1
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Nielsen GH, Schmitz ZD, Hackel BJ. Sequence-developability mapping of affibody and fibronectin paratopes via library-scale variant characterization. Protein Eng Des Sel 2024; 37:gzae010. [PMID: 38836499 PMCID: PMC11170491 DOI: 10.1093/protein/gzae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/29/2024] [Accepted: 06/04/2024] [Indexed: 06/06/2024] Open
Abstract
Protein developability is requisite for use in therapeutic, diagnostic, or industrial applications. Many developability assays are low throughput, which limits their utility to the later stages of protein discovery and evolution. Recent approaches enable experimental or computational assessment of many more variants, yet the breadth of applicability across protein families and developability metrics is uncertain. Here, three library-scale assays-on-yeast protease, split green fluorescent protein (GFP), and non-specific binding-were evaluated for their ability to predict two key developability outcomes (thermal stability and recombinant expression) for the small protein scaffolds affibody and fibronectin. The assays' predictive capabilities were assessed via both linear correlation and machine learning models trained on the library-scale assay data. The on-yeast protease assay is highly predictive of thermal stability for both scaffolds, and the split-GFP assay is informative of affibody thermal stability and expression. The library-scale data was used to map sequence-developability landscapes for affibody and fibronectin binding paratopes, which guides future design of variants and libraries.
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Affiliation(s)
- Gregory H Nielsen
- Department of Chemical Engineering and Materials Science, University of Minnesota, Twin Cities, Minneapolis, MN 55455, United States
| | - Zachary D Schmitz
- Department of Chemical Engineering and Materials Science, University of Minnesota, Twin Cities, Minneapolis, MN 55455, United States
| | - Benjamin J Hackel
- Department of Chemical Engineering and Materials Science, University of Minnesota, Twin Cities, Minneapolis, MN 55455, United States
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2
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Hutchinson M, Ruffolo JA, Haskins N, Iannotti M, Vozza G, Pham T, Mehzabeen N, Shandilya H, Rickert K, Croasdale-Wood R, Damschroder M, Fu Y, Dippel A, Gray JJ, Kaplan G. Toward enhancement of antibody thermostability and affinity by computational design in the absence of antigen. MAbs 2024; 16:2362775. [PMID: 38899735 DOI: 10.1080/19420862.2024.2362775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
Over the past two decades, therapeutic antibodies have emerged as a rapidly expanding domain within the field of biologics. In silico tools that can streamline the process of antibody discovery and optimization are critical to support a pipeline that is growing more numerous and complex every year. High-quality structural information remains critical for the antibody optimization process, but antibody-antigen complex structures are often unavailable and in silico antibody docking methods are still unreliable. In this study, DeepAb, a deep learning model for predicting antibody Fv structure directly from sequence, was used in conjunction with single-point experimental deep mutational scanning (DMS) enrichment data to design 200 potentially optimized variants of an anti-hen egg lysozyme (HEL) antibody. We sought to determine whether DeepAb-designed variants containing combinations of beneficial mutations from the DMS exhibit enhanced thermostability and whether this optimization affected their developability profile. The 200 variants were produced through a robust high-throughput method and tested for thermal and colloidal stability (Tonset, Tm, Tagg), affinity (KD) relative to the parental antibody, and for developability parameters (nonspecific binding, aggregation propensity, self-association). Of the designed clones, 91% and 94% exhibited increased thermal and colloidal stability and affinity, respectively. Of these, 10% showed a significantly increased affinity for HEL (5- to 21-fold increase) and thermostability (>2.5C increase in Tm1), with most clones retaining the favorable developability profile of the parental antibody. Additional in silico tests suggest that these methods would enrich for binding affinity even without first collecting experimental DMS measurements. These data open the possibility of in silico antibody optimization without the need to predict the antibody-antigen interface, which is notoriously difficult in the absence of crystal structures.
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Affiliation(s)
- Mark Hutchinson
- Biologics Engineering, R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Jeffrey A Ruffolo
- Program in Molecular Biophysics, The Johns Hopkins University, Baltimore, MD, USA
- Profluent Bio, Machine Learning, Berkeley, CA, USA
| | - Nantaporn Haskins
- Biologics Engineering, R&D, AstraZeneca, Gaithersburg, MD, USA
- Currently at Protein Engineering, R&D, Amgen Inc, Rockville, MD, USA
| | - Michael Iannotti
- Biologics Engineering, R&D, AstraZeneca, Gaithersburg, MD, USA
- Honigman LLP, Intellectual Property, Washington, DC, United States
| | - Giuliana Vozza
- Biopharmaceuticals Development, R&D, AstraZeneca, Cambridge, UK
| | - Tony Pham
- Biologics Engineering, R&D, AstraZeneca, Gaithersburg, MD, USA
| | | | | | - Keith Rickert
- Biologics Engineering, R&D, AstraZeneca, Gaithersburg, MD, USA
| | | | | | - Ying Fu
- Biologics Engineering, R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Andrew Dippel
- Biologics Engineering, R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Jeffrey J Gray
- Program in Molecular Biophysics, The Johns Hopkins University, Baltimore, MD, USA
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, MD, USA
| | - Gilad Kaplan
- Biologics Engineering, R&D, AstraZeneca, Gaithersburg, MD, USA
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3
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Makowski EK, Chen HT, Wang T, Wu L, Huang J, Mock M, Underhill P, Pelegri-O’Day E, Maglalang E, Winters D, Tessier PM. Reduction of monoclonal antibody viscosity using interpretable machine learning. MAbs 2024; 16:2303781. [PMID: 38475982 PMCID: PMC10939158 DOI: 10.1080/19420862.2024.2303781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 01/05/2024] [Indexed: 03/14/2024] Open
Abstract
Early identification of antibody candidates with drug-like properties is essential for simplifying the development of safe and effective antibody therapeutics. For subcutaneous administration, it is important to identify candidates with low self-association to enable their formulation at high concentration while maintaining low viscosity, opalescence, and aggregation. Here, we report an interpretable machine learning model for predicting antibody (IgG1) variants with low viscosity using only the sequences of their variable (Fv) regions. Our model was trained on antibody viscosity data (>100 mg/mL mAb concentration) obtained at a common formulation pH (pH 5.2), and it identifies three key Fv features of antibodies linked to viscosity, namely their isoelectric points, hydrophobic patch sizes, and numbers of negatively charged patches. Of the three features, most predicted antibodies at risk for high viscosity, including antibodies with diverse antibody germlines in our study (79 mAbs) as well as clinical-stage IgG1s (94 mAbs), are those with low Fv isoelectric points (Fv pIs < 6.3). Our model identifies viscous antibodies with relatively high accuracy not only in our training and test sets, but also for previously reported data. Importantly, we show that the interpretable nature of the model enables the design of mutations that significantly reduce antibody viscosity, which we confirmed experimentally. We expect that this approach can be readily integrated into the drug development process to reduce the need for experimental viscosity screening and improve the identification of antibody candidates with drug-like properties.
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Affiliation(s)
- Emily K. Makowski
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
| | - Hsin-Ting Chen
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Tiexin Wang
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Lina Wu
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Jie Huang
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
| | - Marissa Mock
- Therapeutic Discovery, Research, Amgen Inc, Thousand Oaks, CA, USA
| | - Patrick Underhill
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, USA
| | | | - Erick Maglalang
- Drug Product Technologies, Amgen Inc, Thousand Oaks, CA, USA
| | - Dwight Winters
- Therapeutic Discovery, Research, Amgen Inc, Thousand Oaks, CA, USA
| | - Peter M. Tessier
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
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4
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Shuai RW, Ruffolo JA, Gray JJ. IgLM: Infilling language modeling for antibody sequence design. Cell Syst 2023; 14:979-989.e4. [PMID: 37909045 PMCID: PMC11018345 DOI: 10.1016/j.cels.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 06/14/2023] [Accepted: 10/02/2023] [Indexed: 11/02/2023]
Abstract
Discovery and optimization of monoclonal antibodies for therapeutic applications relies on large sequence libraries but is hindered by developability issues such as low solubility, high aggregation, and high immunogenicity. Generative language models, trained on millions of protein sequences, are a powerful tool for the on-demand generation of realistic, diverse sequences. We present the Immunoglobulin Language Model (IgLM), a deep generative language model for creating synthetic antibody libraries. Compared with prior methods that leverage unidirectional context for sequence generation, IgLM formulates antibody design based on text-infilling in natural language, allowing it to re-design variable-length spans within antibody sequences using bidirectional context. We trained IgLM on 558 million (M) antibody heavy- and light-chain variable sequences, conditioning on each sequence's chain type and species of origin. We demonstrate that IgLM can generate full-length antibody sequences from a variety of species and its infilling formulation allows it to generate infilled complementarity-determining region (CDR) loop libraries with improved in silico developability profiles. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Richard W Shuai
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA
| | - Jeffrey A Ruffolo
- Program in Molecular Biophysics, The Johns Hopkins University, Baltimore, MD, USA
| | - Jeffrey J Gray
- Program in Molecular Biophysics, The Johns Hopkins University, Baltimore, MD, USA; Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, MD, USA.
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5
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Jin X, He B. Combination of On-Line and Off-Line Two-Dimensional Liquid Chromatography-Mass Spectrometry for Comprehensive Characterization of mAb Charge Variants and Precise Instructions for Rapid Process Development. Int J Mol Sci 2023; 24:15184. [PMID: 37894864 PMCID: PMC10607358 DOI: 10.3390/ijms242015184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/04/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
Charge variants, as an important quality attribute of mAbs, must be comprehensively characterized and monitored during development. However, due to their complex structure, the characterization of charge variants is challenging, labor-intensive, and time-consuming when using traditional approaches. This work combines on-line and off-line 2D-LC-MS to comprehensively characterize mAb charge variants and quickly offer precise instructions for process development. Six charge variant peaks of mAb 1 were identified using the developed platform. Off-line 2D-LC-MS analysis at the peptide level showed that the acidic peak P1 and the basic peaks P4 and P5 were caused by the deamidation of asparagine, the oxidation of methionine, and incomplete C-terminal K loss, respectively. On-line 2D-LC-MS at the intact protein level was used to identify the root causes, and it was found that the acidic peak P2 and the basic peak P6 were due to the glutathionylation of cysteine and succinimidation of aspartic acid, respectively, which were not found in off-line 2D-LC-MS because of the loss occurring during pre-treatment. These results suggest that process development could focus on cell culture for adjustment of glutathionylation. In this paper, we propose the concept of precision process development based on on-line 2D-LC-MS, which could quickly offer useful data with only 0.6 mg mAb within 6 h for precise instructions for process development. Overall, the combination of on-line and off-line 2D-LC-MS can characterize mAb charge variants more comprehensively, precisely, and quickly than other approaches. This is a very effective platform with routine operations that provides precise instructions for process development within hours, and will help to accelerate the development of innovative therapeutics.
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Affiliation(s)
- Xiaoqing Jin
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China;
| | - Bingfang He
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China;
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing 211816, China
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6
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Pang KT, Yang YS, Zhang W, Ho YS, Sormanni P, Michaels TCT, Walsh I, Chia S. Understanding and controlling the molecular mechanisms of protein aggregation in mAb therapeutics. Biotechnol Adv 2023; 67:108192. [PMID: 37290583 DOI: 10.1016/j.biotechadv.2023.108192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 05/09/2023] [Accepted: 06/01/2023] [Indexed: 06/10/2023]
Abstract
In antibody development and manufacturing, protein aggregation is a common challenge that can lead to serious efficacy and safety issues. To mitigate this problem, it is important to investigate its molecular origins. This review discusses (1) our current molecular understanding and theoretical models of antibody aggregation, (2) how various stress conditions related to antibody upstream and downstream bioprocesses can trigger aggregation, and (3) current mitigation strategies employed towards inhibiting aggregation. We discuss the relevance of the aggregation phenomenon in the context of novel antibody modalities and highlight how in silico approaches can be exploited to mitigate it.
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Affiliation(s)
- Kuin Tian Pang
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore; School of Chemistry, Chemical Engineering, and Biotechnology, Nanyang Technology University, Singapore
| | - Yuan Sheng Yang
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Wei Zhang
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Ying Swan Ho
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Pietro Sormanni
- Chemistry of Health, Yusuf Hamied Department of Chemistry, University of Cambridge, United Kingdom
| | - Thomas C T Michaels
- Department of Biology, Institute of Biochemistry, ETH Zurich, Otto-Stern-Weg 3, 8093 Zurich, Switzerland; Bringing Materials to Life Initiative, ETH Zurich, Switzerland
| | - Ian Walsh
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore.
| | - Sean Chia
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore.
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7
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Golinski AW, Schmitz ZD, Nielsen GH, Johnson B, Saha D, Appiah S, Hackel BJ, Martiniani S. Predicting and Interpreting Protein Developability Via Transfer of Convolutional Sequence Representation. ACS Synth Biol 2023; 12:2600-2615. [PMID: 37642646 PMCID: PMC10829850 DOI: 10.1021/acssynbio.3c00196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Engineered proteins have emerged as novel diagnostics, therapeutics, and catalysts. Often, poor protein developability─quantified by expression, solubility, and stability─hinders utility. The ability to predict protein developability from amino acid sequence would reduce the experimental burden when selecting candidates. Recent advances in screening technologies enabled a high-throughput (HT) developability dataset for 105 of 1020 possible variants of protein ligand scaffold Gp2. In this work, we evaluate the ability of neural networks to learn a developability representation from a HT dataset and transfer this knowledge to predict recombinant expression beyond observed sequences. The model convolves learned amino acid properties to predict expression levels 44% closer to the experimental variance compared to a non-embedded control. Analysis of learned amino acid embeddings highlights the uniqueness of cysteine, the importance of hydrophobicity and charge, and the unimportance of aromaticity, when aiming to improve the developability of small proteins. We identify clusters of similar sequences with increased recombinant expression through nonlinear dimensionality reduction and we explore the inferred expression landscape via nested sampling. The analysis enables the first direct visualization of the fitness landscape and highlights the existence of evolutionary bottlenecks in sequence space giving rise to competing subpopulations of sequences with different developability. The work advances applied protein engineering efforts by predicting and interpreting protein scaffold expression from a limited dataset. Furthermore, our statistical mechanical treatment of the problem advances foundational efforts to characterize the structure of the protein fitness landscape and the amino acid characteristics that influence protein developability.
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Affiliation(s)
- Alexander W. Golinski
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455
| | - Zachary D. Schmitz
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455
| | - Gregory H. Nielsen
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455
| | - Bryce Johnson
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455
| | - Diya Saha
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455
| | - Sandhya Appiah
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455
| | - Benjamin J. Hackel
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455
| | - Stefano Martiniani
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455
- Center for Soft Matter Research, Department of Physics, New York University, New York, NY 10003
- Simons Center for Computational Physical Chemistry, Departments of Chemistry, New York University, New York, NY 10003
- Courant Institute of Mathematical Sciences, New York University, New York, NY 10003
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8
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Zhang C, Bye JW, Lui LH, Zhang H, Hales J, Brocchini S, Curtis RA, Dalby PA. Enhanced Thermal Stability and Reduced Aggregation in an Antibody Fab Fragment at Elevated Concentrations. Mol Pharm 2023; 20:2650-2661. [PMID: 37040431 PMCID: PMC10155210 DOI: 10.1021/acs.molpharmaceut.3c00081] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
The aggregation of protein therapeutics such as antibodies remains a major challenge in the biopharmaceutical industry. The present study aimed to characterize the impact of the protein concentration on the mechanisms and potential pathways for aggregation, using the antibody Fab fragment A33 as the model protein. Aggregation kinetics were determined for 0.05 to 100 mg/mL Fab A33, at 65 °C. A surprising trend was observed whereby increasing the concentration decreased the relative aggregation rate, ln(v) (% day-1), from 8.5 at 0.05 mg/mL to 4.4 at 100 mg/mL. The absolute aggregation rate (mol L-1 h-1) increased with the concentration following a rate order of approximately 1 up to a concentration of 25 mg/mL. Above this concentration, there was a transition to an apparently negative rate order of -1.1 up to 100 mg/mL. Several potential mechanisms were examined as possible explanations. A greater apparent conformational stability at 100 mg/mL was observed from an increase in the thermal transition midpoint (Tm) by 7-9 °C, relative to those at 1-4 mg/mL. The associated change in unfolding entropy (△Svh) also increased by 14-18% at 25-100 mg/mL, relative to those at 1-4 mg/mL, indicating reduced conformational flexibility in the native ensemble. Addition of Tween or the crowding agents Ficoll and dextran, showed that neither surface adsorption, diffusion limitations nor simple volume crowding affected the aggregation rate. Fitting of kinetic data to a wide range of mechanistic models implied a reversible two-state conformational switch mechanism from aggregation-prone monomers (N*) into non-aggregating native forms (N) at higher concentrations. kD measurements from DLS data also suggested a weak self-attraction while remaining colloidally stable, consistent with macromolecular self-crowding within weakly associated reversible oligomers. Such a model is also consistent with compaction of the native ensemble observed through changes in Tm and △Svh.
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Affiliation(s)
- Cheng Zhang
- Department of Biochemical Engineering, University College London, Gower Street, London WC1E 6BT, U.K
| | - Jordan W Bye
- School of Chemical Engineering and Analytical Science, The University of Manchester, Sackville Street, Manchester M13 9PL, U.K
| | - Lok H Lui
- UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, U.K
| | - Hongyu Zhang
- Department of Biochemical Engineering, University College London, Gower Street, London WC1E 6BT, U.K
| | - John Hales
- Department of Biochemical Engineering, University College London, Gower Street, London WC1E 6BT, U.K
| | - Steve Brocchini
- UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, U.K
| | - Robin A Curtis
- School of Chemical Engineering and Analytical Science, The University of Manchester, Sackville Street, Manchester M13 9PL, U.K
| | - Paul A Dalby
- Department of Biochemical Engineering, University College London, Gower Street, London WC1E 6BT, U.K
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9
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Ausserwöger H, Krainer G, Welsh TJ, Thorsteinson N, de Csilléry E, Sneideris T, Schneider MM, Egebjerg T, Invernizzi G, Herling TW, Lorenzen N, Knowles TPJ. Surface patches induce nonspecific binding and phase separation of antibodies. Proc Natl Acad Sci U S A 2023; 120:e2210332120. [PMID: 37011217 PMCID: PMC10104583 DOI: 10.1073/pnas.2210332120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 02/06/2023] [Indexed: 04/05/2023] Open
Abstract
Nonspecific interactions are a key challenge in the successful development of therapeutic antibodies. The tendency for nonspecific binding of antibodies is often difficult to reduce by rational design, and instead, it is necessary to rely on comprehensive screening campaigns. To address this issue, we performed a systematic analysis of the impact of surface patch properties on antibody nonspecificity using a designer antibody library as a model system and single-stranded DNA as a nonspecificity ligand. Using an in-solution microfluidic approach, we find that the antibodies tested bind to single-stranded DNA with affinities as high as KD = 1 µM. We show that DNA binding is driven primarily by a hydrophobic patch in the complementarity-determining regions. By quantifying the surface patches across the library, the nonspecific binding affinity is shown to correlate with a trade-off between the hydrophobic and total charged patch areas. Moreover, we show that a change in formulation conditions at low ionic strengths leads to DNA-induced antibody phase separation as a manifestation of nonspecific binding at low micromolar antibody concentrations. We highlight that phase separation is driven by a cooperative electrostatic network assembly mechanism of antibodies with DNA, which correlates with a balance between positive and negative charged patches. Importantly, our study demonstrates that both nonspecific binding and phase separation are controlled by the size of the surface patches. Taken together, these findings highlight the importance of surface patches and their role in conferring antibody nonspecificity and its macroscopic manifestation in phase separation.
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Affiliation(s)
- Hannes Ausserwöger
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Georg Krainer
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Timothy J. Welsh
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Nels Thorsteinson
- Research and Development, Chemical Computing Group, Montreal, QuebecH3A 2R7, Canada
| | - Ella de Csilléry
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Tomas Sneideris
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Matthias M. Schneider
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Thomas Egebjerg
- Global Research Technologies, Novo Nordisk A/S2760Måløv, Denmark
| | | | - Therese W. Herling
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Nikolai Lorenzen
- Global Research Technologies, Novo Nordisk A/S2760Måløv, Denmark
| | - Tuomas P. J. Knowles
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, CambridgeCB2 1EW, United Kingdom
- Department of Physics, Cavendish Laboratory, University of Cambridge, CambridgeCB3 0HE, United Kingdom
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10
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Rosace A, Bennett A, Oeller M, Mortensen MM, Sakhnini L, Lorenzen N, Poulsen C, Sormanni P. Automated optimisation of solubility and conformational stability of antibodies and proteins. Nat Commun 2023; 14:1937. [PMID: 37024501 PMCID: PMC10079162 DOI: 10.1038/s41467-023-37668-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 03/24/2023] [Indexed: 04/08/2023] Open
Abstract
Biologics, such as antibodies and enzymes, are crucial in research, biotechnology, diagnostics, and therapeutics. Often, biologics with suitable functionality are discovered, but their development is impeded by developability issues. Stability and solubility are key biophysical traits underpinning developability potential, as they determine aggregation, correlate with production yield and poly-specificity, and are essential to access parenteral and oral delivery. While advances for the optimisation of individual traits have been made, the co-optimization of multiple traits remains highly problematic and time-consuming, as mutations that improve one property often negatively impact others. In this work, we introduce a fully automated computational strategy for the simultaneous optimisation of conformational stability and solubility, which we experimentally validate on six antibodies, including two approved therapeutics. Our results on 42 designs demonstrate that the computational procedure is highly effective at improving developability potential, while not affecting antigen-binding. We make the method available as a webserver at www-cohsoftware.ch.cam.ac.uk.
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Affiliation(s)
- Angelo Rosace
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield road, CB2 1EW, Cambridge, UK
- Master in Bioinformatics for Health Sciences, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
- Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Anja Bennett
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield road, CB2 1EW, Cambridge, UK
- Department of Mammalian Expression, Global Research Technologies, Novo Nordisk A/S, Novo Nordisk Park 1, 2760, Måløv, Denmark
- BRIC, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Marc Oeller
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield road, CB2 1EW, Cambridge, UK
| | - Mie M Mortensen
- Department of Purification Technologies, Global Research Technologies, Novo Nordisk A/S, Novo Nordisk Park 1, 2760, Måløv, Denmark
- Faculty of Engineering and Science, Department of Biotechnology, Chemistry and Environmental Engineering, University of Aalborg, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark
| | - Laila Sakhnini
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield road, CB2 1EW, Cambridge, UK
- Department of Biophysics and Injectable Formulation 2, Global Research Technologies, Novo Nordisk A/S, Måløv, 2760, Denmark
| | - Nikolai Lorenzen
- Department of Biophysics and Injectable Formulation 2, Global Research Technologies, Novo Nordisk A/S, Måløv, 2760, Denmark
| | - Christian Poulsen
- Department of Mammalian Expression, Global Research Technologies, Novo Nordisk A/S, Novo Nordisk Park 1, 2760, Måløv, Denmark
| | - Pietro Sormanni
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield road, CB2 1EW, Cambridge, UK.
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11
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Oeller M, Kang R, Bell R, Ausserwöger H, Sormanni P, Vendruscolo M. Sequence-based prediction of pH-dependent protein solubility using CamSol. Brief Bioinform 2023; 24:7017367. [PMID: 36719110 PMCID: PMC10025429 DOI: 10.1093/bib/bbad004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 12/10/2022] [Accepted: 10/16/2022] [Indexed: 02/01/2023] Open
Abstract
Solubility is a property of central importance for the use of proteins in research in molecular and cell biology and in applications in biotechnology and medicine. Since experimental methods for measuring protein solubility are material intensive and time consuming, computational methods have recently emerged to enable the rapid and inexpensive screening of solubility for large libraries of proteins, as it is routinely required in development pipelines. Here, we describe the development of one such method to include in the predictions the effect of the pH on solubility. We illustrate the resulting pH-dependent predictions on a variety of antibodies and other proteins to demonstrate that these predictions achieve an accuracy comparable with that of experimental methods. We make this method publicly available at https://www-cohsoftware.ch.cam.ac.uk/index.php/camsolph, as the version 3.0 of CamSol.
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Affiliation(s)
- Marc Oeller
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Ryan Kang
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Rosie Bell
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Hannes Ausserwöger
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Pietro Sormanni
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
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12
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Erkamp NA, Oeller M, Sneideris T, Ausserwoger H, Levin A, Welsh TJ, Qi R, Qian D, Lorenzen N, Zhu H, Sormanni P, Vendruscolo M, Knowles TPJ. Multidimensional Protein Solubility Optimization with an Ultrahigh-Throughput Microfluidic Platform. Anal Chem 2023; 95:5362-5368. [PMID: 36930285 PMCID: PMC10061369 DOI: 10.1021/acs.analchem.2c05495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Protein-based biologics are highly suitable for drug development as they exhibit low toxicity and high specificity for their targets. However, for therapeutic applications, biologics must often be formulated to elevated concentrations, making insufficient solubility a critical bottleneck in the drug development pipeline. Here, we report an ultrahigh-throughput microfluidic platform for protein solubility screening. In comparison with previous methods, this microfluidic platform can make, incubate, and measure samples in a few minutes, uses just 20 μg of protein (>10-fold improvement), and yields 10,000 data points (1000-fold improvement). This allows quantitative comparison of formulation excipients, such as sodium chloride, polysorbate, histidine, arginine, and sucrose. Additionally, we can measure how solubility is affected by the combinatorial effect of multiple additives, find a suitable pH for the formulation, and measure the impact of mutations on solubility, thus enabling the screening of large libraries. By reducing material and time costs, this approach makes detailed multidimensional solubility optimization experiments possible, streamlining drug development and increasing our understanding of biotherapeutic solubility and the effects of excipients.
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Affiliation(s)
- Nadia A Erkamp
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Marc Oeller
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Tomas Sneideris
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Hannes Ausserwoger
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Aviad Levin
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Timothy J Welsh
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Runzhang Qi
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Daoyuan Qian
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Nikolai Lorenzen
- Biophysics and Injectable Formulation, Global Research Technology, Novo Nordisk A/S, 2760 Maaloev, Denmark
| | - Hongjia Zhu
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Pietro Sormanni
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Michele Vendruscolo
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Tuomas P J Knowles
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
- Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Ave, Cambridge CB3 0HE, U.K
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13
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Das NC, Chakraborty P, Bayry J, Mukherjee S. Comparative Binding Ability of Human Monoclonal Antibodies against Omicron Variants of SARS-CoV-2: An In Silico Investigation. Antibodies (Basel) 2023; 12:antib12010017. [PMID: 36975364 PMCID: PMC10045060 DOI: 10.3390/antib12010017] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 02/15/2023] [Accepted: 02/17/2023] [Indexed: 02/26/2023] Open
Abstract
Mutation(s) in the spike protein is the major characteristic trait of newly emerged SARS-CoV-2 variants such as Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Delta-plus. Omicron (B.1.1.529) is the latest addition and it has been characterized by high transmissibility and the ability to escape host immunity. Recently developed vaccines and repurposed drugs exert limited action on Omicron strains and hence new therapeutics are immediately needed. Herein, we have explored the efficiency of twelve therapeutic monoclonal antibodies (mAbs) targeting the RBD region of the spike glycoprotein against all the Omicron variants bearing a mutation in spike protein through molecular docking and molecular dynamics simulation. Our in silico evidence reveals that adintivimab, beludivimab, and regadanivimab are the most potent mAbs to form strong biophysical interactions and neutralize most of the Omicron variants. Considering the efficacy of mAbs, we incorporated CDRH3 of beludavimab within the framework of adintrevimab, which displayed a more intense binding affinity towards all of the Omicron variants viz. BA.1, BA.2, BA.2.12.1, BA.4, and BA.5. Furthermore, the cDNA of chimeric mAb was cloned in silico within pET30ax for recombinant production. In conclusion, the present study represents the candidature of human mAbs (beludavimab and adintrevimab) and the therapeutic potential of designed chimeric mAb for treating Omicron-infected patients.
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Affiliation(s)
- Nabarun Chandra Das
- Integrative Biochemistry & Immunology Laboratory, Department of Animal Science, Kazi Nazrul University, Asansol 713 340, India
| | - Pritha Chakraborty
- Integrative Biochemistry & Immunology Laboratory, Department of Animal Science, Kazi Nazrul University, Asansol 713 340, India
| | - Jagadeesh Bayry
- Department of Biological Sciences & Engineering, Indian Institute of Technology Palakkad, Palakkad 678 623, India
- Correspondence: (J.B.); or (S.M.)
| | - Suprabhat Mukherjee
- Integrative Biochemistry & Immunology Laboratory, Department of Animal Science, Kazi Nazrul University, Asansol 713 340, India
- Correspondence: (J.B.); or (S.M.)
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14
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Kopp MRG, Grigolato F, Zürcher D, Das TK, Chou D, Wuchner K, Arosio P. Surface-Induced Protein Aggregation and Particle Formation in Biologics: Current Understanding of Mechanisms, Detection and Mitigation Strategies. J Pharm Sci 2023; 112:377-385. [PMID: 36223809 DOI: 10.1016/j.xphs.2022.10.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 10/05/2022] [Accepted: 10/05/2022] [Indexed: 01/12/2023]
Abstract
Protein stability against aggregation is a major quality concern for the production of safe and effective biopharmaceuticals. Amongst the different drivers of protein aggregation, increasing evidence indicates that interactions between proteins and interfaces represent a major risk factor for the formation of protein aggregates in aqueous solutions. Potentially harmful surfaces relevant to biologics manufacturing and storage include air-water and silicone oil-water interfaces as well as materials from different processing units, storage containers, and delivery devices. The impact of some of these surfaces, for instance originating from impurities, can be difficult to predict and control. Moreover, aggregate formation may additionally be complicated by the simultaneous presence of interfacial, hydrodynamic and mechanical stresses, whose contributions may be difficult to deconvolute. As a consequence, it remains difficult to identify the key chemical and physical determinants and define appropriate analytical methods to monitor and predict protein instability at these interfaces. In this review, we first discuss the main mechanisms of surface-induced protein aggregation. We then review the types of contact materials identified as potentially harmful or detected as potential triggers of proteinaceous particle formation in formulations and discuss proposed mitigation strategies. Finally, we present current methods to probe surface-induced instabilities, which represent a starting point towards assays that can be implemented in early-stage screening and formulation development of biologics.
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Affiliation(s)
- Marie R G Kopp
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Fulvio Grigolato
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Dominik Zürcher
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | | | | | | | - Paolo Arosio
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland.
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15
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Evers A, Malhotra S, Bolick WG, Najafian A, Borisovska M, Warszawski S, Fomekong Nanfack Y, Kuhn D, Rippmann F, Crespo A, Sood V. SUMO: In Silico Sequence Assessment Using Multiple Optimization Parameters. Methods Mol Biol 2023; 2681:383-398. [PMID: 37405660 DOI: 10.1007/978-1-0716-3279-6_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2023]
Abstract
To select the most promising screening hits from antibody and VHH display campaigns for subsequent in-depth profiling and optimization, it is highly desirable to assess and select sequences on properties beyond only their binding signals from the sorting process. In addition, developability risk criteria, sequence diversity, and the anticipated complexity for sequence optimization are relevant attributes for hit selection and optimization. Here, we describe an approach for the in silico developability assessment of antibody and VHH sequences. This method not only allows for ranking and filtering multiple sequences with regard to their predicted developability properties and diversity, but also visualizes relevant sequence and structural features of potentially problematic regions and thereby provides rationales and starting points for multi-parameter sequence optimization.
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Affiliation(s)
- Andreas Evers
- Computational Chemistry & Biologics (CCB), Merck Healthcare KGaA, Darmstadt, Germany.
| | - Shipra Malhotra
- Computational Chemistry & Biologics (CCB), EMD Serono, Billerica, MA, USA
| | | | - Ahmad Najafian
- Computational Chemistry & Biologics (CCB), EMD Serono, Billerica, MA, USA
| | - Maria Borisovska
- Computational Chemistry & Biologics (CCB), EMD Serono, Billerica, MA, USA
| | | | | | - Daniel Kuhn
- Computational Chemistry & Biologics (CCB), Merck Healthcare KGaA, Darmstadt, Germany
| | - Friedrich Rippmann
- Computational Chemistry & Biologics (CCB), Merck Healthcare KGaA, Darmstadt, Germany
| | - Alejandro Crespo
- Computational Chemistry & Biologics (CCB), EMD Serono, Billerica, MA, USA
| | - Vanita Sood
- Computational Chemistry & Biologics (CCB), EMD Serono, Billerica, MA, USA
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16
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Fernández-Quintero ML, Ljungars A, Waibl F, Greiff V, Andersen JT, Gjølberg TT, Jenkins TP, Voldborg BG, Grav LM, Kumar S, Georges G, Kettenberger H, Liedl KR, Tessier PM, McCafferty J, Laustsen AH. Assessing developability early in the discovery process for novel biologics. MAbs 2023; 15:2171248. [PMID: 36823021 PMCID: PMC9980699 DOI: 10.1080/19420862.2023.2171248] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 01/18/2023] [Indexed: 02/25/2023] Open
Abstract
Beyond potency, a good developability profile is a key attribute of a biological drug. Selecting and screening for such attributes early in the drug development process can save resources and avoid costly late-stage failures. Here, we review some of the most important developability properties that can be assessed early on for biologics. These include the influence of the source of the biologic, its biophysical and pharmacokinetic properties, and how well it can be expressed recombinantly. We furthermore present in silico, in vitro, and in vivo methods and techniques that can be exploited at different stages of the discovery process to identify molecules with liabilities and thereby facilitate the selection of the most optimal drug leads. Finally, we reflect on the most relevant developability parameters for injectable versus orally delivered biologics and provide an outlook toward what general trends are expected to rise in the development of biologics.
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Affiliation(s)
- Monica L. Fernández-Quintero
- Center for Molecular Biosciences Innsbruck (CMBI), Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Anne Ljungars
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Franz Waibl
- Center for Molecular Biosciences Innsbruck (CMBI), Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Victor Greiff
- Department of Immunology, University of Oslo, Oslo, Norway
| | - Jan Terje Andersen
- Department of Immunology, University of Oslo, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine and Department of Pharmacology, University of Oslo, Oslo, Norway
| | | | - Timothy P. Jenkins
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Bjørn Gunnar Voldborg
- National Biologics Facility, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Lise Marie Grav
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Sandeep Kumar
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals Inc, Ridgefield, CT, USA
| | - Guy Georges
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Hubert Kettenberger
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Klaus R. Liedl
- Center for Molecular Biosciences Innsbruck (CMBI), Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Peter M. Tessier
- Department of Chemical Engineering, Pharmaceutical Sciences and Biomedical Engineering, Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - John McCafferty
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
- Maxion Therapeutics, Babraham Research Campus, Cambridge, UK
| | - Andreas H. Laustsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
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17
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Trikeriotis M, Akbulatov S, Esposito U, Anastasiou A, Leszczyszyn OI. Analytical Workflows to Unlock Predictive Power in Biotherapeutic Developability. Pharm Res 2023; 40:487-500. [PMID: 36471025 PMCID: PMC9944381 DOI: 10.1007/s11095-022-03448-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 11/24/2022] [Indexed: 12/12/2022]
Abstract
PURPOSE Forming accurate data models that assist the design of developability assays is one area that requires a deep and practical understanding of the problem domain. We aim to incorporate expert knowledge into the model building process by creating new metrics from instrument data and by guiding the choice of input parameters and Machine Learning (ML) techniques. METHODS We generated datasets from the biophysical characterisation of 5 monoclonal antibodies (mAbs). We explored combinations of techniques and parameters to uncover the ones that better describe specific molecular liabilities, such as conformational and colloidal instability. We also employed ML algorithms to predict metrics from the dataset. RESULTS We found that the combination of Differential Scanning Calorimetry (DSC) and Light Scattering thermal ramps enabled us to identify domain-specific aggregation in mAbs that would be otherwise overlooked by common developability workflows. We also found that the response to different salt concentrations provided information about colloidal stability in agreement with charge distribution models. Finally, we predicted DSC transition temperatures from the dataset, and used the order of importance of different metrics to increase the explainability of the model. CONCLUSIONS The new analytical workflows enabled a better description of molecular behaviour and uncovered links between structural properties and molecular liabilities. In the future this new understanding will be coupled with ML algorithms to unlock their predictive power during developability assessment.
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Affiliation(s)
- Markos Trikeriotis
- Research and Development, Malvern Panalytical Limited, Grovewood Road, Malvern, WR14 1XZ, Worcestershire, UK.
| | - Sergey Akbulatov
- Research and Development, Malvern Panalytical Limited, Grovewood Road, Malvern, WR14 1XZ Worcestershire UK
| | - Umberto Esposito
- Research and Development, Malvern Panalytical Limited, Grovewood Road, Malvern, WR14 1XZ Worcestershire UK
| | - Athanasios Anastasiou
- Research and Development, Malvern Panalytical Limited, Grovewood Road, Malvern, WR14 1XZ Worcestershire UK
| | - Oksana I. Leszczyszyn
- Research and Development, Malvern Panalytical Limited, Grovewood Road, Malvern, WR14 1XZ Worcestershire UK
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18
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Thorsteinson N, Comeau SR, Kumar S. Structure-Based Optimization of Antibody-Based Biotherapeutics for Improved Developability: A Practical Guide for Molecular Modelers. Methods Mol Biol 2023; 2552:219-235. [PMID: 36346594 DOI: 10.1007/978-1-0716-2609-2_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
A great effort to avoid known developability risks is now more often being made earlier during the lead candidate discovery and optimization phase of biotherapeutic drug development. Predictive computational strategies, used in the early stages of antibody discovery and development, to mitigate the risk of late-stage failure of antibody candidates, are highly valuable. Various structure-based methods exist for accurately predicting properties critical to developability, and, in this chapter, we discuss the history of their development and demonstrate how they can be used to filter large sets of candidates arising from target affinity screening and to optimize lead candidates for developability. Methods for modeling antibody structures from sequence and detecting post-translational modifications and chemical degradation liabilities are also discussed.
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Affiliation(s)
- Nels Thorsteinson
- Scientific Services Manager, Biologics, Chemical Computing Group ULC, Montreal, QC, Canada
| | - Stephen R Comeau
- Computational Biochemistry and Bioinformatics Group, Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
| | - Sandeep Kumar
- Computational Biochemistry and Bioinformatics Group, Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA.
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19
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Licari G, Martin KP, Crames M, Mozdzierz J, Marlow MS, Karow-Zwick AR, Kumar S, Bauer J. Embedding Dynamics in Intrinsic Physicochemical Profiles of Market-Stage Antibody-Based Biotherapeutics. Mol Pharm 2022; 20:1096-1111. [PMID: 36573887 PMCID: PMC9906779 DOI: 10.1021/acs.molpharmaceut.2c00838] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Adequate stability, manufacturability, and safety are crucial to bringing an antibody-based biotherapeutic to the market. Following the concept of holistic in silico developability, we introduce a physicochemical description of 91 market-stage antibody-based biotherapeutics based on orthogonal molecular properties of variable regions (Fvs) embedded in different simulation environments, mimicking conditions experienced by antibodies during manufacturing, formulation, and in vivo. In this work, the evaluation of molecular properties includes conformational flexibility of the Fvs using molecular dynamics (MD) simulations. The comparison between static homology models and simulations shows that MD significantly affects certain molecular descriptors like surface molecular patches. Moreover, the structural stability of a subset of Fv regions is linked to changes in their specific molecular interactions with ions in different experimental conditions. This is supported by the observation of differences in protein melting temperatures upon addition of NaCl. A DEvelopability Navigator In Silico (DENIS) is proposed to compare mAb candidates for their similarity with market-stage biotherapeutics in terms of physicochemical properties and conformational stability. Expanding on our previous developability guidelines (Ahmed et al. Proc. Natl. Acad. Sci. 2021, 118 (37), e2020577118), the hydrodynamic radius and the protein strand ratio are introduced as two additional descriptors that enable a more comprehensive in silico characterization of biotherapeutic drug candidates. Test cases show how this approach can facilitate identification and optimization of intrinsically developable lead candidates. DENIS represents an advanced computational tool to progress biotherapeutic drug candidates from discovery into early development by predicting drug properties in different aqueous environments.
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Affiliation(s)
- Giuseppe Licari
- Early
Stage Pharmaceutical Development, Pharmaceutical Development Biologicals
& In silico Team, Boehringer Ingelheim
International GmbH & Co. KG, Biberach/Riss 88397, Germany
| | - Kyle P. Martin
- Biotherapeutics
Discovery & In silico Team, Boehringer
Ingelheim Pharmaceuticals Inc., Ridgefield, Connecticut 06877, United States
| | - Maureen Crames
- Biotherapeutics
Discovery & In silico Team, Boehringer
Ingelheim Pharmaceuticals Inc., Ridgefield, Connecticut 06877, United States
| | - Joseph Mozdzierz
- Biotherapeutics
Discovery & In silico Team, Boehringer
Ingelheim Pharmaceuticals Inc., Ridgefield, Connecticut 06877, United States
| | - Michael S. Marlow
- Biotherapeutics
Discovery & In silico Team, Boehringer
Ingelheim Pharmaceuticals Inc., Ridgefield, Connecticut 06877, United States
| | - Anne R. Karow-Zwick
- Early
Stage Pharmaceutical Development, Pharmaceutical Development Biologicals
& In silico Team, Boehringer Ingelheim
International GmbH & Co. KG, Biberach/Riss 88397, Germany
| | - Sandeep Kumar
- Biotherapeutics
Discovery & In silico Team, Boehringer
Ingelheim Pharmaceuticals Inc., Ridgefield, Connecticut 06877, United States,
| | - Joschka Bauer
- Early
Stage Pharmaceutical Development, Pharmaceutical Development Biologicals
& In silico Team, Boehringer Ingelheim
International GmbH & Co. KG, Biberach/Riss 88397, Germany,
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20
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Beck A, Nowak C, Meshulam D, Reynolds K, Chen D, Pacardo DB, Nicholls SB, Carven GJ, Gu Z, Fang J, Wang D, Katiyar A, Xiang T, Liu H. Risk-Based Control Strategies of Recombinant Monoclonal Antibody Charge Variants. Antibodies (Basel) 2022; 11:73. [PMID: 36412839 PMCID: PMC9703962 DOI: 10.3390/antib11040073] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/27/2022] [Accepted: 11/11/2022] [Indexed: 09/28/2023] Open
Abstract
Since the first approval of the anti-CD3 recombinant monoclonal antibody (mAb), muromonab-CD3, a mouse antibody for the prevention of transplant rejection, by the US Food and Drug Administration (FDA) in 1986, mAb therapeutics have become increasingly important to medical care. A wealth of information about mAbs regarding their structure, stability, post-translation modifications, and the relationship between modification and function has been reported. Yet, substantial resources are still required throughout development and commercialization to have appropriate control strategies to maintain consistent product quality, safety, and efficacy. A typical feature of mAbs is charge heterogeneity, which stems from a variety of modifications, including modifications that are common to many mAbs or unique to a specific molecule or process. Charge heterogeneity is highly sensitive to process changes and thus a good indicator of a robust process. It is a high-risk quality attribute that could potentially fail the specification and comparability required for batch disposition. Failure to meet product specifications or comparability can substantially affect clinical development timelines. To mitigate these risks, the general rule is to maintain a comparable charge profile when process changes are inevitably introduced during development and even after commercialization. Otherwise, new peaks or varied levels of acidic and basic species must be justified based on scientific knowledge and clinical experience for a specific molecule. Here, we summarize the current understanding of mAb charge variants and outline risk-based control strategies to support process development and ultimately commercialization.
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Affiliation(s)
- Alain Beck
- Centre d’Immunologie Pierre-Fabre (CIPF), 5 Avenue Napoléon III, 74160 Saint-Julien-en-Genevois, France
| | - Christine Nowak
- Protein Characterization, Alexion AstraZeneca Rare Disease, 100 College St., New Haven, CT 06510, USA
| | - Deborah Meshulam
- Technical Operations/CMC, Scholar Rock, 301 Binney Street, 3rd Floor, Cambridge, MA 02142, USA
| | - Kristina Reynolds
- Technical Operations/CMC, Scholar Rock, 301 Binney Street, 3rd Floor, Cambridge, MA 02142, USA
| | - David Chen
- Technical Operations/CMC, Scholar Rock, 301 Binney Street, 3rd Floor, Cambridge, MA 02142, USA
| | - Dennis B. Pacardo
- Technical Operations/CMC, Scholar Rock, 301 Binney Street, 3rd Floor, Cambridge, MA 02142, USA
| | - Samantha B. Nicholls
- Protein Sciences, Scholar Rock, 301 Binney Street, 3rd Floor, Cambridge, MA 02142, USA
| | - Gregory J. Carven
- Research, Scholar Rock, 301 Binney Street, 3rd Floor, Cambridge, MA 02142, USA
| | - Zhenyu Gu
- Jasper Therapeutics, Inc., 2200 Bridge Pkwy Suite 102, Redwood City, CA 94065, USA
| | - Jing Fang
- Biological Drug Discovery, Biogen, 225 Binney St., Cambridge, MA 02142, USA
| | - Dongdong Wang
- Global Biologics, Takeda Pharmaceuticals, 300 Shire Way, Lexington, MA 02421, USA
| | - Amit Katiyar
- CMC Technical Operations, Magenta Therapeutics, 100 Technology Square, Cambridge, MA 02139, USA
| | - Tao Xiang
- Downstream Process and Analytical Development, Boston Institute of Biotechnology, 225 Turnpike Rd., Southborough, MA 01772, USA
| | - Hongcheng Liu
- Technical Operations/CMC, Scholar Rock, 301 Binney Street, 3rd Floor, Cambridge, MA 02142, USA
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21
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Ausserwöger H, Schneider MM, Herling TW, Arosio P, Invernizzi G, Knowles TPJ, Lorenzen N. Non-specificity as the sticky problem in therapeutic antibody development. Nat Rev Chem 2022; 6:844-861. [PMID: 37117703 DOI: 10.1038/s41570-022-00438-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2022] [Indexed: 11/16/2022]
Abstract
Antibodies are highly potent therapeutic scaffolds with more than a hundred different products approved on the market. Successful development of antibody-based drugs requires a trade-off between high target specificity and target binding affinity. In order to better understand this problem, we here review non-specific interactions and explore their fundamental physicochemical origins. We discuss the role of surface patches - clusters of surface-exposed amino acid residues with similar physicochemical properties - as inducers of non-specific interactions. These patches collectively drive interactions including dipole-dipole, π-stacking and hydrophobic interactions to complementary moieties. We elucidate links between these supramolecular assembly processes and macroscopic development issues, such as decreased physical stability and poor in vivo half-life. Finally, we highlight challenges and opportunities for optimizing protein binding specificity and minimizing non-specificity for future generations of therapeutics.
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22
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Aubrey N, Gouilleux-Gruart V, Dhommée C, Mariot J, Boursin F, Albrecht N, Bergua C, Croix C, Gilotin M, Haudebourg E, Horiot C, Matthias L, Mouline C, Lajoie L, Munos A, Ferry G, Viaud-Massuard MC, Thibault G, Velge-Roussel F. Anticalin N- or C-Terminal on a Monoclonal Antibody Affects Both Production and In Vitro Functionality. Antibodies (Basel) 2022; 11:antib11030054. [PMID: 35997348 PMCID: PMC9397084 DOI: 10.3390/antib11030054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/03/2022] [Accepted: 08/08/2022] [Indexed: 11/16/2022] Open
Abstract
Bispecific antibodies (BsAbs) represent an important advance in innovative therapeutic strategies. Among the countless formats of BsAbs, fusion with molecules such as anticalins linked to a monoclonal antibody (mAb), represents an easy and low-cost way to obtain innovative molecules. We fused an anticalin against human fibronectin to a molecule biosimilar to trastuzumab (H0) or rituximab (R0), in four different positions, two on the N terminal region of heavy or light chains and two on the C terminal region. The eight BsAbs (H family (HF) 1 to 4 and R family (RF) 1 to 4) were produced and their affinity parameters and functional properties evaluated. The presence of anticalin did not change the glycosylation of the BsAb, shape or yield. The antigenic recognition of each BsAb family, Her2 for HF1 to 4 and CD20 for RF1 to 4, was slightly decreased (HF) or absent (RF) for the anticalin N-terminal in the light chain position. The anticalin recognition of FN was slightly decreased for the HF family, but a dramatic decrease was observed for RF members with lowest affinity for RF1. Moreover, functional properties of Abs, such as CD16 activation of NK, CD32-dependent phagocytosis and FcRn transcytosis, confirmed that this anticalin position leads to less efficient BsAbs, more so for RF than HF molecules. Nevertheless, all BsAbs demonstrated affinities for CD16, CD32 and FcRn, which suggests that more than affinity for FcRs is needed for a functioning antibody. Our strategy using anticalin and Abs allows for rapid generation of BsAbs, but as suggested by our results, some positions of anticalins on Abs result in less functionality.
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Affiliation(s)
- Nicolas Aubrey
- ISP UMR 1282, INRA, Team BioMAP, University of Tours, 31 Avenue Monge, 37200 Tours, France
| | | | - Christine Dhommée
- GICC EA7501, Team FRAME, University of Tours, 10 boulevard Tonnellé, 37032 Tours, France
| | - Julie Mariot
- GICC EA7501, Team FRAME, University of Tours, 10 boulevard Tonnellé, 37032 Tours, France
| | - Fanny Boursin
- ISP UMR 1282, INRA, Team BioMAP, University of Tours, 31 Avenue Monge, 37200 Tours, France
| | - Nicolas Albrecht
- GICC EA7501, Team IMT, University of Tours, 10 boulevard Tonnellé, 37032 Tours, France
| | - Cécile Bergua
- GICC EA7501, Team FRAME, University of Tours, 10 boulevard Tonnellé, 37032 Tours, France
| | - Cécile Croix
- GICC EA7501, Team IMT, University of Tours, 10 boulevard Tonnellé, 37032 Tours, France
| | - Mäelle Gilotin
- GICC EA7501, Team FRAME, University of Tours, 10 boulevard Tonnellé, 37032 Tours, France
| | - Eloi Haudebourg
- GICC EA7501, Team IMT, University of Tours, 10 boulevard Tonnellé, 37032 Tours, France
| | - Catherine Horiot
- ISP UMR 1282, INRA, Team BioMAP, University of Tours, 31 Avenue Monge, 37200 Tours, France
| | - Laetitia Matthias
- GICC EA7501, Team FRAME, University of Tours, 10 boulevard Tonnellé, 37032 Tours, France
| | - Caroline Mouline
- GICC EA7501, Team FRAME, University of Tours, 10 boulevard Tonnellé, 37032 Tours, France
| | - Laurie Lajoie
- GICC EA7501, Team FRAME, University of Tours, 10 boulevard Tonnellé, 37032 Tours, France
| | - Audrey Munos
- Institut du Médicament de Tours, BIO3, 15 rue du plat d’étain, 37000 Tours, France
| | - Gilles Ferry
- Chemistry Manufacturing and Control—Biologics, Institut de Recherches SERVIER, 78290 Croissy-sur-Seine, France
| | | | - Gilles Thibault
- GICC EA7501, Team FRAME, University of Tours, 10 boulevard Tonnellé, 37032 Tours, France
| | - Florence Velge-Roussel
- GICC EA7501, Team FRAME, University of Tours, 10 boulevard Tonnellé, 37032 Tours, France
- Correspondence: ; Tel.: +33-247366058
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23
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Spassov VZ, Kemmish H, Yan L. Two physics‐based models for
pH
‐dependent calculations of protein solubility. Protein Sci 2022; 31:e4299. [PMID: 35481654 PMCID: PMC8996476 DOI: 10.1002/pro.4299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 02/01/2022] [Accepted: 02/28/2022] [Indexed: 11/11/2022]
Abstract
When engineering a protein for its biological function, many physicochemical properties are also optimized throughout the engineering process, and the protein's solubility is among the most important properties to consider. Here, we report two novel computational methods to calculate the pH-dependent protein solubility, and to rank the solubility of mutants. The first is an empirical method developed for fast ranking of the solubility of a large number of mutants of a protein. It takes into account electrostatic solvation energy term calculated using Generalized Born approximation, hydrophobic patches, protein charge, and charge asymmetry, as well as the changes of protein stability upon mutation. This method has been tested on over 100 mutations for 17 globular proteins, as well as on 44 variants of five different antibodies. The prediction rate is over 80%. The antibody tests showed a Pearson correlation coefficient, R, with experimental data from .83 to .91. The second method is based on a novel, completely force-field-based approach using CHARMm program modules to calculate the binding energy of the protein to a part of the crystal lattice, generated from X-ray structure. The method predicted with very high accuracy the solubility of Ribonuclease SA and its 3K and 5K mutants as a function of pH without any parameter adjustments of the existing BIOVIA Discovery Studio binding affinity model. Our methods can be used for rapid screening of large numbers of design candidates based on solubility, and to guide the design of solution conditions for antibody formulation.
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Affiliation(s)
- Velin Z. Spassov
- BIOVIA Dassault Systemes, 5005 Wateridge Vista Drive San Diego California USA
| | - Helen Kemmish
- BIOVIA Dassault Systemes, 5005 Wateridge Vista Drive San Diego California USA
| | - Lisa Yan
- BIOVIA Dassault Systemes, 5005 Wateridge Vista Drive San Diego California USA
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24
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Blanco MA. Computational models for studying physical instabilities in high concentration biotherapeutic formulations. MAbs 2022; 14:2044744. [PMID: 35282775 PMCID: PMC8928847 DOI: 10.1080/19420862.2022.2044744] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Computational prediction of the behavior of concentrated protein solutions is particularly advantageous in early development stages of biotherapeutics when material availability is limited and a large set of formulation conditions needs to be explored. This review provides an overview of the different computational paradigms that have been successfully used in modeling undesirable physical behaviors of protein solutions with a particular emphasis on high-concentration drug formulations. This includes models ranging from all-atom simulations, coarse-grained representations to macro-scale mathematical descriptions used to study physical instability phenomena of protein solutions such as aggregation, elevated viscosity, and phase separation. These models are compared and summarized in the context of the physical processes and their underlying assumptions and limitations. A detailed analysis is also given for identifying protein interaction processes that are explicitly or implicitly considered in the different modeling approaches and particularly their relations to various formulation parameters. Lastly, many of the shortcomings of existing computational models are discussed, providing perspectives and possible directions toward an efficient computational framework for designing effective protein formulations.
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Affiliation(s)
- Marco A. Blanco
- Materials and Biophysical Characterization, Analytical R & D, Merck & Co., Inc, Kenilworth, NJ USA
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25
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Das NC, Chakraborty P, Bayry J, Mukherjee S. In Silico Analyses on the Comparative Potential of Therapeutic Human Monoclonal Antibodies Against Newly Emerged SARS-CoV-2 Variants Bearing Mutant Spike Protein. Front Immunol 2022; 12:782506. [PMID: 35082779 PMCID: PMC8784557 DOI: 10.3389/fimmu.2021.782506] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 12/07/2021] [Indexed: 12/19/2022] Open
Abstract
Since the start of the pandemic, SARS-CoV-2 has already infected more than 250 million people globally, with more than five million fatal cases and huge socio-economic losses. In addition to corticosteroids, and antiviral drugs like remdesivir, various immunotherapies including monoclonal antibodies (mAbs) to S protein of SARS-CoV-2 have been investigated to treat COVID-19 patients. These mAbs were initially developed against the wild-type SARS-CoV-2; however, emergence of variant forms of SARS-CoV-2 having mutations in the spike protein in several countries including India raised serious questions on the potential use of these mAbs against SARS-CoV-2 variants. In this study, using an in silico approach, we have examined the binding abilities of eight mAbs against several SARS-CoV-2 variants of Alpha (B.1.1.7) and Delta (B.1.617.2) lineages. The structure of the Fab region of each mAb was designed in silico and subjected to molecular docking against each mutant protein. mAbs were subjected to two levels of selection based on their binding energy, stability, and conformational flexibility. Our data reveal that tixagevimab, regdanvimab, and cilgavimab can efficiently neutralize most of the SARS-CoV-2 Alpha strains while tixagevimab, bamlanivimab, and sotrovimab can form a stable complex with the Delta variants. Based on these data, we have designed, by in silico, a chimeric antibody by conjugating the CDRH3 of regdanivimab with a sotrovimab framework to combat the variants that could potentially escape from the mAb-mediated neutralization. Our finding suggests that though currently available mAbs could be used to treat COVID-19 caused by the variants of SARS-CoV-2, better results could be expected with the chimeric antibodies.
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Affiliation(s)
- Nabarun Chandra Das
- Integrative Biochemistry and Immunology Laboratory, Department of Animal Science, Kazi Nazrul University, Asansol, India
| | - Pritha Chakraborty
- Integrative Biochemistry and Immunology Laboratory, Department of Animal Science, Kazi Nazrul University, Asansol, India
| | - Jagadeesh Bayry
- Department of Biological Sciences and Engineering, Indian Institute of Technology Palakkad, Palakkad, India
| | - Suprabhat Mukherjee
- Integrative Biochemistry and Immunology Laboratory, Department of Animal Science, Kazi Nazrul University, Asansol, India
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26
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Khetan R, Curtis R, Deane CM, Hadsund JT, Kar U, Krawczyk K, Kuroda D, Robinson SA, Sormanni P, Tsumoto K, Warwicker J, Martin ACR. Current advances in biopharmaceutical informatics: guidelines, impact and challenges in the computational developability assessment of antibody therapeutics. MAbs 2022; 14:2020082. [PMID: 35104168 PMCID: PMC8812776 DOI: 10.1080/19420862.2021.2020082] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Therapeutic monoclonal antibodies and their derivatives are key components of clinical pipelines in the global biopharmaceutical industry. The availability of large datasets of antibody sequences, structures, and biophysical properties is increasingly enabling the development of predictive models and computational tools for the "developability assessment" of antibody drug candidates. Here, we provide an overview of the antibody informatics tools applicable to the prediction of developability issues such as stability, aggregation, immunogenicity, and chemical degradation. We further evaluate the opportunities and challenges of using biopharmaceutical informatics for drug discovery and optimization. Finally, we discuss the potential of developability guidelines based on in silico metrics that can be used for the assessment of antibody stability and manufacturability.
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Affiliation(s)
- Rahul Khetan
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Robin Curtis
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | | | | | - Uddipan Kar
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | | | - Daisuke Kuroda
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.,Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Tokyo, Japan.,Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan
| | | | - Pietro Sormanni
- Chemistry of Health, Yusuf Hamied Department of Chemistry, University of Cambridge
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.,Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Tokyo, Japan.,Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan.,The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Jim Warwicker
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Andrew C R Martin
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
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27
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Assessment of Therapeutic Antibody Developability by Combinations of In Vitro and In Silico Methods. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2313:57-113. [PMID: 34478132 DOI: 10.1007/978-1-0716-1450-1_4] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Although antibodies have become the fastest-growing class of therapeutics on the market, it is still challenging to develop them for therapeutic applications, which often require these molecules to withstand stresses that are not present in vivo. We define developability as the likelihood of an antibody candidate with suitable functionality to be developed into a manufacturable, stable, safe, and effective drug that can be formulated to high concentrations while retaining a long shelf life. The implementation of reliable developability assessments from the early stages of antibody discovery enables flagging and deselection of potentially problematic candidates, while focussing available resources on the development of the most promising ones. Currently, however, thorough developability assessment requires multiple in vitro assays, which makes it labor intensive and time consuming to implement at early stages. Furthermore, accurate in vitro analysis at the early stage is compromised by the high number of potential candidates that are often prepared at low quantities and purity. Recent improvements in the performance of computational predictors of developability potential are beginning to change this scenario. Many computational methods only require the knowledge of the amino acid sequences and can be used to identify possible developability issues or to rank available candidates according to a range of biophysical properties. Here, we describe how the implementation of in silico tools into antibody discovery pipelines is increasingly offering time- and cost-effective alternatives to in vitro experimental screening, thus streamlining the drug development process. We discuss in particular the biophysical and biochemical properties that underpin developability potential and their trade-offs, review various in vitro assays to measure such properties or parameters that are predictive of developability, and give an overview of the growing number of in silico tools available to predict properties important for antibody development, including the CamSol method developed in our laboratory.
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28
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Heads JT, Kelm S, Tyson K, Lawson ADG. A computational method for predicting the aggregation propensity of IgG1 and IgG4(P) mAbs in common storage buffers. MAbs 2022; 14:2138092. [PMID: 36418193 PMCID: PMC9704409 DOI: 10.1080/19420862.2022.2138092] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The propensity for some monoclonal antibodies (mAbs) to aggregate at physiological and manufacturing pH values can prevent their use as therapeutic molecules or delay time to market. Consequently, developability assessments are essential to select optimum candidates, or inform on mitigation strategies to avoid potential late-stage failures. These studies are typically performed in a range of buffer solutions because factors such as pH can dramatically alter the aggregation propensity of the test mAbs (up to 100-fold in extreme cases). A computational method capable of robustly predicting the aggregation propensity at the pH values of common storage buffers would have substantial value. Here, we describe a mAb aggregation prediction tool (MAPT) that builds on our previously published isotype-dependent, charge-based model of aggregation. We show that the addition of a homology model-derived hydrophobicity descriptor to our electrostatic aggregation model enabled the generation of a robust mAb developability indicator. To contextualize our aggregation scoring system, we analyzed 97 clinical-stage therapeutic mAbs. To further validate our approach, we focused on six mAbs (infliximab, tocilizumab, rituximab, CNTO607, MEDI1912 and MEDI1912_STT) which have been reported to cover a large range of aggregation propensities. The different aggregation propensities of the case study molecules at neutral and slightly acidic pH were correctly predicted, verifying the utility of our computational method.
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Affiliation(s)
- James T. Heads
- UCB Pharma, 208 Bath Road, SloughSL1 3WE, UK,CONTACT James T. Heads UCB Pharma, 208 Bath Road, SloughSL1 3WE, UK
| | | | - Kerry Tyson
- UCB Pharma, 208 Bath Road, SloughSL1 3WE, UK
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29
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Kunz P. Assessing the Aggregation Propensity of Single-Domain Antibodies upon Heat-Denaturation Employing the ΔT m Shift. Methods Mol Biol 2022; 2446:233-244. [PMID: 35157276 DOI: 10.1007/978-1-0716-2075-5_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Nano differential scanning fluorimetry is used to quantify protein thermostability and has substantially expanded the spectrum of convenient biophysical parameters used to characterize proteins. Here, this technique is used to measure the ΔTm shift for single-domain antibodies (sdAbs), which represents a comprehensive metric for the aggregation propensity of sdAbs upon heat-denaturation. By relating two melting curves at different protein concentrations, the ΔTm shift described in this protocol is ideally suited for high-throughput measurements to guide protein engineering, formulation development, and developability assessment of sdAbs.
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Affiliation(s)
- Patrick Kunz
- Coriolis Pharma Research GmbH, Martinsried, Germany.
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30
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Das TK, Chou DK, Jiskoot W, Arosio P. Nucleation in protein aggregation in biotherapeutic development: a look into the heart of the event. J Pharm Sci 2022; 111:951-959. [DOI: 10.1016/j.xphs.2022.01.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 01/24/2022] [Accepted: 01/24/2022] [Indexed: 12/26/2022]
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31
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Ye W, Liu X, He R, Gou L, Lu M, Yang G, Wen J, Wang X, Liu F, Ma S, Qian W, Jia S, Ding T, Sun L, Gao W. Improving antibody affinity through <i>in vitro</i> mutagenesis in complementarity determining regions. J Biomed Res 2022; 36:155-166. [PMID: 35545451 PMCID: PMC9179109 DOI: 10.7555/jbr.36.20220003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
High-affinity antibodies are widely used in diagnostics and for the treatment of human diseases. However, most antibodies are isolated from semi-synthetic libraries by phage display and do not possess in vivo affinity maturation, which is triggered by antigen immunization. It is therefore necessary to engineer the affinity of these antibodies by way of in vitro assaying. In this study, we optimized the affinity of two human monoclonal antibodies which were isolated by phage display in a previous related study. For the 42A1 antibody, which targets the liver cancer antigen glypican-3, the variant T57H in the second complementarity-determining region of the heavy chain (CDR-H2) exhibited a 2.6-fold improvement in affinity, as well as enhanced cell-binding activity. For the I4A3 antibody to severe acute respiratory syndrome coronavirus 2, beneficial single mutations in CDR-H2 and CDR-H3 were randomly combined to select the best synergistic mutations. Among these, the mutation S53P-S98T improved binding affinity (about 3.7 fold) and the neutralizing activity (about 12 fold) compared to the parent antibody. Taken together, single mutations of key residues in antibody CDRs were enough to increase binding affinity with improved antibody functions. The mutagenic combination of key residues in different CDRs creates additive enhancements. Therefore, this study provides a safe and effective in vitro strategy for optimizing antibody affinity.
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Affiliation(s)
- Wei Ye
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Key Laboratory of Human Functional Genomics of Jiangsu Province, National Health Commission Key Laboratory of Antibody Techniques, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Xiaoyu Liu
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Key Laboratory of Human Functional Genomics of Jiangsu Province, National Health Commission Key Laboratory of Antibody Techniques, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Ruiting He
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Key Laboratory of Human Functional Genomics of Jiangsu Province, National Health Commission Key Laboratory of Antibody Techniques, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Liming Gou
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Key Laboratory of Human Functional Genomics of Jiangsu Province, National Health Commission Key Laboratory of Antibody Techniques, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Ming Lu
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Key Laboratory of Human Functional Genomics of Jiangsu Province, National Health Commission Key Laboratory of Antibody Techniques, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Gang Yang
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Key Laboratory of Human Functional Genomics of Jiangsu Province, National Health Commission Key Laboratory of Antibody Techniques, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Jiaqi Wen
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Key Laboratory of Human Functional Genomics of Jiangsu Province, National Health Commission Key Laboratory of Antibody Techniques, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Xufei Wang
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Key Laboratory of Human Functional Genomics of Jiangsu Province, National Health Commission Key Laboratory of Antibody Techniques, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Fang Liu
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Key Laboratory of Human Functional Genomics of Jiangsu Province, National Health Commission Key Laboratory of Antibody Techniques, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Sujuan Ma
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Key Laboratory of Human Functional Genomics of Jiangsu Province, National Health Commission Key Laboratory of Antibody Techniques, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Weifeng Qian
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu 215001, China
| | - Shaochang Jia
- Department of Biotherapy, Nanjing Jinling Hospital, Nanjing, Jiangsu 210002, China
| | - Tong Ding
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Key Laboratory of Human Functional Genomics of Jiangsu Province, National Health Commission Key Laboratory of Antibody Techniques, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Luan Sun
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Key Laboratory of Human Functional Genomics of Jiangsu Province, National Health Commission Key Laboratory of Antibody Techniques, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Wei Gao and Luan Sun, School of Basic Medical Sciences, Nanjing Medical University, 101 Longmian Road, Nanjing, Jiangsu 211166, China. Tel/Fax: +86-25-86869471/+86-25-86869471, E-mails:
and
| | - Wei Gao
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Key Laboratory of Human Functional Genomics of Jiangsu Province, National Health Commission Key Laboratory of Antibody Techniques, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Wei Gao and Luan Sun, School of Basic Medical Sciences, Nanjing Medical University, 101 Longmian Road, Nanjing, Jiangsu 211166, China. Tel/Fax: +86-25-86869471/+86-25-86869471, E-mails:
and
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32
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Expanding the toolbox for predictive parameters describing antibody stability considering thermodynamic and kinetic determinants. Pharm Res 2021; 38:2065-2089. [PMID: 34904201 DOI: 10.1007/s11095-021-03120-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 10/03/2021] [Indexed: 10/19/2022]
Abstract
PURPOSE Introduction of the activation energy (Ea) as a kinetic parameter to describe and discriminate monoclonal antibody (mAb) stability. METHODS Ea is derived from intrinsic fluorescence (IF) unfolding thermograms. An apparent irreversible three-state fit model based on the Arrhenius integral is developed to determine Ea of respective unfolding transitions. These activation energies are compared to the thermodynamic parameter of van´t Hoff enthalpies (∆Hvh). Using a set of 34 mAbs formulated in four different formulations, both the apparent thermodynamic and kinetic parameters together with apparent melting temperatures are correlated collectively with each other to storage stabilities to evaluate its predictive power with respect to long-term effects potentially reflected in shelf-life. RESULTS Ea allows for the discrimination of (i) different parent mAbs, (ii) different variants that originate from parent mAbs, and (iii) different formulations. Interestingly, we observed that the Ea of the CH2 unfolding transition shows strongest correlations with monomer and aggregate content after storage at accelerated and stress conditions when collectively compared to ∆Hvh and Tm of the CH2 transition. Moreover, the predictive parameters determined for the CH2 domain show generally stronger correlations with monomer and aggregate content than those derived for the Fab. Qualitative assessment by ranking Ea of the Fab domain showed good agreement with monomer content in storage stabilities of individual mAb sub-sets. CONCLUSION Ea from IF unfolding transitions can be used in addition to other commonly used thermodynamic predictive parameters to discriminate and characterize thermal stability of different mAbs in different formulations. Hence, it shows great potential for antibody engineering and formulation scientists.
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33
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Depetris RS, Lu D, Polonskaya Z, Zhang Z, Luna X, Tankard A, Kolahi P, Drummond M, Williams C, Ebert MCCJC, Patel JP, Poyurovsky MV. Functional antibody characterization via direct structural analysis and information-driven protein-protein docking. Proteins 2021; 90:919-935. [PMID: 34773424 PMCID: PMC9544432 DOI: 10.1002/prot.26280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 08/28/2021] [Accepted: 11/07/2021] [Indexed: 12/02/2022]
Abstract
Detailed description of the mechanism of action of the therapeutic antibodies is essential for the functional characterization and future optimization of potential clinical agents. We recently developed KD035, a fully human antibody targeting vascular endothelial growth factor receptor 2 (VEGFR2). KD035 blocked VEGF‐A, and VEGF‐C‐mediated VEGFR2 activation, as demonstrated by the in vitro binding and competition assays and functional cellular assays. Here, we report a computational model of the complex between the variable fragment of KD035 (KD035(Fv)) and the domains 2 and 3 of the extracellular portion of VEGFR2 (VEGFR2(D2‐3)). Our modeling was guided by a priori experimental information including the X‐ray structures of KD035 and related antibodies, binding assays, target domain mapping and comparison of KD035 affinity for VEGFR2 from different species. The accuracy of the model was assessed by molecular dynamics simulations, and subsequently validated by mutagenesis and binding analysis. Importantly, the steps followed during the generation of this model can set a precedent for future in silico efforts aimed at the accurate description of the antibody–antigen and more broadly protein–protein complexes.
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Affiliation(s)
| | - Dan Lu
- Kadmon Corporation, LLC, New York, New York, USA
| | | | - Zhikai Zhang
- Kadmon Corporation, LLC, New York, New York, USA
| | - Xenia Luna
- Kadmon Corporation, LLC, New York, New York, USA
| | | | - Pegah Kolahi
- Kadmon Corporation, LLC, New York, New York, USA
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34
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Oeller M, Sormanni P, Vendruscolo M. An open-source automated PEG precipitation assay to measure the relative solubility of proteins with low material requirement. Sci Rep 2021; 11:21932. [PMID: 34753962 PMCID: PMC8578320 DOI: 10.1038/s41598-021-01126-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/18/2021] [Indexed: 02/02/2023] Open
Abstract
The solubility of proteins correlates with a variety of their properties, including function, production yield, pharmacokinetics, and formulation at high concentrations. High solubility is therefore a key requirement for the development of protein-based reagents for applications in life sciences, biotechnology, diagnostics, and therapeutics. Accurate solubility measurements, however, remain challenging and resource intensive, which limits their throughput and hence their applicability at the early stages of development pipelines, when long-lists of candidates are typically available in minute amounts. Here, we present an automated method based on the titration of a crowding agent (polyethylene glycol, PEG) to quantitatively assess relative solubility of proteins using about 200 µg of purified material. Our results demonstrate that this method is accurate and economical in material requirement and costs of reagents, which makes it suitable for high-throughput screening. This approach is freely-shared and based on a low cost, open-source liquid-handling robot. We anticipate that this method will facilitate the assessment of the developability of proteins and make it substantially more accessible.
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Affiliation(s)
- Marc Oeller
- grid.5335.00000000121885934Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, UK
| | - Pietro Sormanni
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, UK.
| | - Michele Vendruscolo
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, UK.
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35
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Lin J, Figazzolo C, Metrick MA, Sormanni P, Vendruscolo M. Computational maturation of a single-domain antibody against Aβ42 aggregation. Chem Sci 2021; 12:13940-13948. [PMID: 35475123 PMCID: PMC8901120 DOI: 10.1039/d1sc03898b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 08/23/2021] [Indexed: 02/02/2023] Open
Abstract
The expansion of structural databases and the increase in computing power are enabling approaches for antibody discovery based on computational design. It has already been shown that it is possible to use this approach to generate antibodies for specific epitopes on challenging targets. Here we describe an application of this procedure for antibody maturation through the computational design of mutational variants of increased potency. We illustrate this procedure in the case of a single-domain antibody targeting an epitope in the N-terminal region of Aβ42, a peptide whose aggregation is closely associated with Alzheimer's disease. We show that this approach enables the generation of an antibody variant with over 200-fold increased potency against the primary nucleation process in Aβ42 aggregation. Our results thus demonstrate that potentiated antibody variants can be obtained by computational maturation. A computational maturation method enables the generation of an antibody variant with over 200-fold increased potency against the primary nucleation process in Aβ42 aggregation.![]()
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Affiliation(s)
- Jiacheng Lin
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge Cambridge CB2 1EW UK
| | - Chiara Figazzolo
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge Cambridge CB2 1EW UK
| | - Michael A Metrick
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge Cambridge CB2 1EW UK
| | - Pietro Sormanni
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge Cambridge CB2 1EW UK
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge Cambridge CB2 1EW UK
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36
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Thorsteinson N, Gunn JR, Kelly K, Long W, Labute P. Structure-based charge calculations for predicting isoelectric point, viscosity, clearance, and profiling antibody therapeutics. MAbs 2021; 13:1981805. [PMID: 34632944 PMCID: PMC8510563 DOI: 10.1080/19420862.2021.1981805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
The effect of hydrophobicity on antibody aggregation is well understood, and it has been shown that charge calculations can be useful for high-concentration viscosity and pharmacokinetic (PK) clearance predictions. In this work, structure-based charge descriptors are evaluated for their predictive performance on recently published antibody pI, viscosity, and clearance data. From this, we devised four rules for therapeutic antibody profiling which address developability issues arising from hydrophobicity and charged-based solution behavior, PK, and the ability to enrich for those that are approved by the U.S. Food and Drug Administration. Differences in strategy for optimizing the solution behavior of human IgG1 antibodies versus the IgG2 and IgG4 isotypes and the impact of pH alterations in formulation are discussed.
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Affiliation(s)
- Nels Thorsteinson
- Research and Development, Chemical Computing Group ULC, Montreal, Quebec, Canada
| | - John R Gunn
- Research and Development, Chemical Computing Group ULC, Montreal, Quebec, Canada
| | - Kenneth Kelly
- Research and Development, Chemical Computing Group ULC, Montreal, Quebec, Canada
| | - Will Long
- Research and Development, Chemical Computing Group ULC, Montreal, Quebec, Canada
| | - Paul Labute
- Research and Development, Chemical Computing Group ULC, Montreal, Quebec, Canada
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37
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Narayanan H, Dingfelder F, Condado Morales I, Patel B, Heding KE, Bjelke JR, Egebjerg T, Butté A, Sokolov M, Lorenzen N, Arosio P. Design of Biopharmaceutical Formulations Accelerated by Machine Learning. Mol Pharm 2021; 18:3843-3853. [PMID: 34519511 DOI: 10.1021/acs.molpharmaceut.1c00469] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
In addition to activity, successful biological drugs must exhibit a series of suitable developability properties, which depend on both protein sequence and buffer composition. In the context of this high-dimensional optimization problem, advanced algorithms from the domain of machine learning are highly beneficial in complementing analytical screening and rational design. Here, we propose a Bayesian optimization algorithm to accelerate the design of biopharmaceutical formulations. We demonstrate the power of this approach by identifying the formulation that optimizes the thermal stability of three tandem single-chain Fv variants within 25 experiments, a number which is less than one-third of the experiments that would be required by a classical DoE method and several orders of magnitude smaller compared to detailed experimental analysis of full combinatorial space. We further show the advantage of this method over conventional approaches to efficiently transfer historical information as prior knowledge for the development of new biologics or when new buffer agents are available. Moreover, we highlight the benefit of our technique in engineering multiple biophysical properties by simultaneously optimizing both thermal and interface stabilities. This optimization minimizes the amount of surfactant in the formulation, which is important to decrease the risks associated with corresponding degradation processes. Overall, this method can provide high speed of converging to optimal conditions, the ability to transfer prior knowledge, and the identification of new nonlinear combinations of excipients. We envision that these features can lead to a considerable acceleration in formulation design and to parallelization of operations during drug development.
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Affiliation(s)
- Harini Narayanan
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
| | - Fabian Dingfelder
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland.,Department of Biophysics and Injectable Formulation, Global Research Technologies, Novo Nordisk A/S, Måløv 2760, Denmark
| | - Itzel Condado Morales
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland.,Department of Biophysics and Injectable Formulation, Global Research Technologies, Novo Nordisk A/S, Måløv 2760, Denmark
| | - Bhargav Patel
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
| | - Kristine Enemærke Heding
- Department of Biophysics and Injectable Formulation, Global Research Technologies, Novo Nordisk A/S, Måløv 2760, Denmark
| | - Jais Rose Bjelke
- Department of Purification Technologies, Global Research Technologies, Novo Nordisk A/S, Måløv 2760, Denmark
| | - Thomas Egebjerg
- Department of Mammalian Expression, Global Research Technologies, Novo Nordisk A/S, Måløv 2760, Denmark
| | | | | | - Nikolai Lorenzen
- Department of Biophysics and Injectable Formulation, Global Research Technologies, Novo Nordisk A/S, Måløv 2760, Denmark
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
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38
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Kopp MRG, Wolf Pérez AM, Zucca MV, Capasso Palmiero U, Friedrichsen B, Lorenzen N, Arosio P. An accelerated surface-mediated stress assay of antibody instability for developability studies. MAbs 2021; 12:1815995. [PMID: 32954930 PMCID: PMC7577746 DOI: 10.1080/19420862.2020.1815995] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
High physical stability is required for the development of monoclonal antibodies (mAbs) into successful therapeutic products. Developability assays are used to predict physical stability issues such as high viscosity and poor conformational stability, but protein aggregation remains a challenging property to predict. Among different types of stresses, air–water and solid–liquid interfaces are well known to potentially trigger protein instability and induce aggregation. Yet, in contrast to the increasing number of developability assays to evaluate bulk properties, there is still a lack of experimental methods to evaluate antibody stability against interfaces. Here, we investigate the potential of a hydrophobic nanoparticle surface-mediated stress assay to assess the stability of mAbs during the early stages of development. We evaluate this surface-mediated accelerated stability assay on a rationally designed library of 14 variants of a humanized IgG4, featuring a broad span of solubility values and other developability properties. The assay could identify variants characterized by high instability against agitation in the presence of air–water interfaces. Remarkably, for the set of investigated molecules, we observe strong correlations between the extent of aggregation induced by the surface-mediated stress assay and other developability properties of the molecules, such as aggregation upon storage at 45°C, self-association (evaluated by affinity-capture self-interaction nanoparticle spectroscopy) and nonspecific interactions (estimated by cross-interaction chromatography, stand-up monolayer chromatography (SMAC), SMAC*). This highly controlled surface-mediated stress assay has the potential to complement and increase the ability of the current set of screening techniques to assess protein aggregation and developability potential of mAbs during the early stages of drug development. Abbreviations:AC-SINS: Affinity-Capture Self-Interaction Nanoparticle Spectroscopy; AMS: Ammonium sulfate precipitation; ANS: 1-anilinonaphtalene-8-sulfonate; CIC: Cross-interaction chromatography; DLS: Dynamic light scattering; HIC: Hydrophobic interaction chromatography; HNSSA: Hydrophobic nanoparticles surface-stress assay; mAb: Monoclonal antibody; NP: Nanoparticle; SEC: Size exclusion chromatography; SMAC: Stand-up monolayer chromatography; WT: Wild type
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Affiliation(s)
- Marie R G Kopp
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, Swiss Federal Institute of Technology , Zurich, Switzerland
| | - Adriana-Michelle Wolf Pérez
- Department of Biophysics, Biophysics and Injectable Formulation, Novo Nordisk , Måløv, Denmark.,Aarhus University, iNANO , Aarhus C, Denmark
| | - Marta Virginia Zucca
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, Swiss Federal Institute of Technology , Zurich, Switzerland
| | - Umberto Capasso Palmiero
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, Swiss Federal Institute of Technology , Zurich, Switzerland
| | | | - Nikolai Lorenzen
- Department of Biophysics, Biophysics and Injectable Formulation, Novo Nordisk , Måløv, Denmark
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, Swiss Federal Institute of Technology , Zurich, Switzerland
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39
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Golinski AW, Mischler KM, Laxminarayan S, Neurock NL, Fossing M, Pichman H, Martiniani S, Hackel BJ. High-throughput developability assays enable library-scale identification of producible protein scaffold variants. Proc Natl Acad Sci U S A 2021; 118:e2026658118. [PMID: 34078670 PMCID: PMC8201827 DOI: 10.1073/pnas.2026658118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Proteins require high developability-quantified by expression, solubility, and stability-for robust utility as therapeutics, diagnostics, and in other biotechnological applications. Measuring traditional developability metrics is low throughput in nature, often slowing the developmental pipeline. We evaluated the ability of 10 variations of three high-throughput developability assays to predict the bacterial recombinant expression of paratope variants of the protein scaffold Gp2. Enabled by a phenotype/genotype linkage, assay performance for 105 variants was calculated via deep sequencing of populations sorted by proxied developability. We identified the most informative assay combination via cross-validation accuracy and correlation feature selection and demonstrated the ability of machine learning models to exploit nonlinear mutual information to increase the assays' predictive utility. We trained a random forest model that predicts expression from assay performance that is 35% closer to the experimental variance and trains 80% more efficiently than a model predicting from sequence information alone. Utilizing the predicted expression, we performed a site-wise analysis and predicted mutations consistent with enhanced developability. The validated assays offer the ability to identify developable proteins at unprecedented scales, reducing the bottleneck of protein commercialization.
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Affiliation(s)
- Alexander W Golinski
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455
| | - Katelynn M Mischler
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455
| | - Sidharth Laxminarayan
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455
| | - Nicole L Neurock
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455
| | - Matthew Fossing
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455
| | - Hannah Pichman
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455
| | - Stefano Martiniani
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455
| | - Benjamin J Hackel
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455
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40
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Optimization of therapeutic antibodies by predicting antigen specificity from antibody sequence via deep learning. Nat Biomed Eng 2021; 5:600-612. [PMID: 33859386 DOI: 10.1038/s41551-021-00699-9] [Citation(s) in RCA: 103] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 02/15/2021] [Indexed: 02/06/2023]
Abstract
The optimization of therapeutic antibodies is time-intensive and resource-demanding, largely because of the low-throughput screening of full-length antibodies (approximately 1 × 103 variants) expressed in mammalian cells, which typically results in few optimized leads. Here we show that optimized antibody variants can be identified by predicting antigen specificity via deep learning from a massively diverse space of antibody sequences. To produce data for training deep neural networks, we deep-sequenced libraries of the therapeutic antibody trastuzumab (about 1 × 104 variants), expressed in a mammalian cell line through site-directed mutagenesis via CRISPR-Cas9-mediated homology-directed repair, and screened the libraries for specificity to human epidermal growth factor receptor 2 (HER2). We then used the trained neural networks to screen a computational library of approximately 1 × 108 trastuzumab variants and predict the HER2-specific subset (approximately 1 × 106 variants), which can then be filtered for viscosity, clearance, solubility and immunogenicity to generate thousands of highly optimized lead candidates. Recombinant expression and experimental testing of 30 randomly selected variants from the unfiltered library showed that all 30 retained specificity for HER2. Deep learning may facilitate antibody engineering and optimization.
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41
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Berner C, Menzen T, Winter G, Svilenov HL. Combining Unfolding Reversibility Studies and Molecular Dynamics Simulations to Select Aggregation-Resistant Antibodies. Mol Pharm 2021; 18:2242-2253. [PMID: 33928776 DOI: 10.1021/acs.molpharmaceut.1c00017] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The efficient development of new therapeutic antibodies relies on developability assessment with biophysical and computational methods to find molecules with drug-like properties such as resistance to aggregation. Despite the many novel approaches to select well-behaved proteins, antibody aggregation during storage is still challenging to predict. For this reason, there is a high demand for methods that can identify aggregation-resistant antibodies. Here, we show that three straightforward techniques can select the aggregation-resistant antibodies from a dataset with 13 molecules. The ReFOLD assay provided information about the ability of the antibodies to refold to monomers after unfolding with chemical denaturants. Modulated scanning fluorimetry (MSF) yielded the temperatures that start causing irreversible unfolding of the proteins. Aggregation was the main reason for poor unfolding reversibility in both ReFOLD and MSF experiments. We therefore performed temperature ramps in molecular dynamics (MD) simulations to obtain partially unfolded antibody domains in silico and used CamSol to assess their aggregation potential. We compared the information from ReFOLD, MSF, and MD to size-exclusion chromatography (SEC) data that shows whether the antibodies aggregated during storage at 4, 25, and 40 °C. Contrary to the aggregation-prone molecules, the antibodies that were resistant to aggregation during storage at 40 °C shared three common features: (i) higher tendency to refold to monomers after unfolding with chemical denaturants, (ii) higher onset temperature of nonreversible unfolding, and (iii) unfolding of regions containing aggregation-prone sequences at higher temperatures in MD simulations.
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Affiliation(s)
- Carolin Berner
- Department of Pharmacy, Ludwig-Maximilians-Universität München, Butenandtstr. 5, 81377 Munich, Germany
| | - Tim Menzen
- Coriolis Pharma Research GmbH, Fraunhoferstr. 18 b, 82152 Martinsried, Germany
| | - Gerhard Winter
- Department of Pharmacy, Ludwig-Maximilians-Universität München, Butenandtstr. 5, 81377 Munich, Germany
| | - Hristo L Svilenov
- Department of Pharmacy, Ludwig-Maximilians-Universität München, Butenandtstr. 5, 81377 Munich, Germany
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42
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Chi B, De Oliveira G, Gallagher T, Mitchell L, Knightley L, Gonzalez CC, Russell S, Germaschewski V, Pearce C, Sellick CA. Pragmatic mAb lead molecule engineering from a developability perspective. Biotechnol Bioeng 2021; 118:3733-3743. [PMID: 33913507 DOI: 10.1002/bit.27802] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/26/2021] [Accepted: 04/15/2021] [Indexed: 01/08/2023]
Abstract
As the number of antibody drugs being approved and marketed increases, our knowledge of what makes potential drug candidates a successful product has increased tremendously. One of the critical parameters that have become clear in the field is the importance of mAb "developability." Efforts are being increasingly focused on simultaneously selecting molecules that exhibit both desirable biological potencies and manufacturability attributes. In the current study mutations to improve the developability profile of a problematic antibody that inconsistently precipitates in a batch scale-dependent fashion using a standard platform purification process are described. Initial bioinformatic analysis showed the molecule has no obvious sequence or structural liabilities that might lead it to precipitate. Subsequent analysis of the molecule revealed the presence of two unusual positively charged mutations on the light chain at the interface of VH and VL domains, which were hypothesized to be the primary contributor to molecule precipitation during process development. To investigate this hypothesis, straightforward reversion to the germline of these residues was carried out. The resulting mutants have improved expression titers and recovered stability within a forced precipitation assay, without any change to biological activity. Given the time pressures of drug development in industry, process optimization of the lead molecule was carried out in parallel to the "retrospective" mutagenesis approach. Bespoke process optimization for large-scale manufacturing was successful. However, we propose that such context-dependent sequence liabilities should be included in the arsenal of in silico developability screening early in development; particularly since this specific issue can be efficiently mitigated without the requirement for extensive screening of lead molecule variants.
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Affiliation(s)
| | | | - Tom Gallagher
- Kymab Ltd., Cambridge, UK.,F-star Therapeutics Ltd., Cambridge, UK
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43
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Wahlund PO, Lorenzen N, Rischel C. Screening for protein-protein interactions with asymmetrical flow field-flow fractionation. J Pharm Sci 2021; 110:2336-2339. [PMID: 33640337 DOI: 10.1016/j.xphs.2021.02.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 01/27/2021] [Accepted: 02/19/2021] [Indexed: 11/30/2022]
Abstract
We describe a new method for screening protein-protein interaction of biopharmaceutical molecules at dilute concentrations to predict development issues at high concentration. The method is based on Asymmetrical Flow Field-Flow Fractionation (AF4) measurements using well known effects of protein-protein attraction on the fractionation profile due to elevated protein concentrations occurring close to the membrane. We explore the effect for 4 different monoclonal antibodies and show that the profiles obtained are quite different. Interestingly, we find that the recovery in AF4 correlates with the diffusion interaction parameter, which is a standard method for the analysis of protein-protein attraction. The results are insensitive to the protein concentration and buffer composition of the sample solution and only depend on the absolute amount of protein loaded and on the running buffer. This makes the method highly suitable for developability assessment in a compound discovery workflow.
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Affiliation(s)
- Per-Olof Wahlund
- Department Biophysics and Injectable Formulation 2, Global Research Technologies, Novo Nordisk A/S, 2760 Måløv, Denmark.
| | - Nikolai Lorenzen
- Department Biophysics and Injectable Formulation 2, Global Research Technologies, Novo Nordisk A/S, 2760 Måløv, Denmark
| | - Christian Rischel
- Department Biophysics and Injectable Formulation 2, Global Research Technologies, Novo Nordisk A/S, 2760 Måløv, Denmark
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44
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Makowski EK, Wu L, Gupta P, Tessier PM. Discovery-stage identification of drug-like antibodies using emerging experimental and computational methods. MAbs 2021; 13:1895540. [PMID: 34313532 PMCID: PMC8346245 DOI: 10.1080/19420862.2021.1895540] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 02/05/2021] [Accepted: 02/22/2021] [Indexed: 11/30/2022] Open
Abstract
There is intense and widespread interest in developing monoclonal antibodies as therapeutic agents to treat diverse human disorders. During early-stage antibody discovery, hundreds to thousands of lead candidates are identified, and those that lack optimal physical and chemical properties must be deselected as early as possible to avoid problems later in drug development. It is particularly challenging to characterize such properties for large numbers of candidates with the low antibody quantities, concentrations, and purities that are available at the discovery stage, and to predict concentrated antibody properties (e.g., solubility, viscosity) required for efficient formulation, delivery, and efficacy. Here we review key recent advances in developing and implementing high-throughput methods for identifying antibodies with desirable in vitro and in vivo properties, including favorable antibody stability, specificity, solubility, pharmacokinetics, and immunogenicity profiles, that together encompass overall drug developability. In particular, we highlight impressive recent progress in developing computational methods for improving rational antibody design and prediction of drug-like behaviors that hold great promise for reducing the amount of required experimentation. We also discuss outstanding challenges that will need to be addressed in the future to fully realize the great potential of using such analysis for minimizing development times and improving the success rate of antibody candidates in the clinic.
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Affiliation(s)
- Emily K. Makowski
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
| | - Lina Wu
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Chemical Engineering
| | - Priyanka Gupta
- Department of Biochemistry and Biophysics, Rensselaer Polytechnic Institute, Troy, NY, USA
- Biotherapeutics Discovery Department, Boehringer Ingelheim, Ridgefield, CT, USA
| | - Peter M. Tessier
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Chemical Engineering
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
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45
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Sawant MS, Streu CN, Wu L, Tessier PM. Toward Drug-Like Multispecific Antibodies by Design. Int J Mol Sci 2020; 21:E7496. [PMID: 33053650 PMCID: PMC7589779 DOI: 10.3390/ijms21207496] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/02/2020] [Accepted: 10/02/2020] [Indexed: 12/18/2022] Open
Abstract
The success of antibody therapeutics is strongly influenced by their multifunctional nature that couples antigen recognition mediated by their variable regions with effector functions and half-life extension mediated by a subset of their constant regions. Nevertheless, the monospecific IgG format is not optimal for many therapeutic applications, and this has led to the design of a vast number of unique multispecific antibody formats that enable targeting of multiple antigens or multiple epitopes on the same antigen. Despite the diversity of these formats, a common challenge in generating multispecific antibodies is that they display suboptimal physical and chemical properties relative to conventional IgGs and are more difficult to develop into therapeutics. Here we review advances in the design and engineering of multispecific antibodies with drug-like properties, including favorable stability, solubility, viscosity, specificity and pharmacokinetic properties. We also highlight emerging experimental and computational methods for improving the next generation of multispecific antibodies, as well as their constituent antibody fragments, with natural IgG-like properties. Finally, we identify several outstanding challenges that need to be addressed to increase the success of multispecific antibodies in the clinic.
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Affiliation(s)
- Manali S. Sawant
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA; (M.S.S.); (C.N.S.)
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Craig N. Streu
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA; (M.S.S.); (C.N.S.)
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA;
- Department of Chemistry, Albion College, Albion, MI 49224, USA
| | - Lina Wu
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA;
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter M. Tessier
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA; (M.S.S.); (C.N.S.)
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA;
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
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46
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Norman RA, Ambrosetti F, Bonvin AMJJ, Colwell LJ, Kelm S, Kumar S, Krawczyk K. Computational approaches to therapeutic antibody design: established methods and emerging trends. Brief Bioinform 2020; 21:1549-1567. [PMID: 31626279 PMCID: PMC7947987 DOI: 10.1093/bib/bbz095] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/07/2019] [Accepted: 07/05/2019] [Indexed: 12/31/2022] Open
Abstract
Antibodies are proteins that recognize the molecular surfaces of potentially noxious molecules to mount an adaptive immune response or, in the case of autoimmune diseases, molecules that are part of healthy cells and tissues. Due to their binding versatility, antibodies are currently the largest class of biotherapeutics, with five monoclonal antibodies ranked in the top 10 blockbuster drugs. Computational advances in protein modelling and design can have a tangible impact on antibody-based therapeutic development. Antibody-specific computational protocols currently benefit from an increasing volume of data provided by next generation sequencing and application to related drug modalities based on traditional antibodies, such as nanobodies. Here we present a structured overview of available databases, methods and emerging trends in computational antibody analysis and contextualize them towards the engineering of candidate antibody therapeutics.
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47
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Ikenoue T, Aprile FA, Sormanni P, Ruggeri FS, Perni M, Heller GT, Haas CP, Middel C, Limbocker R, Mannini B, Michaels TCT, Knowles TPJ, Dobson CM, Vendruscolo M. A rationally designed bicyclic peptide remodels Aβ42 aggregation in vitro and reduces its toxicity in a worm model of Alzheimer's disease. Sci Rep 2020; 10:15280. [PMID: 32943652 PMCID: PMC7498612 DOI: 10.1038/s41598-020-69626-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 06/26/2020] [Indexed: 01/01/2023] Open
Abstract
Bicyclic peptides have great therapeutic potential since they can bridge the gap between small molecules and antibodies by combining a low molecular weight of about 2 kDa with an antibody-like binding specificity. Here we apply a recently developed in silico rational design strategy to produce a bicyclic peptide to target the C-terminal region (residues 31–42) of the 42-residue form of the amyloid β peptide (Aβ42), a protein fragment whose aggregation into amyloid plaques is linked with Alzheimer’s disease. We show that this bicyclic peptide is able to remodel the aggregation process of Aβ42 in vitro and to reduce its associated toxicity in vivo in a C. elegans worm model expressing Aβ42. These results provide an initial example of a computational approach to design bicyclic peptides to target specific epitopes on disordered proteins.
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Affiliation(s)
- Tatsuya Ikenoue
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.,Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Francesco A Aprile
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.,Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, W12 0BZ, UK
| | - Pietro Sormanni
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Francesco S Ruggeri
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Michele Perni
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Gabriella T Heller
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Christian P Haas
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Christoph Middel
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Ryan Limbocker
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.,Department of Chemistry and Life Science, United States Military Academy, West Point, NY, 10996, USA
| | - Benedetta Mannini
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Thomas C T Michaels
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Christopher M Dobson
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
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48
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Alfaleh MA, Alsaab HO, Mahmoud AB, Alkayyal AA, Jones ML, Mahler SM, Hashem AM. Phage Display Derived Monoclonal Antibodies: From Bench to Bedside. Front Immunol 2020; 11:1986. [PMID: 32983137 PMCID: PMC7485114 DOI: 10.3389/fimmu.2020.01986] [Citation(s) in RCA: 129] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/23/2020] [Indexed: 12/12/2022] Open
Abstract
Monoclonal antibodies (mAbs) have become one of the most important classes of biopharmaceutical products, and they continue to dominate the universe of biopharmaceutical markets in terms of approval and sales. They are the most profitable single product class, where they represent six of the top ten selling drugs. At the beginning of the 1990s, an in vitro antibody selection technology known as antibody phage display was developed by John McCafferty and Sir. Gregory Winter that enabled the discovery of human antibodies for diverse applications, particularly antibody-based drugs. They created combinatorial antibody libraries on filamentous phage to be utilized for generating antigen specific antibodies in a matter of weeks. Since then, more than 70 phage–derived antibodies entered clinical studies and 14 of them have been approved. These antibodies are indicated for cancer, and non-cancer medical conditions, such as inflammatory, optical, infectious, or immunological diseases. This review will illustrate the utility of phage display as a powerful platform for therapeutic antibodies discovery and describe in detail all the approved mAbs derived from phage display.
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Affiliation(s)
- Mohamed A Alfaleh
- Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia.,Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hashem O Alsaab
- Department of Pharmaceutics and Pharmaceutical Technology, College of Pharmacy, Taif University, Taif, Saudi Arabia
| | - Ahmad Bakur Mahmoud
- College of Applied Medical Sciences, Taibah University, Medina, Saudi Arabia
| | - Almohanad A Alkayyal
- Department of Medical Laboratory Technology, University of Tabuk, Tabuk, Saudi Arabia
| | - Martina L Jones
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia.,Australian Research Council Training Centre for Biopharmaceutical Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Stephen M Mahler
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia.,Australian Research Council Training Centre for Biopharmaceutical Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Anwar M Hashem
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
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49
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Heads JT, Lamb R, Kelm S, Adams R, Elliott P, Tyson K, Topia S, West S, Nan R, Turner A, Lawson ADG. Electrostatic interactions modulate the differential aggregation propensities of IgG1 and IgG4P antibodies and inform charged residue substitutions for improved developability. Protein Eng Des Sel 2020; 32:277-288. [PMID: 31868219 PMCID: PMC7036597 DOI: 10.1093/protein/gzz046] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 10/17/2019] [Accepted: 11/19/2019] [Indexed: 11/14/2022] Open
Abstract
Native state aggregation is an important concern in the development of therapeutic antibodies. Enhanced knowledge of mAb native state aggregation mechanisms would permit sequence-based selection and design of therapeutic mAbs with improved developability. We investigated how electrostatic interactions affect the native state aggregation of seven human IgG1 and IgG4P mAb isotype pairs, each pair having identical variable domains that are different for each set of IgG1 and IgG4P constructs. Relative aggregation propensities were determined at pH 7.4, representing physiological conditions, and pH 5.0, representing commonly used storage conditions. Our work indicates that the net charge state of variable domains relative to the net charge state of the constant domains is predominantly responsible for the different native state aggregation behavior of IgG1 and IgG4P mAbs. This observation suggests that the global net charge of a multi domain protein is not a reliable predictor of aggregation propensity. Furthermore, we demonstrate a design strategy in the frameworks of variable domains to reduce the native state aggregation propensity of mAbs identified as being aggregation-prone. Importantly, substitution of specifically identified residues with alternative, human germline residues, to optimize Fv charge, resulted in decreased aggregation potential at pH 5.0 and 7.4, thus increasing developability.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Ruodan Nan
- UCB Pharma, Slough, Berkshire SL1 3WE, UK
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50
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Willis LF, Kumar A, Jain T, Caffry I, Xu Y, Radford SE, Kapur N, Vásquez M, Brockwell DJ. The uniqueness of flow in probing the aggregation behavior of clinically relevant antibodies. ENGINEERING REPORTS : OPEN ACCESS 2020; 2:e12147. [PMID: 34901768 PMCID: PMC8638667 DOI: 10.1002/eng2.12147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 02/18/2020] [Accepted: 02/19/2020] [Indexed: 06/10/2023]
Abstract
The development of therapeutic monoclonal antibodies (mAbs) can be hindered by their tendency to aggregate throughout their lifetime, which can illicit immunogenic responses and render mAb manufacturing unfeasible. Consequently, there is a need to identify mAbs with desirable thermodynamic stability, solubility, and lack of self-association. These behaviors are assessed using an array of in silico and in vitro assays, as no single assay can predict aggregation and developability. We have developed an extensional and shear flow device (EFD), which subjects proteins to defined hydrodynamic forces which mimic those experienced in bioprocessing. Here, we utilize the EFD to explore the aggregation propensity of 33 IgG1 mAbs, whose variable domains are derived from clinical antibodies. Using submilligram quantities of material per replicate, wide-ranging EFD-induced aggregation (9-81% protein in pellet) was observed for these mAbs, highlighting the EFD as a sensitive method to assess aggregation propensity. By comparing the EFD-induced aggregation data to those obtained previously from 12 other biophysical assays, we show that the EFD provides distinct information compared with current measures of adverse biophysical behavior. Assessing a candidate's liability to hydrodynamic force thus adds novel insight into the rational selection of developable mAbs that complements other assays.
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Affiliation(s)
- Leon F. Willis
- School of Molecular and Cellular Biology, Faculty of Biological SciencesUniversity of LeedsLeedsUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsUK
| | - Amit Kumar
- School of Molecular and Cellular Biology, Faculty of Biological SciencesUniversity of LeedsLeedsUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsUK
- Department of Life SciencesImperial College LondonLondonUK
| | | | - Isabelle Caffry
- Adimab LLCLebanonNew HampshireUSA
- Cornell Johnson Graduate School of ManagementIthacaNew YorkUSA
| | - Yingda Xu
- Adimab LLCLebanonNew HampshireUSA
- Biotheus Inc.ZhuhaiGuangdong ProvinceChina
| | - Sheena E. Radford
- School of Molecular and Cellular Biology, Faculty of Biological SciencesUniversity of LeedsLeedsUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsUK
| | - Nikil Kapur
- School of Mechanical Engineering, Faculty of EngineeringUniversity of LeedsLeedsUK
| | | | - David J. Brockwell
- School of Molecular and Cellular Biology, Faculty of Biological SciencesUniversity of LeedsLeedsUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsUK
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