformational epitope mapping using comprehensive mutagenesis and deep sequencing. J Biol Chem 2015; 290:26457-70. [PMID: 26296891 DOI: 10.1074/jbc.m115.676635] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Indexed: 12/29/2022] Open
Abstract
Knowledge of the fine location of neutralizing and non-neutralizing epitopes on human pathogens affords a better understanding of the structural basis of antibody efficacy, which will expedite rational design of vaccines, prophylactics, and therapeutics. However, full utilization of the wealth of information from single cell techniques and antibody repertoire sequencing awaits the development of a high throughput, inexpensive method to map the conformational epitopes for antibody-antigen interactions. Here we show such an approach that combines comprehensive mutagenesis, cell surface display, and DNA deep sequencing. We develop analytical equations to identify epitope positions and show the method effectiveness by mapping the fine epitope for different antibodies targeting TNF, pertussis toxin, and the cancer target TROP2. In all three cases, the experimentally determined conformational epitope was consistent with previous experimental datasets, confirming the reliability of the experimental pipeline. Once the comprehensive library is generated, fine conformational epitope maps can be prepared at a rate of four per day.
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Entzminger KC, Johnson JL, Hyun J, Lieberman RL, Maynard JA. Increased Fab thermoresistance via VH-targeted directed evolution. Protein Eng Des Sel 2015; 28:365-77. [PMID: 26283664 DOI: 10.1093/protein/gzv037] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 07/15/2015] [Indexed: 01/17/2023] Open
Abstract
Antibody aggregation is frequently mediated by the complementarity determining regions within the variable domains and can significantly decrease purification yields, shorten shelf-life and increase the risk of anti-drug immune responses. Aggregation-resistant antibodies could offset these risks; accordingly, we have developed a directed evolution strategy to improve Fab stability. A Fab-phage display vector was constructed and the VH domain targeted for mutagenesis by error-prone PCR. To enrich for thermoresistant clones, the resulting phage library was transiently heated, followed by selection for binding to an anti-light chain constant domain antibody. Five unique variants were identified, each possessing one to three amino acid substitutions. Each engineered Fab possessed higher, Escherichia coli expression yield, a 2-3°C increase in apparent melting temperature and improved aggregation resistance upon heating at high concentration. Select mutations were combined and shown to confer additive improvements to these biophysical characteristics. Finally, the wild-type and most stable triple variant Fab variant were converted into a human IgG1 and expressed in mammalian cells. Both expression level and aggregation resistance were similarly improved in the engineered IgG1. Analysis of the wild-type Fab crystal structure provided a structural rationale for the selected residues changes. This approach can help guide future Fab stabilization efforts.
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Johnson JL, Entzminger KC, Hyun J, Kalyoncu S, Heaner DP, Morales IA, Sheppard A, Gumbart JC, Maynard JA, Lieberman RL. Structural and biophysical characterization of an epitope-specific engineered Fab fragment and complexation with membrane proteins: implications for co-crystallization. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:896-906. [PMID: 25849400 PMCID: PMC4388267 DOI: 10.1107/s1399004715001856] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Accepted: 01/28/2015] [Indexed: 12/22/2022]
Abstract
Crystallization chaperones are attracting increasing interest as a route to crystal growth and structure elucidation of difficult targets such as membrane proteins. While strategies to date have typically employed protein-specific chaperones, a peptide-specific chaperone to crystallize multiple cognate peptide epitope-containing client proteins is envisioned. This would eliminate the target-specific chaperone-production step and streamline the co-crystallization process. Previously, protein engineering and directed evolution were used to generate a single-chain variable (scFv) antibody fragment with affinity for the peptide sequence EYMPME (scFv/EE). This report details the conversion of scFv/EE to an anti-EE Fab format (Fab/EE) followed by its biophysical characterization. The addition of constant chains increased the overall stability and had a negligible impact on the antigen affinity. The 2.0 Å resolution crystal structure of Fab/EE reveals contacts with larger surface areas than those of scFv/EE. Surface plasmon resonance, an enzyme-linked immunosorbent assay, and size-exclusion chromatography were used to assess Fab/EE binding to EE-tagged soluble and membrane test proteins: namely, the β-barrel outer membrane protein intimin and α-helical A2a G protein-coupled receptor (A2aR). Molecular-dynamics simulation of the intimin constructs with and without Fab/EE provides insight into the energetic complexities of the co-crystallization approach.
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Wang X, Gray MC, Hewlett EL, Maynard JA. The Bordetella adenylate cyclase repeat-in-toxin (RTX) domain is immunodominant and elicits neutralizing antibodies. J Biol Chem 2014; 290:3576-91. [PMID: 25505186 DOI: 10.1074/jbc.m114.585281] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The adenylate cyclase toxin (ACT) is a multifunctional virulence factor secreted by Bordetella species. Upon interaction of its C-terminal hemolysin moiety with the cell surface receptor αMβ2 integrin, the N-terminal cyclase domain translocates into the host cell cytosol where it rapidly generates supraphysiological cAMP concentrations, which inhibit host cell anti-bacterial activities. Although ACT has been shown to induce protective immunity in mice, it is not included in any current acellular pertussis vaccines due to protein stability issues and a poor understanding of its role as a protective antigen. Here, we aimed to determine whether any single domain could recapitulate the antibody responses induced by the holo-toxin and to characterize the dominant neutralizing antibody response. We first immunized mice with ACT and screened antibody phage display libraries for binding to purified ACT. The vast majority of unique antibodies identified bound the C-terminal repeat-in-toxin (RTX) domain. Representative antibodies binding two nonoverlapping, neutralizing epitopes in the RTX domain prevented ACT association with J774A.1 macrophages and soluble αMβ2 integrin, suggesting that these antibodies inhibit the ACT-receptor interaction. Sera from mice immunized with the RTX domain showed similar neutralizing activity as ACT-immunized mice, indicating that this domain induced an antibody response similar to that induced by ACT. These data demonstrate that RTX can elicit neutralizing antibodies and suggest it may present an alternative to ACT.
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Beeden RJ, Turner MA, Dryden J, Merida F, Goudkamp K, Malone C, Marshall PA, Birtles A, Maynard JA. Rapid survey protocol that provides dynamic information on reef condition to managers of the Great Barrier Reef. ENVIRONMENTAL MONITORING AND ASSESSMENT 2014; 186:8527-8540. [PMID: 25179944 DOI: 10.1007/s10661-014-4022-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 08/21/2014] [Indexed: 06/03/2023]
Abstract
Managing to support coral reef resilience as the climate changes requires strategic and responsive actions that reduce anthropogenic stress. Managers can only target and tailor these actions if they regularly receive information on system condition and impact severity. In large coral reef areas like the Great Barrier Reef Marine Park (GBRMP), acquiring condition and impact data with good spatial and temporal coverage requires using a large network of observers. Here, we describe the result of ~10 years of evolving and refining participatory monitoring programs used in the GBR that have rangers, tourism operators and members of the public as observers. Participants complete Reef Health and Impact Surveys (RHIS) using a protocol that meets coral reef managers' needs for up-to-date information on the following: benthic community composition, reef condition and impacts including coral diseases, damage, predation and the presence of rubbish. Training programs ensure that the information gathered is sufficiently precise to inform management decisions. Participants regularly report because the demands of the survey methodology have been matched to their time availability. Undertaking the RHIS protocol we describe involves three ~20 min surveys at each site. Participants enter data into an online data management system that can create reports for managers and participants within minutes of data being submitted. Since 2009, 211 participants have completed a total of more than 10,415 surveys at more than 625 different reefs. The two-way exchange of information between managers and participants increases the capacity to manage reefs adaptively, meets education and outreach objectives and can increase stewardship. The general approach used and the survey methodology are both sufficiently adaptable to be used in all reef regions.
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Kalyoncu S, Hyun J, Pai JC, Johnson JL, Entzminger K, Jain A, Heaner DP, Morales IA, Truskett TM, Maynard JA, Lieberman RL. Effects of protein engineering and rational mutagenesis on crystal lattice of single chain antibody fragments. Proteins 2014; 82:1884-95. [PMID: 24615866 PMCID: PMC4142072 DOI: 10.1002/prot.24542] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 02/12/2014] [Accepted: 02/20/2014] [Indexed: 11/06/2022]
Abstract
Protein crystallization is dependent upon, and sensitive to, the intermolecular contacts that assist in ordering proteins into a three-dimensional lattice. Here we used protein engineering and mutagenesis to affect the crystallization of single chain antibody fragments (scFvs) that recognize the EE epitope (EYMPME) with high affinity. These hypercrystallizable scFvs are under development to assist difficult proteins, such as membrane proteins, in forming crystals, by acting as crystallization chaperones. Guided by analyses of intermolecular crystal lattice contacts, two second-generation anti-EE scFvs were produced, which bind to proteins with installed EE tags. Surprisingly, although noncomplementarity determining region (CDR) lattice residues from the parent scFv framework remained unchanged through the processes of protein engineering and rational design, crystal lattices of the derivative scFvs differ. Comparison of energy calculations and the experimentally-determined lattice interactions for this basis set provides insight into the complexity of the forces driving crystal lattice choice and demonstrates the availability of multiple well-ordered surface features in our scFvs capable of forming versatile crystal contacts.
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Kalyoncu S, Johnson JL, Heaner DP, Morales IA, Hyun J, Pai JC, Etzminger K, Maynard JA, Lieberman RL. The Use of Engineered Antibody Fragments to Promote Crystallization of Membrane Proteins. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Abstract
Antibody therapeutics are one of the fastest growing classes of pharmaceuticals, with an annual US market over $20 billion, developed to treat a variety of diseases including cancer, auto-immune and infectious diseases. Most are currently administered as a single molecule to treat a single disease, however there is mounting evidence that cocktails of multiple antibodies, each with a unique binding specificity and protective mechanism, may improve clinical efficacy. Here, we review progress in the development of oligoclonal combinations of antibodies to treat disease, focusing on identification of synergistic antibodies. We then discuss the application of modern antibody engineering technologies to produce highly potent antibody preparations, including oligoclonal antibody cocktails and truly recombinant polyclonal antibodies. Specific examples illustrating the synergy conferred by multiple antibodies will be provided for diseases caused by botulinum toxin, cancer and immune thrombocytopenia. The bioprocessing and regulatory options for these preparations will be discussed.
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Panthani MG, Khan TA, Reid DK, Hellebusch DJ, Rasch MR, Maynard JA, Korgel BA. In vivo whole animal fluorescence imaging of a microparticle-based oral vaccine containing (CuInSe(x)S(2-x))/ZnS core/shell quantum dots. NANO LETTERS 2013; 13:4294-8. [PMID: 23915166 PMCID: PMC3796198 DOI: 10.1021/nl402054w] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Zinc sulfide-coated copper indium sulfur selenide (CuInSexS2-x/ZnS core/shell) nanocrystals were synthesized with size-tunable red to near-infrared (NIR) fluorescence with high quantum yield (40%) in water. These nanocrystals were tested as an imaging agent to track a microparticle-based oral vaccine administered to mice. Poly(lactic-co-glycolic acid) (PLGA) microparticle-encapsulated CuInSexSe2-x/ZnS quantum dots were orally administered to mice and were found to provide a distinct visible fluorescent marker in the gastrointestinal tract of living mice.
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Miller MA, Rodrigues MA, Glass MA, Singh SK, Johnston KP, Maynard JA. Frozen-state storage stability of a monoclonal antibody: aggregation is impacted by freezing rate and solute distribution. J Pharm Sci 2013; 102:1194-208. [PMID: 23400717 DOI: 10.1002/jps.23473] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 01/08/2013] [Accepted: 01/22/2013] [Indexed: 01/13/2023]
Abstract
Freezing of protein solutions perturbs protein conformation, potentially leading to aggregate formation during long-term storage in the frozen state. Macroscopic protein concentration profiles in small cylindrical vessels were determined for a monoclonal antibody frozen in a trehalose-based formulation for various freezing protocols. Slow cooling rates led to concentration differences between outer edges of the tank and the center, up to twice the initial concentration. Fast cooling rates resulted in much smaller differences in protein distribution, likely due to the formation of dendritic ice, which traps solutes in micropockets, limiting their transport by convection and diffusion. Analysis of protein stability after more than 6 months storage at either -10°C or -20°C [above glass transition temperature (T'g )] or -80°C (below T'g ) revealed that aggregation correlated with the cooling rate. Slow-cooled vessels stored above T'g exhibited increased aggregation with time. In contrast, fast-cooled vessels and those stored below T'g showed small to no increase in aggregation at any position. Rapid entrapment of protein in a solute matrix by fast freezing results in improved stability even when stored above T'g . © 2013 Wiley Periodicals, Inc. and the American Pharmacists Association J Pharm Sci 102:1194-1208, 2013.
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Roy BM, Zhukov DV, Maynard JA. Flanking residues are central to DO11.10 T cell hybridoma stimulation by ovalbumin 323-339. PLoS One 2012; 7:e47585. [PMID: 23110081 PMCID: PMC3479146 DOI: 10.1371/journal.pone.0047585] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Accepted: 09/18/2012] [Indexed: 11/30/2022] Open
Abstract
T cell activation requires formation of a tri-molecular interaction between a major histocompatibility complex (MHC), peptide, and T cell receptor. In a common model system, the ovalbumin epitope 323–339 binds the murine class II MHC, I-Ad, in at least three distinct registers. The DO11.10 T cell recognizes the least stable of these, as determined by peptide-MHC dissociation rates. Using exogenous peptides and peptide insertions into a carrier protein in combination with IL-2 secretion assays, we show that the alternate registers do not competitively inhibit display of the active register four. In contrast, this weakly binding register is stabilized by the presence of n-terminal flanking residues active in MHC binding. The DO11.10 hybridoma is sensitive to the presence of specific wild-type residues extending to at least the P-3 peptide position. Transfer of the P-4 to P-2 flanking residues to a hen egg lysozyme epitope also presented by I-Ad increases the activity of that epitope substantially. These results illustrate the inherent complexity in delineating the interaction of multiple registers based on traditional thermodynamic measurements and demonstrate the potential of flanking residue modification for increasing the activity of weakly bound epitopes. The latter technique represents an alternative to substitution of anchor residues within a weakly bound register, which we show can significantly decrease the activity of the epitope to a responding T cell.
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Miller MA, Khan TA, Kaczorowski KJ, Wilson BK, Dinin AK, Borwankar AU, Rodrigues MA, Truskett TM, Johnston KP, Maynard JA. Antibody nanoparticle dispersions formed with mixtures of crowding molecules retain activity and in vivo bioavailability. J Pharm Sci 2012; 101:3763-78. [PMID: 22777686 DOI: 10.1002/jps.23256] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Revised: 06/01/2012] [Accepted: 06/14/2012] [Indexed: 01/07/2023]
Abstract
Monoclonal antibodies continue to command a large market for treatment of a variety of diseases. In many cases, the doses required for therapeutic efficacy are large, limiting options for antibody delivery and administration. We report a novel formulation strategy based on dispersions of antibody nanoclusters that allows for subcutaneous injection of highly concentrated antibody (≈ 190 mg/mL). A solution of monoclonal antibody 1B7 was rapidly frozen and lyophilized using a novel spiral-wound in-situ freezing technology to generate amorphous particles. Upon gentle stirring, a translucent dispersion of approximately 430 nm protein clusters with low apparent viscosity (≈ 24 cp) formed rapidly in buffer containing the pharmaceutically acceptable crowding agents such as trehalose, polyethylene glycol, and n-methyl-2-pyrrolidone. Upon in vitro dilution of the dispersion, the nanoclusters rapidly reverted to monomeric protein with full activity, as monitored by dynamic light scattering and antigen binding. When administered to mice as an intravenous solution, subcutaneous solution, or subcutaneous dispersion at similar (4.6-7.3 mg/kg) or ultra-high dosages (51.6 mg/kg), the distribution and elimination kinetics were within error and the protein retained full activity. Overall, this method of generating high-concentration, low-viscosity dispersions of antibody nanoclusters could lead to improved administration and patient compliance, providing new opportunities for the biotechnology industry.
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Entzminger KC, Chang C, Myhre RO, McCallum KC, Maynard JA. The Skp chaperone helps fold soluble proteins in vitro by inhibiting aggregation. Biochemistry 2012; 51:4822-34. [PMID: 22650963 DOI: 10.1021/bi300412y] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The periplasmic seventeen kilodalton protein (Skp) chaperone has been characterized primarily for its role in outer membrane protein (OMP) biogenesis, during which the jellyfish-like trimeric protein encapsulates partially folded OMPs, protecting them from the aqueous environment until delivery to the BAM outer membrane protein insertion complex. However, Skp is increasingly recognized as a chaperone that also assists in folding soluble proteins in the bacterial periplasm. In this capacity, Skp coexpression increases the active yields of many recombinant proteins and bacterial virulence factors. Using a panel of single-chain antibodies and a single-chain T-cell receptor (collectively termed scFvs) possessing varying stabilities and biophysical characteristics, we performed in vivo expression and in vitro folding and aggregation assays in the presence or absence of Skp. For Skp-sensitive scFvs, the presence of Skp during in vitro refolding assays reduced aggregation but did not alter the observed folding rates, resulting in a higher overall yield of active protein. Of the proteins analyzed, Skp sensitivity in all assays correlated with the presence of folding intermediates, as observed with urea denaturation studies. These results are consistent with Skp acting as a holdase, sequestering partially folded intermediates and thereby preventing aggregation. Because not all soluble proteins are sensitive to Skp coexpression, we hypothesize that the presence of a long-lived protein folding intermediate renders a protein sensitive to Skp. Improved understanding of the bacterial periplasmic protein folding machinery may assist in high-level recombinant protein expression and may help identify novel approaches to block bacterial virulence.
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Johnston KP, Maynard JA, Truskett TM, Borwankar AU, Miller MA, Wilson BK, Dinin AK, Khan TA, Kaczorowski KJ. Concentrated dispersions of equilibrium protein nanoclusters that reversibly dissociate into active monomers. ACS NANO 2012; 6:1357-1369. [PMID: 22260218 DOI: 10.1021/nn204166z] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Stabilizing proteins at high concentration is of broad interest in drug delivery, for treatment of cancer and many other diseases. Herein, we create highly concentrated antibody dispersions (up to 260 mg/mL) comprising dense equilibrium nanoclusters of protein (monoclonal antibody 1B7, polyclonal sheep immunoglobulin G, and bovine serum albumin) molecules which, upon dilution in vitro or administration in vivo, remain conformationally stable and biologically active. The extremely concentrated environment within the nanoclusters (∼700 mg/mL) provides conformational stability to the protein through a novel self-crowding mechanism, as shown by computer simulation, while the primarily repulsive nanocluster interactions result in colloidally stable, transparent dispersions. The nanoclusters are formed by adding trehalose as a cosolute which strengthens the short-ranged attraction between protein molecules. The protein cluster diameter was reversibly tuned from 50 to 300 nm by balancing short-ranged attraction against long-ranged electrostatic repulsion of weakly charged protein at a pH near the isoelectric point. This behavior is described semiquantitatively with a free energy model which includes the fractal dimension of the clusters. Upon dilution of the dispersion in vitro, the clusters rapidly dissociated into fully active protein monomers as shown with biophysical analysis (SEC, DLS, CD, and SDS-PAGE) and sensitive biological assays. Since the concept of forming nanoclusters by tuning colloid interactions is shown to be general, it is likely applicable to a variety of biological therapeutics, mitigating the need to engineer protein stability through amino acid modification. In vivo subcutaneous injection into mice results in indistinguishable pharmacokinetics versus a standard antibody solution. Stable protein dispersions with low viscosities may potentially enable patient self-administration by subcutaneous injection of antibody therapeutics being discovered and developed.
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