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Renawala HK, Chandrababu KB, Smith KJ, D'Addio SM, Topp EM. A Model Study to Assess Fibrillation and Product Stability to Support Peptide Drug Design. Mol Pharm 2024; 21:2223-2237. [PMID: 38552144 DOI: 10.1021/acs.molpharmaceut.3c00996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
The fibrillation of therapeutic peptides can present significant quality concerns and poses challenges for manufacturing and storage. A fundamental understanding of the mechanisms of fibrillation is critical for the rational design of fibrillation-resistant peptide drugs and can accelerate product development by guiding the selection of solution-stable candidates and formulations. The studies reported here investigated the effects of structural modifications on the fibrillation of a 29-residue peptide (PepA) and two sequence modified variants (PepB, PepC). The C-terminus of PepA was amidated, whereas both PepB and PepC retained the carboxylate, and Ser16 in PepA and PepB was substituted with a helix-stabilizing residue, α-aminoisobutyric acid (Aib), in PepC. In thermal denaturation studies by far-UV CD spectroscopy and fibrillation kinetic studies by fluorescence and turbidity measurements, PepA and PepB showed heat-induced conformational changes and were found to form fibrils, whereas PepC did not fibrillate and showed only minor changes in the CD signal. Pulsed hydrogen-deuterium exchange mass spectrometry (HDX-MS) showed a high degree of protection from HD exchange in mature PepA fibrils and its proteolytic fragments, indicating that most of the sequence had been incorporated into the fibril structure and occurred nearly simultaneously throughout the sequence. The effects of the net peptide charge and formulation pH on fibrillation kinetics were investigated. In real-time stability studies of two formulations of PepA at pH's 7.4 and 8.0, analytical methods detected significant changes in the stability of the formulations at different time points during the study, which were not observed during accelerated studies. Additionally, PepA samples were withdrawn from real-time stability and subjected to additional stress (40 °C, continuous shaking) to induce fibrillation; an approach that successfully amplified oligomers or prefibrillar species previously undetected in a thioflavin T assay. Taken together, these studies present an approach to differentiate and characterize fibrillation risk in structurally related peptides under accelerated and real-time conditions, providing a model for rapid, iterative structural design to optimize the stability of therapeutic peptides.
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Affiliation(s)
- Harshil K Renawala
- Department of Industrial and Molecular Pharmaceutics, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Karthik B Chandrababu
- Department of Industrial and Molecular Pharmaceutics, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Katelyn J Smith
- Pharmaceutical Sciences and Clinical Supply, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Suzanne M D'Addio
- Pharmaceutical Sciences and Clinical Supply, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Elizabeth M Topp
- Department of Industrial and Molecular Pharmaceutics, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
- Davidson School of Chemical Engineering, College of Engineering, Purdue University, West Lafayette, Indiana 47907, United States
- National Institute for Bioprocessing Research and Training, Belfield, Blackrock, Co. Dublin A94 X099, Ireland
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2
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Peng F, Liu J, Chen J, Wu W, Zhang Y, Zhao G, Kang Y, Gong D, He L, Wang J, Zhang W, Qiu F. Nanocrystals Slow-Releasing Ropivacaine and Doxorubicin to Synergistically Suppress Tumor Recurrence and Relieve Postoperative Pain. ACS NANO 2023; 17:20135-20152. [PMID: 37805931 DOI: 10.1021/acsnano.3c05831] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Although surgical resection provides a straightforward and effective treatment for most malignant solid tumors, tumor recurrence and acute postoperative pain continue to be two big problems associated with this treatment. To resolve these problems, a nanocrystal composite slow-releasing ropivacaine and doxorubicin was fabricated in this study. Briefly, a self-assembling peptide was used to form nanoparticle complexes with the two drugs, based on which homogeneous nanocrystals were obtained by adjusting the pH. In cultured human melanoma cells, the nanocrystals exhibited improved antitumor activity due to a synergistic effect and enhanced cellular uptake of the two drugs. On the other hand, the nanocrystals could slowly release ropivacaine in vitro and in vivo, generating long-acting analgesia on the rat sciatic nerve block model and incisional pain model. On a nude mouse tumor resection model, the nanocrystals simultaneously suppressed the recurrence of solid tumor and relieved postoperative pain, indicating a potential postoperative treatment for tumor resection patients. This nanocrystal system also suggested a promising and facile strategy for developing multifunctional formulations combining different drugs, which could achieve better therapeutic outcomes in a synergistic and sustained manner.
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Affiliation(s)
- Fei Peng
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu, 610041, China
- Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Center of Translational Medicine of Anesthesiology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jing Liu
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu, 610041, China
- Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Center of Translational Medicine of Anesthesiology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Junjie Chen
- Department of Burn and Plastic Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Weiwei Wu
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu, 610041, China
- Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Center of Translational Medicine of Anesthesiology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yujun Zhang
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu, 610041, China
- Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Center of Translational Medicine of Anesthesiology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Guoyan Zhao
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu, 610041, China
- Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Center of Translational Medicine of Anesthesiology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yi Kang
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu, 610041, China
- Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Center of Translational Medicine of Anesthesiology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Deying Gong
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu, 610041, China
- Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Center of Translational Medicine of Anesthesiology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Liu He
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu, 610041, China
- Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Center of Translational Medicine of Anesthesiology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jing Wang
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu, 610041, China
- Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Center of Translational Medicine of Anesthesiology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Wensheng Zhang
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu, 610041, China
- Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Center of Translational Medicine of Anesthesiology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Feng Qiu
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu, 610041, China
- Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Center of Translational Medicine of Anesthesiology, West China Hospital, Sichuan University, Chengdu, 610041, China
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3
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Crook OM, Gittens N, Chung CW, Deane CM. A Functional Bayesian Model for Hydrogen-Deuterium Exchange Mass Spectrometry. J Proteome Res 2023; 22:2959-2972. [PMID: 37582225 PMCID: PMC10476270 DOI: 10.1021/acs.jproteome.3c00297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Indexed: 08/17/2023]
Abstract
Proteins often undergo structural perturbations upon binding to other proteins or ligands or when they are subjected to environmental changes. Hydrogen-deuterium exchange mass spectrometry (HDX-MS) can be used to explore conformational changes in proteins by examining differences in the rate of deuterium incorporation in different contexts. To determine deuterium incorporation rates, HDX-MS measurements are typically made over a time course. Recently introduced methods show that incorporating the temporal dimension into the statistical analysis improves power and interpretation. However, these approaches have technical assumptions that hinder their flexibility. Here, we propose a more flexible methodology by reframing these methods in a Bayesian framework. Our proposed framework has improved algorithmic stability, allows us to perform uncertainty quantification, and can calculate statistical quantities that are inaccessible to other approaches. We demonstrate the general applicability of the method by showing it can perform rigorous model selection on a spike-in HDX-MS experiment, improved interpretation in an epitope mapping experiment, and increased sensitivity in a small molecule case-study. Bayesian analysis of an HDX experiment with an antibody dimer bound to an E3 ubiquitin ligase identifies at least two interaction interfaces where previous methods obtained confounding results due to the complexities of conformational changes on binding. Our findings are consistent with the cocrystal structure of these proteins, demonstrating a bayesian approach can identify important binding epitopes from HDX data. We also generate HDX-MS data of the bromodomain-containing protein BRD4 in complex with GSK1210151A to demonstrate the increased sensitivity of adopting a Bayesian approach.
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Affiliation(s)
- Oliver M. Crook
- Department
of Statistics, University of Oxford, Oxford OX1 3LB, United Kingdom
| | - Nathan Gittens
- Structural
and Biophysical Sciences, GlaxoSmithKline
R&D, Stevenage SG1 2NY, United
Kingdom
| | - Chun-wa Chung
- Structural
and Biophysical Sciences, GlaxoSmithKline
R&D, Stevenage SG1 2NY, United
Kingdom
| | - Charlotte M. Deane
- Department
of Statistics, University of Oxford, Oxford OX1 3LB, United Kingdom
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4
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Crook OM, Chung CW, Deane CM. Empirical Bayes functional models for hydrogen deuterium exchange mass spectrometry. Commun Biol 2022; 5:588. [PMID: 35705679 PMCID: PMC9200815 DOI: 10.1038/s42003-022-03517-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 05/20/2022] [Indexed: 11/23/2022] Open
Abstract
Hydrogen deuterium exchange mass spectrometry (HDX-MS) is a technique to explore differential protein structure by examining the rate of deuterium incorporation for specific peptides. This rate will be altered upon structural perturbation and detecting significant changes to this rate requires a statistical test. To determine rates of incorporation, HDX-MS measurements are frequently made over a time course. However, current statistical testing procedures ignore the correlations in the temporal dimension of the data. Using tools from functional data analysis, we develop a testing procedure that explicitly incorporates a model of hydrogen deuterium exchange. To further improve statistical power, we develop an empirical Bayes version of our method, allowing us to borrow information across peptides and stabilise variance estimates for low sample sizes. Our approach has increased power, reduces false positives and improves interpretation over linear model-based approaches. Due to the improved flexibility of our method, we can apply it to a multi-antibody epitope-mapping experiment where current approaches are inapplicable due insufficient flexibility. Hence, our approach allows HDX-MS to be applied in more experimental scenarios and reduces the burden on experimentalists to produce excessive replicates. Our approach is implemented in the R-package “hdxstats”: https://github.com/ococrook/hdxstats. A statistical analysis approach for HDX-MS time series data incorporates correlations in time, reducing false positives and improving statistical power and data interpretation.
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Affiliation(s)
- Oliver M Crook
- Department of Statistics, University of Oxford, Oxford, OX1 3LB, UK.
| | - Chun-Wa Chung
- Structural and Biophysical Sciences, GlaxoSmithKline R&D, Stevenage, SG1 2NY, UK
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Sharma A, Khamar D, Cullen S, Hayden A, Hughes H. Innovative Drying Technologies for Biopharmaceuticals. Int J Pharm 2021; 609:121115. [PMID: 34547393 DOI: 10.1016/j.ijpharm.2021.121115] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 08/24/2021] [Accepted: 09/15/2021] [Indexed: 01/30/2023]
Abstract
In the past two decades, biopharmaceuticals have been a breakthrough in improving the quality of lives of patients with various cancers, autoimmune, genetic disorders etc. With the growing demand of biopharmaceuticals, the need for reducing manufacturing costs is essential without compromising on the safety, quality, and efficacy of products. Batch Freeze-drying is the primary commercial means of manufacturing solid biopharmaceuticals. However, Freeze-drying is an economically unfriendly means of production with long production cycles, high energy consumption and heavy capital investment, resulting in high overall costs. This review compiles some potential, innovative drying technologies that have not gained popularity for manufacturing parenteral biopharmaceuticals. Some of these technologies such as Spin-freeze-drying, Spray-drying, Lynfinity® Technology etc. offer a paradigm shift towards continuous manufacturing, whereas PRINT® Technology and MicroglassificationTM allow controlled dry particle characteristics. Also, some of these drying technologies can be easily scaled-up with reduced requirement for different validation processes. The inclusion of Process Analytical Technology (PAT) and offline characterization techniques in tandem can provide additional information on the Critical Process Parameters (CPPs) and Critical Quality Attributes (CQAs) during biopharmaceutical processing. These processing technologies can be envisaged to increase the manufacturing capacity for biopharmaceutical products at reduced costs.
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Affiliation(s)
- Ashutosh Sharma
- Pharmaceutical and Molecular Biotechnology Research Centre (PMBRC), Waterford Institute of Technology, Main Campus, Cork Road, Waterford X91K0EK, Ireland.
| | - Dikshitkumar Khamar
- Sanofi, Manufacturing Science, Analytics and Technology (MSAT), IDA Industrial Park, Waterford X91TP27, Ireland
| | - Sean Cullen
- Gilead Sciences, Commercial Manufacturing, IDA Business & Technology Park, Carrigtwohill, Co. Cork T45DP77, Ireland
| | - Ambrose Hayden
- Pharmaceutical and Molecular Biotechnology Research Centre (PMBRC), Waterford Institute of Technology, Main Campus, Cork Road, Waterford X91K0EK, Ireland
| | - Helen Hughes
- Pharmaceutical and Molecular Biotechnology Research Centre (PMBRC), Waterford Institute of Technology, Main Campus, Cork Road, Waterford X91K0EK, Ireland
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6
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James EI, Murphree TA, Vorauer C, Engen JR, Guttman M. Advances in Hydrogen/Deuterium Exchange Mass Spectrometry and the Pursuit of Challenging Biological Systems. Chem Rev 2021; 122:7562-7623. [PMID: 34493042 PMCID: PMC9053315 DOI: 10.1021/acs.chemrev.1c00279] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Solution-phase hydrogen/deuterium
exchange (HDX) coupled to mass
spectrometry (MS) is a widespread tool for structural analysis across
academia and the biopharmaceutical industry. By monitoring the exchangeability
of backbone amide protons, HDX-MS can reveal information about higher-order
structure and dynamics throughout a protein, can track protein folding
pathways, map interaction sites, and assess conformational states
of protein samples. The combination of the versatility of the hydrogen/deuterium
exchange reaction with the sensitivity of mass spectrometry has enabled
the study of extremely challenging protein systems, some of which
cannot be suitably studied using other techniques. Improvements over
the past three decades have continually increased throughput, robustness,
and expanded the limits of what is feasible for HDX-MS investigations.
To provide an overview for researchers seeking to utilize and derive
the most from HDX-MS for protein structural analysis, we summarize
the fundamental principles, basic methodology, strengths and weaknesses,
and the established applications of HDX-MS while highlighting new
developments and applications.
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Affiliation(s)
- Ellie I James
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Taylor A Murphree
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Clint Vorauer
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - John R Engen
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
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Thakral S, Sonje J, Munjal B, Suryanarayanan R. Stabilizers and their interaction with formulation components in frozen and freeze-dried protein formulations. Adv Drug Deliv Rev 2021; 173:1-19. [PMID: 33741437 DOI: 10.1016/j.addr.2021.03.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 02/06/2021] [Accepted: 03/03/2021] [Indexed: 02/06/2023]
Abstract
This review aims to provide an overview of the current knowledge on protein stabilization during freezing and freeze-drying in relation to stress conditions commonly encountered during these processes. The traditional as well as refined mechanisms by which excipients may stabilize proteins are presented. These stabilizers encompass a wide variety of compounds including sugars, sugar alcohols, amino acids, surfactants, buffers and polymers. The rational selection of excipients for use in frozen and freeze-dried protein formulations is presented. Lyophilized protein formulations are generally multicomponent systems, providing numerous possibilities of excipient-excipient and protein-excipient interactions. The interplay of different formulation components on the protein stability and excipient functionality in the frozen and freeze-dried systems are reviewed, with discussion of representative examples of such interactions.
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