1
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Chen H, Fan X, Zhu S, Pei Y, Zhang X, Zhang X, Liu L, Qian F, Tian B. Accurate prediction of CDR-H3 loop structures of antibodies with deep learning. eLife 2024; 12:RP91512. [PMID: 38921957 PMCID: PMC11208048 DOI: 10.7554/elife.91512] [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: 06/27/2024] Open
Abstract
Accurate prediction of the structurally diverse complementarity determining region heavy chain 3 (CDR-H3) loop structure remains a primary and long-standing challenge for antibody modeling. Here, we present the H3-OPT toolkit for predicting the 3D structures of monoclonal antibodies and nanobodies. H3-OPT combines the strengths of AlphaFold2 with a pre-trained protein language model and provides a 2.24 Å average RMSDCα between predicted and experimentally determined CDR-H3 loops, thus outperforming other current computational methods in our non-redundant high-quality dataset. The model was validated by experimentally solving three structures of anti-VEGF nanobodies predicted by H3-OPT. We examined the potential applications of H3-OPT through analyzing antibody surface properties and antibody-antigen interactions. This structural prediction tool can be used to optimize antibody-antigen binding and engineer therapeutic antibodies with biophysical properties for specialized drug administration route.
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Affiliation(s)
- Hedi Chen
- MOE Key Laboratory of Bioinformatics, State Key Laboratory of Molecular Oncology, School of Pharmaceutical Sciences, Tsinghua UniversityBeijingChina
| | - Xiaoyu Fan
- MOE Key Laboratory of Bioinformatics, State Key Laboratory of Molecular Oncology, School of Pharmaceutical Sciences, Tsinghua UniversityBeijingChina
| | - Shuqian Zhu
- MOE Key Laboratory of Bioinformatics, State Key Laboratory of Molecular Oncology, School of Pharmaceutical Sciences, Tsinghua UniversityBeijingChina
| | - Yuchan Pei
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua UniversityBeijingChina
| | - Xiaochun Zhang
- MOE Key Laboratory of Bioinformatics, State Key Laboratory of Molecular Oncology, School of Pharmaceutical Sciences, Tsinghua UniversityBeijingChina
| | - Xiaonan Zhang
- Department of Natural Language Processing, Baidu International Technology (Shenzhen) Co LtdShenzhenChina
| | - Lihang Liu
- Department of Natural Language Processing, Baidu International Technology (Shenzhen) Co LtdShenzhenChina
| | - Feng Qian
- MOE Key Laboratory of Bioinformatics, State Key Laboratory of Molecular Oncology, School of Pharmaceutical Sciences, Tsinghua UniversityBeijingChina
| | - Boxue Tian
- MOE Key Laboratory of Bioinformatics, State Key Laboratory of Molecular Oncology, School of Pharmaceutical Sciences, Tsinghua UniversityBeijingChina
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2
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Bauer J, Rajagopal N, Gupta P, Gupta P, Nixon AE, Kumar S. How can we discover developable antibody-based biotherapeutics? Front Mol Biosci 2023; 10:1221626. [PMID: 37609373 PMCID: PMC10441133 DOI: 10.3389/fmolb.2023.1221626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/10/2023] [Indexed: 08/24/2023] Open
Abstract
Antibody-based biotherapeutics have emerged as a successful class of pharmaceuticals despite significant challenges and risks to their discovery and development. This review discusses the most frequently encountered hurdles in the research and development (R&D) of antibody-based biotherapeutics and proposes a conceptual framework called biopharmaceutical informatics. Our vision advocates for the syncretic use of computation and experimentation at every stage of biologic drug discovery, considering developability (manufacturability, safety, efficacy, and pharmacology) of potential drug candidates from the earliest stages of the drug discovery phase. The computational advances in recent years allow for more precise formulation of disease concepts, rapid identification, and validation of targets suitable for therapeutic intervention and discovery of potential biotherapeutics that can agonize or antagonize them. Furthermore, computational methods for de novo and epitope-specific antibody design are increasingly being developed, opening novel computationally driven opportunities for biologic drug discovery. Here, we review the opportunities and limitations of emerging computational approaches for optimizing antigens to generate robust immune responses, in silico generation of antibody sequences, discovery of potential antibody binders through virtual screening, assessment of hits, identification of lead drug candidates and their affinity maturation, and optimization for developability. The adoption of biopharmaceutical informatics across all aspects of drug discovery and development cycles should help bring affordable and effective biotherapeutics to patients more quickly.
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Affiliation(s)
- Joschka Bauer
- Early Stage Pharmaceutical Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach/Riss, Germany
- In Silico Team, Boehringer Ingelheim, Hannover, Germany
| | - Nandhini Rajagopal
- In Silico Team, Boehringer Ingelheim, Hannover, Germany
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, United States
| | - Priyanka Gupta
- In Silico Team, Boehringer Ingelheim, Hannover, Germany
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, United States
| | - Pankaj Gupta
- In Silico Team, Boehringer Ingelheim, Hannover, Germany
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, United States
| | - Andrew E. Nixon
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, United States
| | - Sandeep Kumar
- In Silico Team, Boehringer Ingelheim, Hannover, Germany
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, United States
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3
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Shrivastava A, Mandal S, Pattanayek SK, Rathore AS. Rapid Estimation of Size-Based Heterogeneity in Monoclonal Antibodies by Machine Learning-Enhanced Dynamic Light Scattering. Anal Chem 2023; 95:8299-8309. [PMID: 37200383 DOI: 10.1021/acs.analchem.3c00650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Aggregation of monoclonal antibody therapeutics is a serious concern that is believed to impact product safety and efficacy. There is a need for analytical approaches that enable rapid estimation of mAb aggregates. Dynamic light scattering (DLS) is a well-established technique for estimating the average size of protein aggregates or for evaluating sample stability. It is usually used to measure the size and size distribution over a wide range of nano- to micro-sized particles using time-dependent fluctuations in the intensity of scattered light arising from the Brownian motion of particles. In this study, we present a novel DLS-based approach that allows us to quantify the relative percentage of multimers (monomer, dimer, trimer, and tetramer) in a monoclonal antibody (mAb) therapeutic product. The proposed approach uses a machine learning (ML) algorithm and regression to model the system and predict the amount of relevant species such as monomer, dimer, trimer, and tetramer of a mAb in the size range of 10-100 nm. The proposed DLS-ML technique compares favorably to all potential alternatives with respect to the key method attributes, including per sample cost of analysis, per sample time of data acquisition along with ML-based aggregate prediction (<2 min), sample requirements (<3 μg), and user-friendliness of analysis. The proposed rapid method can serve as an orthogonal tool to size exclusion chromatography, which is the current industry workhorse for aggregate assessment.
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Affiliation(s)
- Anuj Shrivastava
- Department of Chemical Engineering, IIT Delhi, Hauz Khas, New Delhi 110016, India
| | - Shyamapada Mandal
- Department of Chemical Engineering, IIT Delhi, Hauz Khas, New Delhi 110016, India
| | - Sudip K Pattanayek
- Department of Chemical Engineering, IIT Delhi, Hauz Khas, New Delhi 110016, India
| | - Anurag S Rathore
- Department of Chemical Engineering, IIT Delhi, Hauz Khas, New Delhi 110016, India
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4
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Kulakova A, Augustijn D, El Bialy I, Gentiluomo L, Greco ML, Hervø-Hansen S, Indrakumar S, Mahapatra S, Martinez Morales M, Pohl C, Polimeni M, Roche A, Svilenov HL, Tosstorff A, Zalar M, Curtis R, Derrick JP, Frieß W, Golovanov AP, Lund M, Nørgaard A, Khan TA, Peters GHJ, Pluen A, Roessner D, Streicher WW, van der Walle CF, Warwicker J, Uddin S, Winter G, Bukrinski JT, Rinnan Å, Harris P. Chemometrics in Protein Formulation: Stability Governed by Repulsion and Protein Unfolding. Mol Pharm 2023. [PMID: 37146162 DOI: 10.1021/acs.molpharmaceut.3c00013] [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: 05/07/2023]
Abstract
Therapeutic proteins can be challenging to develop due to their complexity and the requirement of an acceptable formulation to ensure patient safety and efficacy. To date, there is no universal formulation development strategy that can identify optimal formulation conditions for all types of proteins in a fast and reliable manner. In this work, high-throughput characterization, employing a toolbox of five techniques, was performed on 14 structurally different proteins formulated in 6 different buffer conditions and in the presence of 4 different excipients. Multivariate data analysis and chemometrics were used to analyze the data in an unbiased way. First, observed changes in stability were primarily determined by the individual protein. Second, pH and ionic strength are the two most important factors determining the physical stability of proteins, where there exists a significant statistical interaction between protein and pH/ionic strength. Additionally, we developed prediction methods by partial least-squares regression. Colloidal stability indicators are important for prediction of real-time stability, while conformational stability indicators are important for prediction of stability under accelerated stress conditions at 40 °C. In order to predict real-time storage stability, protein-protein repulsion and the initial monomer fraction are the most important properties to monitor.
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Affiliation(s)
- Alina Kulakova
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, Kongens, Lyngby 2800, Denmark
| | - Dillen Augustijn
- Department of Food Science, Faculty of Science, University of Copenhagen, Rolighedsvej 26, Frederiksberg 1958, Denmark
| | - Inas El Bialy
- Department of Pharmacy, Pharmaceutical Technology and Biopharmaceutics, Ludwig-Maximilians-Universitaet Muenchen, Butenandtstrasse 5, Munich 81377, Germany
| | - Lorenzo Gentiluomo
- Department of Pharmacy, Pharmaceutical Technology and Biopharmaceutics, Ludwig-Maximilians-Universitaet Muenchen, Butenandtstrasse 5, Munich 81377, Germany
- Wyatt Technology Europe GmbH, Hochstrasse 18, Dernbach 56307, Germany
| | - Maria Laura Greco
- Dosage Form Design and Development, AstraZeneca, Sir Aaron Klug Building, Granta Park, Cambridge CB21 6GH, U.K
| | - Stefan Hervø-Hansen
- Division of Theoretical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, Lund 22100, Sweden
| | - Sowmya Indrakumar
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, Kongens, Lyngby 2800, Denmark
| | | | - Marcello Martinez Morales
- Dosage Form Design and Development, AstraZeneca, Sir Aaron Klug Building, Granta Park, Cambridge CB21 6GH, U.K
| | - Christin Pohl
- Novozymes A/S, Krogshoejvej 36, Bagsvaerd 2880, Denmark
| | - Marco Polimeni
- Division of Theoretical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, Lund 22100, Sweden
| | - Aisling Roche
- Department of Chemical Engineering, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Hristo L Svilenov
- Department of Pharmacy, Pharmaceutical Technology and Biopharmaceutics, Ludwig-Maximilians-Universitaet Muenchen, Butenandtstrasse 5, Munich 81377, Germany
| | - Andreas Tosstorff
- Department of Pharmacy, Pharmaceutical Technology and Biopharmaceutics, Ludwig-Maximilians-Universitaet Muenchen, Butenandtstrasse 5, Munich 81377, Germany
| | - Matja Zalar
- Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, and Manchester Institute of Biotechnology, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Robin Curtis
- Department of Chemical Engineering, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Jeremy P Derrick
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Oxford Road, Manchester M13 9PT, U.K
| | - Wolfgang Frieß
- Department of Pharmacy, Pharmaceutical Technology and Biopharmaceutics, Ludwig-Maximilians-Universitaet Muenchen, Butenandtstrasse 5, Munich 81377, Germany
| | - Alexander P Golovanov
- Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, and Manchester Institute of Biotechnology, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Mikael Lund
- Division of Theoretical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, Lund 22100, Sweden
| | | | - Tarik A Khan
- Pharmaceutical Development & Supplies, Pharma Technical Development Biologics Europe, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel 4070, Switzerland
| | - Günther H J Peters
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, Kongens, Lyngby 2800, Denmark
| | - Alain Pluen
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, U.K
| | - Dierk Roessner
- Wyatt Technology Europe GmbH, Hochstrasse 18, Dernbach 56307, Germany
| | | | - Christopher F van der Walle
- Dosage Form Design and Development, AstraZeneca, Sir Aaron Klug Building, Granta Park, Cambridge CB21 6GH, U.K
| | - Jim Warwicker
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Oxford Road, Manchester M13 9PT, U.K
| | - Shahid Uddin
- Dosage Form Design and Development, AstraZeneca, Sir Aaron Klug Building, Granta Park, Cambridge CB21 6GH, U.K
| | - Gerhard Winter
- Department of Pharmacy, Pharmaceutical Technology and Biopharmaceutics, Ludwig-Maximilians-Universitaet Muenchen, Butenandtstrasse 5, Munich 81377, Germany
| | | | - Åsmund Rinnan
- Department of Food Science, Faculty of Science, University of Copenhagen, Rolighedsvej 26, Frederiksberg 1958, Denmark
| | - Pernille Harris
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, Kongens, Lyngby 2800, Denmark
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5
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Low-data interpretable deep learning prediction of antibody viscosity using a biophysically meaningful representation. Sci Rep 2023; 13:2917. [PMID: 36806303 PMCID: PMC9941094 DOI: 10.1038/s41598-023-28841-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 01/25/2023] [Indexed: 02/22/2023] Open
Abstract
Deep learning, aided by the availability of big data sets, has led to substantial advances across many disciplines. However, many scientific problems of practical interest lack sufficiently large datasets amenable to deep learning. Prediction of antibody viscosity is one such problem where deep learning methods have not yet been explored due to the relative scarcity of relevant training data. In this work, we overcome this limitation using a biophysically meaningful representation that enables us to develop generalizable models even under limited training data. We present, PfAbNet-viscosity, a 3D convolutional neural network architecture, to predict high-concentration viscosity of therapeutic antibodies. We show that with the electrostatic potential surface of the antibody variable region as the only input to the network, the models trained on as few as couple dozen datapoints can generalize with high accuracy. Our feature attribution analysis shows that PfAbNet-viscosity has learned key biophysical drivers of viscosity. The applicability of our approach to other biological systems is discussed.
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6
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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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7
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Ghosh I, Gutka H, Krause ME, Clemens R, Kashi RS. A systematic review of commercial high concentration antibody drug products approved in the US: formulation composition, dosage form design and primary packaging considerations. MAbs 2023; 15:2205540. [PMID: 37243580 DOI: 10.1080/19420862.2023.2205540] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 04/15/2023] [Accepted: 04/18/2023] [Indexed: 05/29/2023] Open
Abstract
Three critical aspects that define high concentration antibody products (HCAPs) are as follows: 1) formulation composition, 2) dosage form, and 3) primary packaging configuration. HCAPs have become successful in the therapeutic sector due to their unique advantage of allowing subcutaneous self-administration. Technical challenges, such as physical and chemical instability, viscosity, delivery volume limitations, and product immunogenicity, can hinder successful development and commercialization of HCAPs. Such challenges can be overcome by robust formulation and process development strategies, as well as rational selection of excipients and packaging components. We compiled and analyzed data from US Food and Drug Administration-approved and marketed HCAPs that are ≥100 mg/mL to identify trends in formulation composition and quality target product profile. This review presents our findings and discusses novel formulation and processing technologies that enable the development of improved HCAPs at ≥200 mg/mL. The observed trends can be used as a guide for further advancements in the development of HCAPs as more complex antibody-based modalities enter biologics product development.
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Affiliation(s)
- Indrajit Ghosh
- Sterile Product Development, Bristol Myers Squibb, New Brunswick, NJ, USA
| | - Hiten Gutka
- Sterile Product Development, Bristol Myers Squibb, New Brunswick, NJ, USA
| | - Mary E Krause
- Sterile Product Development, Bristol Myers Squibb, New Brunswick, NJ, USA
| | - Ryan Clemens
- College of Pharmacy, University of Illinois at Chicago, Chicago, USA
| | - Ramesh S Kashi
- Sterile Product Development, Bristol Myers Squibb, Summit, NJ, USA
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8
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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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9
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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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10
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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: 0] [Impact Index Per Article: 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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11
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Shimomura T, Sekiguchi M, Honda R, Yamazaki M, Yokoyama M, Uchiyama S. Estimation of the Viscosity of an Antibody Solution from the Diffusion Interaction Parameter. Biol Pharm Bull 2022; 45:1300-1305. [DOI: 10.1248/bpb.b22-00263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
| | | | - Reisa Honda
- Department of Pharmaceutical Technology, Astellas Pharma Inc
| | - Miki Yamazaki
- Department of Pharmaceutical Technology, Astellas Pharma Inc
| | - Masami Yokoyama
- Department of Biotechnology, Graduate School of Engineering, Osaka University
| | - Susumu Uchiyama
- Department of Biotechnology, Graduate School of Engineering, Osaka University
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12
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Laber JR, Laue TM, Filoti DI. Use of Debye-Hückel-Henry charge measurements in early antibody development elucidates effects of non-specific association. Antib Ther 2022; 5:211-215. [PMID: 35983303 PMCID: PMC9380711 DOI: 10.1093/abt/tbac018] [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] [Received: 01/10/2022] [Revised: 06/21/2022] [Accepted: 07/10/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
The diffusion interaction parameter (kD) has been demonstrated to be a high-throughput technique for characterizing interactions between proteins in solution. kD reflects both attractive and repulsive interactions, including long-ranged electrostatic repulsions. Here, we plot the mutual diffusion coefficient (Dm) as a function of the experimentally determined Debye-Hückel-Henry surface charge (ZDHH) for seven human monoclonal antibodies (mAbs) in 15 mM histidine, pH 6. We find that graphs of Dm versus ZDHH intersect at ZDHH, ~ 2.6, independent of protein concentration. The same data plotted as kD vs. ZDHH shows a transition from net attractive to net repulsive interactions in the same region of the ZDHH intersection point. These data suggest that there is a minimum surface charge necessary on these mAbs needed to overcome attractive interactions.
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Affiliation(s)
- Joshua R Laber
- Formulation and Biologics Product Development, Nektar Therapeutics , 455 Mission Bay Boulevard South, San Francisco, CA 94158, USA
| | - Thomas M Laue
- Carpenter Professor Emeritus, University of New Hampshire , Durham, NH 03824, USA
| | - Dana I Filoti
- Analytical Research and Development, AbbVie , 100 Research Drive, Worcester, MA 01605, USA
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13
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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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14
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Han X, Shih J, Lin Y, Chai Q, Cramer SM. Development of QSAR models for in silico screening of antibody solubility. MAbs 2022; 14:2062807. [PMID: 35442164 PMCID: PMC9037471 DOI: 10.1080/19420862.2022.2062807] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Although monoclonal antibodies (mAbs) have been shown to be extremely effective in treating a number of diseases, they often suffer from poor developability attributes, such as high viscosity and low solubility at elevated concentrations. Since experimental candidate screening is often materials and labor intensive, there is substantial interest in developing in silico tools for expediting mAb design. Here, we present a strategy using machine learning-based QSAR models for the a priori estimation of mAb solubility. The extrapolated protein solubilities of a set of 111 antibodies in a histidine buffer were determined using a high throughput PEG precipitation assay. 3D homology models of the antibodies were determined, and a large set of in house and commercially available molecular descriptors were then calculated. The resulting experimental and descriptor data were then used for the development of QSAR models of mAb solubilities. After feature selection and training with different machine learning algorithms, the models were evaluated with external test sets. The resulting regression models were able to estimate the solubility values of external test set data with R2 of 0.81 and 0.85 for the two regression models developed. In addition, three class and binary classification models were developed and shown to be good estimators of mAb solubility behavior, with overall test set accuracies of 0.70 and 0.95, respectively. The analysis of the selected molecular descriptors in these models was also found to be informative and suggested that several charge-based descriptors and isotype may play important roles in mAb solubility. The combination of high throughput relative solubility experimental techniques in concert with efficient machine learning QSAR models offers an opportunity to rapidly screen potential mAb candidates and to design therapeutics with improved solubility characteristics.
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Affiliation(s)
- Xuan Han
- Department of Chemical and Biological Engineering and Center for Biotechnology and interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - James Shih
- Biotechnology Discovery Research, Eli Lilly Biotechnology Center, San Diego, California, USA
| | - Yuhao Lin
- Research Information & Digital Solutions, Eli Lilly Biotechnology Center, San Diego, California, USA
| | - Qing Chai
- Biotechnology Discovery Research, Eli Lilly Biotechnology Center, San Diego, California, USA
| | - Steven M Cramer
- Department of Chemical and Biological Engineering and Center for Biotechnology and interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA
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15
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Liu Y, Tsang K, Mays M, Hansen G, Chiecko J, Crames M, Wei Y, Zhou W, Fredrick C, Hu J, Liu D, Gebhard D, Huang ZF, Datar A, Kronkaitis A, Gueneva-Boucheva K, Seeliger D, Han F, Sen S, Kasturirangan S, Scheer JM, Nixon AE, Panavas T, Marlow MS, Kumar S. An adapted consensus protein design strategy for identifying globally optimal biotherapeutics. MAbs 2022; 14:2073632. [PMID: 35613320 PMCID: PMC9135432 DOI: 10.1080/19420862.2022.2073632] [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] [Indexed: 10/27/2022] Open
Abstract
Biotherapeutic optimization, whether to improve general properties or to engineer specific attributes, is a time-consuming process with uncertain outcomes. Conversely, Consensus Protein Design has been shown to be a viable approach to enhance protein stability while retaining function. In adapting this method for a more limited number of protein sequences, we studied 21 consensus single-point variants from eight publicly available CD3 binding sequences with high similarity but diverse biophysical and pharmacological properties. All single-point consensus variants retained CD3 binding and performed similarly in cell-based functional assays. Using Ridge regression analysis, we identified the variants and sequence positions with overall beneficial effects on developability attributes of the CD3 binders. A second round of sequence generation that combined these substitutions into a single molecule yielded a unique CD3 binder with globally optimized developability attributes. In this first application to therapeutic antibodies, adapted Consensus Protein Design was found to be highly beneficial within lead optimization, conserving resources and minimizing iterations. Future implementations of this general strategy may help accelerate drug discovery and improve success rates in bringing novel biotherapeutics to market.
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Affiliation(s)
- Yanyun Liu
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
| | - Kenny Tsang
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
| | - Michelle Mays
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
| | - Gale Hansen
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
| | - Jeffrey Chiecko
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
| | - Maureen Crames
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
| | - Yangjie Wei
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
| | - Weijie Zhou
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
| | - Chase Fredrick
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
| | - James Hu
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
| | - Dongmei Liu
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
| | - Douglas Gebhard
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
| | - Zhong-Fu Huang
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
| | - Akshita Datar
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
| | - Anthony Kronkaitis
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
| | | | - Daniel Seeliger
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co KG, Biberach, Germany
| | - Fei Han
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
| | - Saurabh Sen
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
| | - Srinath Kasturirangan
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
| | - Justin M Scheer
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
| | - Andrew E Nixon
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
| | - Tadas Panavas
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
| | - Michael S Marlow
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
| | - Sandeep Kumar
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
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16
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Tomar DS, Licari G, Bauer J, Singh SK, Li L, Kumar S. Stress-dependent flexibility of a full-length human monoclonal antibody: Insights from molecular dynamics to support biopharmaceutical development. J Pharm Sci 2021; 111:628-637. [PMID: 34742728 DOI: 10.1016/j.xphs.2021.10.039] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/30/2021] [Accepted: 10/30/2021] [Indexed: 01/15/2023]
Abstract
After several decades of advancements in drug discovery, product development of biopharmaceuticals remains a time- and resource-consuming endeavor. One of the main reasons is associated to the lack of fundamental understanding of conformational dynamics of such biologic entities, and how they respond to various stresses encountered during manufacturing. In this work, we have studied the conformational dynamics of human IgG1κ b12 monoclonal antibody (mAb) using molecular dynamics simulations. The hundreds of nanoseconds long trajectories reveal that b12 mAb is highly flexible. Its variable domains show greater conformational fluctuations than the constant domains. Additionally, it collapses towards a more globular shape in response to thermal stress, leading to decrease in the total solvent exposed surface area and radius of gyration. This behavior is more pronounced for the deglycosylated b12 mAb, and it appears to correlate with increase in inter-domain contacts between specific regions of the antibody. Conformational fluctuations also cause temporary formation and disruption of hydrophobic and charged patches on the antibody surface, which is particularly important for the prediction of CMC properties during development phases of antibody-based biotherapeutics. The insights gained through these simulations may help the development of biologic drugs, especially with regards to manufacturing processes where antibodies may undergo significant thermal stress.
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Affiliation(s)
- Dheeraj S Tomar
- Biotherapeutics Pharmaceutical Sciences Research and Development, Pfizer Inc., 700 Chesterfield Parkway West, Chesterfield, MO, 63017, USA
| | - Giuseppe Licari
- Pharmaceuticals Development Biologicals, Boehringer Ingelheim Pharmaceuticals, Inc., D-88397 Biberach an der Riss, Germany
| | - Joschka Bauer
- Pharmaceuticals Development Biologicals, Boehringer Ingelheim Pharmaceuticals, Inc., D-88397 Biberach an der Riss, Germany
| | - Satish K Singh
- Biotherapeutics Pharmaceutical Sciences Research and Development, Pfizer Inc., 700 Chesterfield Parkway West, Chesterfield, MO, 63017, USA
| | - Li Li
- Biotherapeutics Pharmaceutical Sciences Research and Development, Pfizer Inc., 1 Burtt Road, Andover, Massachusetts, 01810, USA
| | - Sandeep Kumar
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, CT 06877.
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17
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Scannell MJ, Hyatt MW, Budyak IL, Woldeyes MA, Wang Y. Revisit PEG-Induced Precipitation Assay for Protein Solubility Assessment of Monoclonal Antibody Formulations. Pharm Res 2021; 38:1947-1960. [PMID: 34647231 DOI: 10.1007/s11095-021-03119-4] [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: 06/19/2021] [Accepted: 09/22/2021] [Indexed: 11/27/2022]
Abstract
PURPOSE Protein solubility is an important attribute of pharmaceutical monoclonal antibody (MAb) formulations, particularly at high MAb concentrations. PEG-induced protein precipitation has been routinely used to assess protein solubility. To provide insights for better understanding and implementation of PEG-induced protein precipitation assay, this work compares different solubility measures and examines their relevance to loss of protein solubility in concentrated formulations. METHODS Solubility of a MAb in 15 formulations was evaluated using PEG-induced precipitation assay. Three apparent protein solubility measures, the middle-point and onset PEG concentrations (cmid and conset) as well as the binding free energy (μB), were obtained from the PEG-induced protein precipitation assay and compared to the DLS protein interaction parameter (kD). Visual inspection of loss of protein solubility in concentrated formulations during storage was used to further examine the discrepancy of protein solubility ranking by these measures. RESULTS PEG-induced precipitation assay predicted overall protein solubility ranking similar to that by DLS kD. However, for three formulations with ionic excipients NaCl, Arg·Cl, and Arg·Glu·Cl, PEG-induced precipitation assay yielded more accurate predictions compared to DLS kD measurements. Furthermore, μB showed superior ability in distinguishing protein solubility for these formulations. CONCLUSIONS This study demonstrated good correlations between the protein solubility measures obtained from PEG-induced precipitation experiments and DLS kD measurement. It also provides one example in which protein solubility ranking by binding free energy is more accurate than the other measures. The results support the theoretical proposition that μB has a potential to serve as standard protein solubility measure.
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Affiliation(s)
- Martha J Scannell
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, 601 S. College Road, Wilmington, NC, 28403, USA
| | - Matthew W Hyatt
- Lilly Research Laboratories, Bioproduct Research and Development, Eli Lilly and Company, Indianapolis, IN, 46285, USA
| | - Ivan L Budyak
- Lilly Research Laboratories, Bioproduct Research and Development, Eli Lilly and Company, Indianapolis, IN, 46285, USA
| | - Mahlet A Woldeyes
- Lilly Research Laboratories, Bioproduct Research and Development, Eli Lilly and Company, Indianapolis, IN, 46285, USA.
| | - Ying Wang
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, 601 S. College Road, Wilmington, NC, 28403, USA.
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18
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Intrinsic physicochemical profile of marketed antibody-based biotherapeutics. Proc Natl Acad Sci U S A 2021; 118:2020577118. [PMID: 34504010 PMCID: PMC8449350 DOI: 10.1073/pnas.2020577118] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2021] [Indexed: 01/28/2023] Open
Abstract
Successful biologic drug discovery and development involves finding functional as well as developable candidates. Once a candidate has been demonstrated to be functional, the next step is to determine whether it can be translated into a drug product. This requires that the candidate can withstand stresses encountered during manufacturing, shipping, and storage. Additionally, it must be safe, efficacious, and possess good pharmacology. In silico analyses of the variable regions of 77 marketed antibody-based biotherapeutics have revealed five nonredundant physicochemical descriptors. Distributions of these descriptors, observed for marketed biotherapeutics, can help prioritize a drug candidate for experimental testing at early discovery stages, guide engineering efforts to further optimize it, and help increase the productivity of biologic drug discovery and development. Feeding biopharma pipelines with biotherapeutic candidates that possess desirable developability profiles can help improve the productivity of biologic drug discovery and development. Here, we have derived an in silico profile by analyzing computed physicochemical descriptors for the variable regions (Fv) found in 77 marketed antibody-based biotherapeutics. Fv regions of these biotherapeutics demonstrate significant diversities in their germlines, complementarity determining region loop lengths, hydrophobicity, and charge distributions. Furthermore, an analysis of 24 physicochemical descriptors, calculated using homology-based molecular models, has yielded five nonredundant descriptors whose distributions represent stability, isoelectric point, and molecular surface characteristics of their Fv regions. Fv regions of candidates from our internal discovery campaigns, human next-generation sequencing repertoires, and those in clinical-stages (CST) were assessed for similarity with the physicochemical profile derived here. The Fv regions in 33% of CST antibodies show physicochemical properties that are dissimilar to currently marketed biotherapeutics. In comparison, physicochemical characteristics of ∼29% of the Fv regions in human antibodies and ∼27% of our internal hits deviated significantly from those of marketed biotherapeutics. The early availability of this information can help guide hit selection, lead identification, and optimization of biotherapeutic candidates. Insights from this work can also help support portfolio risk assessment, in-licensing, and biopharma collaborations.
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19
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Bailly M, Mieczkowski C, Juan V, Metwally E, Tomazela D, Baker J, Uchida M, Kofman E, Raoufi F, Motlagh S, Yu Y, Park J, Raghava S, Welsh J, Rauscher M, Raghunathan G, Hsieh M, Chen YL, Nguyen HT, Nguyen N, Cipriano D, Fayadat-Dilman L. Predicting Antibody Developability Profiles Through Early Stage Discovery Screening. MAbs 2021; 12:1743053. [PMID: 32249670 PMCID: PMC7153844 DOI: 10.1080/19420862.2020.1743053] [Citation(s) in RCA: 116] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Monoclonal antibodies play an increasingly important role for the development of new drugs across multiple therapy areas. The term 'developability' encompasses the feasibility of molecules to successfully progress from discovery to development via evaluation of their physicochemical properties. These properties include the tendency for self-interaction and aggregation, thermal stability, colloidal stability, and optimization of their properties through sequence engineering. Selection of the best antibody molecule based on biological function, efficacy, safety, and developability allows for a streamlined and successful CMC phase. An efficient and practical high-throughput developability workflow (100 s-1,000 s of molecules) implemented during early antibody generation and screening is crucial to select the best lead candidates. This involves careful assessment of critical developability parameters, combined with binding affinity and biological properties evaluation using small amounts of purified material (<1 mg), as well as an efficient data management and database system. Herein, a panel of 152 various human or humanized monoclonal antibodies was analyzed in biophysical property assays. Correlations between assays for different sets of properties were established. We demonstrated in two case studies that physicochemical properties and key assay endpoints correlate with key downstream process parameters. The workflow allows the elimination of antibodies with suboptimal properties and a rank ordering of molecules for further evaluation early in the candidate selection process. This enables any further engineering for problematic sequence attributes without affecting program timelines.
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Affiliation(s)
- Marc Bailly
- Discovery Biologics, Protein Sciences, South San Francisco, CA, USA
| | - Carl Mieczkowski
- Discovery Biologics, Protein Sciences, South San Francisco, CA, USA
| | - Veronica Juan
- Discovery Biologics, Protein Sciences, South San Francisco, CA, USA
| | - Essam Metwally
- Computation and Structural Chemistry, South San Francisco, CA, USA
| | - Daniela Tomazela
- Discovery Biologics, Protein Sciences, South San Francisco, CA, USA
| | - Jeanne Baker
- Discovery Biologics, Protein Sciences, South San Francisco, CA, USA
| | - Makiko Uchida
- Discovery Biologics, Protein Sciences, South San Francisco, CA, USA
| | - Ester Kofman
- Discovery Biologics, Protein Sciences, South San Francisco, CA, USA
| | - Fahimeh Raoufi
- Discovery Biologics, Protein Sciences, South San Francisco, CA, USA
| | - Soha Motlagh
- Discovery Biologics, Protein Sciences, South San Francisco, CA, USA
| | - Yao Yu
- Discovery Biologics, Protein Sciences, South San Francisco, CA, USA
| | - Jihea Park
- Discovery Biologics, Protein Sciences, South San Francisco, CA, USA
| | - Smita Raghava
- Pharmaceutical Sciences, Sterile FormulationSciences, Kenilworth, NJ, USA
| | - John Welsh
- Downstream Process Development andEngineering, Kenilworth, NJ, USA
| | - Michael Rauscher
- Downstream Process Development andEngineering, Kenilworth, NJ, USA
| | | | - Mark Hsieh
- Discovery Biologics, Protein Sciences, South San Francisco, CA, USA
| | - Yi-Ling Chen
- Discovery Biologics, Protein Sciences, South San Francisco, CA, USA
| | - Hang Thu Nguyen
- Discovery Biologics, Protein Sciences, South San Francisco, CA, USA
| | - Nhung Nguyen
- Discovery Biologics, Protein Sciences, South San Francisco, CA, USA
| | - Dan Cipriano
- Discovery Biologics, Protein Sciences, South San Francisco, CA, USA
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20
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Lai PK, Fernando A, Cloutier TK, Gokarn Y, Zhang J, Schwenger W, Chari R, Calero-Rubio C, Trout BL. Machine Learning Applied to Determine the Molecular Descriptors Responsible for the Viscosity Behavior of Concentrated Therapeutic Antibodies. Mol Pharm 2021; 18:1167-1175. [PMID: 33450157 DOI: 10.1021/acs.molpharmaceut.0c01073] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Predicting the solution viscosity of monoclonal antibody (mAb) drug products remains as one of the main challenges in antibody drug design, manufacturing, and delivery. In this work, the concentration-dependent solution viscosity of 27 FDA-approved mAbs was measured at pH 6.0 in 10 mM histidine-HCl. Six mAbs exhibited high viscosity (>30 cP) in solutions at 150 mg/mL mAb concentration. Combining molecular modeling and machine learning feature selection, we found that the net charge in the mAbs and the amino acid composition in the Fv region are key features which govern the viscosity behavior. For mAbs whose behavior was not dominated by charge effects, we observed that high viscosity is correlated with more hydrophilic and fewer hydrophobic residues in the Fv region. A predictive model based on the net charges of mAbs and a high viscosity index is presented as a fast screening tool for classifying low- and high-viscosity mAbs.
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Affiliation(s)
- Pin-Kuang Lai
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Amendra Fernando
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Theresa K Cloutier
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Yatin Gokarn
- Biologics Development, Sanofi, Framingham, Massachusetts 01701, United States
| | - Jifeng Zhang
- Biologics Development, Sanofi, Framingham, Massachusetts 01701, United States
| | - Walter Schwenger
- Biologics Development, Sanofi, Framingham, Massachusetts 01701, United States
| | - Ravi Chari
- Biologics Development, Sanofi, Framingham, Massachusetts 01701, United States
| | - Cesar Calero-Rubio
- Biologics Development, Sanofi, Framingham, Massachusetts 01701, United States
| | - Bernhardt L Trout
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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21
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Tilegenova C, Izadi S, Yin J, Huang CS, Wu J, Ellerman D, Hymowitz SG, Walters B, Salisbury C, Carter PJ. Dissecting the molecular basis of high viscosity of monospecific and bispecific IgG antibodies. MAbs 2021; 12:1692764. [PMID: 31779513 PMCID: PMC6927759 DOI: 10.1080/19420862.2019.1692764] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Some antibodies exhibit elevated viscosity at high concentrations, making them poorly suited for therapeutic applications requiring administration by injection such as subcutaneous or ocular delivery. Here we studied an anti-IL-13/IL-17 bispecific IgG4 antibody, which has anomalously high viscosity compared to its parent monospecific antibodies. The viscosity of the bispecific IgG4 in solution was decreased by only ~30% in the presence of NaCl, suggesting electrostatic interactions are insufficient to fully explain the drivers of viscosity. Intriguingly, addition of arginine-HCl reduced the viscosity of the bispecific IgG4 by ~50% to its parent IgG level. These data suggest that beyond electrostatics, additional types of interactions such as cation-π and/or π-π may contribute to high viscosity more significantly than previously understood. Molecular dynamics simulations of antibody fragments in the mixed solution of free arginine and explicit water were conducted to identify hotspots involved in self-interactions. Exposed surface aromatic amino acids displayed an increased number of contacts with arginine. Mutagenesis of the majority of aromatic residues pinpointed by molecular dynamics simulations effectively decreased the solution's viscosity when tested experimentally. This mutational method to reduce the viscosity of a bispecific antibody was extended to a monospecific anti-GCGR IgG1 antibody with elevated viscosity. In all cases, point mutants were readily identified that both reduced viscosity and retained antigen-binding affinity. These studies demonstrate a new approach to mitigate high viscosity of some antibodies by mutagenesis of surface-exposed aromatic residues on complementarity-determining regions that may facilitate some clinical applications.
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Affiliation(s)
| | - Saeed Izadi
- Early Stage Pharmaceutical Development, Genentech Inc., South San Francisco, CA, USA
| | - Jianping Yin
- Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | | | - Jiansheng Wu
- Protein Chemistry, Genentech Inc., South San Francisco, CA, USA
| | - Diego Ellerman
- Protein Chemistry, Genentech Inc., South San Francisco, CA, USA
| | - Sarah G Hymowitz
- Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | - Benjamin Walters
- Biochemical and Cellular Pharmacology, Genentech Inc., South San Francisco, CA, USA
| | - Cleo Salisbury
- Early Stage Pharmaceutical Development, Genentech Inc., South San Francisco, CA, USA
| | - Paul J Carter
- Antibody Engineering, Genentech Inc., South San Francisco, CA, USA
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22
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Lai PK, Fernando A, Cloutier TK, Kingsbury JS, Gokarn Y, Halloran KT, Calero-Rubio C, Trout BL. Machine Learning Feature Selection for Predicting High Concentration Therapeutic Antibody Aggregation. J Pharm Sci 2020; 110:1583-1591. [PMID: 33346034 DOI: 10.1016/j.xphs.2020.12.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/25/2020] [Accepted: 12/11/2020] [Indexed: 02/03/2023]
Abstract
Protein aggregation can hinder the development, safety and efficacy of therapeutic antibody-based drugs. Developing a predictive model that evaluates aggregation behaviors during early stage development is therefore desirable. Machine learning is a widely used tool to train models that predict data with different attributes. However, most machine learning techniques require more data than is typically available in antibody development. In this work, we describe a rational feature selection framework to develop accurate models with a small number of features. We applied this framework to predict aggregation behaviors of 21 approved monospecific monoclonal antibodies at high concentration (150 mg/mL), yielding a correlation coefficient of 0.71 on validation tests with only two features using a linear model. The nearest neighbors and support vector regression models further improved the performance, which have correlation coefficients of 0.86 and 0.80, respectively. This framework can be extended to train other models that predict different physical properties.
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Affiliation(s)
- Pin-Kuang Lai
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Amendra Fernando
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Theresa K Cloutier
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Yatin Gokarn
- Biologics Development, Sanofi, Framingham, MA, USA
| | | | | | - Bernhardt L Trout
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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23
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Matsuoka T, Miyauchi R, Nagaoka N, Hasegawa J. Mitigation of liquid-liquid phase separation of a monoclonal antibody by mutations of negative charges on the Fab surface. PLoS One 2020; 15:e0240673. [PMID: 33125371 PMCID: PMC7598502 DOI: 10.1371/journal.pone.0240673] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 09/30/2020] [Indexed: 01/02/2023] Open
Abstract
Some monoclonal antibodies undergo liquid-liquid phase separation owing to self-attractive associations involving electrostatic and other soft interactions, thereby rendering monoclonal antibodies unsuitable as therapeutics. To mitigate the phase separation, formulation optimization is often performed. However, this is sometimes unsuccessful because of the limited time for the development of therapeutic antibodies. Thus, protein mutations with appropriate design are required. In this report, we describe a case study involving the design of mutants of negatively charged surface residues to reduce liquid-liquid phase separation propensity. Physicochemical analysis of the resulting mutants demonstrated the mutual correlation between the sign of second virial coefficient B2, the Fab dipole moment, and the reduction of liquid-liquid phase separation propensity. Moreover, both the magnitude and direction of the dipole moment appeared to be essential for liquid-liquid phase separation propensity, where electrostatic interaction was the dominant mechanism. These findings could contribute to a better design of mutants with reduced liquid-liquid phase separation propensity and improved drug-like biophysical properties.
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Affiliation(s)
- Tatsuji Matsuoka
- Modality Research Laboratories, Daiichi Sankyo, Co., Ltd., Shinagawa, Tokyo, Japan
| | - Ryuki Miyauchi
- Modality Research Laboratories, Daiichi Sankyo, Co., Ltd., Shinagawa, Tokyo, Japan
| | - Nobumi Nagaoka
- Modality Research Laboratories, Daiichi Sankyo, Co., Ltd., Shinagawa, Tokyo, Japan
| | - Jun Hasegawa
- Modality Research Laboratories, Daiichi Sankyo, Co., Ltd., Shinagawa, Tokyo, Japan
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Smiatek J, Jung A, Bluhmki E. Towards a Digital Bioprocess Replica: Computational Approaches in Biopharmaceutical Development and Manufacturing. Trends Biotechnol 2020; 38:1141-1153. [DOI: 10.1016/j.tibtech.2020.05.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 05/11/2020] [Accepted: 05/13/2020] [Indexed: 12/11/2022]
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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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26
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Kingsbury JS, Saini A, Auclair SM, Fu L, Lantz MM, Halloran KT, Calero-Rubio C, Schwenger W, Airiau CY, Zhang J, Gokarn YR. A single molecular descriptor to predict solution behavior of therapeutic antibodies. SCIENCE ADVANCES 2020; 6:eabb0372. [PMID: 32923611 PMCID: PMC7457339 DOI: 10.1126/sciadv.abb0372] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 06/17/2020] [Indexed: 05/02/2023]
Abstract
Despite the therapeutic success of monoclonal antibodies (mAbs), early identification of developable mAb drug candidates with optimal manufacturability, stability, and delivery attributes remains elusive. Poor solution behavior, which manifests as high solution viscosity or opalescence, profoundly affects the developability of mAb drugs. Using a diverse dataset of 59 mAbs, including 43 approved products, and an array of molecular descriptors spanning colloidal, conformational, charge-based, hydrodynamic, and hydrophobic properties, we show that poor solution behavior is prevalent (>30%) in mAbs and is singularly predicted (>90%) by the diffusion interaction parameter (k D), a dilute-solution measure of colloidal self-interaction. No other descriptor, individually or in combination, was found to be as effective as k D. We also show that well-behaved mAbs, a substantial subset of which bear high positive charge and pI, present no disadvantages with respect to pharmacokinetics in humans. Here, we provide a systematic framework with quantitative thresholds for selecting well-behaved therapeutic mAbs during drug discovery.
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27
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Kuroda D, Tsumoto K. Engineering Stability, Viscosity, and Immunogenicity of Antibodies by Computational Design. J Pharm Sci 2020; 109:1631-1651. [DOI: 10.1016/j.xphs.2020.01.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 12/25/2019] [Accepted: 01/10/2020] [Indexed: 12/18/2022]
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Izadi S, Patapoff TW, Walters BT. Multiscale Coarse-Grained Approach to Investigate Self-Association of Antibodies. Biophys J 2020; 118:2741-2754. [PMID: 32416079 DOI: 10.1016/j.bpj.2020.04.022] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 03/12/2020] [Accepted: 04/13/2020] [Indexed: 11/20/2022] Open
Abstract
Self-association of therapeutic monoclonal antibodies (mabs) are thought to modulate the undesirably high viscosity observed in their concentrated solutions. Computational prediction of such a self-association behavior is advantageous early during mab drug candidate selection when material availability is limited. Here, we present a coarse-grained (CG) simulation method that enables microsecond molecular dynamics simulations of full-length antibodies at high concentrations. The proposed approach differs from others in two ways: first, charges are assigned to CG beads in an effort to reproduce molecular multipole moments and charge asymmetry of full-length antibodies instead of only localized charges. This leads to great improvements in the agreement between CG and all-atom electrostatic fields. Second, the distinctive hydrophobic character of each antibody is incorporated through empirical adjustments to the short-range van der Waals terms dictated by cosolvent all-atom molecular dynamics simulations of antibody variable regions. CG simulations performed on a set of 15 different mabs reveal that diffusion coefficients in crowded environments are markedly impacted by intermolecular interactions. Diffusion coefficients computed from the simulations are in correlation with experimentally measured observables, including viscosities at a high concentration. Further, we show that the evaluation of electrostatic and hydrophobic characters of the mabs is useful in predicting the nonuniform effect of salt on the viscosity of mab solutions. This CG modeling approach is particularly applicable as a material-free screening tool for selecting antibody candidates with desirable viscosity properties.
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Affiliation(s)
- Saeed Izadi
- Pharmaceutical Development, Genentech, South San Francisco, California.
| | - Thomas W Patapoff
- Pharmaceutical Development, Genentech, South San Francisco, California
| | - Benjamin T Walters
- Biochemical and Cellular Pharmacology, Genentech, South San Francisco, California.
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29
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Gentiluomo L, Svilenov HL, Augustijn D, El Bialy I, Greco ML, Kulakova A, Indrakumar S, Mahapatra S, Morales MM, Pohl C, Roche A, Tosstorff A, Curtis R, Derrick JP, Nørgaard A, Khan TA, Peters GHJ, Pluen A, Rinnan Å, Streicher WW, van der Walle CF, Uddin S, Winter G, Roessner D, Harris P, Frieß W. Advancing Therapeutic Protein Discovery and Development through Comprehensive Computational and Biophysical Characterization. Mol Pharm 2020; 17:426-440. [PMID: 31790599 DOI: 10.1021/acs.molpharmaceut.9b00852] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Therapeutic protein candidates should exhibit favorable properties that render them suitable to become drugs. Nevertheless, there are no well-established guidelines for the efficient selection of proteinaceous molecules with desired features during early stage development. Such guidelines can emerge only from a large body of published research that employs orthogonal techniques to characterize therapeutic proteins in different formulations. In this work, we share a study on a diverse group of proteins, including their primary sequences, purity data, and computational and biophysical characterization at different pH and ionic strength. We report weak linear correlations between many of the biophysical parameters. We suggest that a stability comparison of diverse therapeutic protein candidates should be based on a computational and biophysical characterization in multiple formulation conditions, as the latter can largely determine whether a protein is above or below a certain stability threshold. We use the presented data set to calculate several stability risk scores obtained with an increasing level of analytical effort and show how they correlate with protein aggregation during storage. Our work highlights the importance of developing combined risk scores that can be used for early stage developability assessment. We suggest that such scores can have high prediction accuracy only when they are based on protein stability characterization in different solution conditions.
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Affiliation(s)
- Lorenzo Gentiluomo
- Wyatt Technology Europe GmbH , Hochstrasse 18 , 56307 Dernbach , Germany.,Department of Pharmacy, Pharmaceutical Technology and Biopharmaceutics , Ludwig-Maximilians-Universitaet Muenchen , Butenandtstrasse 5 , 81377 Munich , Germany
| | - Hristo L Svilenov
- Department of Pharmacy, Pharmaceutical Technology and Biopharmaceutics , Ludwig-Maximilians-Universitaet Muenchen , Butenandtstrasse 5 , 81377 Munich , Germany
| | - Dillen Augustijn
- Department of Food Science, Faculty of Science , Copenhagen University , Rolighedsvej 26 , 1958 Frederiksberg , Denmark
| | - Inas El Bialy
- Department of Pharmacy, Pharmaceutical Technology and Biopharmaceutics , Ludwig-Maximilians-Universitaet Muenchen , Butenandtstrasse 5 , 81377 Munich , Germany
| | - Maria Laura Greco
- Dosage Form Design and Development , AstraZeneca , Sir Aaron Klug Building, Granta Park , Cambridge CB21 6GH , U.K
| | - Alina Kulakova
- Department of Chemistry , Technical University of Denmark , Kemitorvet 207 , 2800 Kongens Lyngby , Denmark
| | - Sowmya Indrakumar
- Department of Chemistry , Technical University of Denmark , Kemitorvet 207 , 2800 Kongens Lyngby , Denmark
| | | | - Marcello Martinez Morales
- Dosage Form Design and Development , AstraZeneca , Sir Aaron Klug Building, Granta Park , Cambridge CB21 6GH , U.K
| | - Christin Pohl
- Novozymes A/S , Krogshoejvej 36 , 2880 Bagsvaerd , Denmark
| | - Aisling Roche
- School of Chemical Engineering and Analytical Science, Manchester Institute of Biotechnology , The University of Manchester , 131 Princess Street , Manchester M1 7DN , U.K
| | - Andreas Tosstorff
- Department of Pharmacy, Pharmaceutical Technology and Biopharmaceutics , Ludwig-Maximilians-Universitaet Muenchen , Butenandtstrasse 5 , 81377 Munich , Germany
| | - Robin Curtis
- School of Chemical Engineering and Analytical Science, Manchester Institute of Biotechnology , The University of Manchester , 131 Princess Street , Manchester M1 7DN , U.K
| | - Jeremy P Derrick
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre , The University of Manchester , Oxford Road , Manchester M13 9PT , U.K
| | - Allan Nørgaard
- Novozymes A/S , Krogshoejvej 36 , 2880 Bagsvaerd , Denmark
| | - Tarik A Khan
- Pharmaceutical Development & Supplies, Pharma Technical Development Biologics Europe , F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124 , 4070 Basel , Switzerland
| | - Günther H J Peters
- Department of Chemistry , Technical University of Denmark , Kemitorvet 207 , 2800 Kongens Lyngby , Denmark
| | - Alain Pluen
- School of Chemical Engineering and Analytical Science, Manchester Institute of Biotechnology , The University of Manchester , 131 Princess Street , Manchester M1 7DN , U.K
| | - Åsmund Rinnan
- Department of Food Science, Faculty of Science , Copenhagen University , Rolighedsvej 26 , 1958 Frederiksberg , Denmark
| | | | - Christopher F van der Walle
- Dosage Form Design and Development , AstraZeneca , Sir Aaron Klug Building, Granta Park , Cambridge CB21 6GH , U.K
| | - Shahid Uddin
- Dosage Form Design and Development , AstraZeneca , Sir Aaron Klug Building, Granta Park , Cambridge CB21 6GH , U.K
| | - Gerhard Winter
- Department of Pharmacy, Pharmaceutical Technology and Biopharmaceutics , Ludwig-Maximilians-Universitaet Muenchen , Butenandtstrasse 5 , 81377 Munich , Germany
| | - Dierk Roessner
- Wyatt Technology Europe GmbH , Hochstrasse 18 , 56307 Dernbach , Germany
| | - Pernille Harris
- Department of Chemistry , Technical University of Denmark , Kemitorvet 207 , 2800 Kongens Lyngby , Denmark
| | - Wolfgang Frieß
- Department of Pharmacy, Pharmaceutical Technology and Biopharmaceutics , Ludwig-Maximilians-Universitaet Muenchen , Butenandtstrasse 5 , 81377 Munich , Germany
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30
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Wang W, Ohtake S. Science and art of protein formulation development. Int J Pharm 2019; 568:118505. [PMID: 31306712 DOI: 10.1016/j.ijpharm.2019.118505] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 07/08/2019] [Accepted: 07/08/2019] [Indexed: 02/07/2023]
Abstract
Protein pharmaceuticals have become a significant class of marketed drug products and are expected to grow steadily over the next decade. Development of a commercial protein product is, however, a rather complex process. A critical step in this process is formulation development, enabling the final product configuration. A number of challenges still exist in the formulation development process. This review is intended to discuss these challenges, to illustrate the basic formulation development processes, and to compare the options and strategies in practical formulation development.
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Affiliation(s)
- Wei Wang
- Biological Development, Bayer USA, LLC, 800 Dwight Way, Berkeley, CA 94710, United States.
| | - Satoshi Ohtake
- Pharmaceutical Research and Development, Pfizer Biotherapeutics Pharmaceutical Sciences, Chesterfield, MO 63017, United States
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31
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Shan L, Mody N, Sormani P, Rosenthal KL, Damschroder MM, Esfandiary R. Developability Assessment of Engineered Monoclonal Antibody Variants with a Complex Self-Association Behavior Using Complementary Analytical and in Silico Tools. Mol Pharm 2018; 15:5697-5710. [DOI: 10.1021/acs.molpharmaceut.8b00867] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
| | | | - Pietro Sormani
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
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