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Arslan M, Karadag D, Kalyoncu S. Conformational changes in a Vernier zone region: Implications for antibody dual specificity. Proteins 2020; 88:1447-1457. [PMID: 32526069 DOI: 10.1002/prot.25964] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 03/23/2020] [Accepted: 06/06/2020] [Indexed: 11/07/2022]
Abstract
Understanding the determinants of antibody specificity is one of the challenging tasks in antibody development. Monospecific antibodies are still dominant in approved antibody therapeutics but there is a significant body of work to show that multispecific antibodies can increase the overall therapeutic effect. Dual-specific or "Two-in-One" antibodies can bind to two different antigens separately with the same antigen-binding site as opposed to bispecifics, which simultaneously bind to two different antigens through separate antigen-binding units. These nonstandard dual-specific antibodies were recently shown to be promising for new antibody-based therapeutics. Here, we physicochemically and structurally analyzed six different antibodies of which two are monospecific and four are dual-specific antibodies derived from monospecific templates to gain insight about dual-specificity determinants. These dual-specific antibodies can target both human epidermal growth factor receptor 2 and vascular endothelial growth factor at different binding affinities. We showed that a particular region of clustered Vernier zone residues might play key roles in gaining dual specificity. While there are minimal intramolecular interactions between a certain Vernier zone region, namely LV4 and LCDR1 of monospecific template, there is a significant structural change and consequently close contact formation between LV4-LCDR1 loops of derived dual-specific antibodies. Although Vernier zone residues were previously shown to be important for humanization applications, they are mostly underestimated in the literature. Here, we also aim to resurrect Vernier zone residues for antibody engineering efforts.
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Affiliation(s)
- Merve Arslan
- Izmir Biomedicine and Genome Center, Izmir, Turkey.,Izmir Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
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52
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Gentiluomo L, Svilenov HL, Augustijn D, El Bialy I, Greco ML, Kulakova A, Indrakumar S, Mahapatra S, Morales MM, Pohl C, Roche A, Tosstorff A, Curtis R, Derrick JP, Nørgaard A, Khan TA, Peters GHJ, Pluen A, Rinnan Å, Streicher WW, van der Walle CF, Uddin S, Winter G, Roessner D, Harris P, Frieß W. Advancing Therapeutic Protein Discovery and Development through Comprehensive Computational and Biophysical Characterization. Mol Pharm 2020; 17:426-440. [PMID: 31790599 DOI: 10.1021/acs.molpharmaceut.9b00852] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Therapeutic protein candidates should exhibit favorable properties that render them suitable to become drugs. Nevertheless, there are no well-established guidelines for the efficient selection of proteinaceous molecules with desired features during early stage development. Such guidelines can emerge only from a large body of published research that employs orthogonal techniques to characterize therapeutic proteins in different formulations. In this work, we share a study on a diverse group of proteins, including their primary sequences, purity data, and computational and biophysical characterization at different pH and ionic strength. We report weak linear correlations between many of the biophysical parameters. We suggest that a stability comparison of diverse therapeutic protein candidates should be based on a computational and biophysical characterization in multiple formulation conditions, as the latter can largely determine whether a protein is above or below a certain stability threshold. We use the presented data set to calculate several stability risk scores obtained with an increasing level of analytical effort and show how they correlate with protein aggregation during storage. Our work highlights the importance of developing combined risk scores that can be used for early stage developability assessment. We suggest that such scores can have high prediction accuracy only when they are based on protein stability characterization in different solution conditions.
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Affiliation(s)
- Lorenzo Gentiluomo
- Wyatt Technology Europe GmbH , Hochstrasse 18 , 56307 Dernbach , Germany.,Department of Pharmacy, Pharmaceutical Technology and Biopharmaceutics , Ludwig-Maximilians-Universitaet Muenchen , Butenandtstrasse 5 , 81377 Munich , Germany
| | - Hristo L Svilenov
- Department of Pharmacy, Pharmaceutical Technology and Biopharmaceutics , Ludwig-Maximilians-Universitaet Muenchen , Butenandtstrasse 5 , 81377 Munich , Germany
| | - Dillen Augustijn
- Department of Food Science, Faculty of Science , Copenhagen University , Rolighedsvej 26 , 1958 Frederiksberg , Denmark
| | - Inas El Bialy
- Department of Pharmacy, Pharmaceutical Technology and Biopharmaceutics , Ludwig-Maximilians-Universitaet Muenchen , Butenandtstrasse 5 , 81377 Munich , Germany
| | - Maria Laura Greco
- Dosage Form Design and Development , AstraZeneca , Sir Aaron Klug Building, Granta Park , Cambridge CB21 6GH , U.K
| | - Alina Kulakova
- Department of Chemistry , Technical University of Denmark , Kemitorvet 207 , 2800 Kongens Lyngby , Denmark
| | - Sowmya Indrakumar
- Department of Chemistry , Technical University of Denmark , Kemitorvet 207 , 2800 Kongens Lyngby , Denmark
| | | | - Marcello Martinez Morales
- Dosage Form Design and Development , AstraZeneca , Sir Aaron Klug Building, Granta Park , Cambridge CB21 6GH , U.K
| | - Christin Pohl
- Novozymes A/S , Krogshoejvej 36 , 2880 Bagsvaerd , Denmark
| | - Aisling Roche
- School of Chemical Engineering and Analytical Science, Manchester Institute of Biotechnology , The University of Manchester , 131 Princess Street , Manchester M1 7DN , U.K
| | - Andreas Tosstorff
- Department of Pharmacy, Pharmaceutical Technology and Biopharmaceutics , Ludwig-Maximilians-Universitaet Muenchen , Butenandtstrasse 5 , 81377 Munich , Germany
| | - Robin Curtis
- School of Chemical Engineering and Analytical Science, Manchester Institute of Biotechnology , The University of Manchester , 131 Princess Street , Manchester M1 7DN , U.K
| | - Jeremy P Derrick
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre , The University of Manchester , Oxford Road , Manchester M13 9PT , U.K
| | - Allan Nørgaard
- Novozymes A/S , Krogshoejvej 36 , 2880 Bagsvaerd , Denmark
| | - Tarik A Khan
- Pharmaceutical Development & Supplies, Pharma Technical Development Biologics Europe , F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124 , 4070 Basel , Switzerland
| | - Günther H J Peters
- Department of Chemistry , Technical University of Denmark , Kemitorvet 207 , 2800 Kongens Lyngby , Denmark
| | - Alain Pluen
- School of Chemical Engineering and Analytical Science, Manchester Institute of Biotechnology , The University of Manchester , 131 Princess Street , Manchester M1 7DN , U.K
| | - Åsmund Rinnan
- Department of Food Science, Faculty of Science , Copenhagen University , Rolighedsvej 26 , 1958 Frederiksberg , Denmark
| | | | - Christopher F van der Walle
- Dosage Form Design and Development , AstraZeneca , Sir Aaron Klug Building, Granta Park , Cambridge CB21 6GH , U.K
| | - Shahid Uddin
- Dosage Form Design and Development , AstraZeneca , Sir Aaron Klug Building, Granta Park , Cambridge CB21 6GH , U.K
| | - Gerhard Winter
- Department of Pharmacy, Pharmaceutical Technology and Biopharmaceutics , Ludwig-Maximilians-Universitaet Muenchen , Butenandtstrasse 5 , 81377 Munich , Germany
| | - Dierk Roessner
- Wyatt Technology Europe GmbH , Hochstrasse 18 , 56307 Dernbach , Germany
| | - Pernille Harris
- Department of Chemistry , Technical University of Denmark , Kemitorvet 207 , 2800 Kongens Lyngby , Denmark
| | - Wolfgang Frieß
- Department of Pharmacy, Pharmaceutical Technology and Biopharmaceutics , Ludwig-Maximilians-Universitaet Muenchen , Butenandtstrasse 5 , 81377 Munich , Germany
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53
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Goulet DR, Atkins WM. Considerations for the Design of Antibody-Based Therapeutics. J Pharm Sci 2020; 109:74-103. [PMID: 31173761 PMCID: PMC6891151 DOI: 10.1016/j.xphs.2019.05.031] [Citation(s) in RCA: 146] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 05/02/2019] [Accepted: 05/29/2019] [Indexed: 02/06/2023]
Abstract
Antibody-based proteins have become an important class of biologic therapeutics, due in large part to the stability, specificity, and adaptability of the antibody framework. Indeed, antibodies not only have the inherent ability to bind both antigens and endogenous immune receptors but also have proven extremely amenable to protein engineering. Thus, several derivatives of the monoclonal antibody format, including bispecific antibodies, antibody-drug conjugates, and antibody fragments, have demonstrated efficacy for treating human disease, particularly in the fields of immunology and oncology. Reviewed here are considerations for the design of antibody-based therapeutics, including immunological context, therapeutic mechanisms, and engineering strategies. First, characteristics of antibodies are introduced, with emphasis on structural domains, functionally important receptors, isotypic and allotypic differences, and modifications such as glycosylation. Then, aspects of therapeutic antibody design are discussed, including identification of antigen-specific variable regions, choice of expression system, use of multispecific formats, and design of antibody derivatives based on fragmentation, oligomerization, or conjugation to other functional moieties. Finally, strategies to enhance antibody function through protein engineering are reviewed while highlighting the impact of fundamental biophysical properties on protein developability.
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Affiliation(s)
- Dennis R Goulet
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195.
| | - William M Atkins
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195
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Ferreira GM, Shahfar H, Sathish HA, Remmele RL, Roberts CJ. Identifying Key Residues That Drive Strong Electrostatic Attractions between Therapeutic Antibodies. J Phys Chem B 2019; 123:10642-10653. [PMID: 31739660 DOI: 10.1021/acs.jpcb.9b08355] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Attractive electrostatic protein-protein interactions (PPI) necessarily involve identifying oppositely charged regions of the protein surface that interact favorably. This cannot be done reliably if one only considers a single protein in isolation unless there are obvious charge "patches" that result in extreme molecular dipoles. Prior work [ J. Pharm. Sci. 2019 , 108 , 120 - 132 ] identified three monoclonal antibodies (MAbs) that displayed experimental behavior ranging from net repulsive to strongly attractive electrostatic interactions. The present work provides a systematic computational approach for identifying the origin of diverse PPI, in terms of which sets of amino acids or individual amino acids are most influential, and determining if there are different patterns of pairwise amino acid interaction "maps" that result in different behaviors. The charge was eliminated computationally, one by one, for each charged residue in the wild-type sequences, which resulted in predicted changes in the second osmotic virial coefficient. The results highlight interaction "maps" that correspond to cases with qualitatively different net electrostatic PPI for the different MAbs and solution conditions, as well as key sets of residues that contribute to strongly attractive PPI. A more computationally efficient method is also proposed to identify key amino acids based on Mayer-weighted interaction energies.
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Affiliation(s)
- Glenn M Ferreira
- Department of Chemical and Biomolecular Engineering , University of Delaware , Newark , Delaware 19716 , United States
| | - Hassan Shahfar
- Department of Chemical and Biomolecular Engineering , University of Delaware , Newark , Delaware 19716 , United States.,Department of Physics and Astronomy , University of Delaware , Newark , Delaware 19716 , United States
| | | | | | - Christopher J Roberts
- Department of Chemical and Biomolecular Engineering , University of Delaware , Newark , Delaware 19716 , United States
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Julian MC, Rabia LA, Desai AA, Arsiwala A, Gerson JE, Paulson HL, Kane RS, Tessier PM. Nature-inspired design and evolution of anti-amyloid antibodies. J Biol Chem 2019; 294:8438-8451. [PMID: 30918024 DOI: 10.1074/jbc.ra118.004731] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 03/21/2019] [Indexed: 12/17/2022] Open
Abstract
Antibodies that recognize amyloidogenic aggregates with high conformational and sequence specificity are important for detecting and potentially treating a wide range of neurodegenerative disorders, including Alzheimer's and Parkinson's diseases. However, these types of antibodies are challenging to generate because of the large size, hydrophobicity, and heterogeneity of protein aggregates. To address this challenge, we developed a method for generating antibodies specific for amyloid aggregates. First, we grafted amyloidogenic peptide segments from the target polypeptide [Alzheimer's amyloid-β (Aβ) peptide] into the complementarity-determining regions (CDRs) of a stable antibody scaffold. Next, we diversified the grafted and neighboring CDR sites using focused mutagenesis to sample each WT or grafted residue, as well as one to five of the most commonly occurring amino acids at each site in human antibodies. Finally, we displayed these antibody libraries on the surface of yeast cells and selected antibodies that strongly recognize Aβ-amyloid fibrils and only weakly recognize soluble Aβ. We found that this approach enables the generation of monovalent and bivalent antibodies with nanomolar affinity for Aβ fibrils. These antibodies display high conformational and sequence specificity as well as low levels of nonspecific binding and recognize a conformational epitope at the extreme N terminus of human Aβ. We expect that this systematic approach will be useful for generating antibodies with conformational and sequence specificity against a wide range of peptide and protein aggregates associated with neurodegenerative disorders.
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Affiliation(s)
- Mark C Julian
- Isermann Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Lilia A Rabia
- Isermann Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180; Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, Michigan 48109; Department of Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109; Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109
| | - Alec A Desai
- Department of Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109; Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109
| | - Ammar Arsiwala
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Julia E Gerson
- Department of Neurology, University of Michigan, Ann Arbor, Michigan 48109
| | - Henry L Paulson
- Department of Neurology, University of Michigan, Ann Arbor, Michigan 48109; Department of Protein Folding Disease Initiative, University of Michigan, Ann Arbor, Michigan 48109; Department of Michigan Alzheimer's Disease Center, University of Michigan, Ann Arbor, Michigan 48109
| | - Ravi S Kane
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Peter M Tessier
- Isermann Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180; Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, Michigan 48109; Department of Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109; Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109; Department of Protein Folding Disease Initiative, University of Michigan, Ann Arbor, Michigan 48109; Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109.
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