1
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Romei MG, Leonard B, Katz ZB, Le D, Yang Y, Day ES, Koo CW, Sharma P, Bevers Iii J, Kim I, Dai H, Farahi F, Lin M, Shaw AS, Nakamura G, Sockolosky JT, Lazar GA. i-shaped antibody engineering enables conformational tuning of biotherapeutic receptor agonists. Nat Commun 2024; 15:642. [PMID: 38245524 PMCID: PMC10799922 DOI: 10.1038/s41467-024-44985-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 01/11/2024] [Indexed: 01/22/2024] Open
Abstract
The ability to leverage antibodies to agonize disease relevant biological pathways has tremendous potential for clinical investigation. Yet while antibodies have been successful as antagonists, immune mediators, and targeting agents, they are not readily effective at recapitulating the biology of natural ligands. Among the important determinants of antibody agonist activity is the geometry of target receptor engagement. Here, we describe an engineering approach inspired by a naturally occurring Fab-Fab homotypic interaction that constrains IgG in a unique i-shaped conformation. i-shaped antibody (iAb) engineering enables potent intrinsic agonism of five tumor necrosis factor receptor superfamily (TNFRSF) targets. When applied to bispecific antibodies against the heterodimeric IL-2 receptor pair, constrained bispecific IgG formats recapitulate IL-2 agonist activity. iAb engineering provides a tool to tune agonist antibody function and this work provides a framework for the development of intrinsic antibody agonists with the potential for generalization across broad receptor classes.
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Affiliation(s)
- Matthew G Romei
- Department of Antibody Engineering, Genentech Inc., South San Francisco, CA, USA
| | - Brandon Leonard
- Department of Antibody Engineering, Genentech Inc., South San Francisco, CA, USA
| | - Zachary B Katz
- Department of Research Biology, Genentech Inc., South San Francisco, CA, USA
| | - Daniel Le
- Department of Microchemistry, Proteomic, Lipidomics, and Next Generation Sequencing, Genentech Inc., South San Francisco, CA, USA
| | - Yanli Yang
- Department of Antibody Engineering, Genentech Inc., South San Francisco, CA, USA
| | - Eric S Day
- Department of Pharma Technical Development, Genentech Inc., South San Francisco, CA, USA
| | - Christopher W Koo
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | - Preeti Sharma
- Department of Antibody Engineering, Genentech Inc., South San Francisco, CA, USA
| | - Jack Bevers Iii
- Department of Antibody Engineering, Genentech Inc., South San Francisco, CA, USA
| | - Ingrid Kim
- Department of Antibody Engineering, Genentech Inc., South San Francisco, CA, USA
| | - Huiguang Dai
- Department of Antibody Engineering, Genentech Inc., South San Francisco, CA, USA
| | - Farzam Farahi
- Department of Antibody Engineering, Genentech Inc., South San Francisco, CA, USA
| | - May Lin
- Department of Protein Chemistry, Genentech Inc., South San Francisco, CA, USA
| | - Andrey S Shaw
- Department of Research Biology, Genentech Inc., South San Francisco, CA, USA
| | - Gerald Nakamura
- Department of Antibody Engineering, Genentech Inc., South San Francisco, CA, USA
| | | | - Greg A Lazar
- Department of Antibody Engineering, Genentech Inc., South San Francisco, CA, USA.
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2
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Tennenhouse A, Khmelnitsky L, Khalaila R, Yeshaya N, Noronha A, Lindzen M, Makowski EK, Zaretsky I, Sirkis YF, Galon-Wolfenson Y, Tessier PM, Abramson J, Yarden Y, Fass D, Fleishman SJ. Computational optimization of antibody humanness and stability by systematic energy-based ranking. Nat Biomed Eng 2024; 8:30-44. [PMID: 37550425 PMCID: PMC10842793 DOI: 10.1038/s41551-023-01079-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 07/13/2023] [Indexed: 08/09/2023]
Abstract
Conventional methods for humanizing animal-derived antibodies involve grafting their complementarity-determining regions onto homologous human framework regions. However, this process can substantially lower antibody stability and antigen-binding affinity, and requires iterative mutational fine-tuning to recover the original antibody properties. Here we report a computational method for the systematic grafting of animal complementarity-determining regions onto thousands of human frameworks. The method, which we named CUMAb (for computational human antibody design; available at http://CUMAb.weizmann.ac.il ), starts from an experimental or model antibody structure and uses Rosetta atomistic simulations to select designs by energy and structural integrity. CUMAb-designed humanized versions of five antibodies exhibited similar affinities to those of the parental animal antibodies, with some designs showing marked improvement in stability. We also show that (1) non-homologous frameworks are often preferred to highest-homology frameworks, and (2) several CUMAb designs that differ by dozens of mutations and that use different human frameworks are functionally equivalent.
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Affiliation(s)
- Ariel Tennenhouse
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Lev Khmelnitsky
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Razi Khalaila
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Noa Yeshaya
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ashish Noronha
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Moshit Lindzen
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Emily K Makowski
- Biointerfaces Institute and Departments of Chemical Engineering, Pharmaceutical Sciences and Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Ira Zaretsky
- Antibody Engineering Unit, Weizmann Institute of Science, Rehovot, Israel
| | | | | | - Peter M Tessier
- Biointerfaces Institute and Departments of Chemical Engineering, Pharmaceutical Sciences and Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Jakub Abramson
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yosef Yarden
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Deborah Fass
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sarel J Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.
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3
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Heisler J, Kovner D, Izadi S, Zarzar J, Carter PJ. Modulation of the high concentration viscosity of IgG 1 antibodies using clinically validated Fc mutations. MAbs 2024; 16:2379560. [PMID: 39028186 PMCID: PMC11262234 DOI: 10.1080/19420862.2024.2379560] [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: 04/04/2024] [Accepted: 07/09/2024] [Indexed: 07/20/2024] Open
Abstract
The self-association of therapeutic antibodies can result in elevated viscosity and create problems in manufacturing and formulation, as well as limit delivery by subcutaneous injection. The high concentration viscosity of some antibodies has been reduced by variable domain mutations or by the addition of formulation excipients. In contrast, the impact of Fc mutations on antibody viscosity has been minimally explored. Here, we studied the effect of a panel of common and clinically validated Fc mutations on the viscosity of two closely related humanized IgG1, κ antibodies, omalizumab (anti-IgE) and trastuzumab (anti-HER2). Data presented here suggest that both Fab-Fab and Fab-Fc interactions contribute to the high viscosity of omalizumab, in a four-contact model of self-association. Most strikingly, the high viscosity of omalizumab (176 cP) was reduced 10.7- and 2.2-fold by Fc modifications for half-life extension (M252Y:S254T:T256E) and aglycosylation (N297G), respectively. Related single mutations (S254T and T256E) each reduced the viscosity of omalizumab by ~6-fold. An alternative half-life extension Fc mutant (M428L:N434S) had the opposite effect in increasing the viscosity of omalizumab by 1.5-fold. The low viscosity of trastuzumab (8.6 cP) was unchanged or increased by ≤ 2-fold by the different Fc variants. Molecular dynamics simulations provided mechanistic insight into the impact of Fc mutations in modulating electrostatic and hydrophobic surface properties as well as conformational stability of the Fc. This study demonstrates that high viscosity of some IgG1 antibodies can be mitigated by Fc mutations, and thereby offers an additional tool to help design future antibody therapeutics potentially suitable for subcutaneous delivery.
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Affiliation(s)
- Joel Heisler
- Department of Antibody Engineering, Genentech, Inc, South San Francisco, CA, USA
| | - Daniel Kovner
- Department of Pharmaceutical Development, Genentech, Inc, South San Francisco, CA, USA
| | - Saeed Izadi
- Department of Pharmaceutical Development, Genentech, Inc, South San Francisco, CA, USA
| | - Jonathan Zarzar
- Department of Pharmaceutical Development, Genentech, Inc, South San Francisco, CA, USA
| | - Paul J. Carter
- Department of Antibody Engineering, Genentech, Inc, South San Francisco, CA, USA
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4
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Amash A, Volkers G, Farber P, Griffin D, Davison KS, Goodman A, Tonikian R, Yamniuk A, Barnhart B, Jacobs T. Developability considerations for bispecific and multispecific antibodies. MAbs 2024; 16:2394229. [PMID: 39189686 DOI: 10.1080/19420862.2024.2394229] [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: 06/13/2024] [Revised: 08/08/2024] [Accepted: 08/15/2024] [Indexed: 08/28/2024] Open
Abstract
Bispecific antibodies (bsAb) and multispecific antibodies (msAb) encompass a diverse variety of formats that can concurrently bind multiple epitopes, unlocking mechanisms to address previously difficult-to-treat or incurable diseases. Early assessment of candidate developability enables demotion of antibodies with low potential and promotion of the most promising candidates for further development. Protein-based therapies have a stringent set of developability requirements in order to be competitive (e.g. high-concentration formulation, and long half-life) and their assessment requires a robust toolkit of methods, few of which are validated for interrogating bsAbs/msAbs. Important considerations when assessing the developability of bsAbs/msAbs include their molecular format, likelihood for immunogenicity, specificity, stability, and potential for high-volume production. Here, we summarize the critical aspects of developability assessment, and provide guidance on how to develop a comprehensive plan tailored to a given bsAb/msAb.
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Affiliation(s)
- Alaa Amash
- AbCellera Biologics Inc, Vancouver, BC, Canada
| | | | | | | | | | | | | | | | | | - Tim Jacobs
- AbCellera Biologics Inc, Vancouver, BC, Canada
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5
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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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6
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Dai J, Izadi S, Zarzar J, Wu P, Oh A, Carter PJ. Variable domain mutational analysis to probe the molecular mechanisms of high viscosity of an IgG 1 antibody. MAbs 2024; 16:2304282. [PMID: 38269489 PMCID: PMC10813588 DOI: 10.1080/19420862.2024.2304282] [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: 10/19/2023] [Accepted: 01/08/2024] [Indexed: 01/26/2024] Open
Abstract
Subcutaneous injection is the preferred route of administration for many antibody therapeutics for reasons that include its speed and convenience. However, the small volume limit (typically ≤ 2 mL) for subcutaneous delivery often necessitates antibody formulations at high concentrations (commonly ≥100 mg/mL), which may lead to physicochemical problems. For example, antibodies with large hydrophobic or charged patches can be prone to self-interaction giving rise to high viscosity. Here, we combined X-ray crystallography with computational modeling to predict regions of an anti-glucagon receptor (GCGR) IgG1 antibody prone to self-interaction. An extensive mutational analysis was undertaken of the complementarity-determining region residues residing in hydrophobic surface patches predicted by spatial aggregation propensity, in conjunction with residue-level solvent accessibility, averaged over conformational ensembles from molecular dynamics simulations. Dynamic light scattering (DLS) was used as a medium throughput screen for self-interaction of ~ 200 anti-GCGR IgG1 variants. A negative correlation was found between the viscosity determined at high concentration (180 mg/mL) and the DLS interaction parameter measured at low concentration (2-10 mg/mL). Additionally, anti-GCGR variants were readily identified with reduced viscosity and antigen-binding affinity within a few fold of the parent antibody, with no identified impact on overall developability. The methods described here may be useful in the optimization of other antibodies to facilitate their therapeutic administration at high concentration.
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Affiliation(s)
- Jing Dai
- Department of Antibody Engineering, Genentech, Inc, South San Francisco, CA, USA
| | - Saeed Izadi
- Department of Pharmaceutical Development, Genentech, Inc, South San Francisco, CA, USA
| | - Jonathan Zarzar
- Department of Pharmaceutical Development, Genentech, Inc, South San Francisco, CA, USA
| | - Patrick Wu
- Department of Bioanalytical Sciences, Genentech, Inc, South San Francisco, CA, USA
| | - Angela Oh
- Department of Structural Biology, Genentech, Inc, South San Francisco, CA, USA
| | - Paul J. Carter
- Department of Antibody Engineering, Genentech, Inc, South San Francisco, CA, USA
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7
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Jain T, Prinz B, Marker A, Michel A, Reichel K, Czepczor V, Klieber S, Sun W, Kathuria S, Oezguer Bruederle S, Lange C, Wahl L, Starr C, Masiero A, Avery L. Assessment and incorporation of in vitro correlates to pharmacokinetic outcomes in antibody developability workflows. MAbs 2024; 16:2384104. [PMID: 39083118 PMCID: PMC11296533 DOI: 10.1080/19420862.2024.2384104] [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: 04/24/2024] [Revised: 06/27/2024] [Accepted: 07/19/2024] [Indexed: 08/04/2024] Open
Abstract
In vitro assessments for the prediction of pharmacokinetic (PK) behavior of biotherapeutics can help identify corresponding liabilities significantly earlier in the discovery timeline. This can minimize the need for extensive early in vivo PK characterization, thereby reducing animal usage and optimizing resources. In this study, we recommend bolstering classical developability workflows with in vitro measures correlated with PK. In agreement with current literature, in vitro measures assessing nonspecific interactions, self-interaction, and FcRn interaction are demonstrated to have the highest correlations to clearance in hFcRn Tg32 mice. Crucially, the dataset used in this study has broad sequence diversity and a range of physicochemical properties, adding robustness to our recommendations. Finally, we demonstrate a computational approach that combines multiple in vitro measurements with a multivariate regression model to improve the correlation to PK compared to any individual assessment. Our work demonstrates that a judicious choice of high throughput in vitro measurements and computational predictions enables the prioritization of candidate molecules with desired PK properties.
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Affiliation(s)
- Tushar Jain
- Department of Computational Biology, Adimab LLC, Mountain View, CA, USA
| | - Bianka Prinz
- Department of Antibody Discovery, Adimab LLC, Lebanon, NH, USA
| | - Alexander Marker
- Department of Drug Metabolism and Pharmacokinetics, Sanofi, Frankfurt, Germany
| | - Alexander Michel
- Department of Drug Metabolism and Pharmacokinetics, Sanofi, Cambridge, MA, USA
| | - Katrin Reichel
- Department of Large Molecule Research, Sanofi, Frankfurt, Germany
| | - Valerie Czepczor
- Department of Drug Metabolism and Pharmacokinetics, Sanofi, Paris, France
| | - Sylvie Klieber
- Department of Drug Metabolism and Pharmacokinetics, Sanofi, Paris, France
| | - Wei Sun
- Department of Drug Metabolism and Pharmacokinetics, Sanofi, Cambridge, MA, USA
| | - Sagar Kathuria
- Department of Large Molecule Research, Sanofi, Cambridge, MA, USA
| | | | - Christian Lange
- Department of Large Molecule Research, Sanofi, Frankfurt, Germany
| | - Lena Wahl
- Department of Large Molecule Research, Sanofi, Frankfurt, Germany
| | | | | | - Lindsay Avery
- Department of Drug Metabolism and Pharmacokinetics, Sanofi, Cambridge, MA, USA
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8
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Makowski EK, Wang T, Zupancic JM, Huang J, Wu L, Schardt JS, De Groot AS, Elkins SL, Martin WD, Tessier PM. Optimization of therapeutic antibodies for reduced self-association and non-specific binding via interpretable machine learning. Nat Biomed Eng 2024; 8:45-56. [PMID: 37666923 PMCID: PMC10842909 DOI: 10.1038/s41551-023-01074-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 06/29/2023] [Indexed: 09/06/2023]
Abstract
Antibody development, delivery, and efficacy are influenced by antibody-antigen affinity interactions, off-target interactions that reduce antibody bioavailability and pharmacokinetics, and repulsive self-interactions that increase the stability of concentrated antibody formulations and reduce their corresponding viscosity. Yet identifying antibody variants with optimal combinations of these three types of interactions is challenging. Here we show that interpretable machine-learning classifiers, leveraging antibody structural features descriptive of their variable regions and trained on experimental data for a panel of 80 clinical-stage monoclonal antibodies, can identify antibodies with optimal combinations of low off-target binding in a common physiological-solution condition and low self-association in a common antibody-formulation condition. For three clinical-stage antibodies with suboptimal combinations of off-target binding and self-association, the classifiers predicted variable-region mutations that optimized non-affinity interactions while maintaining high-affinity antibody-antigen interactions. Interpretable machine-learning models may facilitate the optimization of antibody candidates for therapeutic applications.
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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
| | - Tiexin Wang
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Jennifer M Zupancic
- 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
| | - Lina Wu
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - John S Schardt
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, 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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9
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Desai AA, Zupancic JM, Trzeciakiewicz H, Gerson JE, DuBois KN, Skinner ME, Sharkey LM, McArthur N, Ferris SP, Bhatt NN, Makowski EK, Smith MD, Chen H, Huang J, Jerez C, Kane RS, Kanaan NM, Paulson HL, Tessier PM. Flow cytometric isolation of drug-like conformational antibodies specific for amyloid fibrils. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.04.547698. [PMID: 37461643 PMCID: PMC10349928 DOI: 10.1101/2023.07.04.547698] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
Abstract
Antibodies that recognize specific protein conformational states are broadly important for research, diagnostic and therapeutic applications, yet they are difficult to generate in a predictable and systematic manner using either immunization or in vitro antibody display methods. This problem is particularly severe for conformational antibodies that recognize insoluble antigens such as amyloid fibrils associated with many neurodegenerative disorders. Here we report a quantitative fluorescence-activated cell sorting (FACS) method for directly selecting high-quality conformational antibodies against different types of insoluble (amyloid fibril) antigens using a single, off-the-shelf human library. Our approach uses quantum dots functionalized with antibodies to capture insoluble antigens, and the resulting quantum dot conjugates are used in a similar manner as conventional soluble antigens for multi-parameter FACS selections. Notably, we find that this approach is robust for isolating high-quality conformational antibodies against tau and α-synuclein fibrils from the same human library with combinations of high affinity, high conformational specificity and, in some cases, low off-target binding that rival or exceed those of clinical-stage antibodies specific for tau (zagotenemab) and α-synuclein (cinpanemab). This approach is expected to enable conformational antibody selection and engineering against diverse types of protein aggregates and other insoluble antigens (e.g., membrane proteins) that are compatible with presentation on the surface of antibody-functionalized quantum dots.
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10
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Condado-Morales I, Sokolova V, Wahlund PO, Heding KE, Auclair S, Kingsbury JS, Arosio P, Lorenzen N. AF4 and PEG Precipitation as Predictive Assays for Antibody Self-Association. Mol Pharm 2023; 20:1323-1330. [PMID: 36668814 DOI: 10.1021/acs.molpharmaceut.2c00946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Monoclonal antibodies (mAbs) are often formulated as high-protein-concentration solutions, which in some cases can exhibit physical stability issues such as high viscosity and opalescence. To ensure that mAb-based drugs can meet their manufacturing, stability, and delivery requirements, it is advantageous to screen for and select mAbs during discovery that are not prone to such behaviors. It has been recently shown that both these macroscopic properties can be predicted to a certain extent from the diffusion interaction parameter (kD), which is a measure of self-association under dilute conditions.1 However, kD can be challenging to measure at the early stage of discovery, where a relatively large amount of a high-purity material, which is required by traditional methods, is often not available. In this study, we demonstrate asymmetric field-flow fractionation (AF4) as a tool to measure self-association and therefore identify antibodies with problematic issues at high concentrations. The principle lies on the ability to concentrate the sample close to the membrane during the injection mode, which can reach formulation-relevant concentrations (>100 mg/mL).2 By analyzing a well-characterized library of commercial antibodies, we show that the measured retention time of the antibodies allows us to pinpoint molecules that exhibit issues at high concentrations. Remarkably, our AF4 assay requires very little (30 μg) sample under dilute conditions and does not need extensive sample purification. Furthermore, we show that a polyethylene glycol (PEG) precipitation assay provides results consistent with AF4 and moreover can further differentiate molecules with issues of opalescence or high viscosity. Overall, our results delineate a two-step strategy for the identification of problematic variants at high concentrations, with AF4 for early developability screening, followed by a PEG assay to validate the problematic molecules and further discriminate between opalescence or high-viscosity issues. This two-step antibody selection strategy enables us to select antibodies early in the discovery process, which are compatible with high-concentration formulations.
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Affiliation(s)
- Itzel Condado-Morales
- Global Research Technology, Novo Nordisk A/S, Maaloev 2760, Denmark.,Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zürich, Zürich 8093, Switzerland
| | - Viktoria Sokolova
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zürich, Zürich 8093, Switzerland
| | - Per-Olof Wahlund
- Global Research Technology, Novo Nordisk A/S, Maaloev 2760, Denmark
| | | | - Sarah Auclair
- Global CMC Development, Sanofi, Framingham, Massachusetts 02210, United States
| | | | - Paolo Arosio
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zürich, Zürich 8093, Switzerland
| | - Nikolai Lorenzen
- Global Research Technology, Novo Nordisk A/S, Maaloev 2760, Denmark
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11
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Jain T, Boland T, Vásquez M. Identifying developability risks for clinical progression of antibodies using high-throughput in vitro and in silico approaches. MAbs 2023; 15:2200540. [PMID: 37072706 PMCID: PMC10114995 DOI: 10.1080/19420862.2023.2200540] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 04/20/2023] Open
Abstract
With the growing significance of antibodies as a therapeutic class, identifying developability risks early during development is of paramount importance. Several high-throughput in vitro assays and in silico approaches have been proposed to de-risk antibodies during early stages of the discovery process. In this review, we have compiled and collectively analyzed published experimental assessments and computational metrics for clinical antibodies. We show that flags assigned based on in vitro measurements of polyspecificity and hydrophobicity are more predictive of clinical progression than their in silico counterparts. Additionally, we assessed the performance of published models for developability predictions on molecules not used during model training. We find that generalization to data outside of those used for training remains a challenge for models. Finally, we highlight the challenges of reproducibility in computed metrics arising from differences in homology modeling, in vitro assessments relying on complex reagents, as well as curation of experimental data often used to assess the utility of high-throughput approaches. We end with a recommendation to enable assay reproducibility by inclusion of controls with disclosed sequences, as well as sharing of structural models to enable the critical assessment and improvement of in silico predictions.
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Affiliation(s)
| | - Todd Boland
- Computational Biology, Adimab LLC, Lebanon, NH, USA
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12
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Svilenov HL, Arosio P, Menzen T, Tessier P, Sormanni P. Approaches to expand the conventional toolbox for discovery and selection of antibodies with drug-like physicochemical properties. MAbs 2023; 15:2164459. [PMID: 36629855 PMCID: PMC9839375 DOI: 10.1080/19420862.2022.2164459] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/22/2022] [Accepted: 12/29/2022] [Indexed: 01/12/2023] Open
Abstract
Antibody drugs should exhibit not only high-binding affinity for their target antigens but also favorable physicochemical drug-like properties. Such drug-like biophysical properties are essential for the successful development of antibody drug products. The traditional approaches used in antibody drug development require significant experimentation to produce, optimize, and characterize many candidates. Therefore, it is attractive to integrate new methods that can optimize the process of selecting antibodies with both desired target-binding and drug-like biophysical properties. Here, we summarize a selection of techniques that can complement the conventional toolbox used to de-risk antibody drug development. These techniques can be integrated at different stages of the antibody development process to reduce the frequency of physicochemical liabilities in antibody libraries during initial discovery and to co-optimize multiple antibody features during early-stage antibody engineering and affinity maturation. Moreover, we highlight biophysical and computational approaches that can be used to predict physical degradation pathways relevant for long-term storage and in-use stability to reduce the need for extensive experimentation.
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Affiliation(s)
- Hristo L. Svilenov
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Gent, Belgium
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland
| | - Tim Menzen
- Coriolis Pharma Research GmbH, Martinsried, 82152, Germany
| | - Peter 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
| | - Pietro Sormanni
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
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13
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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: 20] [Impact Index Per Article: 20.0] [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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14
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Zarzar J, Khan T, Bhagawati M, Weiche B, Sydow-Andersen J, Alavattam S. High concentration formulation developability approaches and considerations. MAbs 2023; 15:2211185. [PMID: 37191233 DOI: 10.1080/19420862.2023.2211185] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
The growing need for biologics to be administered subcutaneously and ocularly, coupled with certain indications requiring high doses, has resulted in an increase in drug substance (DS) and drug product (DP) protein concentrations. With this increase, more emphasis must be placed on identifying critical physico-chemical liabilities during drug development, including protein aggregation, precipitation, opalescence, particle formation, and high viscosity. Depending on the molecule, liabilities, and administration route, different formulation strategies can be used to overcome these challenges. However, due to the high material requirements, identifying optimal conditions can be slow, costly, and often prevent therapeutics from moving rapidly into the clinic/market. In order to accelerate and derisk development, new experimental and in-silico methods have emerged that can predict high concentration liabilities. Here, we review the challenges in developing high concentration formulations, the advances that have been made in establishing low mass and high-throughput predictive analytics, and advances in in-silico tools and algorithms aimed at identifying risks and understanding high concentration protein behavior.
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Affiliation(s)
- Jonathan Zarzar
- Pharmaceutical Development, Genentech Inc, South San Francisco, CA, USA
| | - Tarik Khan
- Pharma Technical Development Europe, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Maniraj Bhagawati
- Large Molecule Research, Pharma Research and Early Development (pRED), Roche Diagnostics GmbH, Penzberg, Germany
| | - Benjamin Weiche
- Large Molecule Research, Pharma Research and Early Development (pRED), Roche Diagnostics GmbH, Penzberg, Germany
| | - Jasmin Sydow-Andersen
- Large Molecule Research, Pharma Research and Early Development (pRED), Roche Diagnostics GmbH, Penzberg, Germany
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15
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Feng J, Jiang M, Shih J, Chai Q. Antibody apparent solubility prediction from sequence by transfer learning. iScience 2022; 25:105173. [PMID: 36212021 PMCID: PMC9535432 DOI: 10.1016/j.isci.2022.105173] [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] [Received: 06/03/2022] [Revised: 08/16/2022] [Accepted: 09/14/2022] [Indexed: 11/25/2022] Open
Abstract
Developing therapeutic monoclonal antibodies (mAbs) for the subcutaneous administration requires identifying mAbs with superior solubility that are amenable for high-concentration formulation. However, experimental screening is often material and labor intensive. Here, we present a strategy (named solPredict) that employs the embeddings from pretrained protein language modeling to predict the apparent solubility of mAbs in histidine (pH 6.0) buffer. A dataset of 220 diverse, in-house mAbs were used for model training and hyperparameter tuning through 5-fold cross validation. solPredict achieves high correlation with experimental solubility on an independent test set of 40 mAbs. Importantly, solPredict performs well for both IgG1 and IgG4 subclasses despite the distinct solubility behaviors. This approach eliminates the need of 3D structure modeling of mAbs, descriptor computation, and expert-crafted input features. The minimal computational expense of solPredict enables rapid, large-scale, and high-throughput screening of mAbs using sequence information alone during early antibody discovery.
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Affiliation(s)
- Jiangyan Feng
- BioTechnology Discovery Research, Eli Lilly Biotechnology Center, San Diego, CA 92121, USA
| | - Min Jiang
- Advanced Analytics and Data Sciences, Eli Lilly Corporate Center, Indianapolis, IN 46225, USA
| | - James Shih
- BioTechnology Discovery Research, Eli Lilly Biotechnology Center, San Diego, CA 92121, USA
| | - Qing Chai
- BioTechnology Discovery Research, Eli Lilly Biotechnology Center, San Diego, CA 92121, USA
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16
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Designing antibodies as therapeutics. Cell 2022; 185:2789-2805. [PMID: 35868279 DOI: 10.1016/j.cell.2022.05.029] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/18/2022] [Accepted: 05/31/2022] [Indexed: 12/25/2022]
Abstract
Antibody therapeutics are a large and rapidly expanding drug class providing major health benefits. We provide a snapshot of current antibody therapeutics including their formats, common targets, therapeutic areas, and routes of administration. Our focus is on selected emerging directions in antibody design where progress may provide a broad benefit. These topics include enhancing antibodies for cancer, antibody delivery to organs such as the brain, gastrointestinal tract, and lungs, plus antibody developability challenges including immunogenicity risk assessment and mitigation and subcutaneous delivery. Machine learning has the potential, albeit as yet largely unrealized, for a transformative future impact on antibody discovery and engineering.
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17
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Makowski EK, Kinnunen PC, Huang J, Wu L, Smith MD, Wang T, Desai AA, Streu CN, Zhang Y, Zupancic JM, Schardt JS, Linderman JJ, Tessier PM. Co-optimization of therapeutic antibody affinity and specificity using machine learning models that generalize to novel mutational space. Nat Commun 2022; 13:3788. [PMID: 35778381 PMCID: PMC9249733 DOI: 10.1038/s41467-022-31457-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 06/20/2022] [Indexed: 11/08/2022] Open
Abstract
Therapeutic antibody development requires selection and engineering of molecules with high affinity and other drug-like biophysical properties. Co-optimization of multiple antibody properties remains a difficult and time-consuming process that impedes drug development. Here we evaluate the use of machine learning to simplify antibody co-optimization for a clinical-stage antibody (emibetuzumab) that displays high levels of both on-target (antigen) and off-target (non-specific) binding. We mutate sites in the antibody complementarity-determining regions, sort the antibody libraries for high and low levels of affinity and non-specific binding, and deep sequence the enriched libraries. Interestingly, machine learning models trained on datasets with binary labels enable predictions of continuous metrics that are strongly correlated with antibody affinity and non-specific binding. These models illustrate strong tradeoffs between these two properties, as increases in affinity along the co-optimal (Pareto) frontier require progressive reductions in specificity. Notably, models trained with deep learning features enable prediction of novel antibody mutations that co-optimize affinity and specificity beyond what is possible for the original antibody library. These findings demonstrate the power of machine learning models to greatly expand the exploration of novel antibody sequence space and accelerate the development of highly potent, drug-like antibodies.
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Affiliation(s)
- Emily K Makowski
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, 48109, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Patrick C Kinnunen
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jie Huang
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, 48109, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, 48109, 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
| | - Matthew D Smith
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Tiexin Wang
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Alec A Desai
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Craig N Streu
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, 48109, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Chemistry, Albion College, Albion, MI, 49224, USA
| | - Yulei Zhang
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jennifer M Zupancic
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - John S Schardt
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, 48109, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jennifer J Linderman
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Peter M Tessier
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, 48109, USA.
- 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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18
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Lai PK. DeepSCM: An efficient convolutional neural network surrogate model for the screening of therapeutic antibody viscosity. Comput Struct Biotechnol J 2022; 20:2143-2152. [PMID: 35832619 PMCID: PMC9092385 DOI: 10.1016/j.csbj.2022.04.035] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 04/26/2022] [Accepted: 04/26/2022] [Indexed: 11/24/2022] Open
Abstract
Predicting high concentration antibody viscosity is essential for developing subcutaneous administration. Computer simulations provide promising tools to reach this aim. One such model is the spatial charge map (SCM) proposed by Agrawal and coworkers (mAbs. 2015, 8(1):43-48). SCM applies molecular dynamics simulations to calculate a score for the screening of antibody viscosity at high concentrations. However, molecular dynamics simulations are computationally costly and require structural information, a significant application bottleneck. In this work, high throughput computing was performed to calculate the SCM scores for 6596 nonredundant antibody variable regions. A convolutional neural network surrogate model, DeepSCM, requiring only sequence information, was then developed based on this dataset. The linear correlation coefficient of the DeepSCM and SCM scores achieved 0.9 on the test set (N = 1320). The DeepSCM model was applied to screen the viscosity of 38 therapeutic antibodies that SCM correctly classified and resulted in only one misclassification. The DeepSCM model will facilitate high concentration antibody viscosity screening. The code and parameters are freely available at https://github.com/Lailabcode/DeepSCM.
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Affiliation(s)
- Pin-Kuang Lai
- Department of Chemical Engineering and Materials Science, Stevens Institute of Technology, Hoboken 07030, NJ, United States
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19
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Gupta P, Makowski EK, Kumar S, Zhang Y, Scheer JM, Tessier PM. Antibodies with Weakly Basic Isoelectric Points Minimize Trade-offs between Formulation and Physiological Colloidal Properties. Mol Pharm 2022; 19:775-787. [PMID: 35108018 PMCID: PMC9350878 DOI: 10.1021/acs.molpharmaceut.1c00373] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The widespread interest in antibody therapeutics has led to much focus on identifying antibody candidates with favorable developability properties. In particular, there is broad interest in identifying antibody candidates with highly repulsive self-interactions in standard formulations (e.g., low ionic strength buffers at pH 5-6) for high solubility and low viscosity. Likewise, there is also broad interest in identifying antibody candidates with low levels of non-specific interactions in physiological solution conditions (PBS, pH 7.4) to promote favorable pharmacokinetic properties. To what extent antibodies that possess both highly repulsive self-interactions in standard formulations and weak non-specific interactions in physiological solution conditions can be systematically identified remains unclear and is a potential impediment to successful therapeutic drug development. Here, we evaluate these two properties for 42 IgG1 variants based on the variable fragments (Fvs) from four clinical-stage antibodies and complementarity-determining regions from 10 clinical-stage antibodies. Interestingly, we find that antibodies with the strongest repulsive self-interactions in a standard formulation (pH 6 and 10 mM histidine) display the strongest non-specific interactions in physiological solution conditions. Conversely, antibodies with the weakest non-specific interactions under physiological conditions display the least repulsive self-interactions in standard formulations. This behavior can be largely explained by the antibody isoelectric point, as highly basic antibodies that are highly positively charged under standard formulation conditions (pH 5-6) promote repulsive self-interactions that mediate high colloidal stability but also mediate strong non-specific interactions with negatively charged biomolecules at physiological pH and vice versa for antibodies with negatively charged Fv regions. Therefore, IgG1s with weakly basic isoelectric points between 8 and 8.5 and Fv isoelectric points between 7.5 and 9 typically display the best combinations of strong repulsive self-interactions and weak non-specific interactions. We expect that these findings will improve the identification and engineering of antibody candidates with drug-like biophysical properties.
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Affiliation(s)
- Priyanka Gupta
- Biochemistry and Biophysics Department, Rensselaer Polytechnic Institute, Troy, New York 12180, United States.,Biotherapeutics Molecule Discovery Department, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, Connecticut 06877, United States
| | - Emily K Makowski
- Department of Pharmaceutical Sciences, Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Sandeep Kumar
- Biotherapeutics Molecule Discovery Department, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, Connecticut 06877, United States
| | - Yulei Zhang
- Department of Chemical Engineering, Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Justin M Scheer
- Biotherapeutics Molecule Discovery Department, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, Connecticut 06877, United States.,Janssen R&D, South San Francisco, California 94080, United States
| | - Peter M Tessier
- Biochemistry and Biophysics Department, Rensselaer Polytechnic Institute, Troy, New York 12180, United States.,Department of Pharmaceutical Sciences, Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States.,Department of Chemical Engineering, Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States.,Department of Biomedical Engineering, Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
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20
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Phan S, Walmer A, Shaw EW, Chai Q. High-throughput profiling of antibody self-association in multiple formulation conditions by PEG stabilized self-interaction nanoparticle spectroscopy. MAbs 2022; 14:2094750. [PMID: 35830420 PMCID: PMC9291693 DOI: 10.1080/19420862.2022.2094750] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Affinity-capture self-interaction nanoparticle spectroscopy (AC-SINS) is an assay developed to monitor the propensity of antibody self-association, hence assessing its colloidal stability. It has been widely used by pharmaceutical companies to screen antibodies at the early discovery stages, aiming to flag potential issues with high concentration formulation. However, the original assay format is not suitable for certain formulation conditions, in particular histidine buffer. In addition, the previous data extrapolation method is suboptimal and cumbersome for processing large amounts of data (100s of molecules) in a high-throughput fashion. To address these limitations, we developed an assay workflow with two major improvements: 1) use of a stabilizing reagent to enable screening of a broader range of formulation conditions beyond phosphate-buffered saline, pH 7.4; and 2) inclusion of a novel algorithm and robust data processing schema that empowers streamlined data analysis. The optimized assay format expands the screening applicability to a wider range of formulation conditions critical for downstream development. Such capability is enhanced by a custom data management workflow for optimal data extraction, analysis, and automation. Our protocol and the R/Shiny application for analysis are publicly available and open-source to benefit the broader scientific community.
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Affiliation(s)
- Samantha Phan
- Biotechnology Discovery Research, Lilly Research Laboratories, Lilly Biotechnology Center, San Diego, CA, USA
| | - Auralee Walmer
- Research Information & Digital Solutions, Lilly Biotechnology Center, San Diego, CA, USA
| | - Eudean W Shaw
- Research Information & Digital Solutions, Lilly Biotechnology Center, San Diego, CA, USA
| | - Qing Chai
- Biotechnology Discovery Research, Lilly Research Laboratories, Lilly Biotechnology Center, San Diego, CA, USA
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21
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Makowski EK, Chen H, Lambert M, Bennett EM, Eschmann NS, Zhang Y, Zupancic JM, Desai AA, Smith MD, Lou W, Fernando A, Tully T, Gallo CJ, Lin L, Tessier PM. Reduction of therapeutic antibody self-association using yeast-display selections and machine learning. MAbs 2022; 14:2146629. [PMID: 36433737 PMCID: PMC9704398 DOI: 10.1080/19420862.2022.2146629] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Self-association governs the viscosity and solubility of therapeutic antibodies in high-concentration formulations used for subcutaneous delivery, yet it is difficult to reliably identify candidates with low self-association during antibody discovery and early-stage optimization. Here, we report a high-throughput protein engineering method for rapidly identifying antibody candidates with both low self-association and high affinity. We find that conjugating quantum dots to IgGs that strongly self-associate (pH 7.4, PBS), such as lenzilumab and bococizumab, results in immunoconjugates that are highly sensitive for detecting other high self-association antibodies. Moreover, these conjugates can be used to rapidly enrich yeast-displayed bococizumab sub-libraries for variants with low levels of immunoconjugate binding. Deep sequencing and machine learning analysis of the enriched bococizumab libraries, along with similar library analysis for antibody affinity, enabled identification of extremely rare variants with co-optimized levels of low self-association and high affinity. This analysis revealed that co-optimizing bococizumab is difficult because most high-affinity variants possess positively charged variable domains and most low self-association variants possess negatively charged variable domains. Moreover, negatively charged mutations in the heavy chain CDR2 of bococizumab, adjacent to its paratope, were effective at reducing self-association without reducing affinity. Interestingly, most of the bococizumab variants with reduced self-association also displayed improved folding stability and reduced nonspecific binding, revealing that this approach may be particularly useful for identifying antibody candidates with attractive combinations of drug-like properties.Abbreviations: AC-SINS: affinity-capture self-interaction nanoparticle spectroscopy; CDR: complementarity-determining region; CS-SINS: charge-stabilized self-interaction nanoparticle spectroscopy; FACS: fluorescence-activated cell sorting; Fab: fragment antigen binding; Fv: fragment variable; IgG: immunoglobulin; QD: quantum dot; PBS: phosphate-buffered saline; VH: variable heavy; VL: variable light.
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Affiliation(s)
- Emily K. Makowski
- Departments of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA,Biointerfaces Institute, University of Michigan, Ann Arbor, MI48109, USA
| | - Hongwei Chen
- Departments of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA,Biointerfaces Institute, University of Michigan, Ann Arbor, MI48109, USA,Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | | | | | | | - Yulei Zhang
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI48109, USA,Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jennifer M. Zupancic
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI48109, USA,Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alec A. Desai
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI48109, USA,Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Matthew D. Smith
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI48109, USA,Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Wenjia Lou
- Departments of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA,Biointerfaces Institute, University of Michigan, Ann Arbor, MI48109, USA,Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Timothy Tully
- Bioprocess Research & Development, Pfizer Inc., St. Louis, MO, USA
| | | | - Laura Lin
- BioMedicine Design, Pfizer Inc, Cambridge, MA, USA
| | - Peter M. Tessier
- Departments of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA,Biointerfaces Institute, University of Michigan, Ann Arbor, MI48109, 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,CONTACT Peter M. Tessier Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA
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22
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Makowski EK, Schardt JS, Tessier PM. Improving antibody drug development using bionanotechnology. Curr Opin Biotechnol 2021; 74:137-145. [PMID: 34890875 DOI: 10.1016/j.copbio.2021.10.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 10/25/2021] [Accepted: 10/31/2021] [Indexed: 12/20/2022]
Abstract
Monoclonal antibodies are being used to treat a remarkable breadth of human disorders. Nevertheless, there are several key challenges at the earliest stages of antibody drug development that need to be addressed using simple and widely accessible methods, especially related to generating antibodies against membrane proteins and identifying antibody candidates with drug-like biophysical properties (high solubility and low viscosity). Here we highlight key bionanotechnologies for preparing functional and stable membrane proteins in diverse types of lipoparticles that are being used to improve antibody discovery and engineering efforts. We also highlight key bionanotechnologies for high-throughput and ultra-dilute screening of antibody biophysical properties during antibody discovery and optimization that are being used for identifying antibodies with superior combinations of in vitro (formulation) and in vivo (half-life) properties.
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Affiliation(s)
- Emily K Makowski
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA; Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - John S Schardt
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA; Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter M Tessier
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA; Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; Departmant of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA.
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