1
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Bárcenas O, Kuriata A, Zalewski M, Iglesias V, Pintado-Grima C, Firlik G, Burdukiewicz M, Kmiecik S, Ventura S. Aggrescan4D: structure-informed analysis of pH-dependent protein aggregation. Nucleic Acids Res 2024; 52:W170-W175. [PMID: 38738618 PMCID: PMC11223845 DOI: 10.1093/nar/gkae382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/11/2024] [Accepted: 04/29/2024] [Indexed: 05/14/2024] Open
Abstract
Protein aggregation is behind the genesis of incurable diseases and imposes constraints on drug discovery and the industrial production and formulation of proteins. Over the years, we have been advancing the Aggresscan3D (A3D) method, aiming to deepen our comprehension of protein aggregation and assist the engineering of protein solubility. Since its inception, A3D has become one of the most popular structure-based aggregation predictors because of its performance, modular functionalities, RESTful service for extensive screenings, and intuitive user interface. Building on this foundation, we introduce Aggrescan4D (A4D), significantly extending A3D's functionality. A4D is aimed at predicting the pH-dependent aggregation of protein structures, and features an evolutionary-informed automatic mutation protocol to engineer protein solubility without compromising structure and stability. It also integrates precalculated results for the nearly 500,000 jobs in the A3D Model Organisms Database and structure retrieval from the AlphaFold database. Globally, A4D constitutes a comprehensive tool for understanding, predicting, and designing solutions for specific protein aggregation challenges. The A4D web server and extensive documentation are available at https://biocomp.chem.uw.edu.pl/a4d/. This website is free and open to all users without a login requirement.
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Affiliation(s)
- Oriol Bárcenas
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Aleksander Kuriata
- Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Mateusz Zalewski
- Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Valentín Iglesias
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
- Clinical Research Centre, Medical University of Białystok, Kilińskiego 1, 15-369 Białystok, Poland
| | - Carlos Pintado-Grima
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Grzegorz Firlik
- Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Michał Burdukiewicz
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
- Clinical Research Centre, Medical University of Białystok, Kilińskiego 1, 15-369 Białystok, Poland
| | - Sebastian Kmiecik
- Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
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2
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Ali M, Greenig M, Oeller M, Atkinson M, Xu X, Sormanni P. Automated optimization of the solubility of a hyper-stable α-amylase. Open Biol 2024; 14:240014. [PMID: 38745462 DOI: 10.1098/rsob.240014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 03/27/2024] [Indexed: 05/16/2024] Open
Abstract
Most successes in computational protein engineering to date have focused on enhancing one biophysical trait, while multi-trait optimization remains a challenge. Different biophysical properties are often conflicting, as mutations that improve one tend to worsen the others. In this study, we explored the potential of an automated computational design strategy, called CamSol Combination, to optimize solubility and stability of enzymes without affecting their activity. Specifically, we focus on Bacillus licheniformis α-amylase (BLA), a hyper-stable enzyme that finds diverse application in industry and biotechnology. We validate the computational predictions by producing 10 BLA variants, including the wild-type (WT) and three designed models harbouring between 6 and 8 mutations each. Our results show that all three models have substantially improved relative solubility over the WT, unaffected catalytic rate and retained hyper-stability, supporting the algorithm's capacity to optimize enzymes. High stability and solubility embody enzymes with superior resilience to chemical and physical stresses, enhance manufacturability and allow for high-concentration formulations characterized by extended shelf lives. This ability to readily optimize solubility and stability of enzymes will enable the rapid and reliable generation of highly robust and versatile reagents, poised to contribute to advancements in diverse scientific and industrial domains.
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Affiliation(s)
- Montader Ali
- Yusuf Hamied Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, UK
| | - Matthew Greenig
- Yusuf Hamied Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, UK
| | - Marc Oeller
- Yusuf Hamied Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, UK
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry , Martinsried 82152, Germany
| | - Misha Atkinson
- Yusuf Hamied Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, UK
| | - Xing Xu
- Yusuf Hamied Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, UK
| | - Pietro Sormanni
- Yusuf Hamied Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, UK
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3
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Lindberg M, Axell E, Sparr E, Linse S. A label-free high-throughput protein solubility assay and its application to Aβ40. Biophys Chem 2024; 307:107165. [PMID: 38309218 DOI: 10.1016/j.bpc.2023.107165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/18/2023] [Accepted: 12/25/2023] [Indexed: 02/05/2024]
Abstract
A major hallmark of Alzheimer's disease is the accumulation of aggregated amyloid β peptide (Aβ) in the brain. Here we develop a solubility assay for proteins and measure the solubility of Aβ40. In brief, the method utilizes 96-well filter plates to separate monomeric Aβ from aggregated Aβ, and the small species are quantified with the amine reactive dye o-phthalaldehyde (OPA). This procedure ensures that solubility is measured for unlabeled species, and makes the assay high-throughput and inexpensive. We demonstrate that the filter plates successfully separate fibrils from monomer, with negligible monomer adsorption, and that OPA can quantify Aβ peptides in a concentration range from 40 nM to 20 μM. We also show that adding a methionine residue to the N-terminus of Aβ1-40 decreases the solubility by <3-fold. The method will facilitate further solubility studies, and contribute to the understanding of the thermodynamics of amyloid fibril formation.
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Affiliation(s)
- Max Lindberg
- Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | - Emil Axell
- Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | - Emma Sparr
- Division of Physical Chemistry, Department of Chemistry, Lund University, Lund, Sweden
| | - Sara Linse
- Biochemistry and Structural Biology, Lund University, Lund, Sweden.
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4
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Oeller M, Kang RJD, Bolt HL, Gomes Dos Santos AL, Weinmann AL, Nikitidis A, Zlatoidsky P, Su W, Czechtizky W, De Maria L, Sormanni P, Vendruscolo M. Sequence-based prediction of the intrinsic solubility of peptides containing non-natural amino acids. Nat Commun 2023; 14:7475. [PMID: 37978172 PMCID: PMC10656490 DOI: 10.1038/s41467-023-42940-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 10/26/2023] [Indexed: 11/19/2023] Open
Abstract
Non-natural amino acids are increasingly used as building blocks in the development of peptide-based drugs as they expand the available chemical space to tailor function, half-life and other key properties. However, while the chemical space of modified amino acids (mAAs) such as residues containing post-translational modifications (PTMs) is potentially vast, experimental methods for measuring the developability properties of mAA-containing peptides are expensive and time consuming. To facilitate developability programs through computational methods, we present CamSol-PTM, a method that enables the fast and reliable sequence-based prediction of the intrinsic solubility of mAA-containing peptides in aqueous solution at room temperature. From a computational screening of 50,000 mAA-containing variants of three peptides, we selected five different small-size mAAs for a total number of 37 peptide variants for experimental validation. We demonstrate the accuracy of the predictions by comparing the calculated and experimental solubility values. Our results indicate that the computational screening of mAA-containing peptides can extend by over four orders of magnitude the ability to explore the solubility chemical space of peptides and confirm that our method can accurately assess the solubility of peptides containing mAAs. This method is available as a web server at https://www-cohsoftware.ch.cam.ac.uk/index.php/camsolptm .
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Affiliation(s)
- Marc Oeller
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ryan J D Kang
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Hannah L Bolt
- Hit Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Ana L Gomes Dos Santos
- Advanced Drug Delivery, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Annika Langborg Weinmann
- Early Chemical Development, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Antonios Nikitidis
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Pavol Zlatoidsky
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Wu Su
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Werngard Czechtizky
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Leonardo De Maria
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Pietro Sormanni
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
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5
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Rosace A, Bennett A, Oeller M, Mortensen MM, Sakhnini L, Lorenzen N, Poulsen C, Sormanni P. Automated optimisation of solubility and conformational stability of antibodies and proteins. Nat Commun 2023; 14:1937. [PMID: 37024501 PMCID: PMC10079162 DOI: 10.1038/s41467-023-37668-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 03/24/2023] [Indexed: 04/08/2023] Open
Abstract
Biologics, such as antibodies and enzymes, are crucial in research, biotechnology, diagnostics, and therapeutics. Often, biologics with suitable functionality are discovered, but their development is impeded by developability issues. Stability and solubility are key biophysical traits underpinning developability potential, as they determine aggregation, correlate with production yield and poly-specificity, and are essential to access parenteral and oral delivery. While advances for the optimisation of individual traits have been made, the co-optimization of multiple traits remains highly problematic and time-consuming, as mutations that improve one property often negatively impact others. In this work, we introduce a fully automated computational strategy for the simultaneous optimisation of conformational stability and solubility, which we experimentally validate on six antibodies, including two approved therapeutics. Our results on 42 designs demonstrate that the computational procedure is highly effective at improving developability potential, while not affecting antigen-binding. We make the method available as a webserver at www-cohsoftware.ch.cam.ac.uk.
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Affiliation(s)
- Angelo Rosace
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield road, CB2 1EW, Cambridge, UK
- Master in Bioinformatics for Health Sciences, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
- Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Anja Bennett
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield road, CB2 1EW, Cambridge, UK
- Department of Mammalian Expression, Global Research Technologies, Novo Nordisk A/S, Novo Nordisk Park 1, 2760, Måløv, Denmark
- BRIC, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Marc Oeller
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield road, CB2 1EW, Cambridge, UK
| | - Mie M Mortensen
- Department of Purification Technologies, Global Research Technologies, Novo Nordisk A/S, Novo Nordisk Park 1, 2760, Måløv, Denmark
- Faculty of Engineering and Science, Department of Biotechnology, Chemistry and Environmental Engineering, University of Aalborg, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark
| | - Laila Sakhnini
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield road, CB2 1EW, Cambridge, UK
- Department of Biophysics and Injectable Formulation 2, Global Research Technologies, Novo Nordisk A/S, Måløv, 2760, Denmark
| | - Nikolai Lorenzen
- Department of Biophysics and Injectable Formulation 2, Global Research Technologies, Novo Nordisk A/S, Måløv, 2760, Denmark
| | - Christian Poulsen
- Department of Mammalian Expression, Global Research Technologies, Novo Nordisk A/S, Novo Nordisk Park 1, 2760, Måløv, Denmark
| | - Pietro Sormanni
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield road, CB2 1EW, Cambridge, UK.
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6
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Oeller M, Kang R, Bell R, Ausserwöger H, Sormanni P, Vendruscolo M. Sequence-based prediction of pH-dependent protein solubility using CamSol. Brief Bioinform 2023; 24:7017367. [PMID: 36719110 PMCID: PMC10025429 DOI: 10.1093/bib/bbad004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 12/10/2022] [Accepted: 10/16/2022] [Indexed: 02/01/2023] Open
Abstract
Solubility is a property of central importance for the use of proteins in research in molecular and cell biology and in applications in biotechnology and medicine. Since experimental methods for measuring protein solubility are material intensive and time consuming, computational methods have recently emerged to enable the rapid and inexpensive screening of solubility for large libraries of proteins, as it is routinely required in development pipelines. Here, we describe the development of one such method to include in the predictions the effect of the pH on solubility. We illustrate the resulting pH-dependent predictions on a variety of antibodies and other proteins to demonstrate that these predictions achieve an accuracy comparable with that of experimental methods. We make this method publicly available at https://www-cohsoftware.ch.cam.ac.uk/index.php/camsolph, as the version 3.0 of CamSol.
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Affiliation(s)
- Marc Oeller
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Ryan Kang
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Rosie Bell
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Hannes Ausserwöger
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Pietro Sormanni
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
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7
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Erkamp NA, Oeller M, Sneideris T, Ausserwoger H, Levin A, Welsh TJ, Qi R, Qian D, Lorenzen N, Zhu H, Sormanni P, Vendruscolo M, Knowles TPJ. Multidimensional Protein Solubility Optimization with an Ultrahigh-Throughput Microfluidic Platform. Anal Chem 2023; 95:5362-5368. [PMID: 36930285 PMCID: PMC10061369 DOI: 10.1021/acs.analchem.2c05495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Protein-based biologics are highly suitable for drug development as they exhibit low toxicity and high specificity for their targets. However, for therapeutic applications, biologics must often be formulated to elevated concentrations, making insufficient solubility a critical bottleneck in the drug development pipeline. Here, we report an ultrahigh-throughput microfluidic platform for protein solubility screening. In comparison with previous methods, this microfluidic platform can make, incubate, and measure samples in a few minutes, uses just 20 μg of protein (>10-fold improvement), and yields 10,000 data points (1000-fold improvement). This allows quantitative comparison of formulation excipients, such as sodium chloride, polysorbate, histidine, arginine, and sucrose. Additionally, we can measure how solubility is affected by the combinatorial effect of multiple additives, find a suitable pH for the formulation, and measure the impact of mutations on solubility, thus enabling the screening of large libraries. By reducing material and time costs, this approach makes detailed multidimensional solubility optimization experiments possible, streamlining drug development and increasing our understanding of biotherapeutic solubility and the effects of excipients.
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Affiliation(s)
- Nadia A Erkamp
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Marc Oeller
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Tomas Sneideris
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Hannes Ausserwoger
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Aviad Levin
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Timothy J Welsh
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Runzhang Qi
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Daoyuan Qian
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Nikolai Lorenzen
- Biophysics and Injectable Formulation, Global Research Technology, Novo Nordisk A/S, 2760 Maaloev, Denmark
| | - Hongjia Zhu
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Pietro Sormanni
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Michele Vendruscolo
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Tuomas P J Knowles
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
- Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Ave, Cambridge CB3 0HE, U.K
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Condado-Morales I, Sokolova V, Wahlund PO, Heding KE, Auclair S, Kingsbury JS, Arosio P, Lorenzen N. AF4 and PEG Precipitation as Predictive Assays for Antibody Self-Association. Mol Pharm 2023; 20:1323-1330. [PMID: 36668814 DOI: 10.1021/acs.molpharmaceut.2c00946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Monoclonal antibodies (mAbs) are often formulated as high-protein-concentration solutions, which in some cases can exhibit physical stability issues such as high viscosity and opalescence. To ensure that mAb-based drugs can meet their manufacturing, stability, and delivery requirements, it is advantageous to screen for and select mAbs during discovery that are not prone to such behaviors. It has been recently shown that both these macroscopic properties can be predicted to a certain extent from the diffusion interaction parameter (kD), which is a measure of self-association under dilute conditions.1 However, kD can be challenging to measure at the early stage of discovery, where a relatively large amount of a high-purity material, which is required by traditional methods, is often not available. In this study, we demonstrate asymmetric field-flow fractionation (AF4) as a tool to measure self-association and therefore identify antibodies with problematic issues at high concentrations. The principle lies on the ability to concentrate the sample close to the membrane during the injection mode, which can reach formulation-relevant concentrations (>100 mg/mL).2 By analyzing a well-characterized library of commercial antibodies, we show that the measured retention time of the antibodies allows us to pinpoint molecules that exhibit issues at high concentrations. Remarkably, our AF4 assay requires very little (30 μg) sample under dilute conditions and does not need extensive sample purification. Furthermore, we show that a polyethylene glycol (PEG) precipitation assay provides results consistent with AF4 and moreover can further differentiate molecules with issues of opalescence or high viscosity. Overall, our results delineate a two-step strategy for the identification of problematic variants at high concentrations, with AF4 for early developability screening, followed by a PEG assay to validate the problematic molecules and further discriminate between opalescence or high-viscosity issues. This two-step antibody selection strategy enables us to select antibodies early in the discovery process, which are compatible with high-concentration formulations.
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Affiliation(s)
- Itzel Condado-Morales
- Global Research Technology, Novo Nordisk A/S, Maaloev 2760, Denmark.,Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zürich, Zürich 8093, Switzerland
| | - Viktoria Sokolova
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zürich, Zürich 8093, Switzerland
| | - Per-Olof Wahlund
- Global Research Technology, Novo Nordisk A/S, Maaloev 2760, Denmark
| | | | - Sarah Auclair
- Global CMC Development, Sanofi, Framingham, Massachusetts 02210, United States
| | | | - Paolo Arosio
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zürich, Zürich 8093, Switzerland
| | - Nikolai Lorenzen
- Global Research Technology, Novo Nordisk A/S, Maaloev 2760, Denmark
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9
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Molecular Determinants of Fibrillation in a Viral Amyloidogenic Domain from Combined Biochemical and Biophysical Studies. Int J Mol Sci 2022; 24:ijms24010399. [PMID: 36613842 PMCID: PMC9820236 DOI: 10.3390/ijms24010399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/16/2022] [Accepted: 12/19/2022] [Indexed: 12/28/2022] Open
Abstract
The Nipah and Hendra viruses (NiV and HeV) are biosafety level 4 human pathogens classified within the Henipavirus genus of the Paramyxoviridae family. In both NiV and HeV, the gene encoding the Phosphoprotein (P protein), an essential polymerase cofactor, also encodes the V and W proteins. These three proteins, which share an intrinsically disordered N-terminal domain (NTD) and have unique C-terminal domains (CTD), are all known to counteract the host innate immune response, with V and W acting by either counteracting or inhibiting Interferon (IFN) signaling. Recently, the ability of a short region within the shared NTD (i.e., PNT3) to form amyloid-like structures was reported. Here, we evaluated the relevance of each of three contiguous tyrosine residues located in a previously identified amyloidogenic motif (EYYY) within HeV PNT3 to the fibrillation process. Our results indicate that removal of a single tyrosine in this motif significantly decreases the ability to form fibrils independently of position, mainly affecting the elongation phase. In addition, we show that the C-terminal half of PNT3 has an inhibitory effect on fibril formation that may act as a molecular shield and could thus be a key domain in the regulation of PNT3 fibrillation. Finally, the kinetics of fibril formation for the two PNT3 variants with the highest and the lowest fibrillation propensity were studied by Taylor Dispersion Analysis (TDA). The results herein presented shed light onto the molecular mechanisms involved in fibril formation.
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10
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Erkamp NA, Qi R, Welsh TJ, Knowles TPJ. Microfluidics for multiscale studies of biomolecular condensates. LAB ON A CHIP 2022; 23:9-24. [PMID: 36269080 PMCID: PMC9764808 DOI: 10.1039/d2lc00622g] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 09/04/2022] [Indexed: 05/12/2023]
Abstract
Membraneless organelles formed through condensation of biomolecules in living cells have become the focus of sustained efforts to elucidate their mechanisms of formation and function. These condensates perform a range of vital functions in cells and are closely connected to key processes in functional and aberrant biology. Since these systems occupy a size scale intermediate between single proteins and conventional protein complexes on the one hand, and cellular length scales on the other hand, they have proved challenging to probe using conventional approaches from either protein science or cell biology. Additionally, condensate can form, solidify and perform functions on various time-scales. From a physical point of view, biomolecular condensates are colloidal soft matter systems, and microfluidic approaches, which originated in soft condensed matter research, have successfully been used to study biomolecular condensates. This review explores how microfluidics have aided condensate research into the thermodynamics, kinetics and other properties of condensates, by offering high-throughput and novel experimental setups.
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Affiliation(s)
- Nadia A Erkamp
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Runzhang Qi
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Timothy J Welsh
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Tuomas P J Knowles
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
- Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Ave, Cambridge, CB3 0HE, UK
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11
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von Mikecz A. Exposome, Molecular Pathways and One Health: The Invertebrate Caenorhabditis elegans. Int J Mol Sci 2022; 23:ijms23169084. [PMID: 36012346 PMCID: PMC9409025 DOI: 10.3390/ijms23169084] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 12/04/2022] Open
Abstract
Due to its preferred habitats in the environment, the free-living nematode Caenorhabditis elegans has become a realistic target organism for pollutants, including manufactured nanoparticles. In the laboratory, the invertebrate animal model represents a cost-effective tool to investigate the molecular mechanisms of the biological response to nanomaterials. With an estimated number of 22,000 coding genes and short life span of 2–3 weeks, the small worm is a giant when it comes to characterization of molecular pathways, long-term low dose pollutant effects and vulnerable age-groups. Here, we review (i) flows of manufactured nanomaterials and exposition of C. elegans in the environment, (ii) the track record of C. elegans in biomedical research, and (iii) its potential to contribute to the investigation of the exposome and bridge nanotoxicology between higher organisms, including humans. The role of C. elegans in the one health concept is taken one step further by proposing methods to sample wild nematodes and their molecular characterization by single worm proteomics.
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Affiliation(s)
- Anna von Mikecz
- IUF-Leibniz Research Institute for Environmental Medicine GmbH, Auf'm Hennekamp 50, 40225 Duesseldorf, Germany
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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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Pons Royo MDC, Beulay JL, Valery E, Jungbauer A, Satzer P. Design of millidevices to expedite apparent solubility measurements. REACT CHEM ENG 2022. [DOI: 10.1039/d2re00022a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A fast, automated and accurate millidevice for determination of the apparent solubility of proteins and impurities and different industrially relevant precipitating agents.
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Affiliation(s)
- Maria del Carme Pons Royo
- Department of Innovation, Novasep, 81 Boulevard de la Moselle, 54340 Pompey, France
- Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, 1190 Vienna, Austria
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 18, 1190 Vienna, Austria
| | - Jean-Luc Beulay
- Department of Innovation, Novasep, 81 Boulevard de la Moselle, 54340 Pompey, France
| | - Eric Valery
- Department of Innovation, Novasep, 81 Boulevard de la Moselle, 54340 Pompey, France
| | - Alois Jungbauer
- Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, 1190 Vienna, Austria
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 18, 1190 Vienna, Austria
| | - Peter Satzer
- Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, 1190 Vienna, Austria
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