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Kopp MRG, Grigolato F, Zürcher D, Das TK, Chou D, Wuchner K, Arosio P. Surface-Induced Protein Aggregation and Particle Formation in Biologics: Current Understanding of Mechanisms, Detection and Mitigation Strategies. J Pharm Sci 2023; 112:377-385. [PMID: 36223809 DOI: 10.1016/j.xphs.2022.10.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 10/05/2022] [Accepted: 10/05/2022] [Indexed: 01/12/2023]
Abstract
Protein stability against aggregation is a major quality concern for the production of safe and effective biopharmaceuticals. Amongst the different drivers of protein aggregation, increasing evidence indicates that interactions between proteins and interfaces represent a major risk factor for the formation of protein aggregates in aqueous solutions. Potentially harmful surfaces relevant to biologics manufacturing and storage include air-water and silicone oil-water interfaces as well as materials from different processing units, storage containers, and delivery devices. The impact of some of these surfaces, for instance originating from impurities, can be difficult to predict and control. Moreover, aggregate formation may additionally be complicated by the simultaneous presence of interfacial, hydrodynamic and mechanical stresses, whose contributions may be difficult to deconvolute. As a consequence, it remains difficult to identify the key chemical and physical determinants and define appropriate analytical methods to monitor and predict protein instability at these interfaces. In this review, we first discuss the main mechanisms of surface-induced protein aggregation. We then review the types of contact materials identified as potentially harmful or detected as potential triggers of proteinaceous particle formation in formulations and discuss proposed mitigation strategies. Finally, we present current methods to probe surface-induced instabilities, which represent a starting point towards assays that can be implemented in early-stage screening and formulation development of biologics.
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Affiliation(s)
- Marie R G Kopp
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Fulvio Grigolato
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Dominik Zürcher
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | | | | | | | - Paolo Arosio
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland.
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2
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ElGamacy M. Accelerating therapeutic protein design. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 130:85-118. [PMID: 35534117 DOI: 10.1016/bs.apcsb.2022.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Protein structures provide for defined microenvironments that can support complex pharmacological functions, otherwise unachievable by small molecules. The advent of therapeutic proteins has thus greatly broadened the range of manageable disorders. Leveraging the knowledge and recent advances in de novo protein design methods has the prospect of revolutionizing how protein drugs are discovered and developed. This review lays out the main challenges facing therapeutic proteins discovery and development, and how present and future advancements of protein design can accelerate the protein drug pipelines.
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Affiliation(s)
- Mohammad ElGamacy
- University Hospital Tübingen, Division of Translational Oncology, Tübingen, Germany; Max Planck Institute for Biology, Tübingen, Germany.
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3
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Meric G, Naik S, Hunter AK, Robinson AS, Roberts CJ. Challenges for design of aggregation-resistant variants of granulocyte colony-stimulating factor. Biophys Chem 2021; 277:106630. [PMID: 34119805 DOI: 10.1016/j.bpc.2021.106630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 05/14/2021] [Accepted: 05/31/2021] [Indexed: 01/15/2023]
Abstract
Non-native protein aggregation is a long-standing issue in pharmaceutical biotechnology. A rational design approach was used in order to identify variants of recombinant human granulocyte colony-stimulating factor (rhG-CSF) with lower aggregation propensity at solution conditions that are typical of commercial formulation. The approach used aggregation-prone-region (APR) predictors to select single amino acid substitutions that were predicted to decrease intrinsic aggregation propensity (IAP). The results of static light scattering temperature-ramps and chemical unfolding experiments demonstrated that none of the selected variants exhibited improved aggregation resistance, and the apparent conformational stability of each variant was lower than that of WT. Aggregation studies under partly denaturing conditions suggested that the IAP of at least one variant remained unaltered. Overall, this study highlights a general challenge in designing aggregation resistance for proteins, due to the need to accurately predict both APRs and conformational stability.
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Affiliation(s)
- Gulsum Meric
- Chemical & Biomolecular Engineering, University of Delaware, Newark, DE 19716, United States.
| | - Subhashchandra Naik
- Chemical & Biomolecular Engineering, University of Delaware, Newark, DE 19716, United States.
| | - Alan K Hunter
- Biopharmaceuticals Development, R&D, AstraZeneca, Gaithersburg, MD 20878, United States.
| | - Anne S Robinson
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, United States.
| | - Christopher J Roberts
- Chemical & Biomolecular Engineering, University of Delaware, Newark, DE 19716, United States.
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4
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Kopp MRG, Wolf Pérez AM, Zucca MV, Capasso Palmiero U, Friedrichsen B, Lorenzen N, Arosio P. An accelerated surface-mediated stress assay of antibody instability for developability studies. MAbs 2021; 12:1815995. [PMID: 32954930 PMCID: PMC7577746 DOI: 10.1080/19420862.2020.1815995] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
High physical stability is required for the development of monoclonal antibodies (mAbs) into successful therapeutic products. Developability assays are used to predict physical stability issues such as high viscosity and poor conformational stability, but protein aggregation remains a challenging property to predict. Among different types of stresses, air–water and solid–liquid interfaces are well known to potentially trigger protein instability and induce aggregation. Yet, in contrast to the increasing number of developability assays to evaluate bulk properties, there is still a lack of experimental methods to evaluate antibody stability against interfaces. Here, we investigate the potential of a hydrophobic nanoparticle surface-mediated stress assay to assess the stability of mAbs during the early stages of development. We evaluate this surface-mediated accelerated stability assay on a rationally designed library of 14 variants of a humanized IgG4, featuring a broad span of solubility values and other developability properties. The assay could identify variants characterized by high instability against agitation in the presence of air–water interfaces. Remarkably, for the set of investigated molecules, we observe strong correlations between the extent of aggregation induced by the surface-mediated stress assay and other developability properties of the molecules, such as aggregation upon storage at 45°C, self-association (evaluated by affinity-capture self-interaction nanoparticle spectroscopy) and nonspecific interactions (estimated by cross-interaction chromatography, stand-up monolayer chromatography (SMAC), SMAC*). This highly controlled surface-mediated stress assay has the potential to complement and increase the ability of the current set of screening techniques to assess protein aggregation and developability potential of mAbs during the early stages of drug development. Abbreviations:AC-SINS: Affinity-Capture Self-Interaction Nanoparticle Spectroscopy; AMS: Ammonium sulfate precipitation; ANS: 1-anilinonaphtalene-8-sulfonate; CIC: Cross-interaction chromatography; DLS: Dynamic light scattering; HIC: Hydrophobic interaction chromatography; HNSSA: Hydrophobic nanoparticles surface-stress assay; mAb: Monoclonal antibody; NP: Nanoparticle; SEC: Size exclusion chromatography; SMAC: Stand-up monolayer chromatography; WT: Wild type
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Affiliation(s)
- Marie R G Kopp
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, Swiss Federal Institute of Technology , Zurich, Switzerland
| | - Adriana-Michelle Wolf Pérez
- Department of Biophysics, Biophysics and Injectable Formulation, Novo Nordisk , Måløv, Denmark.,Aarhus University, iNANO , Aarhus C, Denmark
| | - Marta Virginia Zucca
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, Swiss Federal Institute of Technology , Zurich, Switzerland
| | - Umberto Capasso Palmiero
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, Swiss Federal Institute of Technology , Zurich, Switzerland
| | | | - Nikolai Lorenzen
- Department of Biophysics, Biophysics and Injectable Formulation, Novo Nordisk , Måløv, Denmark
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, Swiss Federal Institute of Technology , Zurich, Switzerland
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5
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Directed evolution of glycosyltransferase for enhanced efficiency of avermectin glucosylation. Appl Microbiol Biotechnol 2021; 105:4599-4607. [PMID: 34043077 DOI: 10.1007/s00253-021-11279-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 03/15/2021] [Accepted: 04/06/2021] [Indexed: 10/21/2022]
Abstract
Avermectin, produced by Streptomyces avermitilis, is an active compound protective against nematodes, insects, and mites. However, its potential usage is limited by its low aqueous solubility. The uridine diphosphate (UDP)-glycosyltransferase (BLC) from Bacillus licheniformis synthesizes avermectin glycosides with improved water solubility and in vitro antinematodal activity. However, enzymatic glycosylation of avermectin by BLC is limited due to the low conversion rate of this reaction. Thus, improving BLC enzyme activity is necessary for mass production of avermectin glycosides for field application. In this study, the catalytic activity of BLC toward avermectin was enhanced via directed evolution. Three mutants from the BLC mutant library (R57H, V227A, and D252V) had specific glucosylation activity for avermectin 2.0-, 1.8-, and 1.5-fold higher, respectively, than wild-type BLC. Generation of combined mutations via site-directed mutagenesis led to even further enhancement of activity. The triple mutant, R57H/V227A/D252V, had the highest activity, 2.8-fold higher than that of wild-type BLC. The catalytic efficiencies (Kcat/Km) of the best mutant (R57H/V227A/D252V) toward the substrates avermectin and UDP-glucose were improved by 2.71- and 2.29-fold, respectively, compared to those of wild-type BLC. Structural modeling analysis revealed that the free energy of the mutants was - 1.1 to - 7.1 kcal/mol lower than that of wild-type BLC, which was correlated with their improved activity. KEY POINTS: • Directed evolution improved the glucosylation activity of BLC toward avermectin. • Combinatorial site-directed mutagenesis led to further enhanced activity. • The mutants exhibited lower free energy values than wild-type BLC.
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6
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Kopp MRG, Capasso Palmiero U, Arosio P. A Nanoparticle-Based Assay To Evaluate Surface-Induced Antibody Instability. Mol Pharm 2020; 17:909-918. [DOI: 10.1021/acs.molpharmaceut.9b01168] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Marie R. G. Kopp
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich 8093, Switzerland
| | - Umberto Capasso Palmiero
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich 8093, Switzerland
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich 8093, Switzerland
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7
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Chandler PG, Broendum SS, Riley BT, Spence MA, Jackson CJ, McGowan S, Buckle AM. Strategies for Increasing Protein Stability. Methods Mol Biol 2020; 2073:163-181. [PMID: 31612442 DOI: 10.1007/978-1-4939-9869-2_10] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The stability of wild-type proteins is often a hurdle to their practical use in research, industry, and medicine. The route to engineering stability of a protein of interest lies largely with the available data. Where high-resolution structural data is available, rational design, based on fundamental principles of protein chemistry, can improve protein stability. Recent advances in computational biology and the use of nonnatural amino acids have also provided novel rational methods for improving protein stability. Likewise, the explosion of sequence and structural data available in public databases, in combination with improvements in freely available computational tools, has produced accessible phylogenetic approaches. Trawling modern sequence databases can identify the thermostable homologs of a target protein, and evolutionary data can be quickly generated using available phylogenetic tools. Grafting features from those thermostable homologs or ancestors provides stability improvement through a semi-rational approach. Further, molecular techniques such as directed evolution have shown great promise in delivering designer proteins. These strategies are well documented and newly accessible to the molecular biologist, allowing for rapid enhancements of protein stability.
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Affiliation(s)
- Peter G Chandler
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Sebastian S Broendum
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Blake T Riley
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Matthew A Spence
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Canberra, ACT, Australia
| | - Sheena McGowan
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Ashley M Buckle
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
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8
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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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9
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Navarro S, Ventura S. Computational re-design of protein structures to improve solubility. Expert Opin Drug Discov 2019; 14:1077-1088. [DOI: 10.1080/17460441.2019.1637413] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Susanna Navarro
- Institut de Biotecnologia i de Biomedicina, Parc de Recerca UAB, Mòdul B, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina, Parc de Recerca UAB, Mòdul B, Universitat Autònoma de Barcelona, Barcelona, Spain
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10
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Evers A, Pfeiffer-Marek S, Bossart M, Heubel C, Stock U, Tiwari G, Gebauer B, Elshorst B, Pfenninger A, Lukasczyk U, Hessler G, Kamm W, Wagner M. Peptide Optimization at the Drug Discovery-Development Interface: Tailoring of Physicochemical Properties Toward Specific Formulation Requirements. J Pharm Sci 2019; 108:1404-1414. [DOI: 10.1016/j.xphs.2018.11.043] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 11/27/2018] [Indexed: 12/31/2022]
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11
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Robinson MJ, Matejtschuk P, Longstaff C, Dalby PA. Selective Stabilization and Destabilization of Protein Domains in Tissue-Type Plasminogen Activator Using Formulation Excipients. Mol Pharm 2019; 16:744-755. [PMID: 30565948 DOI: 10.1021/acs.molpharmaceut.8b01024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Multidomain biotherapeutic proteins present additional behavioral and analytical challenges for the optimization of their kinetic stability by formulation. Tissue-type plasminogen activator (tPA) comprises six protein domains that exhibit a complex and pH-dependent thermal unfolding profile, due to partially independent domain unfolding. Here we have used tPA as a model for evaluating the relationships between various thermal unfolding and aggregation parameters in multidomain proteins. We show that changes in the thermal unfolding profile of tPA were parametrized by the overall thermal midpoint transition temperature, Tm, and the Van't Hoff entropy for unfolding, Δ Svh, which is a measure of unfolding cooperativity. The kinetics of degradation at 45 °C, leading to aggregation, were measured as rates of monomer and activity loss. These two rates were found to be coincident at all pH. Aggregation accelerated at pH 4 due to the early unfolding of the serine protease N-terminal domain (SP-N), whereas at pH 5-8, the fraction unfolded at 45 °C ( f45) was <1%, resulting in a baseline rate of aggregation from the native ensemble. We used a Design of Experiments (DoE) approach to evaluate how formulation excipients impact and control the thermal unfolding profile for tPA and found that the relative stability of each of the tPA domains was dependent on the formulation. Therefore, the optimization of formulations for complex multidomain proteins such as tPA may need to be multiobjective, with careful selection of the desired attributes that improve stability. As aggregation rates (ln v) correlated well to Tm ( R2 = 0.77) and Δ Svh ( R2 = 0.71) but not Tagg ( R2 = 0.01), we analyzed how formulation excipients and pH would be able to optimize Tm and Δ Svh. Formulation excipient behaviors were found to group according to their combined impact on Tm and Δ Svh. The effects of each excipient were often selectively stabilizing or destabilizing to specific tPA domains and changed the stability of particular domains relative to the others. The types of mechanism by which this could occur might involve specific interactions with the protein surface, or otherwise effects that are mediated via the solvent as a result of the different surface hydrophobicities and polarities of each domain.
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Affiliation(s)
- Mathew J Robinson
- Department of Biochemical Engineering , University College London , Gower Street , London WC1E 6BT , U.K
| | - Paul Matejtschuk
- National Institute for Biological Standards and Control , South Mimms, Potters Bar , Hertfordshire EN6 3QG , U.K
| | - Colin Longstaff
- National Institute for Biological Standards and Control , South Mimms, Potters Bar , Hertfordshire EN6 3QG , U.K
| | - Paul A Dalby
- Department of Biochemical Engineering , University College London , Gower Street , London WC1E 6BT , U.K
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12
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Ferreira GM, Calero-Rubio C, Sathish HA, Remmele RL, Roberts CJ. Electrostatically Mediated Protein-Protein Interactions for Monoclonal Antibodies: A Combined Experimental and Coarse-Grained Molecular Modeling Approach. J Pharm Sci 2019; 108:120-132. [DOI: 10.1016/j.xphs.2018.11.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 10/27/2018] [Accepted: 11/01/2018] [Indexed: 01/05/2023]
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13
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Steric Repulsion Forces Contributed by PEGylation of Interleukin-1 Receptor Antagonist Reduce Gelation and Aggregation at the Silicone Oil-Water Interface. J Pharm Sci 2018; 108:162-172. [PMID: 30395835 DOI: 10.1016/j.xphs.2018.10.045] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 10/24/2018] [Accepted: 10/24/2018] [Indexed: 01/19/2023]
Abstract
Silicone oil, used as a lubricating coating in pharmaceutical containers, has been implicated as a cause of therapeutic protein aggregation. After adsorbing to silicone oil-water interfaces, proteins may form interfacial gels, which can be transported into solution as insoluble aggregates if the interfaces are perturbed. Mechanical interfacial perturbation of both monomeric recombinant human interleukin-1 receptor antagonist (rhIL-1ra) and PEGylated rhIL-1ra (PEG rhIL-1ra) in siliconized syringes resulted in losses of soluble monomeric protein. However, the loss of rhIL-1ra was twice that for PEG rhIL-1ra; even though in solution, PEG rhIL-1ra had a lower ΔGunf and exhibited a more perturbed tertiary structure at the interface. Net protein-protein interactions in solution for rhIL-1ra were attractive but increased steric repulsion because of PEGylation led to net repulsive interactions for PEG rhIL-1ra. Attractive interactions for rhIL-1ra were associated with increases in intermolecular β-sheet content at the interface, whereas no intermolecular β-sheet structures were observed for adsorbed PEG rhIL-1ra. rhIL-1ra formed interfacial gels that were 5 times stronger than those formed by PEG rhIL-1ra. Thus, the steric repulsion contributed by the PEGylation resulted in decreased interfacial gelation and in the reduction of aggregation, in spite of the destabilizing effects of PEGylation on the protein's conformational stability.
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14
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An Evaluation of the Potential of NMR Spectroscopy and Computational Modelling Methods to Inform Biopharmaceutical Formulations. Pharmaceutics 2018; 10:pharmaceutics10040165. [PMID: 30248922 PMCID: PMC6320905 DOI: 10.3390/pharmaceutics10040165] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 09/11/2018] [Accepted: 09/17/2018] [Indexed: 12/22/2022] Open
Abstract
Protein-based therapeutics are considered to be one of the most important classes of pharmaceuticals on the market. The growing need to prolong stability of high protein concentrations in liquid form has proven to be challenging. Therefore, significant effort is being made to design formulations which can enable the storage of these highly concentrated protein therapies for up to 2 years. Currently, the excipient selection approach involves empirical high-throughput screening, but does not reveal details on aggregation mechanisms or the molecular-level effects of the formulations under storage conditions. Computational modelling approaches have the potential to elucidate such mechanisms, and rapidly screen in silico prior to experimental testing. Nuclear Magnetic Resonance (NMR) spectroscopy can also provide complementary insights into excipient–protein interactions. This review will highlight the underpinning principles of molecular modelling and NMR spectroscopy. It will also discuss the advancements in the applications of computational and NMR approaches in investigating excipient–protein interactions.
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15
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Zhang C, Samad M, Yu H, Chakroun N, Hilton D, Dalby PA. Computational Design To Reduce Conformational Flexibility and Aggregation Rates of an Antibody Fab Fragment. Mol Pharm 2018; 15:3079-3092. [PMID: 29897777 DOI: 10.1021/acs.molpharmaceut.8b00186] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Computationally guided semirational design has significant potential for improving the aggregation kinetics of protein biopharmaceuticals. While improvement in the global conformational stability can stabilize proteins to aggregation under some conditions, previous studies suggest that such an approach is limited, because thermal transition temperatures ( Tm) and the fraction of protein unfolded ( fT) tend to only correlate with aggregation kinetics where the protein is incubated at temperatures approaching the Tm. This is because under these conditions, aggregation from globally unfolded protein becomes dominant. However, under native conditions, the aggregation kinetics are presumed to be dependent on local structural fluctuations or partial unfolding of the native state, which reveal regions of high propensity to form protein-protein interactions that lead to aggregation. In this work, we have targeted the design of stabilizing mutations to regions of the A33 Fab surface structure, which were predicted to be more flexible. This Fab already has high global stability, and global unfolding is not the main cause of aggregation under most conditions. Therefore, the aim was to reduce the conformational flexibility and entropy of the native protein at various locations and thus identify which of those regions has the greatest influence on the aggregation kinetics. Highly dynamic regions of structure were identified through both molecular dynamics simulation and B-factor analysis of related X-ray crystal structures. The most flexible residues were mutated into more stable variants, as predicted by Rosetta, which evaluates the ΔΔ GND for each potential point mutation. Additional destabilizing variants were prepared as controls to evaluate the prediction accuracy and also to assess the general influence of conformational stability on aggregation kinetics. The thermal conformational stability, and aggregation rates of 18 variants at 65 °C, were each examined at pH 4, 200 mM ionic strength, under which conditions the initial wild-type protein was <5% unfolded. Variants with decreased Tm values led to more rapid aggregation due to an increase in the fraction of protein unfolded under the conditions studied. As expected, no significant improvements were observed in the global conformational stability as measured by Tm. However, 6 of the 12 stable variants led to an increase in the cooperativity of unfolding, consistent with lower conformational flexibility and entropy in the native ensemble. Three of these had 5-11% lower aggregation rates, and their structural clustering indicated that the local dynamics of the C-terminus of the heavy chain had a role in influencing the aggregation rate.
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Affiliation(s)
- Cheng Zhang
- Department of Biochemical Engineering , University College London , Gordon Street , London WC1E 7JE , U.K
| | - Maariyah Samad
- Department of Biochemical Engineering , University College London , Gordon Street , London WC1E 7JE , U.K
| | - Haoran Yu
- Department of Biochemical Engineering , University College London , Gordon Street , London WC1E 7JE , U.K
| | - Nesrine Chakroun
- Department of Biochemical Engineering , University College London , Gordon Street , London WC1E 7JE , U.K
| | - David Hilton
- Department of Biochemical Engineering , University College London , Gordon Street , London WC1E 7JE , U.K
| | - Paul A Dalby
- Department of Biochemical Engineering , University College London , Gordon Street , London WC1E 7JE , U.K
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16
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Manning MC, Liu J, Li T, Holcomb RE. Rational Design of Liquid Formulations of Proteins. THERAPEUTIC PROTEINS AND PEPTIDES 2018; 112:1-59. [DOI: 10.1016/bs.apcsb.2018.01.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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17
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Meric G, Robinson AS, Roberts CJ. Driving Forces for Nonnative Protein Aggregation and Approaches to Predict Aggregation-Prone Regions. Annu Rev Chem Biomol Eng 2017; 8:139-159. [DOI: 10.1146/annurev-chembioeng-060816-101404] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Gulsum Meric
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716
| | - Anne S. Robinson
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118
| | - Christopher J. Roberts
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716
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18
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O'Brien C, Blanco M, Costanzo J, Enterline M, Fernandez E, Robinson A, Roberts C. Modulating non-native aggregation and electrostatic protein-protein interactions with computationally designed single-point mutations. Protein Eng Des Sel 2016; 29:231-243. [PMID: 27160179 PMCID: PMC4867096 DOI: 10.1093/protein/gzw010] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 02/29/2016] [Accepted: 03/28/2016] [Indexed: 11/14/2022] Open
Abstract
Non-native protein aggregation is a ubiquitous challenge in the production, storage and administration of protein-based biotherapeutics. This study focuses on altering electrostatic protein-protein interactions as a strategy to modulate aggregation propensity in terms of temperature-dependent aggregation rates, using single-charge variants of human γ-D crystallin. Molecular models were combined to predict amino acid substitutions that would modulate protein-protein interactions with minimal effects on conformational stability. Experimental protein-protein interactions were quantified by the Kirkwood-Buff integrals (G22) from laser scattering, and G22 showed semi-quantitative agreement with model predictions. Experimental initial-rates for aggregation showed that increased (decreased) repulsive interactions led to significantly increased (decreased) aggregation resistance, even based solely on single-point mutations. However, in the case of a particular amino acid (E17), the aggregation mechanism was altered by substitution with R or K, and this greatly mitigated improvements in aggregation resistance. The results illustrate that predictions based on native protein-protein interactions can provide a useful design target for engineering aggregation resistance; however, this approach needs to be balanced with consideration of how mutations can impact aggregation mechanisms.
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Affiliation(s)
- C.J. O'Brien
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA
| | - M.A. Blanco
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA
| | - J.A. Costanzo
- Department of Chemical Engineering, University of Virginia, Charlottesville, VA 22903, USA
| | - M. Enterline
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA
| | - E.J. Fernandez
- Department of Chemical Engineering, University of Virginia, Charlottesville, VA 22903, USA
| | - A.S. Robinson
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, LA 70118, USA
| | - C.J. Roberts
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA
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19
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Seeliger D, Schulz P, Litzenburger T, Spitz J, Hoerer S, Blech M, Enenkel B, Studts JM, Garidel P, Karow AR. Boosting antibody developability through rational sequence optimization. MAbs 2016; 7:505-15. [PMID: 25759214 DOI: 10.1080/19420862.2015.1017695] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The application of monoclonal antibodies as commercial therapeutics poses substantial demands on stability and properties of an antibody. Therapeutic molecules that exhibit favorable properties increase the success rate in development. However, it is not yet fully understood how the protein sequences of an antibody translates into favorable in vitro molecule properties. In this work, computational design strategies based on heuristic sequence analysis were used to systematically modify an antibody that exhibited a tendency to precipitation in vitro. The resulting series of closely related antibodies showed improved stability as assessed by biophysical methods and long-term stability experiments. As a notable observation, expression levels also improved in comparison with the wild-type candidate. The methods employed to optimize the protein sequences, as well as the biophysical data used to determine the effect on stability under conditions commonly used in the formulation of therapeutic proteins, are described. Together, the experimental and computational data led to consistent conclusions regarding the effect of the introduced mutations. Our approach exemplifies how computational methods can be used to guide antibody optimization for increased stability.
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Affiliation(s)
- Daniel Seeliger
- a Division Research Germany; Boehringer Ingelheim Pharma GmbH & Co. KG ; Biberach/Riss , Germany
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20
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Kamal MZ, Kumar V, Satyamurthi K, Das KK, Rao NM. Mutational probing of protein aggregates to design aggregation-resistant proteins. FEBS Open Bio 2016; 6:126-34. [PMID: 27239434 PMCID: PMC4821347 DOI: 10.1002/2211-5463.12003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 11/16/2015] [Accepted: 11/30/2015] [Indexed: 11/24/2022] Open
Abstract
Characterization of amorphous protein aggregates may offer insights into the process of aggregation. Eleven single amino acid mutants of lipase (LipA of Bacillus subtilis) were subjected to temperature-induced aggregation, and the resultant aggregates were characterized for recovery of activity in the presence of guanidinium chloride (GdmCl). Based on activity recovery profiles of the aggregates, the mutants could be broadly assigned into four groups. By including at least one mutation from each group, a mutant was generated that showed an increase of ~ 10 °C in melting temperature (T m) compared to the wild-type and did not aggregate even at 75 °C. This method explores characterization of amorphous protein aggregates in the presence of GdmCl and helps in identifying mutations involved in protein aggregation.
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Affiliation(s)
- Mohamad Zahid Kamal
- Centre for Cellular and Molecular Biology Council of Scientific and Industrial Research Hyderabad India
| | - Virender Kumar
- Centre for Cellular and Molecular Biology Council of Scientific and Industrial Research Hyderabad India
| | - Kundarapu Satyamurthi
- Centre for Cellular and Molecular Biology Council of Scientific and Industrial Research Hyderabad India
| | - Kushal Kumar Das
- Centre for Cellular and Molecular Biology Council of Scientific and Industrial Research Hyderabad India
| | - Nalam Madhusudhana Rao
- Centre for Cellular and Molecular Biology Council of Scientific and Industrial Research Hyderabad India
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21
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Qi X, Sun Y, Xiong S. A single freeze-thawing cycle for highly efficient solubilization of inclusion body proteins and its refolding into bioactive form. Microb Cell Fact 2015; 14:24. [PMID: 25879903 PMCID: PMC4343044 DOI: 10.1186/s12934-015-0208-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 02/13/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mild solubilization of inclusion bodies has attracted attention in recent days, with an objective to preserve the existing native-like secondary structure of proteins, reduce protein aggregation during refolding and recovering high amount of bioactive proteins from inclusion bodies. RESULTS Here we presented an efficient method for mild solubilization of inclusion bodies by using a freeze-thawing process in the presence of low concentration of urea. We used two different proteins to demonstrate the advantage of this method over the traditional urea-denatured method: enhanced green fluorescent protein (EGFP) and the catalytic domain of human macrophage metalloelastase (MMP-12_CAT). Firstly, PBS buffer at pH 8 containing different molar concentration of urea (0-8 M) were used to solubilize EGFP and MMP-12-CAT inclusion bodies and the solubility achieved in 2 M urea in PBS buffer by freeze-thawing method was comparable to that of PBS buffer containing 8 M urea by traditional urea-denatured method. Secondly, different solvents were used to solubilize EGFP and MMP-12_CAT from inclusion bodies and the results indicated that a wide range of buffers containing 2 M urea could efficiently solubilize EGFP and MMP-12_CAT inclusion bodies by freeze-thawing method. Thirdly, the effect of pH and freezing temperature on the solubility of EGFP and MMP-12_CAT inclusion bodies were studied, revealing that solubilization of inclusion bodies by freeze-thawing method is pH dependent and the optimal freezing temperature indicated here is -20°C. Forth, the solubilized EGFP and MMP-12_CAT from inclusion bodies were refolded by rapid dilution and dialysis, respectively. The results showed that the refolded efficiency is much higher (more than twice) from freeze-thawing method than the traditional urea-denatured method. The freeze-thawing method containing 2 M urea also effectively solubilized a number of proteins as inclusion bodies in E.coli. CONCLUSIONS Mild solubilization of inclusion body proteins using the freeze-thawing method is simple, highly efficient and generally applicable. The method can be utilized to prepare large quantities of bioactive soluble proteins from inclusion bodies for basic research and industrial purpose.
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Affiliation(s)
- Xingmei Qi
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, Jiangsu, 215123, China.
| | - Yifan Sun
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, Jiangsu, 215123, China.
| | - Sidong Xiong
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, Jiangsu, 215123, China.
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22
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Razinkov VI, Treuheit MJ, Becker GW. Accelerated formulation development of monoclonal antibodies (mAbs) and mAb-based modalities: review of methods and tools. ACTA ACUST UNITED AC 2015; 20:468-83. [PMID: 25576149 DOI: 10.1177/1087057114565593] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
More therapeutic monoclonal antibodies and antibody-based modalities are in development today than ever before, and a faster and more accurate drug discovery process will ensure that the number of candidates coming to the biopharmaceutical pipeline will increase in the future. The process of drug product development and, specifically, formulation development is a critical bottleneck on the way from candidate selection to fully commercialized medicines. This article reviews the latest advances in methods of formulation screening, which allow not only the high-throughput selection of the most suitable formulation but also the prediction of stability properties under manufacturing and long-term storage conditions. We describe how the combination of automation technologies and high-throughput assays creates the opportunity to streamline the formulation development process starting from early preformulation screening through to commercial formulation development. The application of quality by design (QbD) concepts and modern statistical tools are also shown here to be very effective in accelerated formulation development of both typical antibodies and complex modalities derived from them.
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23
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Roberts CJ, Blanco MA. Role of anisotropic interactions for proteins and patchy nanoparticles. J Phys Chem B 2014; 118:12599-611. [PMID: 25302767 PMCID: PMC4226310 DOI: 10.1021/jp507886r] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
Protein–protein
interactions are inherently anisotropic
to some degree, with orientation-dependent interactions between repulsive
and attractive or complementary regions or “patches”
on adjacent proteins. In some cases it has been suggested that such
patch–patch interactions dominate the thermodynamics of dilute
protein solutions, as captured by the osmotic second virial coefficient
(B22), but delineating when this will
or will not be the case remains an open question. A series of simplified
but exactly solvable models are first used to illustrate that a delicate
balance exists between the strength of attractive patch–patch
interactions and the patch size, and that repulsive patch–patch
interactions contribute significantly to B22 for only those conditions where the repulsions are long-ranged.
Finally, B22 is reformulated, without
approximations, in terms of the density of states for a given interaction
energy and particle–particle distance. Doing so illustrates
the inherent balance of entropic and energetic contributions to B22. It highlights that simply having strong
patch–patch interactions will only cause anisotropic interactions
to dominate B22 solution properties if
the unavoidable entropic penalties are overcome, which cannot occur
if patches are too small. The results also indicate that the temperature
dependence of B22 may be a simple experimental
means to assess whether a small number of strongly attractive configurations
dominate the dilute solution behavior.
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Affiliation(s)
- Christopher J Roberts
- Department of Chemical and Biomolecular Engineering, and Center for Molecular and Engineering Thermodynamics, University of Delaware , Newark, Delaware 19716, United States
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