51
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Sulea T, Hussack G, Ryan S, Tanha J, Purisima EO. Application of Assisted Design of Antibody and Protein Therapeutics (ADAPT) improves efficacy of a Clostridium difficile toxin A single-domain antibody. Sci Rep 2018; 8:2260. [PMID: 29396522 PMCID: PMC5797146 DOI: 10.1038/s41598-018-20599-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 01/17/2018] [Indexed: 02/07/2023] Open
Abstract
Assisted Design of Antibody and Protein Therapeutics (ADAPT) is an affinity maturation platform interleaving predictions and testing that was previously validated on monoclonal antibodies (mAbs). This study expands the applicability of ADAPT to single-domain antibodies (sdAbs), a promising class of recombinant antibody-based biologics. As a test case, we used the camelid sdAb A26.8, a VHH that binds Clostridium difficile toxin A (TcdA) relatively weakly but displays a reasonable level of TcdA neutralization. ADAPT-guided A26.8 affinity maturation resulted in an improvement of one order of magnitude by point mutations only, reaching an equilibrium dissociation constant (KD) of 2 nM, with the best binding mutants having similar or improved stabilities relative to the parent sdAb. This affinity improvement generated a 6-fold enhancement of efficacy at the cellular level; the A26.8 double-mutant T56R,T103R neutralizes TcdA cytotoxicity with an IC50 of 12 nM. The designed mutants with increased affinities are predicted to establish novel electrostatic interactions with the antigen. Almost full additivity of mutation effects is observed, except for positively charged residues introduced at adjacent positions. Furthermore, analysis of false-positive predictions points to general directions for improving the ADAPT platform. ADAPT guided the efficacy enhancement of an anti-toxin sdAb, an alternative therapeutic modality for C. difficile.
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Affiliation(s)
- Traian Sulea
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, Quebec, H4P 2R2, Canada.,Institute of Parasitology, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, Quebec, H9X 3V9, Canada
| | - Greg Hussack
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, K1A 0R6, Canada
| | - Shannon Ryan
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, K1A 0R6, Canada
| | - Jamshid Tanha
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, K1A 0R6, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada
| | - Enrico O Purisima
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, Quebec, H4P 2R2, Canada. .,Department of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec, H3G 1Y6, Canada.
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52
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Chew WL. Immunity to CRISPR Cas9 and Cas12a therapeutics. WILEY INTERDISCIPLINARY REVIEWS. SYSTEMS BIOLOGY AND MEDICINE 2018; 10. [PMID: 29083112 DOI: 10.1002/wsbm.1408] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Revised: 09/08/2017] [Accepted: 09/10/2017] [Indexed: 12/27/2022]
Abstract
Genome-editing therapeutics are poised to treat human diseases. As we enter clinical trials with the most promising CRISPR-Cas9 and CRISPR-Cas12a (Cpf1) modalities, the risks associated with administering these foreign biomolecules into human patients become increasingly salient. Preclinical discovery with CRISPR-Cas9 and CRISPR-Cas12a systems and foundational gene therapy studies indicate that the host immune system can mount undesired responses against the administered proteins and nucleic acids, the gene-edited cells, and the host itself. These host defenses include inflammation via activation of innate immunity, antibody induction in humoral immunity, and cell death by T-cell-mediated cytotoxicity. If left unchecked, these immunological reactions can curtail therapeutic benefits and potentially lead to mortality. Ways to assay and reduce the immunogenicity of Cas9 and Cas12a proteins are therefore critical for ensuring patient safety and treatment efficacy, and for bringing us closer to realizing the vision of permanent genetic cures. WIREs Syst Biol Med 2018, 10:e1408. doi: 10.1002/wsbm.1408 This article is categorized under: Laboratory Methods and Technologies > Genetic/Genomic Methods Translational, Genomic, and Systems Medicine > Translational Medicine Translational, Genomic, and Systems Medicine > Therapeutic Methods.
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Affiliation(s)
- Wei Leong Chew
- Synthetic Biology, Genome Institute of Singapore, Singapore, Singapore
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53
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Tao L, Li D, Li Y, Shi X, Wang J, Rao C, Zhang Y. Designing a mutant Candida uricase with improved polymerization state and enzymatic activity. Protein Eng Des Sel 2017; 30:753-759. [PMID: 29161434 DOI: 10.1093/protein/gzx056] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 11/02/2017] [Indexed: 11/12/2022] Open
Abstract
As human uricase has been silenced during evolution, counterparts from other species become an alternative for the treatment of hyperuricemia. Candida uricase is a promising option among them, but its aggregation propensity remains a major obstacle to clinical use. In this study, we designed two mutations according to homology-modeled 3D structure of Candida uricase: Cys249Ser substitution and C-terminal Leu deletion. The wild-type uricase and three mutants containing either or both of the mutations were expressed in Escherichia coli BL21 and validated by mass spectrometry. Size-exclusion chromatography and electrophoresis analysis demonstrated that aggregation was induced by interchain disulfide bonds and could be significantly avoided by Cys249Ser substitution. In combination with Cys249Ser substitution, deletion of Leu increased the enzymatic activity by 8%. Taken together, mutant containing both mutations is chosen as our target protein which is comparatively more suitable for therapeutic use. In addition, homology-modeled 3D structure was proved to be an efficient approach for protein engineering.
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Affiliation(s)
- Lei Tao
- State Key Laboratory of Cancer Biology, Department of Biopharmaceutics, School of Pharmacy, The Fourth Military Medical University, Xi'an, People's Republic of China.,National Institute for Food and Drug Control, Beijing 100050, People's Republic of China
| | - Dandan Li
- National Institute for Food and Drug Control, Beijing 100050, People's Republic of China
| | - Yonghong Li
- National Institute for Food and Drug Control, Beijing 100050, People's Republic of China
| | - Xinchang Shi
- National Institute for Food and Drug Control, Beijing 100050, People's Republic of China
| | - Junzhi Wang
- National Institute for Food and Drug Control, Beijing 100050, People's Republic of China
| | - Chunming Rao
- National Institute for Food and Drug Control, Beijing 100050, People's Republic of China
| | - Yingqi Zhang
- State Key Laboratory of Cancer Biology, Department of Biopharmaceutics, School of Pharmacy, The Fourth Military Medical University, Xi'an, People's Republic of China
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54
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Chevalier A, Silva DA, Rocklin GJ, Hicks DR, Vergara R, Murapa P, Bernard SM, Zhang L, Lam KH, Yao G, Bahl CD, Miyashita SI, Goreshnik I, Fuller JT, Koday MT, Jenkins CM, Colvin T, Carter L, Bohn A, Bryan CM, Fernández-Velasco DA, Stewart L, Dong M, Huang X, Jin R, Wilson IA, Fuller DH, Baker D. Massively parallel de novo protein design for targeted therapeutics. Nature 2017; 550:74-79. [PMID: 28953867 PMCID: PMC5802399 DOI: 10.1038/nature23912] [Citation(s) in RCA: 278] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 08/17/2017] [Indexed: 12/24/2022]
Abstract
De novo protein design holds promise for creating small stable proteins with shapes customized to bind therapeutic targets. We describe a massively parallel approach for designing, manufacturing and screening mini-protein binders, integrating large-scale computational design, oligonucleotide synthesis, yeast display screening and next-generation sequencing. We designed and tested 22,660 mini-proteins of 37-43 residues that target influenza haemagglutinin and botulinum neurotoxin B, along with 6,286 control sequences to probe contributions to folding and binding, and identified 2,618 high-affinity binders. Comparison of the binding and non-binding design sets, which are two orders of magnitude larger than any previously investigated, enabled the evaluation and improvement of the computational model. Biophysical characterization of a subset of the binder designs showed that they are extremely stable and, unlike antibodies, do not lose activity after exposure to high temperatures. The designs elicit little or no immune response and provide potent prophylactic and therapeutic protection against influenza, even after extensive repeated dosing.
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Affiliation(s)
- Aaron Chevalier
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Daniel-Adriano Silva
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Gabriel J Rocklin
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Derrick R Hicks
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington 98195, USA
| | - Renan Vergara
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
- Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria, México City 04510, Mexico
| | - Patience Murapa
- Department of Microbiology, University of Washington, Seattle, Washington 98109, USA
| | - Steffen M Bernard
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Lu Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
- Department of Chemistry and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Kwok-Ho Lam
- Department of Physiology and Biophysics, University of California, Irvine, California 92697, USA
| | - Guorui Yao
- Department of Physiology and Biophysics, University of California, Irvine, California 92697, USA
| | - Christopher D Bahl
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Shin-Ichiro Miyashita
- Department of Urology, Boston Children's Hospital, Boston, Massachusetts 02115, USA
- Department of Microbiology and Immunobiology and Department of Surgery, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Inna Goreshnik
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - James T Fuller
- Department of Microbiology, University of Washington, Seattle, Washington 98109, USA
| | - Merika T Koday
- Department of Microbiology, University of Washington, Seattle, Washington 98109, USA
- Virvio Inc., Seattle, Washington 98195, USA
| | - Cody M Jenkins
- Department of Microbiology, University of Washington, Seattle, Washington 98109, USA
| | - Tom Colvin
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Lauren Carter
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Alan Bohn
- Department of Microbiology, University of Washington, Seattle, Washington 98109, USA
| | - Cassie M Bryan
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - D Alejandro Fernández-Velasco
- Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria, México City 04510, Mexico
| | - Lance Stewart
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Min Dong
- Department of Urology, Boston Children's Hospital, Boston, Massachusetts 02115, USA
- Department of Microbiology and Immunobiology and Department of Surgery, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Xuhui Huang
- Department of Chemistry and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Rongsheng Jin
- Department of Physiology and Biophysics, University of California, Irvine, California 92697, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Deborah H Fuller
- Department of Microbiology, University of Washington, Seattle, Washington 98109, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
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55
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Dhanda SK, Grifoni A, Pham J, Vaughan K, Sidney J, Peters B, Sette A. Development of a strategy and computational application to select candidate protein analogues with reduced HLA binding and immunogenicity. Immunology 2017; 153:118-132. [PMID: 28833085 DOI: 10.1111/imm.12816] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/27/2017] [Accepted: 08/14/2017] [Indexed: 12/13/2022] Open
Abstract
Unwanted immune responses against protein therapeutics can reduce efficacy or lead to adverse reactions. T-cell responses are key in the development of such responses, and are directed against immunodominant regions within the protein sequence, often associated with binding to several allelic variants of HLA class II molecules (promiscuous binders). Herein, we report a novel computational strategy to predict 'de-immunized' peptides, based on previous studies of erythropoietin protein immunogenicity. This algorithm (or method) first predicts promiscuous binding regions within the target protein sequence and then identifies residue substitutions predicted to reduce HLA binding. Further, this method anticipates the effect of any given substitution on flanking peptides, thereby circumventing the creation of nascent HLA-binding regions. As a proof-of-principle, the algorithm was applied to Vatreptacog α, an engineered Factor VII molecule associated with unintended immunogenicity. The algorithm correctly predicted the two immunogenic peptides containing the engineered residues. As a further validation, we selected and evaluated the immunogenicity of seven substitutions predicted to simultaneously reduce HLA binding for both peptides, five control substitutions with no predicted reduction in HLA-binding capacity, and additional flanking region controls. In vitro immunogenicity was detected in 21·4% of the cultures of peptides predicted to have reduced HLA binding and 11·4% of the flanking regions, compared with 46% for the cultures of the peptides predicted to be immunogenic. This method has been implemented as an interactive application, freely available online at http://tools.iedb.org/deimmunization/.
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Affiliation(s)
- Sandeep Kumar Dhanda
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Alba Grifoni
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - John Pham
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Kerrie Vaughan
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
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56
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In silico methods for design of biological therapeutics. Methods 2017; 131:33-65. [PMID: 28958951 DOI: 10.1016/j.ymeth.2017.09.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 09/21/2017] [Accepted: 09/23/2017] [Indexed: 12/18/2022] Open
Abstract
It has been twenty years since the first rationally designed small molecule drug was introduced into the market. Since then, we have progressed from designing small molecules to designing biotherapeutics. This class of therapeutics includes designed proteins, peptides and nucleic acids that could more effectively combat drug resistance and even act in cases where the disease is caused because of a molecular deficiency. Computational methods are crucial in this design exercise and this review discusses the various elements of designing biotherapeutic proteins and peptides. Many of the techniques discussed here, such as the deterministic and stochastic design methods, are generally used in protein design. We have devoted special attention to the design of antibodies and vaccines. In addition to the methods for designing these molecules, we have included a comprehensive list of all biotherapeutics approved for clinical use. Also included is an overview of methods that predict the binding affinity, cell penetration ability, half-life, solubility, immunogenicity and toxicity of the designed therapeutics. Biotherapeutics are only going to grow in clinical importance and are set to herald a new generation of disease management and cure.
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57
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Computationally optimized deimmunization libraries yield highly mutated enzymes with low immunogenicity and enhanced activity. Proc Natl Acad Sci U S A 2017; 114:E5085-E5093. [PMID: 28607051 DOI: 10.1073/pnas.1621233114] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Therapeutic proteins of wide-ranging function hold great promise for treating disease, but immune surveillance of these macromolecules can drive an antidrug immune response that compromises efficacy and even undermines safety. To eliminate widespread T-cell epitopes in any biotherapeutic and thereby mitigate this key source of detrimental immune recognition, we developed a Pareto optimal deimmunization library design algorithm that optimizes protein libraries to account for the simultaneous effects of combinations of mutations on both molecular function and epitope content. Active variants identified by high-throughput screening are thus inherently likely to be deimmunized. Functional screening of an optimized 10-site library (1,536 variants) of P99 β-lactamase (P99βL), a component of ADEPT cancer therapies, revealed that the population possessed high overall fitness, and comprehensive analysis of peptide-MHC II immunoreactivity showed the population possessed lower average immunogenic potential than the wild-type enzyme. Although similar functional screening of an optimized 30-site library (2.15 × 109 variants) revealed reduced population-wide fitness, numerous individual variants were found to have activity and stability better than the wild type despite bearing 13 or more deimmunizing mutations per enzyme. The immunogenic potential of one highly active and stable 14-mutation variant was assessed further using ex vivo cellular immunoassays, and the variant was found to silence T-cell activation in seven of the eight blood donors who responded strongly to wild-type P99βL. In summary, our multiobjective library-design process readily identified large and mutually compatible sets of epitope-deleting mutations and produced highly active but aggressively deimmunized constructs in only one round of library screening.
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58
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Insights into Hunter syndrome from the structure of iduronate-2-sulfatase. Nat Commun 2017; 8:15786. [PMID: 28593992 PMCID: PMC5472762 DOI: 10.1038/ncomms15786] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 04/27/2017] [Indexed: 01/02/2023] Open
Abstract
Hunter syndrome is a rare but devastating childhood disease caused by mutations in the IDS gene encoding iduronate-2-sulfatase, a crucial enzyme in the lysosomal degradation pathway of dermatan sulfate and heparan sulfate. These complex glycosaminoglycans have important roles in cell adhesion, growth, proliferation and repair, and their degradation and recycling in the lysosome is essential for cellular maintenance. A variety of disease-causing mutations have been identified throughout the IDS gene. However, understanding the molecular basis of the disease has been impaired by the lack of structural data. Here, we present the crystal structure of human IDS with a covalently bound sulfate ion in the active site. This structure provides essential insight into multiple mechanisms by which pathogenic mutations interfere with enzyme function, and a compelling explanation for severe Hunter syndrome phenotypes. Understanding the structural consequences of disease-associated mutations will facilitate the identification of patients that may benefit from specific tailored therapies. Hunter syndrome is a lysosomal storage disease caused by mutations in the enzyme iduronate-2-sulfatase (IDS). Here, the authors present the IDS crystal structure and give mechanistic insights into mutations that cause Hunter syndrome.
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59
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Paladino A, Marchetti F, Rinaldi S, Colombo G. Protein design: from computer models to artificial intelligence. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1318] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Antonella Paladino
- Biomolecular Simulations & Computational Chemistry Group; Istituto Istituto di Chimica del Riconoscimento Molecolare, CNR; Milano Italy
| | - Filippo Marchetti
- Biomolecular Simulations & Computational Chemistry Group; Istituto Istituto di Chimica del Riconoscimento Molecolare, CNR; Milano Italy
| | - Silvia Rinaldi
- Biomolecular Simulations & Computational Chemistry Group; Istituto Istituto di Chimica del Riconoscimento Molecolare, CNR; Milano Italy
| | - Giorgio Colombo
- Biomolecular Simulations & Computational Chemistry Group; Istituto Istituto di Chimica del Riconoscimento Molecolare, CNR; Milano Italy
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60
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Jain S, Jou JD, Georgiev IS, Donald BR. A critical analysis of computational protein design with sparse residue interaction graphs. PLoS Comput Biol 2017; 13:e1005346. [PMID: 28358804 PMCID: PMC5391103 DOI: 10.1371/journal.pcbi.1005346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 04/13/2017] [Accepted: 01/03/2017] [Indexed: 11/19/2022] Open
Abstract
Protein design algorithms enumerate a combinatorial number of candidate structures to compute the Global Minimum Energy Conformation (GMEC). To efficiently find the GMEC, protein design algorithms must methodically reduce the conformational search space. By applying distance and energy cutoffs, the protein system to be designed can thus be represented using a sparse residue interaction graph, where the number of interacting residue pairs is less than all pairs of mutable residues, and the corresponding GMEC is called the sparse GMEC. However, ignoring some pairwise residue interactions can lead to a change in the energy, conformation, or sequence of the sparse GMEC vs. the original or the full GMEC. Despite the widespread use of sparse residue interaction graphs in protein design, the above mentioned effects of their use have not been previously analyzed. To analyze the costs and benefits of designing with sparse residue interaction graphs, we computed the GMECs for 136 different protein design problems both with and without distance and energy cutoffs, and compared their energies, conformations, and sequences. Our analysis shows that the differences between the GMECs depend critically on whether or not the design includes core, boundary, or surface residues. Moreover, neglecting long-range interactions can alter local interactions and introduce large sequence differences, both of which can result in significant structural and functional changes. Designs on proteins with experimentally measured thermostability show it is beneficial to compute both the full and the sparse GMEC accurately and efficiently. To this end, we show that a provable, ensemble-based algorithm can efficiently compute both GMECs by enumerating a small number of conformations, usually fewer than 1000. This provides a novel way to combine sparse residue interaction graphs with provable, ensemble-based algorithms to reap the benefits of sparse residue interaction graphs while avoiding their potential inaccuracies. Computational structure-based protein design algorithms have successfully redesigned proteins to fold and bind target substrates in vitro, and even in vivo. Because the complexity of a computational design increases dramatically with the number of mutable residues, many design algorithms employ cutoffs (distance or energy) to neglect some pairwise residue interactions, thereby reducing the effective search space and computational cost. However, the energies neglected by such cutoffs can add up, which may have nontrivial effects on the designed sequence and its function. To study the effects of using cutoffs on protein design, we computed the optimal sequence both with and without cutoffs, and showed that neglecting long-range interactions can significantly change the computed conformation and sequence. Designs on proteins with experimentally measured thermostability showed the benefits of computing the optimal sequences (and their conformations), both with and without cutoffs, efficiently and accurately. Therefore, we also showed that a provable, ensemble-based algorithm can efficiently compute the optimal conformation and sequence, both with and without applying cutoffs, by enumerating a small number of conformations, usually fewer than 1000. This provides a novel way to combine cutoffs with provable, ensemble-based algorithms to reap the computational efficiency of cutoffs while avoiding their potential inaccuracies.
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Affiliation(s)
- Swati Jain
- Computational Biology and Bioinformatics Program, Duke University, Durham, North Carolina, United States of America
- Department of Computer Science, Duke University, Durham, North Carolina, United States of America
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Jonathan D. Jou
- Department of Computer Science, Duke University, Durham, North Carolina, United States of America
| | - Ivelin S. Georgiev
- Department of Computer Science, Duke University, Durham, North Carolina, United States of America
| | - Bruce R. Donald
- Department of Computer Science, Duke University, Durham, North Carolina, United States of America
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Chemistry, Duke University, Durham, North Carolina, United States of America
- * E-mail:
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61
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Mazor R, Kaplan G, Park D, Jang Y, Lee F, Kreitman R, Pastan I. Rational design of low immunogenic anti CD25 recombinant immunotoxin for T cell malignancies by elimination of T cell epitopes in PE38. Cell Immunol 2017; 313:59-66. [PMID: 28087047 DOI: 10.1016/j.cellimm.2017.01.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 01/04/2017] [Accepted: 01/04/2017] [Indexed: 12/15/2022]
Abstract
LMB-2, is a potent recombinant immunotoxin (RIT) that is composed of scFv antibody that targets CD25 (Tac) and a toxin fragment (PE38). It is used to treat T cell leukemias and lymphomas. To make LMB-2 less immunogenic, we introduced a large deletion in domain II and six point mutations in domain III that were previously shown to reduce T cell activation in other RITs. We found that unlike other RITs, deletion of domain II from LMB-2 severely compromised its activity. Rather than deletion, we identified T cell epitopes in domain II and used alanine substitutions to identify point mutations that diminished those epitopes. The novel RIT, LMB-142 contains a 38kDa toxin and nine point mutations that diminished T cell response to the corresponding peptides by an average of 75%. LMB-142 has good cytotoxic activity and has lower nonspecific toxicity in mice. LMB-142 should be more efficient in cancer therapy because more treatment cycles can be given.
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Affiliation(s)
- Ronit Mazor
- Laboratory of Molecular Biology, Center for Cancer Research, National Institutes of Health, Bethesda, MD 20892-4264, USA.
| | - Gilad Kaplan
- Laboratory of Molecular Biology, Center for Cancer Research, National Institutes of Health, Bethesda, MD 20892-4264, USA.
| | - Dong Park
- Laboratory of Molecular Biology, Center for Cancer Research, National Institutes of Health, Bethesda, MD 20892-4264, USA.
| | - Youjin Jang
- Laboratory of Molecular Biology, Center for Cancer Research, National Institutes of Health, Bethesda, MD 20892-4264, USA.
| | - Fred Lee
- Laboratory of Molecular Biology, Center for Cancer Research, National Institutes of Health, Bethesda, MD 20892-4264, USA.
| | - Robert Kreitman
- Laboratory of Molecular Biology, Center for Cancer Research, National Institutes of Health, Bethesda, MD 20892-4264, USA.
| | - Ira Pastan
- Laboratory of Molecular Biology, Center for Cancer Research, National Institutes of Health, Bethesda, MD 20892-4264, USA.
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62
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EpiSweep: Computationally Driven Reengineering of Therapeutic Proteins to Reduce Immunogenicity While Maintaining Function. Methods Mol Biol 2017; 1529:375-398. [PMID: 27914063 DOI: 10.1007/978-1-4939-6637-0_20] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Therapeutic proteins are yielding ever more advanced and efficacious new drugs, but the biological origins of these highly effective therapeutics render them subject to immune surveillance within the patient's body. When recognized by the immune system as a foreign agent, protein drugs elicit a coordinated response that can manifest a range of clinical complications including rapid drug clearance, loss of functionality and efficacy, delayed infusion-like allergic reactions, more serious anaphylactic shock, and even induced auto-immunity. It is thus often necessary to deimmunize an exogenous protein in order to enable its clinical application; critically, the deimmunization process must also maintain the desired therapeutic activity.To meet the growing need for effective, efficient, and broadly applicable protein deimmunization technologies, we have developed the EpiSweep suite of protein design algorithms. EpiSweep seamlessly integrates computational prediction of immunogenic T cell epitopes with sequence- or structure-based assessment of the impacts of mutations on protein stability and function, in order to select combinations of mutations that make Pareto optimal trade-offs between the competing goals of low immunogenicity and high-level function. The methods are applicable both to the design of individual functionally deimmunized variants as well as the design of combinatorial libraries enriched in functionally deimmunized variants. After validating EpiSweep in a series of retrospective case studies providing comparisons to conventional approaches to T cell epitope deletion, we have experimentally demonstrated it to be highly effective in prospective application to deimmunization of a number of different therapeutic candidates. We conclude that our broadly applicable computational protein design algorithms guide the engineer towards the most promising deimmunized therapeutic candidates, and thereby have the potential to accelerate development of new protein drugs by shortening time frames and improving hit rates.
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Abstract
Computational protein design (CPD), a yet evolving field, includes computer-aided engineering for partial or full de novo designs of proteins of interest. Designs are defined by a requested structure, function, or working environment. This chapter describes the birth and maturation of the field by presenting 101 CPD examples in a chronological order emphasizing achievements and pending challenges. Integrating these aspects presents the plethora of CPD approaches with the hope of providing a "CPD 101". These reflect on the broader structural bioinformatics and computational biophysics field and include: (1) integration of knowledge-based and energy-based methods, (2) hierarchical designated approach towards local, regional, and global motifs and the integration of high- and low-resolution design schemes that fit each such region, (3) systematic differential approaches towards different protein regions, (4) identification of key hot-spot residues and the relative effect of remote regions, (5) assessment of shape-complementarity, electrostatics and solvation effects, (6) integration of thermal plasticity and functional dynamics, (7) negative design, (8) systematic integration of experimental approaches, (9) objective cross-assessment of methods, and (10) successful ranking of potential designs. Future challenges also include dissemination of CPD software to the general use of life-sciences researchers and the emphasis of success within an in vivo milieu. CPD increases our understanding of protein structure and function and the relationships between the two along with the application of such know-how for the benefit of mankind. Applied aspects range from biological drugs, via healthier and tastier food products to nanotechnology and environmentally friendly enzymes replacing toxic chemicals utilized in the industry.
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Mazor R, Addissie S, Jang Y, Tai CH, Rose J, Hakim F, Pastan I. Role of HLA-DP in the Presentation of Epitopes from the Truncated Bacterial PE38 Immunotoxin. AAPS JOURNAL 2016; 19:117-129. [PMID: 27796910 DOI: 10.1208/s12248-016-9986-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 08/18/2016] [Indexed: 02/07/2023]
Abstract
Identification of helper T-cell epitopes is important in many fields of medicine. We previously used an experimental approach to identify T-cell epitopes in PE38, a truncated bacterial toxin used in immunotoxins. Here, we evaluated the ability of antibodies to DR, DP, or DQ to block T-cell responses to PE38 epitopes in 36 PBMC samples. We predicted the binding affinities of peptides to DR, DP, and DQ alleles using computational tools and analyzed their ability to predict the T-cell epitopes. We found that HLA-DR is responsible for 65% of the responses, DP 24%, and DQ 4%. One epitope that is presented in 20% of the samples (10/50) is entirely DP restricted and was not predicted to bind to DR or DP reference alleles using binding algorithms. We conclude that DP has an important role in helper T-cell response to PE38.
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Affiliation(s)
- Ronit Mazor
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Room 5106, Bethesda, Maryland, 20892-4264, USA
| | - Selamawit Addissie
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Room 5106, Bethesda, Maryland, 20892-4264, USA
| | - Youjin Jang
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Room 5106, Bethesda, Maryland, 20892-4264, USA
| | - Chin-Hsien Tai
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Room 5106, Bethesda, Maryland, 20892-4264, USA
| | - Jeremy Rose
- Experimental Transplantation and Immunology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Fran Hakim
- Experimental Transplantation and Immunology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Ira Pastan
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Room 5106, Bethesda, Maryland, 20892-4264, USA.
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Altai M, Liu H, Orlova A, Tolmachev V, Gräslund T. Influence of molecular design on biodistribution and targeting properties of an Affibody-fused HER2-recognising anticancer toxin. Int J Oncol 2016; 49:1185-94. [DOI: 10.3892/ijo.2016.3614] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 05/20/2016] [Indexed: 11/05/2022] Open
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Griswold KE, Bailey-Kellogg C. Design and engineering of deimmunized biotherapeutics. Curr Opin Struct Biol 2016; 39:79-88. [PMID: 27322891 DOI: 10.1016/j.sbi.2016.06.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 06/03/2016] [Accepted: 06/06/2016] [Indexed: 12/26/2022]
Abstract
Therapeutic proteins are powerful next-generation drugs able to effectively treat diverse and devastating diseases, but the development and use of biotherapeutics entails unique challenges and risks. In particular, protein drugs are subject to immune surveillance in the human body, and ensuing antidrug immune responses can cause a wide range of problems including altered pharmacokinetics, loss of efficacy, and even life-threating complications. Here we review recent progress in technologies for engineering deimmunized biotherapeutics, placing particular emphasis on deletion of immunogenic antibody and T cell epitopes via experimentally or computationally guided mutagenesis.
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Affiliation(s)
- Karl E Griswold
- Thayer School of Engineering, Dartmouth, Hanover, NH, United States; Stealth Biologics LLC, Lyme, NH, United States.
| | - Chris Bailey-Kellogg
- Stealth Biologics LLC, Lyme, NH, United States; Department of Computer Science, Dartmouth, Hanover, NH, United States.
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Abstract
Recombinant immunotoxins (RITs) are chimeric proteins designed to treat cancer. They are made up of an Fv or Fab that targets an antigen on a cancer cell fused to a 38-kDa portion of Pseudomonas exotoxin A (PE38). Because PE38 is a bacterial protein, it is highly immunogenic in patients with solid tumors that have normal immune systems, but much less immunogenic in patients with hematologic malignancies where the immune system is suppressed. RITs have shown efficacy in refractory hairy cell leukemia and in some children with acute lymphoblastic leukemia, but have been much less effective in solid tumors, because neutralizing antibodies develop and prevent additional treatment cycles. In this paper we will (i) review data from clinical trials describing the immunogenicity of PE38 in different patient populations; (ii) review results from clinical trials using different immunosuppressive drugs; and (iii) describe our efforts to make new less-immunogenic RITs by identifying and removing T- and B-cell epitopes to hide the RIT from the immune system.
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Affiliation(s)
- Ronit Mazor
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Masanori Onda
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ira Pastan
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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Zhao H, Verma D, Li W, Choi Y, Ndong C, Fiering SN, Bailey-Kellogg C, Griswold KE. Depletion of T cell epitopes in lysostaphin mitigates anti-drug antibody response and enhances antibacterial efficacy in vivo. ACTA ACUST UNITED AC 2016; 22:629-39. [PMID: 26000749 DOI: 10.1016/j.chembiol.2015.04.017] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 04/16/2015] [Accepted: 04/17/2015] [Indexed: 01/17/2023]
Abstract
The enzyme lysostaphin possesses potent anti-staphylococcal activity and represents a promising antibacterial drug candidate; however, its immunogenicity poses a barrier to clinical translation. Here, structure-based biomolecular design enabled widespread depletion of lysostaphin DRB1(∗)0401 restricted T cell epitopes, and resulting deimmunized variants exhibited striking reductions in anti-drug antibody responses upon administration to humanized HLA-transgenic mice. This reduced immunogenicity translated into improved efficacy in the form of protection against repeated challenges with methicillin-resistant Staphylococcus aureus (MRSA). In contrast, while wild-type lysostaphin was efficacious against the initial MRSA infection, it failed to clear subsequent bacterial challenges that were coincident with escalating anti-drug antibody titers. These results extend the existing deimmunization literature, in which reduced immunogenicity and retained efficacy are assessed independently of each other. By correlating in vivo efficacy with longitudinal measures of anti-drug antibody development, we provide the first direct evidence that T cell epitope depletion manifests enhanced biotherapeutic efficacy.
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Affiliation(s)
- Hongliang Zhao
- Thayer School of Engineering at Dartmouth, 14 Engineering Drive, Hanover, NH 03755, USA; Laboratory of Microorganism Engineering, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing 100071, People's Republic of China
| | - Deeptak Verma
- Department of Computer Science, Dartmouth, 6211 Sudikoff Laboratory, Hanover, NH 03755, USA
| | - Wen Li
- Thayer School of Engineering at Dartmouth, 14 Engineering Drive, Hanover, NH 03755, USA
| | - Yoonjoo Choi
- Department of Computer Science, Dartmouth, 6211 Sudikoff Laboratory, Hanover, NH 03755, USA
| | - Christian Ndong
- Thayer School of Engineering at Dartmouth, 14 Engineering Drive, Hanover, NH 03755, USA
| | - Steven N Fiering
- Department of Microbiology and Immunology, Dartmouth, Hanover, NH 03755, USA; Norris Cotton Cancer Center at Dartmouth, Lebanon, NH 03766, USA
| | - Chris Bailey-Kellogg
- Department of Computer Science, Dartmouth, 6211 Sudikoff Laboratory, Hanover, NH 03755, USA.
| | - Karl E Griswold
- Thayer School of Engineering at Dartmouth, 14 Engineering Drive, Hanover, NH 03755, USA; Norris Cotton Cancer Center at Dartmouth, Lebanon, NH 03766, USA; Department of Biological Sciences, Dartmouth, Hanover, NH 03755, USA.
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69
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Mettu RR, Charles T, Landry SJ. CD4+ T-cell epitope prediction using antigen processing constraints. J Immunol Methods 2016; 432:72-81. [PMID: 26891811 DOI: 10.1016/j.jim.2016.02.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 12/10/2015] [Accepted: 02/11/2016] [Indexed: 02/02/2023]
Abstract
T-cell CD4+ epitopes are important targets of immunity against infectious diseases and cancer. State-of-the-art methods for MHC class II epitope prediction rely on supervised learning methods in which an implicit or explicit model of sequence specificity is constructed using a training set of peptides with experimentally tested MHC class II binding affinity. In this paper we present a novel method for CD4+ T-cell eptitope prediction based on modeling antigen-processing constraints. Previous work indicates that dominant CD4+ T-cell epitopes tend to occur adjacent to sites of initial proteolytic cleavage. Given an antigen with known three-dimensional structure, our algorithm first aggregates four types of conformational stability data in order to construct a profile of stability that allows us to identify regions of the protein that are most accessible to proteolysis. Using this profile, we then construct a profile of epitope likelihood based on the pattern of transitions from unstable to stable regions. We validate our method using 35 datasets of experimentally measured CD4+ T cell responses of mice bearing I-Ab or HLA-DR4 alleles as well as of human subjects. Overall, our results show that antigen processing constraints provide a significant source of predictive power. For epitope prediction in single-allele systems, our approach can be combined with sequence-based methods, or used in instances where little or no training data is available. In multiple-allele systems, sequence-based methods can only be used if the allele distribution of a population is known. In contrast, our approach does not make use of MHC binding prediction, and is thus agnostic to MHC class II genotypes.
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Affiliation(s)
- Ramgopal R Mettu
- Department of Computer Science, Tulane University, New Orleans, LA, USA; Vector-Borne Infectious Diseases Research Center, Tulane University, New Orleans, LA, USA.
| | - Tysheena Charles
- Department of Biochemistry and Molecular Biology, Tulane School of Medicine, New Orleans, LA, USA
| | - Samuel J Landry
- Department of Biochemistry and Molecular Biology, Tulane School of Medicine, New Orleans, LA, USA
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Jou JD, Jain S, Georgiev IS, Donald BR. BWM*: A Novel, Provable, Ensemble-based Dynamic Programming Algorithm for Sparse Approximations of Computational Protein Design. J Comput Biol 2016; 23:413-24. [PMID: 26744898 DOI: 10.1089/cmb.2015.0194] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Sparse energy functions that ignore long range interactions between residue pairs are frequently used by protein design algorithms to reduce computational cost. Current dynamic programming algorithms that fully exploit the optimal substructure produced by these energy functions only compute the GMEC. This disproportionately favors the sequence of a single, static conformation and overlooks better binding sequences with multiple low-energy conformations. Provable, ensemble-based algorithms such as A* avoid this problem, but A* cannot guarantee better performance than exhaustive enumeration. We propose a novel, provable, dynamic programming algorithm called Branch-Width Minimization* (BWM*) to enumerate a gap-free ensemble of conformations in order of increasing energy. Given a branch-decomposition of branch-width w for an n-residue protein design with at most q discrete side-chain conformations per residue, BWM* returns the sparse GMEC in O([Formula: see text]) time and enumerates each additional conformation in merely O([Formula: see text]) time. We define a new measure, Total Effective Search Space (TESS), which can be computed efficiently a priori before BWM* or A* is run. We ran BWM* on 67 protein design problems and found that TESS discriminated between BWM*-efficient and A*-efficient cases with 100% accuracy. As predicted by TESS and validated experimentally, BWM* outperforms A* in 73% of the cases and computes the full ensemble or a close approximation faster than A*, enumerating each additional conformation in milliseconds. Unlike A*, the performance of BWM* can be predicted in polynomial time before running the algorithm, which gives protein designers the power to choose the most efficient algorithm for their particular design problem.
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Affiliation(s)
- Jonathan D Jou
- 1 Department of Computer Science, Duke University , Durham, North Carolina
| | - Swati Jain
- 1 Department of Computer Science, Duke University , Durham, North Carolina.,2 Department of Biochemistry, Duke University Medical Center , Durham, North Carolina.,3 Department of Computational Biology and Bioinformatics Program, Duke University , Durham, North Carolina
| | - Ivelin S Georgiev
- 1 Department of Computer Science, Duke University , Durham, North Carolina
| | - Bruce R Donald
- 1 Department of Computer Science, Duke University , Durham, North Carolina.,2 Department of Biochemistry, Duke University Medical Center , Durham, North Carolina.,4 Department of Chemistry, Duke University , Durham, North Carolina
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71
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Bakail M, Ochsenbein F. Targeting protein–protein interactions, a wide open field for drug design. CR CHIM 2016. [DOI: 10.1016/j.crci.2015.12.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Rad-Malekshahi M, Lempsink L, Amidi M, Hennink WE, Mastrobattista E. Biomedical Applications of Self-Assembling Peptides. Bioconjug Chem 2015; 27:3-18. [DOI: 10.1021/acs.bioconjchem.5b00487] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mazda Rad-Malekshahi
- Department of Pharmaceutics,
Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, 3584
CG Utrecht, The Netherlands
| | - Ludwijn Lempsink
- Department of Pharmaceutics,
Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, 3584
CG Utrecht, The Netherlands
| | - Maryam Amidi
- Department of Pharmaceutics,
Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, 3584
CG Utrecht, The Netherlands
| | - Wim E. Hennink
- Department of Pharmaceutics,
Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, 3584
CG Utrecht, The Netherlands
| | - Enrico Mastrobattista
- Department of Pharmaceutics,
Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, 3584
CG Utrecht, The Netherlands
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73
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Fernández A, Scott LR. Drug leads for interactive protein targets with unknown structure. Drug Discov Today 2015; 21:531-5. [PMID: 26484433 DOI: 10.1016/j.drudis.2015.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 09/29/2015] [Accepted: 10/12/2015] [Indexed: 11/24/2022]
Abstract
The disruption of protein-protein interfaces (PPIs) remains a challenge in drug discovery. The problem becomes daunting when the structure of the target protein is unknown and is even further complicated when the interface is susceptible to disruptive phosphorylation. Based solely on protein sequence and information about phosphorylation-susceptible sites within the PPI, a new technology has been developed to identify drug leads to inhibit protein associations. Here we reveal this technology and contrast it with current structure-based technologies for the generation of drug leads. The novel technology is illustrated by a patented invention to treat heart failure. The success of this technology shows that it is possible to generate drug leads in the absence of target structure.
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Affiliation(s)
- Ariel Fernández
- Argentine Institute of Mathematics (IAM), National Research Council (CONICET), Buenos Aires 1083, Argentina; AF Innovation, Avenida del Libertador 1092, Buenos Aires 1112, Argentina.
| | - L Ridgway Scott
- Department of Computer Science, The University of Chicago, Chicago, IL 60637, USA; Department of Mathematics, The University of Chicago, Chicago, IL 60637, USA
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Bengtsson NE, Seto JT, Hall JK, Chamberlain JS, Odom GL. Progress and prospects of gene therapy clinical trials for the muscular dystrophies. Hum Mol Genet 2015; 25:R9-17. [PMID: 26450518 DOI: 10.1093/hmg/ddv420] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 09/30/2015] [Indexed: 12/16/2022] Open
Abstract
Clinical trials represent a critical avenue for new treatment development, where early phases (I, I/II) are designed to test safety and effectiveness of new therapeutics or diagnostic indicators. A number of recent advances have spurred renewed optimism toward initiating clinical trials and developing refined therapies for the muscular dystrophies (MD's) and other myogenic disorders. MD's encompass a heterogeneous group of degenerative disorders often characterized by progressive muscle weakness and fragility. Many of these diseases result from mutations in genes encoding proteins of the dystrophin-glycoprotein complex (DGC). The most common and severe form among children is Duchenne muscular dystrophy, caused by mutations in the dystrophin gene, with an average life expectancy around 25 years of age. Another group of MD's referred to as the limb-girdle muscular dystrophies (LGMDs) can affect boys or girls, with different types caused by mutations in different genes. Mutation of the α-sarcoglycan gene, also a DGC component, causes LGMD2D and represents the most common form of LGMD. Early preclinical and clinical trial findings support the feasibility of gene therapy via recombinant adeno-associated viral vectors as a viable treatment approach for many MDs. In this mini-review, we present an overview of recent progress in clinical gene therapy trials of the MD's and touch upon promising preclinical advances.
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Affiliation(s)
| | | | | | - Jeffrey S Chamberlain
- Department of Neurology and Department of Biochemistry, University of Washington School of Medicine, Seattle, WA 98195-7350, USA
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Mazor R, Tai CH, Lee B, Pastan I. Poor correlation between T-cell activation assays and HLA-DR binding prediction algorithms in an immunogenic fragment of Pseudomonas exotoxin A. J Immunol Methods 2015; 425:10-20. [PMID: 26056938 PMCID: PMC4604018 DOI: 10.1016/j.jim.2015.06.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 06/02/2015] [Accepted: 06/03/2015] [Indexed: 12/20/2022]
Abstract
The ability to identify immunogenic determinants that activate T-cells is important for the development of new vaccines, allergy therapy and protein therapeutics. In silico MHC-II binding prediction algorithms are often used for T-cell epitope identification. To understand how well those programs predict immunogenicity, we computed HLA binding to peptides spanning the sequence of PE38, a fragment of an anti-cancer immunotoxin, and compared the predicted and experimentally identified T-cell epitopes. We found that the prediction for individual donors did not correlate well with the experimental data. Furthermore, prediction of T-cell epitopes in an HLA heterogenic population revealed that the two strongest epitopes were predicted at multiple cutoffs but the third epitope was predicted negative at all cutoffs and overall 4/9 epitopes were missed at several cutoffs. We conclude that MHC class-II binding predictions are not sufficient to predict the T-cell epitopes in PE38 and should be supplemented by experimental work.
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Affiliation(s)
- Ronit Mazor
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Chin-Hsien Tai
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Byungkook Lee
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Ira Pastan
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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76
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Manlove LS, Berquam-Vrieze KE, Pauken KE, Williams RT, Jenkins MK, Farrar MA. Adaptive Immunity to Leukemia Is Inhibited by Cross-Reactive Induced Regulatory T Cells. THE JOURNAL OF IMMUNOLOGY 2015; 195:4028-37. [PMID: 26378075 DOI: 10.4049/jimmunol.1501291] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 08/17/2015] [Indexed: 12/21/2022]
Abstract
BCR-ABL(+) acute lymphoblastic leukemia patients have transient responses to current therapies. However, the fusion of BCR to ABL generates a potential leukemia-specific Ag that could be a target for immunotherapy. We demonstrate that the immune system can limit BCR-ABL(+) leukemia progression although ultimately this immune response fails. To address how BCR-ABL(+) leukemia escapes immune surveillance, we developed a peptide: MHC class II tetramer that labels endogenous BCR-ABL-specific CD4(+) T cells. Naive mice harbored a small population of BCR-ABL-specific T cells that proliferated modestly upon immunization. The small number of naive BCR-ABL-specific T cells was due to negative selection in the thymus, which depleted BCR-ABL-specific T cells. Consistent with this observation, we saw that BCR-ABL-specific T cells were cross-reactive with an endogenous peptide derived from ABL. Despite this cross-reactivity, the remaining population of BCR-ABL reactive T cells proliferated upon immunization with the BCR-ABL fusion peptide and adjuvant. In response to BCR-ABL(+) leukemia, BCR-ABL-specific T cells proliferated and converted into regulatory T (Treg) cells, a process that was dependent on cross-reactivity with self-antigen, TGF-β1, and MHC class II Ag presentation by leukemic cells. Treg cells were critical for leukemia progression in C57BL/6 mice, as transient Treg cell ablation led to extended survival of leukemic mice. Thus, BCR-ABL(+) leukemia actively suppresses antileukemia immune responses by converting cross-reactive leukemia-specific T cells into Treg cells.
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Affiliation(s)
- Luke S Manlove
- Center for Immunology, University of Minnesota, Minneapolis, MN 55455; Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455
| | - Katherine E Berquam-Vrieze
- Center for Immunology, University of Minnesota, Minneapolis, MN 55455; Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455
| | - Kristen E Pauken
- Center for Immunology, University of Minnesota, Minneapolis, MN 55455; Institute for Immunology, Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19444
| | | | - Marc K Jenkins
- Center for Immunology, University of Minnesota, Minneapolis, MN 55455; Department of Microbiology, University of Minnesota, Minneapolis, MN 55455
| | - Michael A Farrar
- Center for Immunology, University of Minnesota, Minneapolis, MN 55455; Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455;
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Choi Y, Hua C, Sentman CL, Ackerman ME, Bailey-Kellogg C. Antibody humanization by structure-based computational protein design. MAbs 2015; 7:1045-57. [PMID: 26252731 PMCID: PMC5045135 DOI: 10.1080/19420862.2015.1076600] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 07/06/2015] [Accepted: 07/20/2015] [Indexed: 12/15/2022] Open
Abstract
Antibodies derived from non-human sources must be modified for therapeutic use so as to mitigate undesirable immune responses. While complementarity-determining region (CDR) grafting-based humanization techniques have been successfully applied in many cases, it remains challenging to maintain the desired stability and antigen binding affinity upon grafting. We developed an alternative humanization approach called CoDAH ("Computationally-Driven Antibody Humanization") in which computational protein design methods directly select sets of amino acids to incorporate from human germline sequences to increase humanness while maintaining structural stability. Retrospective studies show that CoDAH is able to identify variants deemed beneficial according to both humanness and structural stability criteria, even for targets lacking crystal structures. Prospective application to TZ47, a murine anti-human B7H6 antibody, demonstrates the approach. Four diverse humanized variants were designed, and all possible unique VH/VL combinations were produced as full-length IgG1 antibodies. Soluble and cell surface expressed antigen binding assays showed that 75% (6 of 8) of the computationally designed VH/VL variants were successfully expressed and competed with the murine TZ47 for binding to B7H6 antigen. Furthermore, 4 of the 6 bound with an estimated KD within an order of magnitude of the original TZ47 antibody. In contrast, a traditional CDR-grafted variant could not be expressed. These results suggest that the computational protein design approach described here can be used to efficiently generate functional humanized antibodies and provide humanized templates for further affinity maturation.
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Affiliation(s)
- Yoonjoo Choi
- Department of Computer Science; Dartmouth College; Hanover, NH USA
| | - Casey Hua
- Thayer School of Engineering; Dartmouth College; Hanover, NH USA
- Department of Microbiology and Immunology; Geisel School of Medicine; Dartmouth College; Lebanon, NH USA
| | - Charles L Sentman
- Department of Microbiology and Immunology; Geisel School of Medicine; Dartmouth College; Lebanon, NH USA
| | - Margaret E Ackerman
- Thayer School of Engineering; Dartmouth College; Hanover, NH USA
- Department of Microbiology and Immunology; Geisel School of Medicine; Dartmouth College; Lebanon, NH USA
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Liu H, Seijsing J, Frejd FY, Tolmachev V, Gräslund T. Target-specific cytotoxic effects on HER2-expressing cells by the tripartite fusion toxin ZHER2:2891-ABD-PE38X8, including a targeting affibody molecule and a half-life extension domain. Int J Oncol 2015; 47:601-9. [PMID: 26046132 DOI: 10.3892/ijo.2015.3027] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 04/02/2015] [Indexed: 11/06/2022] Open
Abstract
Development of cancer treatment regimens including immunotoxins is partly hampered by their immunogenicity. Recently, deimmunized versions of toxins have been described, potentially being better suited for translation to the clinic. In this study, a recombinant tripartite fusion toxin consisting of a deimmunized version of exotoxin A from Pseudomonas aeruginosa (PE38) genetically fused to an affibody molecule specifically interacting with the human epidermal growth factor receptor 2 (HER2), and also an albumin binding domain (ABD) for half-life extension, has been produced and characterized in terms of functionality of the three moieties. Biosensor based assays showed that the fusion toxin was able to interact with human and mouse serum albumin, but not with bovine serum albumin and that it interacted with HER2 (KD=5 nM). Interestingly, a complex of the fusion toxin and human serum albumin also interacted with HER2 but with a somewhat weaker affinity (KD=12 nM). The IC50-values of the fusion toxin ranged from 6 to 300 pM on SKOV-3, SKBR-3 and A549 cells and was lower for cells with higher surface densities of HER2. The fusion toxin was found specific for HER2 as shown by blocking available HER2 receptors with free affibody molecule before subjecting the cells to the toxin. Analysis of contact time showed that 10 min was sufficient to kill 50% of the cells. In conclusion, all three regions of the fusion toxin were found to be functional.
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Affiliation(s)
- Hao Liu
- School of Biotechnology, Division of Protein Technology, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Johan Seijsing
- School of Biotechnology, Division of Protein Technology, KTH - Royal Institute of Technology, Stockholm, Sweden
| | | | - Vladimir Tolmachev
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Torbjörn Gräslund
- School of Biotechnology, Division of Protein Technology, KTH - Royal Institute of Technology, Stockholm, Sweden
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79
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Auger A, Park M, Nitschke F, Minassian LM, Beilhartz GL, Minassian BA, Melnyk RA. Efficient Delivery of Structurally Diverse Protein Cargo into Mammalian Cells by a Bacterial Toxin. Mol Pharm 2015; 12:2962-71. [DOI: 10.1021/acs.molpharmaceut.5b00233] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anick Auger
- Program in Molecular Structure & Function, The Hospital for Sick Children, Toronto, ON, Canada
| | - Minyoung Park
- Program in Molecular Structure & Function, The Hospital for Sick Children, Toronto, ON, Canada
- Department
of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Felix Nitschke
- Program in Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Lori M. Minassian
- Program in Molecular Structure & Function, The Hospital for Sick Children, Toronto, ON, Canada
| | - Greg L. Beilhartz
- Program in Molecular Structure & Function, The Hospital for Sick Children, Toronto, ON, Canada
| | - Berge A. Minassian
- Program in Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department
of Paediatrics, University of Toronto, Toronto, ON, Canada
| | - Roman A. Melnyk
- Program in Molecular Structure & Function, The Hospital for Sick Children, Toronto, ON, Canada
- Department
of Biochemistry, University of Toronto, Toronto, ON, Canada
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80
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Salvat RS, Choi Y, Bishop A, Bailey-Kellogg C, Griswold KE. Protein deimmunization via structure-based design enables efficient epitope deletion at high mutational loads. Biotechnol Bioeng 2015; 112:1306-18. [PMID: 25655032 PMCID: PMC4452428 DOI: 10.1002/bit.25554] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Revised: 01/09/2015] [Accepted: 01/18/2015] [Indexed: 12/31/2022]
Abstract
Anti-drug immune responses are a unique risk factor for biotherapeutics, and undesired immunogenicity can alter pharmacokinetics, compromise drug efficacy, and in some cases even threaten patient safety. To fully capitalize on the promise of biotherapeutics, more efficient and generally applicable protein deimmunization tools are needed. Mutagenic deletion of a protein's T cell epitopes is one powerful strategy to engineer immunotolerance, but deimmunizing mutations must maintain protein structure and function. Here, EpiSweep, a structure-based protein design and deimmunization algorithm, has been used to produce a panel of seven beta-lactamase drug candidates having 27-47% reductions in predicted epitope content. Despite bearing eight mutations each, all seven engineered enzymes maintained good stability and activity. At the same time, the variants exhibited dramatically reduced interaction with human class II major histocompatibility complex proteins, key regulators of anti-drug immune responses. When compared to 8-mutation designs generated with a sequence-based deimmunization algorithm, the structure-based designs retained greater thermostability and possessed fewer high affinity epitopes, the dominant drivers of anti-biotherapeutic immune responses. These experimental results validate the first structure-based deimmunization algorithm capable of mapping optimal biotherapeutic design space. By designing optimal mutations that reduce immunogenic potential while imparting favorable intramolecular interactions, broadly distributed epitopes may be simultaneously targeted using high mutational loads.
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Affiliation(s)
- Regina S Salvat
- Thayer School of Engineering, Dartmouth, 14 Engineering Dr., Hanover, New Hampshire, 03755
| | - Yoonjoo Choi
- Department of Computer Science, Dartmouth, 6211 Sudikoff Laboratory, Hanover, New Hampshire, 03755
| | | | - Chris Bailey-Kellogg
- Department of Computer Science, Dartmouth, 6211 Sudikoff Laboratory, Hanover, New Hampshire, 03755.
| | - Karl E Griswold
- Thayer School of Engineering, Dartmouth, 14 Engineering Dr., Hanover, New Hampshire, 03755.
- Program in Molecular and Cellular Biology, Dartmouth, Hanover, New Hampshire.
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81
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Blazanovic K, Zhao H, Choi Y, Li W, Salvat RS, Osipovitch DC, Fields J, Moise L, Berwin BL, Fiering SN, Bailey-Kellogg C, Griswold KE. Structure-based redesign of lysostaphin yields potent antistaphylococcal enzymes that evade immune cell surveillance. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2015; 2:15021. [PMID: 26151066 PMCID: PMC4470366 DOI: 10.1038/mtm.2015.21] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 04/15/2015] [Accepted: 04/17/2015] [Indexed: 12/22/2022]
Abstract
Staphylococcus aureus infections exert a tremendous burden on the health-care system, and the threat of drug-resistant strains continues to grow. The bacteriolytic enzyme lysostaphin is a potent antistaphylococcal agent with proven efficacy against both drug-sensitive and drug-resistant strains; however, the enzyme's own bacterial origins cause undesirable immunogenicity and pose a barrier to clinical translation. Here, we deimmunized lysostaphin using a computationally guided process that optimizes sets of mutations to delete immunogenic T cell epitopes without disrupting protein function. In vitro analyses showed the methods to be both efficient and effective, producing seven different deimmunized designs exhibiting high function and reduced immunogenic potential. Two deimmunized candidates elicited greatly suppressed proliferative responses in splenocytes from humanized mice, while at the same time the variants maintained wild-type efficacy in a staphylococcal pneumonia model. Overall, the deimmunized enzymes represent promising leads in the battle against S. aureus.
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Affiliation(s)
| | - Hongliang Zhao
- Thayer School of Engineering, Dartmouth , Hanover, New Hampshire, USA ; Laboratory of Microorganism Engineering, Beijing Institute of Biotechnology , Beijing, People's Republic of China
| | - Yoonjoo Choi
- Department of Computer Science, Dartmouth , Hanover, New Hampshire, USA
| | - Wen Li
- Thayer School of Engineering, Dartmouth , Hanover, New Hampshire, USA
| | - Regina S Salvat
- Thayer School of Engineering, Dartmouth , Hanover, New Hampshire, USA
| | - Daniel C Osipovitch
- Program in Experimental and Molecular Medicine, Dartmouth , Hanover, New Hampshire, USA
| | - Jennifer Fields
- Department of Microbiology and Immunology, Dartmouth , Hanover, New Hampshire, USA
| | - Leonard Moise
- Institute for Immunology and Informatics, University of Rhode Island , Providence, Rhode Island, USA
| | - Brent L Berwin
- Department of Microbiology and Immunology, Dartmouth , Hanover, New Hampshire, USA ; Norris Cotton Cancer Center, Dartmouth , Hanover, New Hampshire, USA
| | - Steven N Fiering
- Department of Microbiology and Immunology, Dartmouth , Hanover, New Hampshire, USA ; Norris Cotton Cancer Center, Dartmouth , Hanover, New Hampshire, USA
| | | | - Karl E Griswold
- Thayer School of Engineering, Dartmouth , Hanover, New Hampshire, USA ; Norris Cotton Cancer Center, Dartmouth , Hanover, New Hampshire, USA ; Department of Biological Sciences, Dartmouth , Hanover, New Hampshire, USA
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82
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Tateno H, Onuma Y, Ito Y, Minoshima F, Saito S, Shimizu M, Aiki Y, Asashima M, Hirabayashi J. Elimination of tumorigenic human pluripotent stem cells by a recombinant lectin-toxin fusion protein. Stem Cell Reports 2015; 4:811-20. [PMID: 25866158 PMCID: PMC4437484 DOI: 10.1016/j.stemcr.2015.02.016] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 02/21/2015] [Accepted: 02/23/2015] [Indexed: 12/11/2022] Open
Abstract
The application of stem-cell-based therapies in regenerative medicine is hindered by the tumorigenic potential of residual human pluripotent stem cells. Previously, we identified a human pluripotent stem-cell-specific lectin probe, called rBC2LCN, by comprehensive glycome analysis using high-density lectin microarrays. Here we developed a recombinant lectin-toxin fusion protein of rBC2LCN with a catalytic domain of Pseudomonas aeruginosa exotoxin A, termed rBC2LCN-PE23, which could be expressed as a soluble form from the cytoplasm of Escherichia coli and purified to homogeneity by one-step affinity chromatography. rBC2LCN-PE23 bound to human pluripotent stem cells, followed by its internalization, allowing intracellular delivery of a cargo of cytotoxic protein. The addition of rBC2LCN-PE23 to the culture medium was sufficient to completely eliminate human pluripotent stem cells. Thus, rBC2LCN-PE23 has the potential to contribute to the safety of stem-cell-based therapies.
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Affiliation(s)
- Hiroaki Tateno
- Research Center for Stem Cell Engineering, National Institute of Advanced Industrial Science and Technology, Tsukuba Central 2, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan.
| | - Yasuko Onuma
- Research Center for Stem Cell Engineering, National Institute of Advanced Industrial Science and Technology, Tsukuba Central 4, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8562, Japan
| | - Yuzuru Ito
- Research Center for Stem Cell Engineering, National Institute of Advanced Industrial Science and Technology, Tsukuba Central 4, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8562, Japan
| | - Fumi Minoshima
- Research Center for Stem Cell Engineering, National Institute of Advanced Industrial Science and Technology, Tsukuba Central 2, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Sayoko Saito
- Research Center for Stem Cell Engineering, National Institute of Advanced Industrial Science and Technology, Tsukuba Central 2, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Madoka Shimizu
- Research Center for Stem Cell Engineering, National Institute of Advanced Industrial Science and Technology, Tsukuba Central 4, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8562, Japan
| | - Yasuhiko Aiki
- Research Center for Stem Cell Engineering, National Institute of Advanced Industrial Science and Technology, Tsukuba Central 4, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8562, Japan
| | - Makoto Asashima
- Research Center for Stem Cell Engineering, National Institute of Advanced Industrial Science and Technology, Tsukuba Central 4, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8562, Japan
| | - Jun Hirabayashi
- Research Center for Stem Cell Engineering, National Institute of Advanced Industrial Science and Technology, Tsukuba Central 2, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
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83
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Sliepen K, van Montfort T, Melchers M, Isik G, Sanders RW. Immunosilencing a highly immunogenic protein trimerization domain. J Biol Chem 2015; 290:7436-42. [PMID: 25635058 DOI: 10.1074/jbc.m114.620534] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Many therapeutic proteins and protein subunit vaccines contain heterologous trimerization domains, such as the widely used GCN4-based isoleucine zipper (IZ) and the T4 bacteriophage fibritin foldon (Fd) trimerization domains. We found that these domains induced potent anti-IZ or anti-Fd antibody responses in animals when fused to an HIV-1 envelope glycoprotein (Env) immunogen. To dampen IZ-induced responses, we constructed an IZ domain containing four N-linked glycans (IZN4) to shield the underlying protein surface. When fused to two different vaccine antigens, HIV-1 Env and influenza hemagglutinin (HA), IZN4 strongly reduced the antibody responses against the IZ, but did not affect the antibody titers against Env or HA. Silencing of immunogenic multimerization domains with glycans might be relevant for therapeutic proteins and protein vaccines.
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Affiliation(s)
- Kwinten Sliepen
- From the Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands and
| | - Thijs van Montfort
- From the Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands and
| | - Mark Melchers
- From the Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands and
| | - Gözde Isik
- From the Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands and
| | - Rogier W Sanders
- From the Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands and Weill Medical College of Cornell University, New York, New York 10065
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84
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Jou JD, Jain S, Georgiev I, Donald BR. BWM*: A Novel, Provable, Ensemble-Based Dynamic Programming Algorithm for Sparse Approximations of Computational Protein Design. LECTURE NOTES IN COMPUTER SCIENCE 2015. [DOI: 10.1007/978-3-319-16706-0_16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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85
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Research Highlights. Nat Biotechnol 2014. [DOI: 10.1038/nbt.2992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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86
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van den Berg BA, Reinders MJ, van der Laan JM, Roubos JA, de Ridder D. Protein redesign by learning from data. Protein Eng Des Sel 2014; 27:281-8. [DOI: 10.1093/protein/gzu031] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
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87
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Mazor R, Eberle JA, Hu X, Vassall AN, Onda M, Beers R, Lee EC, Kreitman RJ, Lee B, Baker D, King C, Hassan R, Benhar I, Pastan I. Recombinant immunotoxin for cancer treatment with low immunogenicity by identification and silencing of human T-cell epitopes. Proc Natl Acad Sci U S A 2014; 111:8571-6. [PMID: 24799704 PMCID: PMC4060717 DOI: 10.1073/pnas.1405153111] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Nonhuman proteins have valuable therapeutic properties, but their efficacy is limited by neutralizing antibodies. Recombinant immunotoxins (RITs) are potent anticancer agents that have produced many complete remissions in leukemia, but immunogenicity limits the number of doses that can be given to patients with normal immune systems. Using human cells, we identified eight helper T-cell epitopes in PE38, a portion of the bacterial protein Pseudomonas exotoxin A which consists of the toxin moiety of the RIT, and used this information to make LMB-T18 in which three epitopes were deleted and five others diminished by point mutations in key residues. LMB-T18 has high cytotoxic and antitumor activity and is very resistant to thermal denaturation. The new immunotoxin has a 93% decrease in T-cell epitopes and should have improved efficacy in patients because more treatment cycles can be given. Furthermore, the deimmunized toxin can be used to make RITs targeting other antigens, and the approach we describe can be used to deimmunize other therapeutically useful nonhuman proteins.
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Affiliation(s)
- Ronit Mazor
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892;Department of Molecular Microbiology and Biotechnology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 6998, Israel
| | - Jaime A Eberle
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Xiaobo Hu
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Aaron N Vassall
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Masanori Onda
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Richard Beers
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Elizabeth C Lee
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Robert J Kreitman
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Byungkook Lee
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - David Baker
- Institute for Protein Design, Department of Biochemistry, University of Washington, Seattle, WA 98122; and
| | - Chris King
- Institute for Protein Design, Department of Biochemistry, University of Washington, Seattle, WA 98122; and
| | - Raffit Hassan
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892;Thoracic and Gastrointestinal Oncology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Itai Benhar
- Department of Molecular Microbiology and Biotechnology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 6998, Israel
| | - Ira Pastan
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892;
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