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Wang Y, Williams HD, Dikicioglu D, Dalby PA. Predictive Model Building for Aggregation Kinetics Based on Molecular Dynamics Simulations of an Antibody Fragment. Mol Pharm 2024. [PMID: 39348223 DOI: 10.1021/acs.molpharmaceut.4c00859] [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: 10/02/2024]
Abstract
Computational methods including machine learning and molecular dynamics simulations have strong potential to characterize, understand, and ultimately predict the properties of proteins relevant to their stability and function as therapeutics. Such methods would streamline the development pathway by minimizing the current experimental testing required for many protein variants and formulations. The molecular understanding of thermostability and aggregation propensity has advanced significantly along with predictive algorithms based on the sequence-level or structural-level information on a protein. However, these approaches focus largely on a comparison of protein sequence variations to correlate the properties of proteins to their stability, solubility, and aggregation propensity. For therapeutic protein development, it is of equal importance to take into account the impact of the formulation conditions to elucidate and predict the stability of the antibody drugs. At the macroscopic level, changing temperature, pH, ionic strength, and the addition of excipients can significantly alter the kinetics of protein aggregation. The mechanisms controlling aggregation kinetics have been traced back to a combination of molecular features, including conformational stability, partial unfolding to aggregation-prone states, and the colloidal stability governed by surface charges and hydrophobicity. However, very little has been done to evaluate these features in the context of protein dynamics in different formulations. In this work, we have combined a range of molecular features calculated from the Fab A33 protein sequence and molecular dynamics simulations. Using the power of advanced, yet interpretable, statistical tools, it has been possible to uncover greater insights into the mechanisms behind protein stability, validating previous findings, and also develop models that can predict the aggregation kinetics within a range of 49 different solution conditions.
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Affiliation(s)
- Yuhan Wang
- Department of Biochemical Engineering, University College London, London WC1E 6BT, U.K
| | - Hywel D Williams
- Biopharmaceutical Product Development, CSL Ltd., 45 Poplar Road, Parkville 3052, Australia
| | - Duygu Dikicioglu
- Department of Biochemical Engineering, University College London, London WC1E 6BT, U.K
| | - Paul A Dalby
- Department of Biochemical Engineering, University College London, London WC1E 6BT, U.K
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Carvalho SF, Custódio MH, Pereiro AB, Araújo JMM. Towards Enhanced Tunability of Aqueous Biphasic Systems: Furthering the Grasp of Fluorinated Ionic Liquids in the Purification of Proteins. Int J Mol Sci 2024; 25:5766. [PMID: 38891953 PMCID: PMC11172314 DOI: 10.3390/ijms25115766] [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: 04/12/2024] [Revised: 05/11/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024] Open
Abstract
This work unfolds functionalized ABSs composed of FILs ([C2C1Im][C4F9SO3] and [N1112(OH)][C4F9SO3]), mere fluoro-containing ILs ([C2C1Im][CF3SO3] and [C4C1Im][CF3SO3]), known globular protein stabilizers (sucrose and [N1112(OH)][C4F9SO3]), low-molecular-weight carbohydrate (glucose), and even high-charge density salt (K3PO4). The ternary phase diagrams were determined, stressing that FILs highly increased the ability for ABS formation. The functionalized ABSs (FILs vs. mere fluoro-containing ILs) were used to extract lysozyme (Lys). The ABSs' biphasic regions were screened in terms of protein biocompatibility, analyzing the impact of ABS phase-forming components in Lys by UV-VIS spectrophotometry, CD spectroscopy, fluorescence spectroscopy, DSC, and enzyme assay. Lys partition behavior was characterized in terms of extraction efficiency (% EE). The structure, stability, and function of Lys were maintained or improved throughout the extraction step, as evaluated by CD spectroscopy, DSC, enzyme assay, and SDS-PAGE. Overall, FIL-based ABSs are more versatile and amenable to being tuned by the adequate choice of the phase-forming components and selecting the enriched phase. Binding studies between Lys and ABS phase-forming components were attained by MST, demonstrating the strong interaction between Lys and FILs aggregates. Two of the FIL-based ABSs (30 %wt [C2C1Im][C4F9SO3] + 2 %wt K3PO4 and 30 %wt [C2C1Im][C4F9SO3] + 25 %wt sucrose) allowed the simultaneous purification of Lys and BSA in a single ABS extraction step with high yield (extraction efficiency up to 100%) for both proteins. The purity of both recovered proteins was validated by SDS-PAGE analysis. Even with a high-charge density salt, the FIL-based ABSs developed in this work seem more amenable to be tuned. Lys and BSA were purified through selective partition to opposite phases in a single FIL-based ABS extraction step. FIL-based ABSs are proposed as an improved extraction step for proteins, based on their biocompatibility, customizable properties, and selectivity.
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Affiliation(s)
| | | | | | - João M. M. Araújo
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal; (S.F.C.); (M.H.C.); (A.B.P.)
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3
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Carvalho SF, Pereiro AB, Araújo JMM. Simultaneous Purification of Human Interferon Alpha-2b and Serum Albumin Using Bioprivileged Fluorinated Ionic Liquid-Based Aqueous Biphasic Systems. Int J Mol Sci 2024; 25:2751. [PMID: 38473998 DOI: 10.3390/ijms25052751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 02/14/2024] [Accepted: 02/19/2024] [Indexed: 03/14/2024] Open
Abstract
Interferon alpha-2b (IFN-α2b) is an essential cytokine widely used in the treatment of chronic hepatitis C and hairy cell leukemia, and serum albumin is the most abundant plasma protein with numerous physiological functions. Effective single-step aqueous biphasic system (ABS) extraction for the simultaneous purification of IFN-α2b and BSA (serum albumin protein) was developed in this work. Effects of the ionic liquid (IL)-based ABS functionalization, fluorinated ILs (FILs; [C2C1Im][C4F9SO3] and [N1112(OH)][C4F9SO3]) vs. mere fluoro-containing IL ([C4C1Im][CF3SO3]), in combination with sucrose or [N1112(OH)][H2PO4] (well-known globular protein stabilizers), or high-charge-density salt K3PO4 were investigated. The effects of phase pH, phase water content (%wt), phase composition (%wt), and phase volume ratio were investigated. The phase pH was found to have a significant effect on IFN-α2b and BSA partition. Experimental results show that simultaneous single-step purification was achieved with a high yield (extraction efficiency up to 100%) for both proteins and a purification factor of IFN-α2b high in the enriched IFN-α2b phase (up to 23.22) and low in the BSA-enriched phase (down to 0.00). SDS-PAGE analysis confirmed the purity of both recovered proteins. The stability and structure of IFN-α2b and BSA were preserved or even improved (FIL-rich phase) during the purification step, as evaluated by CD spectroscopy and DSC. Binding studies of IFN-α2b and BSA with the ABS phase-forming components were assessed by MST, showing the strong interaction between FILs aggregates and both proteins. In view of their biocompatibility, customizable properties, and selectivity, FIL-based ABSs are suggested as an improved purification step that could facilitate the development of biologics.
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Affiliation(s)
- Sara F Carvalho
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal
| | - Ana B Pereiro
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal
| | - João M M Araújo
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal
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Tam HH, Zhu D, Ho SSK, Vong HW, Wong VKW, Mok SWF, Wong IN. Potential enhancement of post-stroke angiogenic response by targeting the oligomeric aggregation of p53 protein. Front Cell Neurosci 2023; 17:1193362. [PMID: 37534043 PMCID: PMC10393283 DOI: 10.3389/fncel.2023.1193362] [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: 03/24/2023] [Accepted: 06/30/2023] [Indexed: 08/04/2023] Open
Abstract
Tumor suppressor gene p53 and its aggregate have been found to be involved in many angiogenesis-related pathways. We explored the possible p53 aggregation formation mechanisms commonly occur after ischemic stroke, such as hypoxia and the presence of reactive oxygen species (ROS). The angiogenic pathways involving p53 mainly occur in nucleus or cytoplasm, with one exception that occurs in mitochondria. Considering the high mitochondrial density in brain and endothelial cells, we proposed that the cyclophilin D (CypD)-dependent vascular endothelial cell (VECs) necrosis pathway occurring in the mitochondria is one of the major factors that affects angiogenesis. Hence, targeting p53 aggregation, a key intermediate in the pathway, could be an alternative therapeutic target for post-stroke management.
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Affiliation(s)
- Hoi Hei Tam
- Faculty of Medicine, Macau University of Science and Technology, Macau, Macau SAR, China
| | - Dongxing Zhu
- Guangdong Key Laboratory of Vascular Diseases, State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangzhou Institute of Cardiovascular Disease, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Samuel Sze King Ho
- Faculty of Medicine, Macau University of Science and Technology, Macau, Macau SAR, China
| | - Heng Wai Vong
- Faculty of Medicine, Macau University of Science and Technology, Macau, Macau SAR, China
| | - Vincent Kam Wai Wong
- Dr. Neher’s Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, Macau SAR, China
| | - Simon Wing-Fai Mok
- Faculty of Medicine, Macau University of Science and Technology, Macau, Macau SAR, China
- Dr. Neher’s Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, Macau SAR, China
| | - Io Nam Wong
- Faculty of Medicine, Macau University of Science and Technology, Macau, Macau SAR, China
- Dr. Neher’s Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, Macau SAR, China
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Ferreira ML, Vieira NSM, Oliveira ALS, Araújo JMM, Pereiro AB. Disclosing the Potential of Fluorinated Ionic Liquids as Interferon-Alpha 2b Delivery Systems. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:1851. [PMID: 35683707 PMCID: PMC9181987 DOI: 10.3390/nano12111851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 05/23/2022] [Accepted: 05/27/2022] [Indexed: 11/16/2022]
Abstract
Interferon-alpha 2b (IFN-α 2b) is a therapeutic protein used for the treatment of cancer, viral infections, and auto-immune diseases. Its application is hindered by a low bioavailability and instability in the bloodstream, and the search for new strategies for a target delivery and stabilization of IFN-α 2b to improve its therapeutic efficacy is crucial. Fluorinated ionic liquids (FILs) are promising biomaterials that: (i) can form self-assembled structures; (ii) have complete miscibility in water; and (iii) can be designed to have reduced toxicity. The influence of IFN-α 2b in the aggregation behaviour of FILs and the interactions between them were investigated through conductivity and surface tension measurements, and using electron microscopic and spectroscopy techniques to study FILs feasibility as an interferon-alpha 2b delivery system. The results show that the presence of IFN-α 2b influences the aggregation behaviour of FILs and that strong interaction between the two compounds occurs. The protein might not be fully encapsulated by FILs. However, the FIL can be tailored in the future to carry IFN-α 2b by the formation of a conjugate, which prevents the aggregation of this protein. This work constitutes a first step toward the design and development of FIL-based IFN-α 2b delivery systems.
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Affiliation(s)
| | | | | | - João M. M. Araújo
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal; (M.L.F.); (N.S.M.V.); (A.L.S.O.)
| | - Ana B. Pereiro
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal; (M.L.F.); (N.S.M.V.); (A.L.S.O.)
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Binding of excipients is a poor predictor for aggregation kinetics of biopharmaceutical proteins. Eur J Pharm Biopharm 2020; 151:127-136. [PMID: 32283214 DOI: 10.1016/j.ejpb.2020.04.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 04/03/2020] [Accepted: 04/04/2020] [Indexed: 12/11/2022]
Abstract
One of the major challenges in formulation development of biopharmaceuticals is improving long-term storage stability, which is often achieved by addition of excipients to the final formulation. Finding the optimal excipient for a given protein is usually done using a trial-and-error approach, due to the lack of general understanding of how excipients work for a particular protein. Previously, preferential interactions (binding or exclusion) of excipients with proteins were postulated as a mechanism explaining diversity in the stabilisation effects. Weak preferential binding is however difficult to quantify experimentally, and the question remains whether the formulation process should seek excipients which preferentially bind with proteins, or not. Here, we apply solution NMR spectroscopy to comprehensively evaluate protein-excipient interactions between therapeutically relevant proteins and commonly used excipients. Additionally, we evaluate the effect of excipients on thermal and colloidal protein stability, on aggregation kinetics and protein storage stability at elevated temperatures. We show that there is a weak negative correlation between the strength of protein-excipient interactions and effect on enhancing protein thermal stability. We found that the overall protein-excipient binding per se can be a poor criterion for choosing excipients enhancing formulation stability. Experiments on a diverse set of excipients and test proteins reveal that while excipients affect all of the different aspects of protein stability, the effects are very much protein specific, and care must be taken to avoid apparent generalisations if a smaller dataset is being used.
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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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