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Sun NN, Xu QF, Yang MD, Li YN, Liu H, Tantai W, Shu GW, Li GL. A high-throughput differential scanning fluorimetry method for rapid detection of thermal stability and iron saturation in lactoferrin. Int J Biol Macromol 2024; 267:131285. [PMID: 38583841 DOI: 10.1016/j.ijbiomac.2024.131285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/28/2024] [Accepted: 03/29/2024] [Indexed: 04/09/2024]
Abstract
Thermal stability and iron saturation of lactoferrin (LF) are of great significance not only for the evaluation of the biological activities of LF but also for the optimization of the isolation and drying process parameters. Differential scanning calorimetry (DSC) is a well-established and efficient method for thermal stability and iron saturation detection in LF. However, multiple DSC measurements are typically performed sequentially, thus time-consuming and low throughput. Herein, we introduced the differential scanning fluorimetry (DSF) approach to overcome such limitations. The DSF can monitor LF thermal unfolding with a commonly available real-time PCR instrument and a fluorescent dye (SYPRO orange or Glomelt), and the measured melting temperature of LF is consistent with that determined by DSC. On the basis of that, a new quantification method was established for determination of iron saturation levels using the linear correlation of the degree of ion saturation of LF with DSF measurements. Such DSF method is simple, inexpensive, rapid (<15 min), and high throughput (>96 samples per experiment), and provides a valuable alternative tool for thermal stability detection of LF and other whey proteins.
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Affiliation(s)
- Na-Na Sun
- School of Food Science and Engineering, National R&D Center for Goat Dairy Products Processing Technology, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, China
| | - Qin-Feng Xu
- School of Food Science and Engineering, National R&D Center for Goat Dairy Products Processing Technology, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, China.
| | - Meng-di Yang
- School of Food Science and Engineering, National R&D Center for Goat Dairy Products Processing Technology, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, China
| | - Yan-Ni Li
- School of Food Science and Engineering, National R&D Center for Goat Dairy Products Processing Technology, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, China
| | - Hao Liu
- School of Food Science and Engineering, National R&D Center for Goat Dairy Products Processing Technology, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, China
| | - Wei Tantai
- School of Food Science and Engineering, National R&D Center for Goat Dairy Products Processing Technology, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, China
| | - Guo-Wei Shu
- School of Food Science and Engineering, National R&D Center for Goat Dairy Products Processing Technology, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, China
| | - Guo-Liang Li
- School of Food Science and Engineering, National R&D Center for Goat Dairy Products Processing Technology, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, China
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2
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Gooran N, Kopra K. Fluorescence-Based Protein Stability Monitoring-A Review. Int J Mol Sci 2024; 25:1764. [PMID: 38339045 PMCID: PMC10855643 DOI: 10.3390/ijms25031764] [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: 12/31/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
Proteins are large biomolecules with a specific structure that is composed of one or more long amino acid chains. Correct protein structures are directly linked to their correct function, and many environmental factors can have either positive or negative effects on this structure. Thus, there is a clear need for methods enabling the study of proteins, their correct folding, and components affecting protein stability. There is a significant number of label-free methods to study protein stability. In this review, we provide a general overview of these methods, but the main focus is on fluorescence-based low-instrument and -expertise-demand techniques. Different aspects related to thermal shift assays (TSAs), also called differential scanning fluorimetry (DSF) or ThermoFluor, are introduced and compared to isothermal chemical denaturation (ICD). Finally, we discuss the challenges and comparative aspects related to these methods, as well as future opportunities and assay development directions.
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Affiliation(s)
| | - Kari Kopra
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland;
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3
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Mahran R, Vello N, Komulainen A, Malakoutikhah M, Härmä H, Kopra K. Isothermal chemical denaturation assay for monitoring protein stability and inhibitor interactions. Sci Rep 2023; 13:20066. [PMID: 37973851 PMCID: PMC10654576 DOI: 10.1038/s41598-023-46720-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 11/03/2023] [Indexed: 11/19/2023] Open
Abstract
Thermal shift assay (TSA) with altered temperature has been the most widely used method for monitoring protein stability for drug research. However, there is a pressing need for isothermal techniques as alternatives. This urgent demand arises from the limitations of TSA, which can sometimes provide misleading ranking of protein stability and fail to accurately reflect protein stability under physiological conditions. Although differential scanning fluorimetry has significantly improved throughput in comparison to differential scanning calorimetry and differential static light scattering throughput, all these methods exhibit moderate sensitivity. In contrast, current isothermal chemical denaturation (ICD) techniques may not offer the same throughput capabilities as TSA, but it provides more precise information about protein stability and interactions. Unfortunately, ICD also suffers from limited sensitivity, typically in micromolar range. We have developed a novel method to overcome these challenges, namely throughput and sensitivity. The novel Förster Resonance Energy Transfer (FRET)-Probe as an external probe is highly applicable to isothermal protein stability monitoring but also to conventional TSA. We have investigated ICD for multiple proteins with focus on KRASG12C with covalent inhibitors and three chemical denaturants performed at nanomolar protein concentration. Data showed corresponding inhibitor-induced stabilization of KRASG12C to those reported by nucleotide exchange assay.
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Affiliation(s)
- Randa Mahran
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland.
| | - Niklas Vello
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
| | - Anita Komulainen
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
| | | | - Harri Härmä
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
| | - Kari Kopra
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
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4
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Llowarch P, Usselmann L, Ivanov D, Holdgate GA. Thermal unfolding methods in drug discovery. BIOPHYSICS REVIEWS 2023; 4:021305. [PMID: 38510342 PMCID: PMC10903397 DOI: 10.1063/5.0144141] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 04/13/2023] [Indexed: 03/22/2024]
Abstract
Thermal unfolding methods, applied in both isolated protein and cell-based settings, are increasingly used to identify and characterize hits during early drug discovery. Technical developments over recent years have facilitated their application in high-throughput approaches, and they now are used more frequently for primary screening. Widespread access to instrumentation and automation, the ability to miniaturize, as well as the capability and capacity to generate the appropriate scale and quality of protein and cell reagents have all played a part in these advances. As the nature of drug targets and approaches to their modulation have evolved, these methods have broadened our ability to provide useful chemical start points. Target proteins without catalytic function, or those that may be difficult to express and purify, are amenable to these methods. Here, we provide a review of the applications of thermal unfolding methods applied in hit finding during early drug discovery.
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Affiliation(s)
- Poppy Llowarch
- High Throughput Screening, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, United Kingdom
| | - Laura Usselmann
- High Throughput Screening, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, United Kingdom
| | - Delyan Ivanov
- High Throughput Screening, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, United Kingdom
| | - Geoffrey A. Holdgate
- High Throughput Screening, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, United Kingdom
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5
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Li X, Singh NK, Collins DR, Ng R, Zhang A, Lamothe-Molina PA, Shahinian P, Xu S, Tan K, Piechocka-Trocha A, Urbach JM, Weber JK, Gaiha GD, Takou Mbah OC, Huynh T, Cheever S, Chen J, Birnbaum M, Zhou R, Walker BD, Wang JH. Molecular basis of differential HLA class I-restricted T cell recognition of a highly networked HIV peptide. Nat Commun 2023; 14:2929. [PMID: 37217466 DOI: 10.1038/s41467-023-38573-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 05/09/2023] [Indexed: 05/24/2023] Open
Abstract
Cytotoxic-T-lymphocyte (CTL) mediated control of HIV-1 is enhanced by targeting highly networked epitopes in complex with human-leukocyte-antigen-class-I (HLA-I). However, the extent to which the presenting HLA allele contributes to this process is unknown. Here we examine the CTL response to QW9, a highly networked epitope presented by the disease-protective HLA-B57 and disease-neutral HLA-B53. Despite robust targeting of QW9 in persons expressing either allele, T cell receptor (TCR) cross-recognition of the naturally occurring variant QW9_S3T is consistently reduced when presented by HLA-B53 but not by HLA-B57. Crystal structures show substantial conformational changes from QW9-HLA to QW9_S3T-HLA by both alleles. The TCR-QW9-B53 ternary complex structure manifests how the QW9-B53 can elicit effective CTLs and suggests sterically hindered cross-recognition by QW9_S3T-B53. We observe populations of cross-reactive TCRs for B57, but not B53 and also find greater peptide-HLA stability for B57 in comparison to B53. These data demonstrate differential impacts of HLAs on TCR cross-recognition and antigen presentation of a naturally arising variant, with important implications for vaccine design.
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Affiliation(s)
- Xiaolong Li
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, China.
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA.
| | - Nishant Kumar Singh
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, 02142, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - David R Collins
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Robert Ng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
| | - Angela Zhang
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
| | | | - Peter Shahinian
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Shutong Xu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
| | - Kemin Tan
- Structural Biology Center, X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Alicja Piechocka-Trocha
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | | | - Jeffrey K Weber
- IBM Thomas J. Watson Research Center, Computational Biology Center, Yorktown Heights, NY, 10598, USA
| | - Gaurav D Gaiha
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | | | - Tien Huynh
- IBM Thomas J. Watson Research Center, Computational Biology Center, Yorktown Heights, NY, 10598, USA
| | - Sophia Cheever
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - James Chen
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Michael Birnbaum
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, 02142, USA
| | - Ruhong Zhou
- IBM Thomas J. Watson Research Center, Computational Biology Center, Yorktown Heights, NY, 10598, USA
- Department of Chemistry, Columbia University, New York, NY, 10025, USA
- Institute of Quantitative Biology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
- Institute for Medical Engineering and Science and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Jia-Huai Wang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02215, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02215, USA.
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6
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Leandro P, Lino PR, Lopes R, Leandro J, Amaro MP, Sousa P, Vicente JB, Almeida AJ. Isothermal denaturation fluorimetry vs Differential scanning fluorimetry as tools for screening of stabilizers for protein freeze-drying: human phenylalanine hydroxylase as the case study. Eur J Pharm Biopharm 2023; 187:1-11. [PMID: 37011788 DOI: 10.1016/j.ejpb.2023.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/24/2023] [Accepted: 03/25/2023] [Indexed: 04/03/2023]
Abstract
The structural maintenance of therapeutic proteins during formulation and/or storage is a critical aspect, particularly for multi-domain and/or multimeric proteins which usually exhibit intrinsic structural dynamics leading to aggregation with concomitant loss-of-function. Protein freeze-drying is a widely used technique to preserve protein structure and function during storage. To minimize chemical/physical stresses occurring during this process, protein stabilizers are usually included, their effect being strongly dependent on the target protein. Therefore, they should be screened for on a time-consuming case-by-case basis. Herein, differential scanning fluorimetry (DSF) and isothermal denaturation fluorimetry (ITDF) were employed to screen, among different classes of freeze-drying additives, for the most effective stabilizer of the model protein human phenylalanine hydroxylase (hPAH). Correlation studies among retrieved DSF and ITDF parameters with recovered enzyme amount and activity indicated ITDF as the most appropriate screening method. Biochemical and biophysical characterization of hPAH freeze-dried with ITDF-selected stabilizers and a long-term storage study (12 months, 5 ± 3 °C) showed that the selected compounds prevented protein aggregation and preserved hPAH structural and functional properties throughout time storage. Our results provide a solid basis towards the choice of ITDF as a high-throughput screening step for the identification of protein freeze-drying protectors.
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Affiliation(s)
- Paula Leandro
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal.
| | - Paulo R Lino
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Raquel Lopes
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - João Leandro
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Mariana P Amaro
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Paulo Sousa
- Sofarimex, Indústria Química e Farmacêutica SA, Av. das Indústrias, Alto de Colaride, 2735-521 Agualva, Portugal
| | - João B Vicente
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República 2780-157 Oeiras, Portugal
| | - António J Almeida
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal.
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7
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Structural Basis of Cysteine Ligase MshC Inhibition by Cysteinyl-Sulfonamides. Int J Mol Sci 2022; 23:ijms232315095. [PMID: 36499418 PMCID: PMC9736012 DOI: 10.3390/ijms232315095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 11/25/2022] [Accepted: 11/26/2022] [Indexed: 12/03/2022] Open
Abstract
Mycothiol (MSH), the major cellular thiol in Mycobacterium tuberculosis (Mtb), plays an essential role in the resistance of Mtb to various antibiotics and oxidative stresses. MshC catalyzes the ATP-dependent ligation of 1-O-(2-amino-2-deoxy-α-d-glucopyranosyl)-d-myo-inositol (GlcN-Ins) with l-cysteine (l-Cys) to form l-Cys-GlcN-Ins, the penultimate step in MSH biosynthesis. The inhibition of MshC is lethal to Mtb. In the present study, five new cysteinyl-sulfonamides were synthesized, and their binding affinity with MshC was evaluated using a thermal shift assay. Two of them bind the target with EC50 values of 219 and 231 µM. Crystal structures of full-length MshC in complex with these two compounds showed that they were bound in the catalytic site of MshC, inducing dramatic conformational changes of the catalytic site compared to the apo form. In particular, the observed closure of the KMSKS loop was not detected in the published cysteinyl-sulfamoyl adenosine-bound structure, the latter likely due to trypsin treatment. Despite the confirmed binding to MshC, the compounds did not suppress Mtb culture growth, which might be explained by the lack of adequate cellular uptake. Taken together, these novel cysteinyl-sulfonamide MshC inhibitors and newly reported full-length apo and ligand-bound MshC structures provide a promising starting point for the further development of novel anti-tubercular drugs targeting MshC.
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8
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Li DD, Li J, Huang Y, Shi J, Yang Y, Peng QH. Kaempferol Inhibits Dry Eye-Related Corneal Inflammation In Vitro Via the p38 Pathway. Nat Prod Commun 2022. [DOI: 10.1177/1934578x221131407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
ObjectiveThe purpose of this study is to investigate the effect of kaempferol (KAE), an effective constituent of Buddleja officinalis, on human corneal epithelial cells (HCECs) under a hyperosmolar environment. Methods HCECs were cultured in DMEM/F12 medium and allocated into four groups: normal, model, vehicle, and KAE. Ki67 staining was used to detect HCEC proliferation; TdT-mediated dUTP Nick-End Labeling staining was used to detect HCEC apoptosis; quantified real-time PCR was used to investigate the mRNA relative expression levels of TNF-α, IL-6, and p38. and Western blot was used to reveal the protein expression levels of TNF-α, IL-6, and p38. Results Compared with those in the normal group, the proliferation ability of HCECs was significantly inhibited and the apoptosis rate of HCECs was notably increased in the model group; but KAE could effectively improve HCEC proliferation and reduce HCEC apoptosis. Compared with those in the normal group, the mRNA relative expressions and protein levels of TNF-α, IL-6, and p38 were significantly increased in the model group, which were effectively decreased after KAE intervention. Conclusion KAE could promote HCEC proliferation and reduce cell apoptosis, as well as inhibit the expression of inflammatory factors in a hypertonic-induced HCEC model via the p38MAPK pathway.
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Affiliation(s)
- Dong-dong Li
- Hunan University of Chinese Medicine, Changsha, China
- Key Laboratory of Traditional Chinese Medicine for Prevention and Treatment of Eye, Ear, Nose and Throat Diseases in Hunan Province, Changsha, China
- Hunan Provincial Engineering and Technological Research Center for Prevention and Treatment of Ophthalmology and Otolaryngology Diseases with Chinese Medicine and Protecting Visual Function, Changsha, China
| | - Jie Li
- Hunan University of Chinese Medicine, Changsha, China
- Key Laboratory of Traditional Chinese Medicine for Prevention and Treatment of Eye, Ear, Nose and Throat Diseases in Hunan Province, Changsha, China
- Wenzhou Medical University, Wenzhou, China
| | - Yu Huang
- Hunan University of Chinese Medicine, Changsha, China
- Key Laboratory of Traditional Chinese Medicine for Prevention and Treatment of Eye, Ear, Nose and Throat Diseases in Hunan Province, Changsha, China
- Hunan Provincial Engineering and Technological Research Center for Prevention and Treatment of Ophthalmology and Otolaryngology Diseases with Chinese Medicine and Protecting Visual Function, Changsha, China
| | - Jian Shi
- Hunan University of Chinese Medicine, Changsha, China
- Key Laboratory of Traditional Chinese Medicine for Prevention and Treatment of Eye, Ear, Nose and Throat Diseases in Hunan Province, Changsha, China
- Hunan Provincial Engineering and Technological Research Center for Prevention and Treatment of Ophthalmology and Otolaryngology Diseases with Chinese Medicine and Protecting Visual Function, Changsha, China
| | - Yijing Yang
- Hunan University of Chinese Medicine, Changsha, China
- Key Laboratory of Traditional Chinese Medicine for Prevention and Treatment of Eye, Ear, Nose and Throat Diseases in Hunan Province, Changsha, China
- Hunan Provincial Engineering and Technological Research Center for Prevention and Treatment of Ophthalmology and Otolaryngology Diseases with Chinese Medicine and Protecting Visual Function, Changsha, China
| | - Qing-hua Peng
- Hunan University of Chinese Medicine, Changsha, China
- Key Laboratory of Traditional Chinese Medicine for Prevention and Treatment of Eye, Ear, Nose and Throat Diseases in Hunan Province, Changsha, China
- Hunan Provincial Engineering and Technological Research Center for Prevention and Treatment of Ophthalmology and Otolaryngology Diseases with Chinese Medicine and Protecting Visual Function, Changsha, China
- First Affiliated Hospital of Hunan University of Chinese Medicine, Changsha, China
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9
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Stolzke T, Krieg F, Peng T, Zhang H, Häusler O, Brandenbusch C. Hydroxylpropyl-β-cyclodextrin as Potential Excipient to Prevent Stress-Induced Aggregation in Liquid Protein Formulations. Molecules 2022; 27:molecules27165094. [PMID: 36014329 PMCID: PMC9414600 DOI: 10.3390/molecules27165094] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/30/2022] [Accepted: 08/03/2022] [Indexed: 11/22/2022] Open
Abstract
Due to the growing demand for patient-friendly subcutaneous dosage forms, the ability to increasing protein solubility and stability in formulations to deliver on the required high protein concentrations is crucial. A common approach to ensure protein solubility and stability in high concentration protein formulations is the addition of excipients such as sugars, amino acids, surfactants, approved by the Food and Drug Administration. In a best-case scenario, these excipients fulfil multiple demands simultaneously, such as increasing long-term stability of the formulation, reducing protein adsorption on surfaces/interfaces, and stabilizing the protein against thermal or mechanical stress. 2-Hydroxylpropyl-β-cyclodextrin (derivative of β-cyclodextrin) holds this potential, but has not yet been sufficiently investigated for use in protein formulations. Within this work, we have systematically investigated the relevant molecular interactions to identify the potential of Kleptose®HPB (2-hydroxylpropyl-β-cyclodextrin from Roquette Freres, Lestrem, France) as “multirole” excipient within liquid protein formulations. Based on our results three factors determine the influence of Kleptose®HPB on protein formulation stability: (1) concentration of Kleptose®HPB, (2) protein type and protein concentration, and (3) quality of the protein formulation. Our results not only contribute to the understanding of the relevant interactions but also enable the target-oriented use of Kleptose®HPB within formulation design.
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Affiliation(s)
- Tanja Stolzke
- Laboratory of Thermodynamics, Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany
| | - Franziska Krieg
- Laboratory of Thermodynamics, Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany
| | - Tao Peng
- Roquette Asia Pacific Pte. Ltd., Singapore 138588, Singapore
| | - Hailong Zhang
- Roquette Asia Pacific Pte. Ltd., Singapore 138588, Singapore
| | | | - Christoph Brandenbusch
- Laboratory of Thermodynamics, Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany
- Correspondence:
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10
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Nie M, Liu Y, Huang X, Zhang Z, Zhao Q. Microtiter plate-based differential scanning fluorimetry: a high-throughput method for efficient formulation development. J Pharm Sci 2022; 111:2397-2403. [DOI: 10.1016/j.xphs.2022.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 05/12/2022] [Accepted: 05/12/2022] [Indexed: 10/18/2022]
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11
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Kunz P. Assessing the Aggregation Propensity of Single-Domain Antibodies upon Heat-Denaturation Employing the ΔT m Shift. Methods Mol Biol 2022; 2446:233-244. [PMID: 35157276 DOI: 10.1007/978-1-0716-2075-5_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Nano differential scanning fluorimetry is used to quantify protein thermostability and has substantially expanded the spectrum of convenient biophysical parameters used to characterize proteins. Here, this technique is used to measure the ΔTm shift for single-domain antibodies (sdAbs), which represents a comprehensive metric for the aggregation propensity of sdAbs upon heat-denaturation. By relating two melting curves at different protein concentrations, the ΔTm shift described in this protocol is ideally suited for high-throughput measurements to guide protein engineering, formulation development, and developability assessment of sdAbs.
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Affiliation(s)
- Patrick Kunz
- Coriolis Pharma Research GmbH, Martinsried, Germany.
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12
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Saikia A, Springer S. Peptide-MHC I complex stability measured by nanoscale differential scanning fluorimetry reveals molecular mechanism of thermal denaturation. Mol Immunol 2021; 136:73-81. [PMID: 34091103 DOI: 10.1016/j.molimm.2021.04.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 04/08/2021] [Accepted: 04/29/2021] [Indexed: 12/22/2022]
Abstract
Recombinant major histocompatibility complex class I molecules are used in diagnostic and therapeutic approaches in cancer immunotherapy, with many studies exploring their binding to antigenic peptides. Current techniques for kinetic peptide binding studies are hampered by high sample consumption, low throughput, interference with protein stability, and/or high background signal. Here, we validate nanoscale differential scanning fluorimetry (nanoDSF), a method using the tryptophan fluorescence of class I molecules, for class I/peptide binding, and we use it to determine the molecular mechanism of the thermal denaturation of HLA-A*02:01.
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Affiliation(s)
- Ankur Saikia
- Department of Life Science and Chemistry, Jacobs University Bremen, Germany
| | - Sebastian Springer
- Department of Life Science and Chemistry, Jacobs University Bremen, Germany.
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13
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Huang C, Wang Y, Xu X, Mills J, Jin W, Ghose S, Li ZJ. Hydrophobic property of cation-exchange resins affects monoclonal antibody aggregation. J Chromatogr A 2020; 1631:461573. [DOI: 10.1016/j.chroma.2020.461573] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 09/06/2020] [Accepted: 09/19/2020] [Indexed: 12/29/2022]
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14
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Svilenov HL, Menzen T, Richter K, Winter G. Modulated Scanning Fluorimetry Can Quickly Assess Thermal Protein Unfolding Reversibility in Microvolume Samples. Mol Pharm 2020; 17:2638-2647. [DOI: 10.1021/acs.molpharmaceut.0c00330] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Hristo L. Svilenov
- Department of Pharmacy, Ludwig-Maximilians-University, Butenandtstr. 5, 81377 Munich, Germany
| | - Tim Menzen
- Coriolis Pharma Research GmbH, Fraunhoferstr. 18 b, 82152 Martinsried, Germany
| | - Klaus Richter
- Coriolis Pharma Research GmbH, Fraunhoferstr. 18 b, 82152 Martinsried, Germany
| | - Gerhard Winter
- Department of Pharmacy, Ludwig-Maximilians-University, Butenandtstr. 5, 81377 Munich, Germany
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15
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Effects of electroacupuncture on conjunctival cell apoptosis and the expressions of apoptosis-related proteins Caspase-3, Fas and Bcl-2 in rabbits with dry eye syndrome. JOURNAL OF ACUPUNCTURE AND TUINA SCIENCE 2020. [DOI: 10.1007/s11726-020-1152-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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16
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Sun C, Li Y, Yates EA, Fernig DG. SimpleDSFviewer: A tool to analyze and view differential scanning fluorimetry data for characterizing protein thermal stability and interactions. Protein Sci 2019; 29:19-27. [PMID: 31394001 DOI: 10.1002/pro.3703] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 07/27/2019] [Accepted: 08/06/2019] [Indexed: 02/02/2023]
Abstract
Differential scanning fluorimetry (DSF) is a widely used thermal shift assay for measuring protein stability and protein-ligand interactions that are simple, cheap, and amenable to high throughput. However, data analysis remains a challenge, requiring improved methods. Here, the program SimpleDSFviewer, a user-friendly interface, is described to help the researchers who apply DSF technique in their studies. SimpleDSFviewer integrates melting curve (MC) normalization, smoothing, and melting temperature (Tm) analysis and directly previews analyzed data, providing an efficient analysis tool for DSF. SimpleDSFviewer is developed in Matlab, and it is freely available for all users to use in Matlab workspace or with Matlab Runtime. It is easy to use and an efficient tool for researchers to preview and analyze their data in a very short time.
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Affiliation(s)
- Changye Sun
- Henan Key Laboratory of Medical Tissue Regeneration, Xinxiang Medical University, Xinxiang, Henan, China.,Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Yong Li
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Edwin A Yates
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - David G Fernig
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
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17
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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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18
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Svilenov H, Winter G. The ReFOLD assay for protein formulation studies and prediction of protein aggregation during long-term storage. Eur J Pharm Biopharm 2019; 137:131-139. [DOI: 10.1016/j.ejpb.2019.02.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 02/19/2019] [Accepted: 02/22/2019] [Indexed: 11/28/2022]
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19
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Fabrication of Konjac glucomannan-based composite hydrogel crosslinked by calcium hydroxide for promising lacrimal plugging purpose. Int J Biol Macromol 2019; 127:440-449. [DOI: 10.1016/j.ijbiomac.2019.01.069] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 01/11/2019] [Accepted: 01/16/2019] [Indexed: 01/22/2023]
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20
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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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21
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22
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Pivovarova Y, Liu J, Lesigang J, Koldyka O, Rauschmeier R, Hu K, Dong G. Structure of a Novel Dimeric SET Domain Methyltransferase that Regulates Cell Motility. J Mol Biol 2018; 430:4209-4229. [PMID: 30148980 PMCID: PMC7141177 DOI: 10.1016/j.jmb.2018.08.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 08/17/2018] [Accepted: 08/21/2018] [Indexed: 11/21/2022]
Abstract
Lysine methyltransferases (KMTs) were initially associated with transcriptional control through their methylation of histones and other nuclear proteins, but have since been found to regulate many other cellular activities. The apical complex lysine (K) methyltransferase (AKMT) of the human parasite Toxoplasma gondii was recently shown to play a critical role in regulating cellular motility. Here we report a 2.1-Å resolution crystal structure of the conserved and functional C-terminal portion (aa289-709) of T. gondii AKMT. AKMT dimerizes via a unique intermolecular interface mediated by the C-terminal tetratricopeptide repeat-like domain together with a specific zinc-binding motif that is absent from all other KMTs. Disruption of AKMT dimerization impaired both its enzyme activity and parasite egress from infected host cells in vivo. Structural comparisons reveal that AKMT is related to the KMTs in the SMYD family, with, however, a number of distinct structural features in addition to the unusual dimerization interface. These features are conserved among the apicomplexan parasites and their free-living relatives, but not found in any known KMTs in animals. AKMT therefore is the founding member of a new subclass of KMT that has important implications for the evolution of the apicomplexans.
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Affiliation(s)
- Yulia Pivovarova
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Jun Liu
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Johannes Lesigang
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | | | - Rene Rauschmeier
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Ke Hu
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.
| | - Gang Dong
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, 1030 Vienna, Austria.
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23
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Booth W, Schlachter CR, Pote S, Ussin N, Mank NJ, Klapper V, Offermann LR, Tang C, Hurlburt BK, Chruszcz M. Impact of an N-terminal Polyhistidine Tag on Protein Thermal Stability. ACS OMEGA 2018; 3:760-768. [PMID: 29399652 PMCID: PMC5793033 DOI: 10.1021/acsomega.7b01598] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 01/05/2018] [Indexed: 05/15/2023]
Abstract
For years, the use of polyhistidine tags (His-tags) has been a staple in the isolation of recombinant proteins in immobilized metal affinity chromatography experiments. Their usage has been widely beneficial in increasing protein purity from crude cell lysates. For some recombinant proteins, a consequence of His-tag addition is that it can affect protein function and stability. Functional proteins are essential in the elucidation of their biological, kinetic, structural, and thermodynamic properties. In this study, we determine the effect of N-terminal His-tags on the thermal stability of select proteins using differential scanning fluorimetry and identify that the removal of the His-tag can have both beneficial and deleterious effects on their stability.
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Affiliation(s)
- William
T. Booth
- Department
of Chemistry and Biochemistry, University
of South Carolina, Columbia, South Carolina 29208, United States
| | - Caleb R. Schlachter
- Department
of Chemistry and Biochemistry, University
of South Carolina, Columbia, South Carolina 29208, United States
| | - Swanandi Pote
- Department
of Chemistry and Biochemistry, University
of South Carolina, Columbia, South Carolina 29208, United States
| | - Nikita Ussin
- Department
of Chemistry and Biochemistry, University
of South Carolina, Columbia, South Carolina 29208, United States
| | - Nicholas J. Mank
- Department
of Chemistry and Biochemistry, University
of South Carolina, Columbia, South Carolina 29208, United States
| | - Vincent Klapper
- Department
of Chemistry and Biochemistry, University
of South Carolina, Columbia, South Carolina 29208, United States
| | - Lesa R. Offermann
- Department
of Chemistry and Biochemistry, University
of South Carolina, Columbia, South Carolina 29208, United States
- Department
of Chemistry, Davidson College, Davidson, North Carolina 28035, United States
| | - Chuanbing Tang
- Department
of Chemistry and Biochemistry, University
of South Carolina, Columbia, South Carolina 29208, United States
| | - Barry K. Hurlburt
- United
States Department of Agriculture, Agricultural Research Service, Southern Regional Research Center, New Orleans, Louisiana 70124, United States
| | - Maksymilian Chruszcz
- Department
of Chemistry and Biochemistry, University
of South Carolina, Columbia, South Carolina 29208, United States
- E-mail: . Tel: (803) 777-7399. Fax: (803) 777-9521
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24
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Eek P, Piht MA, Rätsep M, Freiberg A, Järving I, Samel N. A conserved π–cation and an electrostatic bridge are essential for 11R-lipoxygenase catalysis and structural stability. Biochim Biophys Acta Mol Cell Biol Lipids 2015. [DOI: 10.1016/j.bbalip.2015.07.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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25
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Jarasch A, Koll H, Regula JT, Bader M, Papadimitriou A, Kettenberger H. Developability Assessment During the Selection of Novel Therapeutic Antibodies. J Pharm Sci 2015; 104:1885-1898. [DOI: 10.1002/jps.24430] [Citation(s) in RCA: 149] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 02/28/2015] [Accepted: 03/03/2015] [Indexed: 01/02/2023]
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26
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Chaudhuri R, Cheng Y, Middaugh CR, Volkin DB. High-throughput biophysical analysis of protein therapeutics to examine interrelationships between aggregate formation and conformational stability. AAPS JOURNAL 2013; 16:48-64. [PMID: 24174400 DOI: 10.1208/s12248-013-9539-6] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 09/25/2013] [Indexed: 11/30/2022]
Abstract
Stabilization and formulation of therapeutic proteins against physical instability, both structural alterations and aggregation, is particularly challenging not only due to each protein's unique physicochemical characteristics but also their susceptibility to the surrounding milieu (pH, ionic strength, excipients, etc.) as well as various environmental stresses (temperature, agitation, lyophilization, etc.). The use of high-throughput techniques can significantly aid in the evaluation of stabilizing solution conditions by permitting a more rapid evaluation of a large matrix of possible combinations. In this mini-review, we discuss both key physical degradation pathways observed for protein-based drugs and the utility of various high-throughput biophysical techniques to aid in protein formulation development to minimize their occurrence. We then focus on four illustrative case studies with therapeutic protein candidates of varying sizes, shapes and physicochemical properties to explore different analytical challenges in monitoring protein physical instability. These include an IgG2 monoclonal antibody, an albumin-fusion protein, a recombinant pentameric plasma glycoprotein, and an antibody fragment (Fab). Future challenges and opportunities to improve and apply high-throughput approaches to protein formulation development are also discussed.
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Affiliation(s)
- Rajoshi Chaudhuri
- Department of Pharmaceutical Chemistry, Macromolecule and Vaccine Stabilization Center, University of Kansas, Lawrence, Kansas, 66047, USA
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