101
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Filipović L, Kojadinović M, Popović M. Exosomes and exosome-mimetics as targeted drug carriers: Where we stand and what the future holds? J Drug Deliv Sci Technol 2022. [DOI: 10.1016/j.jddst.2021.103057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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102
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Tomak A, Cesmeli S, Hanoglu BD, Winkler D, Oksel Karakus C. Nanoparticle-protein corona complex: understanding multiple interactions between environmental factors, corona formation, and biological activity. Nanotoxicology 2022; 15:1331-1357. [PMID: 35061957 DOI: 10.1080/17435390.2022.2025467] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The surfaces of pristine nanoparticles become rapidly coated by proteins in biological fluids, forming the so-called protein corona. The corona modifies key physicochemical characteristics of nanoparticle surfaces that modulate its biological and pharmacokinetic activity, biodistribution, and safety. In the two decades since the protein corona was identified, the importance of nanoparticles surface properties in regulating biological responses have been recognized. However, there is still a lack of clarity about the relationships between physiological conditions and corona composition over time, and how this controls biological activities/interactions. Here we review recent progress in characterizing the structure and composition of protein corona as a function of biological fluid and time. We summarize the influence of nanoparticle characteristics on protein corona composition and discuss the relevance of protein corona to the biological activity and fate of nanoparticles. The aim is to provide a critical summary of the key factors that affect protein corona formation (e.g. characteristics of nanoparticles and biological environment) and how the corona modulates biological activity, cellular uptake, biodistribution, and drug delivery. In addition to a discussion on the importance of the characterization of protein corona adsorbed on nanoparticle surfaces under conditions that mimic relevant physiological environment, we discuss the unresolved technical issues related to the characterization of nanoparticle-protein corona complexes during their journey in the body. Lastly, the paper offers a perspective on how the existing nanomaterial toxicity data obtained from in vitro studies should be reconsidered in the light of the presence of a protein corona, and how recent advances in fields, such as proteomics and machine learning can be integrated into the quantitative analysis of protein corona components.
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Affiliation(s)
- Aysel Tomak
- Department of Bioengineering, Izmir Institute of Technology, Izmir, Turkey
| | - Selin Cesmeli
- Department of Bioengineering, Izmir Institute of Technology, Izmir, Turkey
| | - Bercem D Hanoglu
- Vocational School of Health Services, Ardahan University, Ardahan, Turkey
| | - David Winkler
- School of Biochemistry & Genetics, La Trobe University, Bundoora, Australia.,Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia.,School of Pharmacy, University of Nottingham, Nottingham, UK
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103
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Assessment of Therapeutic Antibody Developability by Combinations of In Vitro and In Silico Methods. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2313:57-113. [PMID: 34478132 DOI: 10.1007/978-1-0716-1450-1_4] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Although antibodies have become the fastest-growing class of therapeutics on the market, it is still challenging to develop them for therapeutic applications, which often require these molecules to withstand stresses that are not present in vivo. We define developability as the likelihood of an antibody candidate with suitable functionality to be developed into a manufacturable, stable, safe, and effective drug that can be formulated to high concentrations while retaining a long shelf life. The implementation of reliable developability assessments from the early stages of antibody discovery enables flagging and deselection of potentially problematic candidates, while focussing available resources on the development of the most promising ones. Currently, however, thorough developability assessment requires multiple in vitro assays, which makes it labor intensive and time consuming to implement at early stages. Furthermore, accurate in vitro analysis at the early stage is compromised by the high number of potential candidates that are often prepared at low quantities and purity. Recent improvements in the performance of computational predictors of developability potential are beginning to change this scenario. Many computational methods only require the knowledge of the amino acid sequences and can be used to identify possible developability issues or to rank available candidates according to a range of biophysical properties. Here, we describe how the implementation of in silico tools into antibody discovery pipelines is increasingly offering time- and cost-effective alternatives to in vitro experimental screening, thus streamlining the drug development process. We discuss in particular the biophysical and biochemical properties that underpin developability potential and their trade-offs, review various in vitro assays to measure such properties or parameters that are predictive of developability, and give an overview of the growing number of in silico tools available to predict properties important for antibody development, including the CamSol method developed in our laboratory.
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104
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Bou-Assaf GM, Budyak IL, Brenowitz M, Day ES, Hayes D, Hill J, Majumdar R, Ringhieri P, Schuck P, Lin JC. Best Practices for Aggregate Quantitation of Antibody Therapeutics by Sedimentation Velocity Analytical Ultracentrifugation. J Pharm Sci 2022; 111:2121-2133. [PMID: 34986360 DOI: 10.1016/j.xphs.2021.12.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/24/2021] [Accepted: 12/24/2021] [Indexed: 11/18/2022]
Abstract
Analytical ultracentrifugation (AUC) is a critical analytical tool supporting the development and manufacture of protein therapeutics. AUC is routinely used as an assay orthogonal to size exclusion chromatography for aggregate quantitation. This article distills the experimental and analysis procedures used by the authors for sedimentation velocity AUC into a series of best-practices considerations. The goal of this distillation is to help harmonize aggregate quantitation approaches across the biopharmaceutical industry. We review key considerations for sample and instrument suitability, experimental design, and data analysis best practices and conversely, highlight potential pitfalls to accurate aggregate analysis. Our goal is to provide experienced users benchmarks against which they can standardize their analyses and to provide guidance for new AUC analysts that will aid them to become proficient in this fundamental technique.
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Affiliation(s)
| | - Ivan L Budyak
- Bioproduct Research and Development, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - Michael Brenowitz
- Departments of Biochemistry and Molecular Pharmacology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461
| | - Eric S Day
- Pharmaceutical Development, Genentech a Member of the Roche Group, 1 DNA Way, South San Francisco, CA 94080
| | - David Hayes
- IntlSoSci, 23 Washington St., Gorham, NH 03581
| | - John Hill
- Department of Bioengineering, University of Washington, Seattle, WA 98105
| | - Ranajoy Majumdar
- Bioproduct Research and Development, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - Paola Ringhieri
- Analytical Development Biotech Department, Merck Serono S.p.a, Guidonia, RM, Italy; an affiliate of Merck KGaA
| | - Peter Schuck
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, 13 South Drive, Bethesda, MD 20892
| | - Jasper C Lin
- Pharmaceutical Development, Genentech a Member of the Roche Group, 1 DNA Way, South San Francisco, CA 94080.
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105
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Abstract
Food carbohydrates are macronutrients that are found in fruits, grains, vegetables, and milk products. These organic compounds are present in foods in the form of sugars, starches, and fibers and are composed of carbon, hydrogen, and oxygen. These wide ranging macromolecules can be classified according to their chemical structure into three major groups: low molecular weight mono- and disaccharides, intermediate molecular weight oligosaccharides, and high molecular weight polysaccharides. Notably, the digestibility of specific carbohydrate components differ and nondigestible carbohydrates can reach the large intestine intact where they act as food sources for beneficial bacteria. In this review, we give an overview of advances made in food carbohydrate analysis. Overall, this review indicates the importance of carbohydrate analytical techniques in the quest to identify and isolate health-promoting carbohydrates to be used as additives in the functional foods industry.
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Affiliation(s)
- Leonie J Kiely
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Rita M Hickey
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland.
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106
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Xu Z, Ho M, Bordoloi D, Kudchodkar S, Khoshnejad M, Giron L, Zaidi F, Jeong M, Roberts CC, Park YK, Maslow J, Abdel-Mohsen M, Muthumani K. Techniques for Developing and Assessing Immune Responses Induced by Synthetic DNA Vaccines for Emerging Infectious Diseases. Methods Mol Biol 2022; 2410:229-263. [PMID: 34914050 DOI: 10.1007/978-1-0716-1884-4_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Vaccines are one of mankind's greatest medical advances, and their use has drastically reduced and in some cases eliminated (e.g., smallpox) disease and death caused by infectious agents. Traditional vaccine modalities including live-attenuated pathogen vaccines, wholly inactivated pathogen vaccines, and protein-based pathogen subunit vaccines have successfully been used to create efficacious vaccines against measles, mumps, rubella, polio, and yellow fever. These traditional vaccine modalities, however, take many months to years to develop and have thus proven less effective for use in creating vaccines to emerging or reemerging infectious diseases (EIDs) including influenza, Human immunodeficiency virus (HIV), dengue virus (DENV), chikungunya virus (CHIKV), West Nile virus (WNV), Middle East respiratory syndrome (MERS), and the severe acute respiratory syndrome coronaviruses 1 and 2 (SARS-CoV and SARS-CoV-2). As factors such as climate change and increased globalization continue to increase the pace of EID development, newer vaccine modalities are required to develop vaccines that can prevent or attenuate EID outbreaks throughout the world. One such modality, DNA vaccines, has been studied for over 30 years and has numerous qualities that make them ideal for meeting the challenge of EIDs including; (1) DNA vaccine candidates can be designed within hours of publishing of a pathogens genetic sequence; (2) they can be manufactured cheaply and rapidly in large quantities; (3) they are thermostable and have reduced requirement for a cold-chain during distribution, and (4) they have a remarkable safety record in the clinic. Optimizations made in plasmid design as well as in DNA vaccine delivery have greatly improved the immunogenicity of these vaccines. Here we describe the process of making a DNA vaccine to an EID pathogen and describe methods used for assessing the immunogenicity and protective efficacy of DNA vaccines in small animal models.
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Affiliation(s)
- Ziyang Xu
- Vaccine & Immunotherapy Center, The Wistar Institute, Philadelphia, PA, USA
| | - Michelle Ho
- Vaccine & Immunotherapy Center, The Wistar Institute, Philadelphia, PA, USA
| | - Devivasha Bordoloi
- Vaccine & Immunotherapy Center, The Wistar Institute, Philadelphia, PA, USA
| | | | - Makan Khoshnejad
- Vaccine & Immunotherapy Center, The Wistar Institute, Philadelphia, PA, USA
| | - Leila Giron
- Vaccine & Immunotherapy Center, The Wistar Institute, Philadelphia, PA, USA
| | - Faraz Zaidi
- Vaccine & Immunotherapy Center, The Wistar Institute, Philadelphia, PA, USA
| | | | | | | | - Joel Maslow
- GeneOne Life Science Inc., Seoul, South Korea
| | | | - Kar Muthumani
- Vaccine & Immunotherapy Center, The Wistar Institute, Philadelphia, PA, USA.
- GeneOne Life Science Inc., Seoul, South Korea.
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107
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Ioannou E, Labrou NE. Rational Design of Self-Assembling Supramolecular Protein Nanostructures Utilizing the Cucurbit[8]Uril Macrocyclic Host. Methods Mol Biol 2022; 2487:177-187. [PMID: 35687236 DOI: 10.1007/978-1-0716-2269-8_11] [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: 06/15/2023]
Abstract
Self-assembly is a phenomenon that governs molecular structural organization in nature, therefore raising research interest for the fabrication of novel nanomaterials with diverse applications in biocatalysis, biomedicine, material templating, and biosensor development. In this chapter we provide protocols for the development of supramolecular protein complexes based on host-guest interactions in the presence of the macrocyclic host, cucurbit[8]uril (CB[8]). CB[8] is reported to exhibit high binding affinity towards the tripeptide Phe-Gly-Gly (FGG), therefore it can be utilized as a selective adhesive of protein molecules, after fusion of FGG to an accessible protein surface.
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Affiliation(s)
- Elisavet Ioannou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Nikolaos E Labrou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece.
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108
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Tiambeng TN, Wu Z, Melby JA, Ge Y. Size Exclusion Chromatography Strategies and MASH Explorer for Large Proteoform Characterization. Methods Mol Biol 2022; 2500:15-30. [PMID: 35657584 PMCID: PMC9703982 DOI: 10.1007/978-1-0716-2325-1_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Top-down mass spectrometry (MS)-based analysis of larger proteoforms (>50 kDa) is typically challenging due to an exponential decay in the signal-to-noise ratio with increasing protein molecular weight (MW) and coelution with low-MW proteoforms. Size exclusion chromatography (SEC) fractionates proteins based on their size, separating larger proteoforms from those of smaller size in the proteome. In this protocol, we initially describe the use of SEC to fractionate high-MW proteoforms from low-MW proteoforms. Subsequently, the SEC fractions containing the proteoforms of interest are subjected to reverse-phase liquid chromatography (RPLC) coupled online with high-resolution MS. Finally, proteoforms are characterized using MASH Explorer, a user-friendly software environment for in-depth proteoform characterization.
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Affiliation(s)
- Timothy N. Tiambeng
- Department of Chemistry, University of Wisconsin – Madison, Madison, WI 53706
| | - Zhijie Wu
- Department of Chemistry, University of Wisconsin – Madison, Madison, WI 53706
| | - Jake A. Melby
- Department of Chemistry, University of Wisconsin – Madison, Madison, WI 53706
| | - Ying Ge
- Department of Chemistry, University of Wisconsin – Madison, Madison, WI 53706,Department of Cell and Regenerative Biology, University of Wisconsin – Madison, Madison, WI 53705,Human Proteomic Program, University of Wisconsin – Madison, Madison WI 53705,To whom correspondence may be addressed: Dr. Ying Ge, 8551 WIMR-II, 1111 Highland Ave., Madison, Wisconsin 53705, USA. ; Tel: 608-265-4744
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109
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Improving Isolation of Extracellular Vesicles by Utilizing Nanomaterials. MEMBRANES 2021; 12:membranes12010055. [PMID: 35054584 PMCID: PMC8780510 DOI: 10.3390/membranes12010055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 12/16/2021] [Accepted: 12/22/2021] [Indexed: 01/04/2023]
Abstract
Extracellular vesicles (EVs) as the new form of cellular communication have been demonstrated their potential use for disease diagnosis, prognosis and treatment. EVs are vesicles with a lipid bilayer and are present in various biofluids, such as blood, saliva and urine. Therefore, EVs have emerged as one of the most appealing sources for the discovery of clinical biomarkers. However, isolation of the target EVs from different biofluids is required for the use of EVs as diagnostic and therapeutic entities in clinical settings. Owing to their unique properties and versatile functionalities, nanomaterials have been widely investigated for EV isolation with the aim to provide rapid, simple, and efficient EV enrichment. Herein, this review presents the progress of nanomaterial-based isolations for EVs over the past five years (from 2017 to 2021) and discusses the use of nanomaterials for EV isolations based on the underlying mechanism in order to offer insights into the design of nanomaterials for EV isolations.
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110
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Cline EN, Alvarez C, Duan J, Patrie SM. Online μSEC 2-nRPLC-MS for Improved Sensitivity of Intact Protein Detection of IEF-Separated Nonhuman Primate Cerebrospinal Fluid Proteins. Anal Chem 2021; 93:16741-16750. [PMID: 34881887 PMCID: PMC10476446 DOI: 10.1021/acs.analchem.1c00396] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proteoform-resolved information, obtained by top-down (TD) "intact protein" proteomics, is expected to contribute substantially to the understanding of molecular pathogenic mechanisms and, in turn, identify novel therapeutic and diagnostic targets. However, the robustness of mass spectrometry (MS) analysis of intact proteins in complex biological samples is hindered by the high dynamic range in protein concentration and mass, protein instability, and buffer complexity. Here, we describe an evolutionary step for intact protein investigations through the online implementation of tandem microflow size-exclusion chromatography with nanoflow reversed-phase liquid chromatography and MS (μSEC2-nRPLC-MS). Online serial high-/low-pass SEC filtration overcomes the aforementioned hurdles to intact proteomic analysis through automated sample desalting/cleanup and enrichment of target mass ranges (5-155 kDa) prior to nRPLC-MS. The coupling of μSEC to nRPLC is achieved through a novel injection volume control (IVC) strategy of inserting protein trap columns, pre- and post-μSEC columns, to enable injection of dilute samples in high volumes without loss of sensitivity or resolution. Critical characteristics of the approach are tested via rigorous investigations on samples of varied complexity and chemical background. Application of the platform to cerebrospinal fluid (CSF) prefractionated by OFFGEL isoelectric focusing drastically increases the number of intact mass tags (IMTs) detected within the target mass range (5-30 kDa) in comparison to one-dimensional nRPLC-MS with approximately 100× less CSF than previous OFFGEL studies. Furthermore, the modular design of the μSEC2-nRPLC-MS platform is robust and promises significant flexibility for large-scale TDMS analysis of diverse samples either directly or in concert with other multidimensional fractionation steps.
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Affiliation(s)
- Erika N Cline
- Department of Chemistry and the Proteomics Center of Excellence, Northwestern University, 2145 Sheridan Rd, Evanston, Illinois 60208, United States
| | - Carina Alvarez
- Department of Chemistry and the Proteomics Center of Excellence, Northwestern University, 2145 Sheridan Rd, Evanston, Illinois 60208, United States
| | - Jiana Duan
- Department of Chemistry and the Proteomics Center of Excellence, Northwestern University, 2145 Sheridan Rd, Evanston, Illinois 60208, United States
| | - Steven M Patrie
- Department of Chemistry and the Proteomics Center of Excellence, Northwestern University, 2145 Sheridan Rd, Evanston, Illinois 60208, United States
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111
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Hu Y, Yang J, He C, Wei H, Wu G, Xiong H, Ma Y. Fractionation and purification of antioxidant peptides from abalone viscera by a combination of Sephadex G‐15 and Toyopearl HW‐40F chromatography. Int J Food Sci Technol 2021. [DOI: 10.1111/ijfs.15504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Yaqin Hu
- College of Ocean Food and Biological Engineering Fujian Provincial Engineering Technology Research Center of Marine Functional Food Jimei University Xiamen 361021 China
| | - Jiahong Yang
- College of Ocean Food and Biological Engineering Fujian Provincial Engineering Technology Research Center of Marine Functional Food Jimei University Xiamen 361021 China
| | - Chuanbo He
- College of Ocean Food and Biological Engineering Fujian Provincial Engineering Technology Research Center of Marine Functional Food Jimei University Xiamen 361021 China
| | - Haocheng Wei
- College of Ocean Food and Biological Engineering Fujian Provincial Engineering Technology Research Center of Marine Functional Food Jimei University Xiamen 361021 China
| | - Guohong Wu
- College of Ocean Food and Biological Engineering Fujian Provincial Engineering Technology Research Center of Marine Functional Food Jimei University Xiamen 361021 China
| | - Hejian Xiong
- College of Ocean Food and Biological Engineering Fujian Provincial Engineering Technology Research Center of Marine Functional Food Jimei University Xiamen 361021 China
| | - Ying Ma
- Fisheries College of Jimei University Xiamen 361021 China
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112
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Borman P, Campa C, Delpierre G, Hook E, Jackson P, Kelley W, Protz M, Vandeputte O. Selection of Analytical Technology and Development of Analytical Procedures Using the Analytical Target Profile. Anal Chem 2021; 94:559-570. [PMID: 34928590 DOI: 10.1021/acs.analchem.1c03854] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A structured approach to method development can help to ensure an analytical procedure is robust across the lifecycle of its use. The analytical target profile (ATP), which describes the required quality of the reportable value to be produced by the analytical procedure, enables the analytical scientist to select the best analytical technology on which to develop their procedure(s). Once the technology has been identified, screening of potentially fit for purpose analytical procedures should take place. Analytical procedures that have been demonstrated to meet the ATP should be evaluated against business drivers (e.g., operational constraints) to determine the most suitable analytical procedure. Three case studies are covered from across small molecules, vaccines, and biotherapeutics. The case studies cover different aspects of the analytical procedure selection process, such as the use of platform method development processes and procedures, the development of multiattribute analytical procedures, and the use of analytical technologies to provide product characterization knowledge in order to define or redefine the ATP. Challenges associated with method selection are discussed such as where existing pharmacopoeial monographs link acceptance criteria to specific types of analytical technology.
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Affiliation(s)
- Phil Borman
- Product Development and Supply, GSK, Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, U.K
| | - Cristiana Campa
- Technical Research & Development, Vaccines, GSK, Via Fiorentina 1, 53100 Siena, Italy
| | | | - Elliot Hook
- Global Pharma Analytical Science and Technology, Pharma Supply Chain, GSK, Priory Street, Ware, SG12 0DJ, U.K
| | - Patrick Jackson
- Product Development and Supply, GSK, Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, U.K
| | - Wayne Kelley
- Product Development and Supply, GSK, King of Prussia, Pennsylvania 19406, United States
| | - Michel Protz
- Analytical Research and Development, GSK, 1330 Rixensart, Belgium
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113
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Martins CSM, Sousa HBA, Prior JAV. From Impure to Purified Silver Nanoparticles: Advances and Timeline in Separation Methods. NANOMATERIALS 2021; 11:nano11123407. [PMID: 34947761 PMCID: PMC8703312 DOI: 10.3390/nano11123407] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 11/21/2022]
Abstract
AgNPs have exceptional characteristics that depend on their size and shape. Over the past years, there has been an exponential increase in applications of nanoparticles (NPs), especially the silver ones (AgNPs), in several areas, such as, for example, electronics; environmental, pharmaceutical, and toxicological applications; theragnostics; and medical treatments, among others. This growing use has led to a greater exposure of humans to AgNPs and a higher risk to human health and the environment. This risk becomes more aggravated when the AgNPs are used without purification or separation from the synthesis medium, in which the hazardous synthesis precursors remain unseparated from the NPs and constitute a severe risk for unnecessary environmental contamination. This review examines the situation of the available separation methods of AgNPs from crude suspensions or real samples. Different separation techniques are reviewed, and relevant data are discussed, with a focus on the sustainability and efficiency of AgNPs separation methods.
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114
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Particles in Biopharmaceutical Formulations, Part 2: An Update on Analytical Techniques and Applications for Therapeutic Proteins, Viruses, Vaccines and Cells. J Pharm Sci 2021; 111:933-950. [PMID: 34919969 DOI: 10.1016/j.xphs.2021.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 12/09/2021] [Accepted: 12/09/2021] [Indexed: 11/21/2022]
Abstract
Particles in biopharmaceutical formulations remain a hot topic in drug product development. With new product classes emerging it is crucial to discriminate particulate active pharmaceutical ingredients from particulate impurities. Technical improvements, new analytical developments and emerging tools (e.g., machine learning tools) increase the amount of information generated for particles. For a proper interpretation and judgment of the generated data a thorough understanding of the measurement principle, suitable application fields and potential limitations and pitfalls is required. Our review provides a comprehensive overview of novel particle analysis techniques emerging in the last decade for particulate impurities in therapeutic protein formulations (protein-related, excipient-related and primary packaging material-related), as well as particulate biopharmaceutical formulations (virus particles, virus-like particles, lipid nanoparticles and cell-based medicinal products). In addition, we review the literature on applications, describe specific analytical approaches and illustrate advantages and drawbacks of currently available techniques for particulate biopharmaceutical formulations.
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115
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Kim AY, Park SY, Park SH, Jin JS, Kim ES, Kim JY, Park JH, Ko YJ. Validation of Pretreatment Methods for the In-Process Quantification of Foot-and-Mouth Disease Vaccine Antigens. Vaccines (Basel) 2021; 9:vaccines9111361. [PMID: 34835292 PMCID: PMC8624908 DOI: 10.3390/vaccines9111361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/10/2021] [Accepted: 11/18/2021] [Indexed: 01/10/2023] Open
Abstract
Foot-and-mouth disease (FMD), caused by the FMD virus (FMDV), is controlled by vaccine policy in many countries. For vaccine potency, the content of intact virus particles (146S antigens) is critical, and the sucrose density gradient (SDG) fractionation is the gold standard for the quantification of 146S antigens. However, this method has several drawbacks. Although size-exclusion high-performance liquid chromatography (SE-HPLC) was introduced to replace the classic method, its application is generally confined to purified samples owing to the interfering signals. Therefore, we aimed to develop optimal pretreatment methods for SE-HPLC quantification in less purified samples. Crude virus infection supernatant (CVIS) and semi-purified samples with PEG precipitation (PEG-P) were used. Chloroform pretreatment was essential to remove a high level of non-specific signals in CVIS, whereas it caused loss of 146S antigens without the distinctive removal of non-specific signals in PEG-P. Benzonase pretreatment was required to improve the resolution of the target peak in the chromatogram for both CVIS and PEG-P. Through spiking tests with pure 146S antigens, it was verified that the combined pretreatment with chloroform and benzonase was optimal for the CVIS, while the sole pretreatment of benzonase was beneficial for PEG-P.
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Affiliation(s)
| | | | | | | | | | | | | | - Young-Joon Ko
- Correspondence: ; Tel.: +82-54-912-0908; Fax: +82-54-912-0890
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116
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Choy CH, He L, Tulumello D, Gajewska B, Terebiznik MR, Botelho RJ, Azizi A. Aggregation and Size Attributes Analysis of Unadsorbed and Adjuvant-adsorbed Antigens using a Multispectral Imaging Flow Cytometer Platform. J Pharm Sci 2021; 111:672-679. [PMID: 34742727 DOI: 10.1016/j.xphs.2021.10.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 10/30/2021] [Accepted: 10/30/2021] [Indexed: 11/26/2022]
Abstract
Various vaccine quality attributes should be monitored to ensure consistency, potency, purity, and safety of vaccine products prior to lot release. Vaccine particle size and protein antigen aggregation are two important considerations for particle-adsorbed vaccines. In this study, we evaluated the use of imaging flow cytometry as a potential all-in-one platform to measure adjuvant particle size and to detect protein aggregates through a combination of brightfield microscopy, side scatter detection, and fluorescence microscopy. An aluminum phosphate adjuvant was analyzed for size using the brightfield function, and the size measurement was compared against laser diffraction. Heat-induced protein aggregates of either unadsorbed antigens or aluminum phosphate adjuvant-adsorbed antigens were stained with the fluorescent ProteoStat aggregation dye, followed by detection and analysis using a combination of the brightfield and fluorescence microscopy functions. The change in aggregation of unadsorbed antigens was confirmed using dynamic light scattering. These results demonstrate the versatility of the imaging flow cytometry platform for the evaluation of multiple vaccine quality characteristics.
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Affiliation(s)
- Christopher H Choy
- Immunology platform, Analytical Sciences North America, Sanofi Pasteur, 1755 Steeles Avenue West, Toronto, ON, M2R 3T4, Canada; Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, M5B 2K3, Canada
| | - Liwei He
- Immunology platform, Analytical Sciences North America, Sanofi Pasteur, 1755 Steeles Avenue West, Toronto, ON, M2R 3T4, Canada
| | - David Tulumello
- Biochemistry platform, Analytical Sciences North America, Sanofi Pasteur, 1755 Steeles Avenue West, Toronto, Ontario, M2R 3T4, Canada
| | - Beata Gajewska
- Immunology platform, Analytical Sciences North America, Sanofi Pasteur, 1755 Steeles Avenue West, Toronto, ON, M2R 3T4, Canada
| | - Mauricio R Terebiznik
- Department of Biological Sciences, University of Toronto at Scarborough, Toronto, Ontario, M1C 1A4, Canada
| | - Roberto J Botelho
- Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, M5B 2K3, Canada
| | - Ali Azizi
- Immunology platform, Analytical Sciences North America, Sanofi Pasteur, 1755 Steeles Avenue West, Toronto, ON, M2R 3T4, Canada.
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117
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Shivange G, Mondal T, Lyerly E, Bhatnagar S, Landen CN, Reddy S, Kim J, Doan B, Riddle P, Tushir-Singh J. A patch of positively charged residues regulates the efficacy of clinical DR5 antibodies in solid tumors. Cell Rep 2021; 37:109953. [PMID: 34731630 PMCID: PMC8720280 DOI: 10.1016/j.celrep.2021.109953] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 07/19/2021] [Accepted: 10/15/2021] [Indexed: 11/16/2022] Open
Abstract
Receptor clustering is the first and critical step to activate apoptosis by death receptor-5 (DR5). The recent discovery of the autoinhibitory DR5 ectodomain has challenged the long-standing view of its mechanistic activation by the natural ligand Apo2L. Because the autoinhibitory residues have remained unknown, here we characterize a crucial patch of positively charged residues (PPCR) in the highly variable domain of DR5. The PPCR electrostatically separates DR5 receptors to autoinhibit their clustering in the absence of ligand and antibody binding. Mutational substitution and antibody-mediated PPCR interference resulted in increased apoptotic cytotoxic function. A dually specific antibody that enables sustained tampering with PPCR function exceptionally enhanced DR5 clustering and apoptotic activation and distinctively improved the survival of animals bearing aggressive metastatic and recurrent tumors, whereas clinically tested DR5 antibodies without PPCR blockade function were largely ineffective. Our study provides mechanistic insights into DR5 activation and a therapeutic analytical design for potential clinical success.
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MESH Headings
- A549 Cells
- Animals
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/metabolism
- Antibodies, Monoclonal/pharmacology
- Antibodies, Monoclonal, Humanized/immunology
- Antibodies, Monoclonal, Humanized/metabolism
- Antibodies, Monoclonal, Humanized/pharmacology
- Antibody Specificity
- Antineoplastic Agents, Immunological/immunology
- Antineoplastic Agents, Immunological/metabolism
- Antineoplastic Agents, Immunological/pharmacology
- Apoptosis/drug effects
- Epitopes
- Humans
- Mice, Inbred C57BL
- Mice, Inbred NOD
- Mice, SCID
- Neoplasms/drug therapy
- Neoplasms/immunology
- Neoplasms/metabolism
- Receptors, TNF-Related Apoptosis-Inducing Ligand/antagonists & inhibitors
- Receptors, TNF-Related Apoptosis-Inducing Ligand/immunology
- Receptors, TNF-Related Apoptosis-Inducing Ligand/metabolism
- Signal Transduction
- Tumor Burden/drug effects
- Xenograft Model Antitumor Assays
- Mice
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Affiliation(s)
- Gururaj Shivange
- Laboratory of Novel Biologics, Medical Microbiology and Immunology, University of California, Davis, Davis, CA 95616, USA; Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville VA 22908, USA
| | - Tanmoy Mondal
- Laboratory of Novel Biologics, Medical Microbiology and Immunology, University of California, Davis, Davis, CA 95616, USA; Department of Medical Microbiology and Immunology, University of California School of Medicine, University of California, Davis, Davis, CA 95616, USA; Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville VA 22908, USA
| | - Evan Lyerly
- Laboratory of Novel Biologics, Medical Microbiology and Immunology, University of California, Davis, Davis, CA 95616, USA; Undergraduate Research Program Volunteers, University of Virginia, Charlottesville VA; Blavatnik Institute, Harvard Medical School, Boston MA
| | - Sanchita Bhatnagar
- Department of Medical Microbiology and Immunology, University of California School of Medicine, University of California, Davis, Davis, CA 95616, USA; Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville VA 22908, USA
| | | | - Shivani Reddy
- Laboratory of Novel Biologics, Medical Microbiology and Immunology, University of California, Davis, Davis, CA 95616, USA; Undergraduate Research Program Volunteers, University of Virginia, Charlottesville VA
| | - Jonathan Kim
- Laboratory of Novel Biologics, Medical Microbiology and Immunology, University of California, Davis, Davis, CA 95616, USA; Undergraduate Research Program Volunteers, University of Virginia, Charlottesville VA
| | - Britney Doan
- Laboratory of Novel Biologics, Medical Microbiology and Immunology, University of California, Davis, Davis, CA 95616, USA; Undergraduate Research Program Volunteers, University of Virginia, Charlottesville VA
| | - Paula Riddle
- Laboratory of Novel Biologics, Medical Microbiology and Immunology, University of California, Davis, Davis, CA 95616, USA; Undergraduate Research Program Volunteers, University of Virginia, Charlottesville VA
| | - Jogender Tushir-Singh
- Laboratory of Novel Biologics, Medical Microbiology and Immunology, University of California, Davis, Davis, CA 95616, USA; Department of Medical Microbiology and Immunology, University of California School of Medicine, University of California, Davis, Davis, CA 95616, USA; Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville VA 22908, USA; University of Virginia Comprehensive Cancer Center, Charlottesville VA; UC Davis Comprehensive Cancer Center, University of California School of Medicine, University of California, Davis, Davis, CA 95616, USA.
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118
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Shatat SM, Al-Ghobashy MA, Fathalla FA, Abbas SS, Eltanany BM. Coupling of Trastuzumab chromatographic profiling with machine learning tools: A complementary approach for biosimilarity and stability assessment. J Chromatogr B Analyt Technol Biomed Life Sci 2021; 1184:122976. [PMID: 34656909 DOI: 10.1016/j.jchromb.2021.122976] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 09/13/2021] [Accepted: 09/15/2021] [Indexed: 12/14/2022]
Abstract
Biosimilar products present a growing opportunity to improve the global healthcare systems. The amount of accepted variability during the comparative assessments of biosimilar products introduces a significant challenge for both the biosimilar developers and the regulatory authorities. The aim of this study was to explore unsupervised machine learning tools as a mathematical aid for the interpretation and visualization of such comparability under control and stress conditions using data extracted from high throughput analytical techniques. For this purpose, a head-to-head analysis of the physicochemical characteristics of three Trastuzumab (TTZ) approved biosimilars and the originator product (Herceptin®) was performed. The studied quality attributes included the primary structure and identity by peptide mapping (PM) with reversed-phase chromatography-UV detection, size and charge profiles by stability-indicating size exclusion and cation exchange chromatography. Stress conditions involved pH and thermal stress. Principal component analysis (PCA) and two of the widely used cluster analysis tools, namely, K-means and Density-based Spatial Clustering of Applications with Noise (DBSCAN), were explored for clustering and feature representation of varied analytical datasets. It has been shown that the clustering patterns delineated by the used algorithms changed based on the included chromatographic profiles. The applied data analysis tools were found effective in revealing patterns of similarity and variability between i) intact and stressed as well as ii) originator and biosimilar samples.
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Affiliation(s)
- Sara M Shatat
- National Organization for Research and Control of Biologicals, Egypt
| | - Medhat A Al-Ghobashy
- Analytical Chemistry Department, Faculty of Pharmacy, Cairo University, Egypt; Bioanalysis Research Group, School of Pharmacy, Newgiza University, Egypt
| | - Faten A Fathalla
- National Organization for Research and Control of Biologicals, Egypt
| | - Samah S Abbas
- Analytical Chemistry Department, Faculty of Pharmacy, Cairo University, Egypt
| | - Basma M Eltanany
- Analytical Chemistry Department, Faculty of Pharmacy, Cairo University, Egypt.
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119
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Weissman JD, Singh AK, Devaiah BN, Schuck P, LaRue RC, Singer DS. The intrinsic kinase activity of BRD4 spans its BD2-B-BID domains. J Biol Chem 2021; 297:101326. [PMID: 34688663 PMCID: PMC8591364 DOI: 10.1016/j.jbc.2021.101326] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/29/2021] [Accepted: 10/02/2021] [Indexed: 11/26/2022] Open
Abstract
Bromodomain protein 4 (BRD4) is a transcriptional and epigenetic regulator that is a therapeutic target in many cancers and inflammatory diseases. BRD4 plays important roles in transcription as an active kinase, which phosphorylates the carboxy-terminal domain (CTD) of RNA polymerase II (Pol II), the proto-oncogene c-MYC, and transcription factors TAF7 and CDK9. BRD4 is also a passive scaffold that recruits transcription factors. Despite these well-established functions, there has been little characterization of BRD4’s biophysical properties or its kinase activity. We report here that the 156 kD mouse BRD4 exists in an extended dimeric conformation with a sedimentation coefficient of ∼6.7 S and a high frictional ratio. Deletion of the conserved B motif (aa 503–548) disrupts BRD4’s dimerization. BRD4 kinase activity maps to amino acids 351 to 598, which span bromodomain-2, the B motif, and the BID domain (BD2-B-BID) and contributes to the in vivo phosphorylation of its substrates. As further assessed by analytical ultracentrifugation, BRD4 directly binds purified Pol II CTD. Importantly, the conserved A motif of BRD4 is essential for phosphorylation of Pol II CTD, but not for phosphorylation of TAF7, mapping its binding site to the A motif. Peptides of the viral MLV integrase (MLVIN) protein and cellular histone lysine methyltransferase, NSD3, which have been shown by NMR to bind to the extra-terminal (ET) domain, also are phosphorylated by BRD4. Thus, BRD4 has multiple distinct substrate-binding sites and a common kinase domain. These results provide new insights into the structure and kinase function of BRD4.
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Affiliation(s)
- Jocelyn D Weissman
- Experimental Immunology Branch, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Amit K Singh
- Experimental Immunology Branch, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Ballachanda N Devaiah
- Experimental Immunology Branch, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Peter Schuck
- Dynamics of Macromolecular Assembly Section, National Institute of Biomedical Imaging and Bioengineering, NIH, Bethesda, Maryland, USA
| | - Ross C LaRue
- Department of Cancer Biology and Genetics, College of Medicine, and Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio, USA
| | - Dinah S Singer
- Experimental Immunology Branch, National Cancer Institute, NIH, Bethesda, Maryland, USA.
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120
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Singh SM, Furman R, Singh RK, Balakrishnan G, Chennamsetty N, Tao L, Li Z. Size exclusion chromatography for the characterization and quality control of biologics. J LIQ CHROMATOGR R T 2021. [DOI: 10.1080/10826076.2021.1979582] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Surinder M. Singh
- Analytical Development and Attribute Sciences, New Brunswick, NJ, USA
| | - Ran Furman
- Analytical Development and Attribute Sciences, New Brunswick, NJ, USA
| | - Rajesh K. Singh
- Analytical Development and Attribute Sciences, New Brunswick, NJ, USA
| | | | | | - Li Tao
- Analytical Development and Attribute Sciences, New Brunswick, NJ, USA
| | - Zhengjian Li
- Analytical Development and Attribute Sciences, New Brunswick, NJ, USA
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121
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Scaled preparation of extracellular vesicles from conditioned media. Adv Drug Deliv Rev 2021; 177:113940. [PMID: 34419502 DOI: 10.1016/j.addr.2021.113940] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 07/13/2021] [Accepted: 08/16/2021] [Indexed: 12/15/2022]
Abstract
Extracellular vesicles (EVs) especially of mesenchymal stem/stomal cells (MSCs) are increasingly considered as biotherapeutic agents for a variety of different diseases. For translating them effectively into the clinics, scalable production processes fulfilling good manufacturing practice (GMP) are needed. Like for other biotherapeutic agents, the manufacturing of EV products can be subdivided in the upstream and downstream processing and the subsequent quality control, each of them containing several unit operations. During upstream processing (USP), cells are isolated, stored (cell banking) and expanded; furthermore, EV-containing conditioned media are produced. During downstream processing (DSP), conditioned media (CM) are processed to obtain concentrated and purified EV products. CM are either stored until DSP or are directly processed. As first unit operation in DSP, clarification removes remaining cells, debris and other larger impurities. The key operations of each EV DSP is volume-reduction combined with purification of the concentrated EVs. Most of the EV preparation methods used in conventional research labs including differential centrifugation procedures are limited in their scalability. Consequently, it is a major challenge in the therapeutic EV field to identify appropriate EV concentration and purification methods allowing scale up. As EVs share several features with enveloped viruses, that are used for more than two decades in the clinics now, several principles can be adopted to EV manufacturing. Here, we introduce and discuss volume reducing and purification methods frequently used for viruses and analyze their value for the manufacturing of EV-based therapeutics.
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122
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Kato T, Vykoukal JV, Fahrmann JF, Hanash S. Extracellular Vesicles in Lung Cancer: Prospects for Diagnostic and Therapeutic Applications. Cancers (Basel) 2021; 13:cancers13184604. [PMID: 34572829 PMCID: PMC8469977 DOI: 10.3390/cancers13184604] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/08/2021] [Accepted: 09/10/2021] [Indexed: 02/04/2023] Open
Abstract
Extracellular vesicles (EVs) are nano-sized lipid-bound particles containing proteins, nucleic acids and metabolites released by cells. They have been identified in body fluids including blood, saliva, sputum and pleural effusions. In tumors, EVs derived from cancer and immune cells mediate intercellular communication and exchange, and can affect immunomodulatory functions. In the context of lung cancer, emerging evidence implicates EV involvement during various stages of tumor development and progression, including angiogenesis, epithelial to mesenchymal transformation, immune system suppression, metastasis and drug resistance. Additionally, tumor-derived EVs (TDEs) have potential as a liquid biopsy source and as a means of therapeutic targeting, and there is considerable interest in developing clinical applications for EVs in these contexts. In this review, we consider the biogenesis, components, biological functions and isolation methods of EVs, and the implications for their clinical utility for diagnostic and therapeutic applications in lung cancer.
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Affiliation(s)
- Taketo Kato
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA; (T.K.); (J.V.V.); (J.F.F.)
| | - Jody V. Vykoukal
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA; (T.K.); (J.V.V.); (J.F.F.)
- The McCombs Institute for the Early Detection and Treatment of Cancer, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Johannes F. Fahrmann
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA; (T.K.); (J.V.V.); (J.F.F.)
| | - Samir Hanash
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA; (T.K.); (J.V.V.); (J.F.F.)
- The McCombs Institute for the Early Detection and Treatment of Cancer, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Correspondence:
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123
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Madhu P, Mukhopadhyay S. Distinct types of amyloid-β oligomers displaying diverse neurotoxicity mechanisms in Alzheimer's disease. J Cell Biochem 2021; 122:1594-1608. [PMID: 34494298 DOI: 10.1002/jcb.30141] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/21/2021] [Accepted: 08/26/2021] [Indexed: 11/09/2022]
Abstract
Soluble oligomers of amyloid-β (Aβ) are recognized as key pernicious species in Alzheimer's disease (AD) that cause synaptic dysfunction and memory impairments. Numerous studies have identified various types of Aβ oligomers having heterogeneous peptide length, size distribution, structure, appearance, and toxicity. Here, we review the characteristics of soluble Aβ oligomers based on their morphology, size, and structural reactivity toward the conformation-specific antibodies and then describe their formation, localization, and cellular effects in AD brains, in vivo and in vitro. We also summarize the mechanistic pathways by which these soluble Aβ oligomers cause proteasomal impairment, calcium dyshomeostasis, inhibition of long-term potentiation, apoptosis, mitochondrial damage, and cognitive decline. These cellular events include three distinct molecular mechanisms: (i) high-affinity binding with the receptors for Aβ oligomers such as N-methyl- d-aspartate receptors, cellular prion protein, nerve growth factor, insulin receptors, and frizzled receptors; (ii) the interaction of Aβ oligomers with the lipid membranes; (iii) intraneuronal accumulation of Aβ by α7-nicotinic acetylcholine receptors, apolipoprotein E, and receptor for advanced glycation end products. These studies indicate that there is a pressing need to carefully examine the role of size, appearance, and the conformation of oligomers in identifying the specific mechanism of neurotoxicity that may uncover potential targets for designing AD therapeutics.
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Affiliation(s)
- Priyanka Madhu
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER), Mohali, India.,Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Mohali, India
| | - Samrat Mukhopadhyay
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER), Mohali, India.,Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Mohali, India.,Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Mohali, India
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124
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Liang BJ, Lusvarghi S, Ambudkar SV, Huang HC. Use of photoimmunoconjugates to characterize ABCB1 in cancer cells. NANOPHOTONICS 2021; 10:3049-3061. [PMID: 35070633 PMCID: PMC8773461 DOI: 10.1515/nanoph-2021-0252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Accurate detection of ATP-binding cassette drug transporter ABCB1 expression is imperative for precise identification of drug-resistant tumors. Existing detection methods fail to provide the necessary molecular details regarding the functional state of the transporter. Photo-immunoconjugates are a unique class of antibody-dye conjugates for molecular diagnosis and therapeutic treatment. However, conjugating hydrophobic photosensitizers to hydrophilic antibodies is quite challenging. Here, we devise a photoimmunoconjugate that combines a clinically approved benzoporphyrin derivative (BPD) photosensitizer and the conformational-sensitive UIC2 monoclonal antibody to target functionally active human ABCB1 (i.e., ABCB1 in the inward-open conformation). We show that PEGylation of UIC2 enhances the BPD conjugation efficiency and reduces the amount of non-covalently conjugated BPD molecules by 17%. Size exclusion chromatography effectively separates the different molecular weight species found in the UIC2-BPD sample. The binding of UIC2-BPD to ABCB1 was demonstrated in lipidic nanodiscs and ABCB1-overexpressing triple negative breast cancer (TNBC) cells. UIC2-BPD was found to retain the conformation sensitivity of UIC2, as the addition of ABCB1 modulators increases the antibody reactivity in vitro. Thus, the inherent fluorescence capability of BPD can be used to label ABCB1-overexpressing TNBC cells using UIC2-BPD. Our findings provide insight into conjugation of hydrophobic photosensitizers to conformation-sensitive antibodies to target proteins expressed on the surface of cancer cells.
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Affiliation(s)
- Barry J. Liang
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA; and Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sabrina Lusvarghi
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Suresh V. Ambudkar
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Room 2120, Bldg 37, 37 Convent Drive, Bethesda, MD 20892-4256, USA
| | - Huang-Chiao Huang
- Fischell Department of Bioengineering, University of Maryland, 8278 Paint Branch Drive, College Park, MD 20742-5031, USA; and Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201-1595, USA
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125
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Valtonen S, Vuorinen E, Eskonen V, Malakoutikhah M, Kopra K, Härmä H. Sensitive, homogeneous, and label-free protein-probe assay for antibody aggregation and thermal stability studies. MAbs 2021; 13:1955810. [PMID: 34455913 PMCID: PMC8409793 DOI: 10.1080/19420862.2021.1955810] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Protein aggregation is a spontaneous process affected by multiple external and internal properties, such as buffer composition and storage temperature. Aggregation of protein-based drugs can endanger patient safety due, for example, to increased immunogenicity. Aggregation can also inactivate protein drugs and prevent target engagement, and thus regulatory requirements are strict regarding drug stability monitoring during manufacturing and storage. Many of the current technologies for aggregation monitoring are time- and material-consuming and require specific instruments and expertise. These types of assays are not only expensive, but also unsuitable for larger sample panels. Here we report a label-free time-resolved luminescence-based method using an external Eu3+-conjugated probe for the simple and fast detection of protein stability and aggregation. We focused on monitoring the properties of IgG, which is a common format for biological drugs. The Protein-Probe assay enables IgG aggregation detection with a simple single-well mix-and-measure assay performed at room temperature. Further information can be obtained in a thermal ramping, where IgG thermal stability is monitored. We showed that with the Protein-Probe, trastuzumab aggregation was detected already after 18 hours of storage at 60°C, 4 to 8 days earlier compared to SYPRO Orange- and UV250-based assays, respectively. The ultra-high sensitivity of less than 0.1% IgG aggregates enables the Protein-Probe to reduce assay time and material consumption compared to existing techniques.
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Affiliation(s)
- Salla Valtonen
- Department of Chemistry, University of Turku, Turku, Finland
| | | | - Ville Eskonen
- Department of Chemistry, University of Turku, Turku, Finland
| | | | - Kari Kopra
- Department of Chemistry, University of Turku, Turku, Finland
| | - Harri Härmä
- Department of Chemistry, University of Turku, Turku, Finland
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126
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Calvaresi V, Redsted A, Norais N, Rand KD. Hydrogen-Deuterium Exchange Mass Spectrometry with Integrated Size-Exclusion Chromatography for Analysis of Complex Protein Samples. Anal Chem 2021; 93:11406-11414. [PMID: 34387074 DOI: 10.1021/acs.analchem.1c01171] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The growing use of hydrogen-deuterium exchange mass spectrometry (HDX-MS) for studying membrane proteins, large protein assemblies, and highly disulfide-bonded species is often challenged by the presence in the sample of large amounts of lipids, protein ligands, and/or highly ionizable reducing agents. Here, we describe how a short size-exclusion chromatography (SEC) column can be integrated with a conventional temperature-controlled HDX-MS setup to achieve fast and online removal of unwanted species from the HDX sample prior to chromatographic separation and MS analysis. Dual-mode valves permit labeled proteins eluting after SEC to be directed to the proteolytic and chromatographic columns, while unwanted sample components are led to waste. The SEC-coupled HDX-MS method allows analyses to be completed with lower or similar back-exchange compared to conventional experiments. We demonstrate the suitability of the method for the analysis of challenging protein samples, achieving efficient online removal of lipid components from protein-lipid systems, depletion of an antibody from an antigen during epitope mapping, and elimination of MS interfering compounds such as tris(2-carboxyethyl)phosphine (TCEP) during HDX-MS analysis of a disulfide-bonded protein. The implementation of the short SEC column to the conventional HDX-MS setup is straightforward and could be of significant general utility during the HDX-MS analysis of complex protein states.
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Affiliation(s)
- Valeria Calvaresi
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Copenhagen 2100, Denmark.,GSK, Siena 53100, Italy
| | - Andreas Redsted
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Copenhagen 2100, Denmark.,GSK, Siena 53100, Italy
| | | | - Kasper D Rand
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Copenhagen 2100, Denmark
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127
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Sharma S, Modi P, Sharma G, Deep S. Kinetics theories to understand the mechanism of aggregation of a protein and to design strategies for its inhibition. Biophys Chem 2021; 278:106665. [PMID: 34419715 DOI: 10.1016/j.bpc.2021.106665] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 12/14/2022]
Abstract
Protein aggregation phenomenon is closely related to the formation of amyloids which results in many neurodegenerative diseases like Alzheimer's, Parkinson's, Huntington's, and Amyotrophic Lateral Sclerosis. In order to prevent and treat these diseases, a clear understanding of the mechanism of misfolding and self-assembly of peptides and proteins is very crucial. The aggregation of a protein may involve various microscopic events. Multiple simulations utilizing the solutions of the master equation have given a better understanding of the kinetic profiles involved in the presence and absence of a particular microscopic event. This review focuses on understanding the contribution of these molecular events to protein aggregation based on the analysis of kinetic profiles of aggregation. We also discuss the effect of inhibitors, which target various species of aggregation pathways, on the kinetic profile of protein aggregation. At the end of this review, some strategies for the inhibition of aggregation that can be utilized by combining the chemical kinetics approach with thermodynamics are proposed.
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Affiliation(s)
- Shilpa Sharma
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Priya Modi
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Gargi Sharma
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Shashank Deep
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
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128
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Soltermann F, Struwe WB, Kukura P. Label-free methods for optical in vitro characterization of protein-protein interactions. Phys Chem Chem Phys 2021; 23:16488-16500. [PMID: 34342317 PMCID: PMC8359934 DOI: 10.1039/d1cp01072g] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 07/23/2021] [Indexed: 12/13/2022]
Abstract
Protein-protein interactions are involved in the regulation and function of the majority of cellular processes. As a result, much effort has been aimed at the development of methodologies capable of quantifying protein-protein interactions, with label-free methods being of particular interest due to the associated simplified workflows and minimisation of label-induced perturbations. Here, we review recent advances in optical technologies providing label-free in vitro measurements of affinities and kinetics. We provide an overview and comparison of existing techniques and their principles, discussing advantages, limitations, and recent applications.
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Affiliation(s)
- Fabian Soltermann
- Physical and Theoretical Chemistry, Department of Chemistry, University of OxfordUK
| | - Weston B. Struwe
- Physical and Theoretical Chemistry, Department of Chemistry, University of OxfordUK
| | - Philipp Kukura
- Physical and Theoretical Chemistry, Department of Chemistry, University of OxfordUK
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129
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Shirejini SZ, Inci F. The Yin and Yang of exosome isolation methods: conventional practice, microfluidics, and commercial kits. Biotechnol Adv 2021; 54:107814. [PMID: 34389465 DOI: 10.1016/j.biotechadv.2021.107814] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 08/08/2021] [Accepted: 08/08/2021] [Indexed: 12/18/2022]
Abstract
Exosomes are a subset of extracellular vesicles released from various cells, and they can be found in different bodily fluids. Exosomes are used as biomarkers to diagnose many diseases and to monitor therapy efficiency as they represent the status and origin of the cell, which they are released from. Considering that they co-exist in bodily fluids with other types of particles, their isolation still remains challenging since conventional separation methods are time-consuming, user-dependent, and result in low isolation yield. This review summarizes the conventional strategies and microfluidic-based methods for exosome isolation along with their strengths and limitations. Microfluidic devices emerge as a promising approach to overcome the limitations of the conventional methods due to their inherent characteristics, such as the need for minute sample volume and rapid operation, in order to isolate exosomes with a high yield and a high purity in a short amount of time, which make them unprecedented tools for molecular biology and clinical applications. This review elaborates on the existing microfluidic-based exosome isolation methods and denotes their benefits and drawbacks. Herein, we also introduce various commercially available platforms and kits for exosome isolation along with their working principles.
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Affiliation(s)
- Saeedreza Zeibi Shirejini
- UNAM-National Nanotechnology Research Center, Bilkent University, 06800 Ankara, Turkey; Institute of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey
| | - Fatih Inci
- UNAM-National Nanotechnology Research Center, Bilkent University, 06800 Ankara, Turkey; Institute of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey.
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130
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Tacias-Pascacio VG, Morellon-Sterling R, Castañeda-Valbuena D, Berenguer-Murcia Á, Kamli MR, Tavano O, Fernandez-Lafuente R. Immobilization of papain: A review. Int J Biol Macromol 2021; 188:94-113. [PMID: 34375660 DOI: 10.1016/j.ijbiomac.2021.08.016] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/22/2021] [Accepted: 08/03/2021] [Indexed: 12/13/2022]
Abstract
Papain is a cysteine protease from papaya, with many applications due to its broad specificity. This paper reviews for first time the immobilization of papain on different supports (organic, inorganic or hybrid supports) presenting some of the features of the utilized immobilization strategies (e.g., epoxide, glutaraldehyde, genipin, glyoxyl for covalent immobilization). Special focus is placed on the preparation of magnetic biocatalysts, which will permit the simple recovery of the biocatalyst even if the medium is a suspension. Problems specific to the immobilization of proteases (e.g., steric problems when hydrolyzing large proteins) are also defined. The benefits of a proper immobilization (enzyme stabilization, widening of the operation window) are discussed, together with some artifacts that may suggest an enzyme stabilization that may be unrelated to enzyme rigidification.
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Affiliation(s)
- Veymar G Tacias-Pascacio
- Facultad de Ciencias de la Nutrición y Alimentos, Universidad de Ciencias y Artes de Chiapas, Lib. Norte Pte. 1150, 29039 Tuxtla Gutiérrez, Chiapas, Mexico; Tecnológico Nacional de México/Instituto Tecnológico de Tuxtla Gutiérrez, Carretera Panamericana Km. 1080, 29050 Tuxtla Gutiérrez, Chiapas, Mexico
| | - Roberto Morellon-Sterling
- Departamento de Biocatálisis. ICP-CSIC./Marie Curie 2, Campus UAM-CSIC Cantoblanco, 28049 Madrid. Spain; Student of Departamento de Biología Molecular, Universidad Autónoma de Madrid, Darwin 2, Campus UAM-CSIC, Cantoblanco, 28049 Madrid. Spain
| | - Daniel Castañeda-Valbuena
- Tecnológico Nacional de México/Instituto Tecnológico de Tuxtla Gutiérrez, Carretera Panamericana Km. 1080, 29050 Tuxtla Gutiérrez, Chiapas, Mexico
| | - Ángel Berenguer-Murcia
- Departamento de Química Inorgánica e Instituto Universitario de Materiales, Universidad de Alicante, Alicante, Spain
| | - Majid Rasool Kamli
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddad 21589, Saudi Arabia; Center of excellence in Bionanoscience Research, King Abdulaziz University, Jeddad 21589, Saudi Arabia
| | - Olga Tavano
- Faculty of Nutrition, Alfenas Federal Univ., 700 Gabriel Monteiro da Silva St, Alfenas, MG 37130-000, Brazil
| | - Roberto Fernandez-Lafuente
- Departamento de Biocatálisis. ICP-CSIC./Marie Curie 2, Campus UAM-CSIC Cantoblanco, 28049 Madrid. Spain; Center of Excellence in Bionanoscience Research, External advisory board, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
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131
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Arndt JR, Wormwood Moser KL, Van Aken G, Doyle RM, Talamantes T, DeBord D, Maxon L, Stafford G, Fjeldsted J, Miller B, Sherman M. High-Resolution Ion-Mobility-Enabled Peptide Mapping for High-Throughput Critical Quality Attribute Monitoring. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2019-2032. [PMID: 33835810 DOI: 10.1021/jasms.0c00434] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Characterization and monitoring of post-translational modifications (PTMs) by peptide mapping is a ubiquitous assay in biopharmaceutical characterization. Often, this assay is coupled to reversed-phase liquid chromatographic (LC) separations that require long gradients to identify all components of the protein digest and resolve critical modifications for relative quantitation. Incorporating ion mobility (IM) as an orthogonal separation that relies on peptide structure can supplement the LC separation by providing an additional differentiation filter to resolve isobaric peptides, potentially reducing ambiguity in identification through mobility-aligned fragmentation and helping to reduce the run time of peptide mapping assays. A next-generation high-resolution ion mobility (HRIM) technique, based on structures for lossless ion manipulations (SLIM) technology with a 13 m ion path, provides peak capacities and higher resolving power that rivals traditional chromatographic separations and, owing to its ability to resolve isobaric peptides that coelute in faster chromatographic methods, allows for up to 3× shorter run times than conventional peptide mapping methods. In this study, the NIST monoclonal antibody IgG1κ (NIST RM 8671, NISTmAb) was characterized by LC-HRIM-MS and LC-HRIM-MS with collision-induced dissociation (HRIM-CID-MS) using a 20 min analytical method. This approach delivered a sequence coverage of 96.5%. LC-HRIM-CID-MS experiments provided additional confidence in sequence determination. HRIM-MS resolved critical oxidations, deamidations, and isomerizations that coelute with their native counterparts in the chromatographic dimension. Finally, quantitative measurements of % modification were made using only the m/z-extracted HRIM arrival time distributions, showing good agreement with the reference liquid-phase separation. This study shows, for the first time, the analytical capability of HRIM using SLIM technology for enhancing peptide mapping workflows relevant to biopharmaceutical characterization.
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Affiliation(s)
- James R Arndt
- MOBILion Systems, Inc., 4 Hillman Drive, Suite 130, Chadds Ford, Pennsylvania 19317, United States
| | - Kelly L Wormwood Moser
- MOBILion Systems, Inc., 4 Hillman Drive, Suite 130, Chadds Ford, Pennsylvania 19317, United States
| | - Gregory Van Aken
- MOBILion Systems, Inc., 4 Hillman Drive, Suite 130, Chadds Ford, Pennsylvania 19317, United States
| | - Rory M Doyle
- MOBILion Systems, Inc., 4 Hillman Drive, Suite 130, Chadds Ford, Pennsylvania 19317, United States
| | - Tatjana Talamantes
- MOBILion Systems, Inc., 4 Hillman Drive, Suite 130, Chadds Ford, Pennsylvania 19317, United States
| | - Daniel DeBord
- MOBILion Systems, Inc., 4 Hillman Drive, Suite 130, Chadds Ford, Pennsylvania 19317, United States
| | - Laura Maxon
- MOBILion Systems, Inc., 4 Hillman Drive, Suite 130, Chadds Ford, Pennsylvania 19317, United States
| | - George Stafford
- Agilent Technologies Inc., 5301 Stevens Creek Bouelvard, Santa Clara, California 95051, United States
| | - John Fjeldsted
- Agilent Technologies Inc., 5301 Stevens Creek Bouelvard, Santa Clara, California 95051, United States
| | - Bryan Miller
- Agilent Technologies Inc., 5301 Stevens Creek Bouelvard, Santa Clara, California 95051, United States
| | - Melissa Sherman
- MOBILion Systems, Inc., 4 Hillman Drive, Suite 130, Chadds Ford, Pennsylvania 19317, United States
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132
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Detwiler RE, Schlirf AE, Kramer JR. Rethinking Transition Metal Catalyzed N-Carboxyanhydride Polymerization: Polymerization of Pro and AcOPro N-Carboxyanhydrides. J Am Chem Soc 2021; 143:11482-11489. [PMID: 34283588 DOI: 10.1021/jacs.1c03338] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Polyproline (PP) based polypeptides have broad applications as protein mimics, ordered materials, hydrogels, and surface coatings. However, a lack of rapid and efficient preparatory methods has challenged synthesis of well-defined high molecular weight materials. Here, we report facile and high-yielding methods for preparation and polymerization of Pro and trans-4-acetoxy-Pro N-carboxyanhdrides (NCAs). For decades, transition metal initiators of NCA polymerization were assumed to be nonstarters with Pro due to the lack of an amide NH proton. We carefully considered the known steps in the initiation mechanism and applied a Ni initiator that intercepts an intermediate and does not require an NH group. This initiator efficiently catalyzes controlled, living polymerization of Pro NCAs, revealing that routes alternate to the previously proposed mechanism must be at play. We also found Co species can catalyze Pro NCA polymerization, and we improved the synthetic methods to prepare the NCA monomers. Our methods are high-yielding and rapid and give tunable, end-functional PP-based homo, statistical, and block polypeptides. We characterized the conformation of PP and trans-4-hydroxy-PP by CD and confirmed the time scale for quantitative conversion from PPI to PPII helices. Overall, our data shed light on the general propagation mechanism of transition metal catalyzed NCA polymerization and have opened the door for efficient preparation of a desirable class of biomaterials.
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Affiliation(s)
- Rachel E Detwiler
- Department of Biomedical Engineering, University of Utah, Salt Lake City, Utah 84112, United States
| | - Austin E Schlirf
- Department of Biomedical Engineering, University of Utah, Salt Lake City, Utah 84112, United States
| | - Jessica R Kramer
- Department of Biomedical Engineering, University of Utah, Salt Lake City, Utah 84112, United States
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133
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Campuzano IDG, Sandoval W. Denaturing and Native Mass Spectrometric Analytics for Biotherapeutic Drug Discovery Research: Historical, Current, and Future Personal Perspectives. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1861-1885. [PMID: 33886297 DOI: 10.1021/jasms.1c00036] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Mass spectrometry (MS) plays a key role throughout all stages of drug development and is now as ubiquitous as other analytical techniques such as surface plasmon resonance, nuclear magnetic resonance, and supercritical fluid chromatography, among others. Herein, we aim to discuss the history of MS, both electrospray and matrix-assisted laser desorption ionization, specifically for the analysis of antibodies, evolving through to denaturing and native-MS analysis of newer biologic moieties such as antibody-drug conjugates, multispecific antibodies, and interfering nucleic acid-based therapies. We discuss challenging therapeutic target characterization such as membrane protein receptors. Importantly, we compare and contrast the MS and hyphenated analytical chromatographic methods used to characterize these therapeutic modalities and targets within biopharmaceutical research and highlight the importance of appropriate MS deconvolution software and its essential contribution to project progression. Finally, we describe emerging applications and MS technologies that are still predominantly within either a development or academic stage of use but are poised to have significant impact on future drug development within the biopharmaceutic industry once matured. The views reflected herein are personal and are not meant to be an exhaustive list of all relevant MS performed within biopharmaceutical research but are what we feel have been historically, are currently, and will be in the future the most impactful for the drug development process.
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MESH Headings
- Antibodies, Monoclonal/analysis
- Automation, Laboratory
- Biopharmaceutics/methods
- Chromatography, Liquid
- Drug Discovery/methods
- Drug Industry/history
- History, 20th Century
- History, 21st Century
- Humans
- Immunoconjugates/analysis
- Immunoconjugates/chemistry
- Protein Denaturation
- Protein Processing, Post-Translational
- Proteins/analysis
- Spectrometry, Mass, Electrospray Ionization/history
- Spectrometry, Mass, Electrospray Ionization/instrumentation
- Spectrometry, Mass, Electrospray Ionization/methods
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/history
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/instrumentation
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
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Affiliation(s)
- Iain D G Campuzano
- Discovery Attribute Sciences, Amgen Research, 1 Amgen Center Drive, Thousand Oaks, California 92130, United States
| | - Wendy Sandoval
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
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134
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Stability-Indicating Analytical Approach for Stability Evaluation of Lactoferrin. Pharmaceutics 2021; 13:pharmaceutics13071065. [PMID: 34371755 PMCID: PMC8309015 DOI: 10.3390/pharmaceutics13071065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/02/2021] [Accepted: 07/07/2021] [Indexed: 02/07/2023] Open
Abstract
Lactoferrin is a multifunctional iron-binding glycoprotein in milk. Due to its potential for the treatment of various diseases, interest in products containing lactoferrin is increasing. However, as a protein, it is prone to degradation, which critically affects the quality of products. Therefore, the main purpose of our work was to develop a stability-indicating analytical approach for stability evaluation of lactoferrin. We were focused on two complementary methods: reversed-phase and size-exclusion chromatography. The stability-indicating nature of the selected methods was confirmed. They were successfully validated by following the ICH guidelines and applied to preliminary lactoferrin stability studies. Up to three degradation products, as well as aggregates and fragments of lactoferrin, were detected in various samples using complementary reversed-phase and size-exclusion chromatographic methods. The analytical approach was additionally extended with three spectroscopic techniques (absorbance, intrinsic fluorescence, and bicinchoninic acid method), which may provide valuable complementary information in some cases. The presented analytical approach allows the stability evaluation of lactoferrin in various samples, including the ability to detect differences in its degradation mechanisms. Furthermore, it has the potential to be used for the quality control of products containing lactoferrin.
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135
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Do Kwon Y, Wang XE, Bender MF, Yang R, Li Y, McKee K, Rawi R, O’Dell S, Schneck NA, Shaddeau A, Zhang B, Arnold FJ, Connors M, Doria-Rose NA, Kwong PD, Lei QP. Structures of HIV-1 Neutralizing Antibody 10E8 Delineate the Mechanistic Basis of Its Multi-Peak Behavior on Size-Exclusion Chromatography. Antibodies (Basel) 2021; 10:antib10020023. [PMID: 34200826 PMCID: PMC8293163 DOI: 10.3390/antib10020023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 05/20/2021] [Accepted: 05/30/2021] [Indexed: 11/16/2022] Open
Abstract
Antibody 10E8 is capable of effectively neutralizing HIV through its recognition of the membrane-proximal external region (MPER), and a suitably optimized version of 10E8 might have utility in HIV therapy and prophylaxis. However, 10E8 displays a three-peak profile on size-exclusion chromatography (SEC), complicating its manufacture. Here we show cis-trans conformational isomerization of the Tyr-Pro-Pro (YPP) motif in the heavy chain 3rd complementarity-determining region (CDR H3) of antibody 10E8 to be the mechanistic basis of its multipeak behavior. We observed 10E8 to undergo slow conformational isomerization and delineate a mechanistic explanation for effective comodifiers that were able to resolve its SEC heterogeneity and to allow an evaluation of the critical quality attribute of aggregation. We determined crystal structures of single and double alanine mutants of a key di-proline motif and of a light chain variant, revealing alternative conformations of the CDR H3. We also replicated both multi-peak and delayed SEC behavior with MPER-antibodies 4E10 and VRC42, by introducing a Tyr-Pro (YP) motif into their CDR H3s. Our results show how a conformationally dynamic CDR H3 can provide the requisite structural plasticity needed for a highly hydrophobic paratope to recognize its membrane-proximal epitope.
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Affiliation(s)
- Young Do Kwon
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Y.D.K.); (M.F.B.); (K.M.); (R.R.); (S.O.); (B.Z.); (N.A.D.-R.)
| | - Xiangchun E. Wang
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Gaithersburg, MD 20878, USA; (X.E.W.); (R.Y.); (Y.L.); (N.A.S.); (A.S.); (F.J.A.)
| | - Michael F. Bender
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Y.D.K.); (M.F.B.); (K.M.); (R.R.); (S.O.); (B.Z.); (N.A.D.-R.)
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Gaithersburg, MD 20878, USA; (X.E.W.); (R.Y.); (Y.L.); (N.A.S.); (A.S.); (F.J.A.)
| | - Rong Yang
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Gaithersburg, MD 20878, USA; (X.E.W.); (R.Y.); (Y.L.); (N.A.S.); (A.S.); (F.J.A.)
| | - Yile Li
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Gaithersburg, MD 20878, USA; (X.E.W.); (R.Y.); (Y.L.); (N.A.S.); (A.S.); (F.J.A.)
| | - Krisha McKee
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Y.D.K.); (M.F.B.); (K.M.); (R.R.); (S.O.); (B.Z.); (N.A.D.-R.)
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Y.D.K.); (M.F.B.); (K.M.); (R.R.); (S.O.); (B.Z.); (N.A.D.-R.)
| | - Sijy O’Dell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Y.D.K.); (M.F.B.); (K.M.); (R.R.); (S.O.); (B.Z.); (N.A.D.-R.)
| | - Nicole A. Schneck
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Gaithersburg, MD 20878, USA; (X.E.W.); (R.Y.); (Y.L.); (N.A.S.); (A.S.); (F.J.A.)
| | - Andrew Shaddeau
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Gaithersburg, MD 20878, USA; (X.E.W.); (R.Y.); (Y.L.); (N.A.S.); (A.S.); (F.J.A.)
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Y.D.K.); (M.F.B.); (K.M.); (R.R.); (S.O.); (B.Z.); (N.A.D.-R.)
| | - Frank J. Arnold
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Gaithersburg, MD 20878, USA; (X.E.W.); (R.Y.); (Y.L.); (N.A.S.); (A.S.); (F.J.A.)
| | - Mark Connors
- HIV-Specific Immunity Section of the Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Nicole A. Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Y.D.K.); (M.F.B.); (K.M.); (R.R.); (S.O.); (B.Z.); (N.A.D.-R.)
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Y.D.K.); (M.F.B.); (K.M.); (R.R.); (S.O.); (B.Z.); (N.A.D.-R.)
- Correspondence: (P.D.K.); (Q.P.L.)
| | - Q. Paula Lei
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Gaithersburg, MD 20878, USA; (X.E.W.); (R.Y.); (Y.L.); (N.A.S.); (A.S.); (F.J.A.)
- Correspondence: (P.D.K.); (Q.P.L.)
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136
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Wätzig H, Hoffstedt M, Krebs F, Minkner R, Scheller C, Zagst H. Protein analysis and stability: Overcoming trial-and-error by grouping according to physicochemical properties. J Chromatogr A 2021; 1649:462234. [PMID: 34038775 DOI: 10.1016/j.chroma.2021.462234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 12/15/2022]
Abstract
Today proteins are possibly the most important class of substances. Yet new tasks for proteins are still often solved by trial-and-error approaches. However, in some areas these euphemistically called "screening approaches" are not suitable. E.g. stability tests just take too long and therefore require a more strategic, target-orientated concept. This concept is available by grouping proteins according to their physicochemical properties and then pulling out the right drawer for new tasks. These properties include size, then charge and hydrophobicity as well as their patchinesses, and the degree of order. In addition, solubility, the content of (free) enthalpy, aromatic-amino-acid- and α/β-frequency as well as helix capping, and corresponding patchiness, the number of specific motifs and domains as well as the typical concentration range can be helpful to discriminate between different groups of proteins. Analyzing correlations will reduce the necessary amount of parameters and additional ones, which may be still undiscovered at the present time, can be identified looking at protein subgroups with similar physicochemical properties which still behave heterogeneously. Step-by-step the methodology will be improved. Possibly protein stability will be the driver of this process, but all other areas such as production, purification and analytics including sample pre-treatment and the choice of appropriate separation conditions for e.g. chromatography and electrophoresis will profit from a rational strategy.
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Affiliation(s)
- Hermann Wätzig
- Technische Universität Braunschweig, Institute of Medicinal and Pharmaceutical Chemistry, Beethovenstraße 55, Braunschweig 38106, Germany.
| | - Marc Hoffstedt
- Technische Universität Braunschweig, Institute of Medicinal and Pharmaceutical Chemistry, Beethovenstraße 55, Braunschweig 38106, Germany
| | - Finja Krebs
- Technische Universität Braunschweig, Institute of Medicinal and Pharmaceutical Chemistry, Beethovenstraße 55, Braunschweig 38106, Germany
| | - Robert Minkner
- Technische Universität Braunschweig, Institute of Medicinal and Pharmaceutical Chemistry, Beethovenstraße 55, Braunschweig 38106, Germany
| | - Christin Scheller
- Technische Universität Braunschweig, Institute of Medicinal and Pharmaceutical Chemistry, Beethovenstraße 55, Braunschweig 38106, Germany
| | - Holger Zagst
- Technische Universität Braunschweig, Institute of Medicinal and Pharmaceutical Chemistry, Beethovenstraße 55, Braunschweig 38106, Germany
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137
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Taylor A, Warner M, Mendoza C, Memmott C, LeCheminant T, Bailey S, Christensen C, Keller J, Suli A, Mizrachi D. Chimeric Claudins: A New Tool to Study Tight Junction Structure and Function. Int J Mol Sci 2021; 22:ijms22094947. [PMID: 34066630 PMCID: PMC8124314 DOI: 10.3390/ijms22094947] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/02/2021] [Accepted: 05/04/2021] [Indexed: 12/11/2022] Open
Abstract
The tight junction (TJ) is a structure composed of multiple proteins, both cytosolic and membranal, responsible for cell–cell adhesion in polarized endothelium and epithelium. The TJ is intimately connected to the cytoskeleton and plays a role in development and homeostasis. Among the TJ’s membrane proteins, claudins (CLDNs) are key to establishing blood–tissue barriers that protect organismal physiology. Recently, several crystal structures have been reported for detergent extracted recombinant CLDNs. These structural advances lack direct evidence to support quaternary structure of CLDNs. In this article, we have employed protein-engineering principles to create detergent-independent chimeric CLDNs, a combination of a 4-helix bundle soluble monomeric protein (PDB ID: 2jua) and the apical—50% of human CLDN1, the extracellular domain that is responsible for cell–cell adhesion. Maltose-binding protein-fused chimeric CLDNs (MBP-CCs) used in this study are soluble proteins that retain structural and functional aspects of native CLDNs. Here, we report the biophysical characterization of the structure and function of MBP-CCs. MBP-fused epithelial cadherin (MBP-eCAD) is used as a control and point of comparison of a well-characterized cell-adhesion molecule. Our synthetic strategy may benefit other families of 4-α-helix membrane proteins, including tetraspanins, connexins, pannexins, innexins, and more.
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138
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Appearance and Formation Analysis of Multimers in High Concentration Antibodies. Chromatographia 2021. [DOI: 10.1007/s10337-021-04015-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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139
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Bolje A, Gobec S. Analytical Techniques for Structural Characterization of Proteins in Solid Pharmaceutical Forms: An Overview. Pharmaceutics 2021; 13:pharmaceutics13040534. [PMID: 33920461 PMCID: PMC8070348 DOI: 10.3390/pharmaceutics13040534] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/21/2021] [Accepted: 04/08/2021] [Indexed: 11/17/2022] Open
Abstract
Therapeutic proteins as biopharmaceuticals have emerged as a very important class of drugs for the treatment of many diseases. However, they are less stable compared to conventional pharmaceuticals. Their long-term stability in solid forms, which is critical for product performance, depends heavily on the retention of the native protein structure during the lyophilization (freeze-drying) process and, thereafter, in the solid state. Indeed, the biological function of proteins is directly related to the tertiary and secondary structure. Besides physical stability and biological activity, conformational stability (three-dimensional structure) is another important aspect when dealing with protein pharmaceuticals. Moreover, denaturation as loss of higher order structure is often a precursor to aggregation or chemical instability. Careful study of the physical and chemical properties of proteins in the dried state is therefore critical during biopharmaceutical drug development to deliver a final drug product with built-in quality that is safe, high-quality, efficient, and affordable for patients. This review provides an overview of common analytical techniques suitable for characterizing pharmaceutical protein powders, providing structural, and conformational information, as well as insights into dynamics. Such information can be very useful in formulation development, where selecting the best formulation for the drug can be quite a challenge.
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Affiliation(s)
- Aljoša Bolje
- Correspondence: (A.B.); (S.G.); Tel.: +386-147-69500 (A.B.); +386-147-69585 (S.G.)
| | - Stanislav Gobec
- Correspondence: (A.B.); (S.G.); Tel.: +386-147-69500 (A.B.); +386-147-69585 (S.G.)
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140
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Knihtila R, Song Y, Chemmalil L, Ding J, Mussa N, Li ZJ. Systematic Development of a Size Exclusion Chromatography Method for a Monoclonal Antibody with High Surface Aggregation Propensity (SAP) Index. J Pharm Sci 2021; 110:2651-2660. [PMID: 33812889 DOI: 10.1016/j.xphs.2021.03.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 02/27/2021] [Accepted: 03/12/2021] [Indexed: 10/21/2022]
Abstract
Size Exclusion Chromatography (SEC) has been widely used to assess aggregate content in bio-pharmaceutical drugs such as monoclonal antibodies (mAbs), and is routinely used during method development and release testing. Electrostatic interactions between protein analytes and SEC column resin are commonly observed besides the primary mode of size separation during SEC method development, which needs to be minimized. An effective method to minimize electrostatic interactions is through increasing mobile phase (MP) salt concentration. However; increasing salt concentration in MP will induce increased hydrophobicity of proteins and increased hydrophobic interactions between protein and stationary phase, as demonstrated for mAb-A in this paper, a protein with high surface aggregation propensity (SAP) score and an isoelectric point near mobile phase pH. In this work, a systematic, Design of Experimental approach was taken to identify optimal SEC method conditions including column type, buffer composition, ionic strength, pH and additives. The optimized method was demonstrated to be robust towards small changes in method operation conditions and was qualified for use in product release and stability studies. Additionally, biophysical and computational studies were performed to elucidate the role of MP additives, which supports the use of arginine as an essential additive to minimize undesirable hydrophobic interactions between proteins and stationary phase.
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Affiliation(s)
| | | | - Letha Chemmalil
- BMS Process Development Analytical Group, 38 Jackson Rd, Devens, MA 01434, USA.
| | - Julia Ding
- BMS Process Development Analytical Group, 38 Jackson Rd, Devens, MA 01434, USA
| | | | - Zheng Jian Li
- BMS Analytical Development & Analytical Attribute Science in Biologics, 38 Jackson Rd, Devens, MA 01434, USA
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141
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Zhao J, Hu G, Huang Y, Huang Y, Wei X, Shi J. Polysaccharide conjugate vaccine: A kind of vaccine with great development potential. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2020.10.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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142
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Collagen IV α345 dysfunction in glomerular basement membrane diseases. III. A functional framework for α345 hexamer assembly. J Biol Chem 2021; 296:100592. [PMID: 33775696 PMCID: PMC8099640 DOI: 10.1016/j.jbc.2021.100592] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 03/11/2021] [Accepted: 03/24/2021] [Indexed: 12/15/2022] Open
Abstract
We identified a genetic variant, an 8-residue appendage, of the α345 hexamer of collagen IV present in patients with glomerular basement membrane diseases, Goodpasture’s disease and Alport syndrome, and determined the long-awaited crystal structure of the hexamer. We sought to elucidate how variants cause glomerular basement membrane disease by exploring the mechanism of the hexamer assembly. Chloride ions induced in vitro hexamer assembly in a composition-specific manner in the presence of equimolar concentrations of α3, α4, and α5 NC1 monomers. Chloride ions, together with sulfilimine crosslinks, stabilized the assembled hexamer. Furthermore, the chloride ion–dependent assembly revealed the conformational plasticity of the loop-crevice-loop bioactive sites, a critical property underlying bioactivity and pathogenesis. We explored the native mechanism by expressing recombinant α345 miniprotomers in the cell culture and characterizing the expressed proteins. Our findings revealed NC1-directed trimerization, forming protomers inside the cell; hexamerization, forming scaffolds outside the cell; and a Cl gradient–signaled hexamerization. This assembly detail, along with a crystal structure, provides a framework for understanding hexamer dysfunction. Restoration of the native conformation of bioactive sites and α345 hexamer replacement are prospective approaches to therapeutic intervention.
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143
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Lubomirsky E, Khodabandeh A, Preis J, Susewind M, Hofe T, Hilder EF, Arrua RD. Polymeric stationary phases for size exclusion chromatography: A review. Anal Chim Acta 2021; 1151:338244. [PMID: 33608083 DOI: 10.1016/j.aca.2021.338244] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 11/17/2022]
Abstract
Synthetic and natural macromolecules are commonly used in a variety of fields such as plastics, nanomedicine, biotherapeutics, drug delivery and tissue engineering. Characterising macromolecules in terms of their structural parameters (size, molar mass and distribution, architecture) is key to have a better understanding of their structure-property relationships. Size exclusion chromatography (SEC) is a commonly used technique for polymer characterization since it offers access to the determination of the size of a macromolecule, its molar mass and the molar mass distribution. Moreover, detectors that allow the determination of true molar masses, macromolecule's architecture and the composition of copolymers can be coupled to the chromatographic system. Like other chromatographic techniques, the stationary phase is of paramount importance for efficient SEC separations. This review presents the basic principles for the design of stationary phases for SEC as well as synthetic methods currently used in the field. Current status of fully-porous polymeric stationary phases used in SEC is reviewed and their advantages and limitations are also discussed. Finally, the potential of polymer monoliths in SEC is also covered, highlighting the limitations this column technology could address. However, further development in the polymer structure is needed to consider this column technology in the field of macromolecule separation.
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Affiliation(s)
- Ester Lubomirsky
- Future Industries Institute, University of South Australia, Mawson Lakes Campus, South Australia, 5095, Australia
| | - Aminreza Khodabandeh
- Future Industries Institute, University of South Australia, Mawson Lakes Campus, South Australia, 5095, Australia
| | - Jasmin Preis
- Polymer Standards Service GmbH, In der Dalheimer Wiese 5, Mainz, 55120, Germany
| | - Moritz Susewind
- Polymer Standards Service GmbH, In der Dalheimer Wiese 5, Mainz, 55120, Germany
| | - Thorsten Hofe
- Polymer Standards Service GmbH, In der Dalheimer Wiese 5, Mainz, 55120, Germany
| | - Emily F Hilder
- Future Industries Institute, University of South Australia, Mawson Lakes Campus, South Australia, 5095, Australia
| | - R Dario Arrua
- Future Industries Institute, University of South Australia, Mawson Lakes Campus, South Australia, 5095, Australia.
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144
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Mondal T, Shivange GN, Tihagam RGT, Lyerly E, Battista M, Talwar D, Mosavian R, Urbanek K, Rashid NS, Harrell JC, Bos PD, Stelow EB, Stack MS, Bhatnagar S, Tushir‐Singh J. Unexpected PD-L1 immune evasion mechanism in TNBC, ovarian, and other solid tumors by DR5 agonist antibodies. EMBO Mol Med 2021; 13:e12716. [PMID: 33587338 PMCID: PMC7933954 DOI: 10.15252/emmm.202012716] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 12/03/2020] [Accepted: 12/07/2020] [Indexed: 12/11/2022] Open
Abstract
Lack of effective immune infiltration represents a significant barrier to immunotherapy in solid tumors. Thus, solid tumor-enriched death receptor-5 (DR5) activating antibodies, which generates tumor debulking by extrinsic apoptotic cytotoxicity, remains a crucial alternate therapeutic strategy. Over past few decades, many DR5 antibodies moved to clinical trials after successfully controlling tumors in immunodeficient tumor xenografts. However, DR5 antibodies failed to significantly improve survival in phase-II trials, leading in efforts to generate second generation of DR5 agonists to supersize apoptotic cytotoxicity in tumors. Here we have discovered that clinical DR5 antibodies activate an unexpected immunosuppressive PD-L1 stabilization pathway, which potentially had contributed to their limited success in clinics. The DR5 agonist stimulated caspase-8 signaling not only activates ROCK1 but also undermines proteasome function, both of which contributes to increased PD-L1 stability on tumor cell surface. Targeting DR5-ROCK1-PD-L1 axis markedly increases immune effector T-cell function, promotes tumor regression, and improves overall survival in animal models. These insights have identified a potential clinically viable combinatorial strategy to revive solid cancer immunotherapy using death receptor agonism.
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Affiliation(s)
- Tanmoy Mondal
- Laboratory of Novel BiologicsUniversity of VirginiaCharlottesvilleVAUSA
- Department of Biochemistry and Molecular GeneticsUniversity of VirginiaCharlottesvilleVAUSA
| | - Gururaj N Shivange
- Laboratory of Novel BiologicsUniversity of VirginiaCharlottesvilleVAUSA
- Department of Biochemistry and Molecular GeneticsUniversity of VirginiaCharlottesvilleVAUSA
| | - Rachisan GT Tihagam
- Department of Biochemistry and Molecular GeneticsUniversity of VirginiaCharlottesvilleVAUSA
| | - Evan Lyerly
- Laboratory of Novel BiologicsUniversity of VirginiaCharlottesvilleVAUSA
- Department of Biochemistry and Molecular GeneticsUniversity of VirginiaCharlottesvilleVAUSA
- Undergraduate Research ProgramUniversity of VirginiaCharlottesvilleVAUSA
| | - Michael Battista
- Laboratory of Novel BiologicsUniversity of VirginiaCharlottesvilleVAUSA
- Department of Biochemistry and Molecular GeneticsUniversity of VirginiaCharlottesvilleVAUSA
- Undergraduate Research ProgramUniversity of VirginiaCharlottesvilleVAUSA
| | - Divpriya Talwar
- Laboratory of Novel BiologicsUniversity of VirginiaCharlottesvilleVAUSA
- Department of Biochemistry and Molecular GeneticsUniversity of VirginiaCharlottesvilleVAUSA
- Undergraduate Research ProgramUniversity of VirginiaCharlottesvilleVAUSA
| | - Roxanna Mosavian
- Laboratory of Novel BiologicsUniversity of VirginiaCharlottesvilleVAUSA
- Department of Biochemistry and Molecular GeneticsUniversity of VirginiaCharlottesvilleVAUSA
- Undergraduate Research ProgramUniversity of VirginiaCharlottesvilleVAUSA
| | - Karol Urbanek
- Laboratory of Novel BiologicsUniversity of VirginiaCharlottesvilleVAUSA
- Department of Biochemistry and Molecular GeneticsUniversity of VirginiaCharlottesvilleVAUSA
| | | | - J Chuck Harrell
- Department of PathologyMassey Cancer Center, VCURichmondVAUSA
| | - Paula D Bos
- Department of PathologyMassey Cancer Center, VCURichmondVAUSA
| | - Edward B Stelow
- Department of PathologyUniversity of VirginiaCharlottesvilleVAUSA
| | - M Sharon Stack
- Harper Cancer Research InstituteUniversity of Notre DameNotre DameINUSA
| | - Sanchita Bhatnagar
- Department of Biochemistry and Molecular GeneticsUniversity of VirginiaCharlottesvilleVAUSA
- University of Virginia Cancer Center and Medical SchoolCharlottesvilleVAUSA
| | - Jogender Tushir‐Singh
- Laboratory of Novel BiologicsUniversity of VirginiaCharlottesvilleVAUSA
- Department of Biochemistry and Molecular GeneticsUniversity of VirginiaCharlottesvilleVAUSA
- University of Virginia Cancer Center and Medical SchoolCharlottesvilleVAUSA
- DoD Ovarian Cancer Academy Early Career InvestigatorCharlottesvilleVAUSA
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145
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Lin B, Lei Y, Wang J, Zhu L, Wu Y, Zhang H, Wu L, Zhang P, Yang C. Microfluidic-Based Exosome Analysis for Liquid Biopsy. SMALL METHODS 2021; 5:e2001131. [PMID: 34927834 DOI: 10.1002/smtd.202001131] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/29/2020] [Indexed: 06/14/2023]
Abstract
Liquid biopsy offers non-invasive and real-time molecular profiling of individual patients, and is thus considered a revolutionary technology in precision medicine. Exosomes have been acknowledged as significant biomarkers in liquid biopsy, as they play a central role in cell-cell communication and are closely related to the pathogenesis of most human malignancies. Nevertheless, in biofluids exosomes always co-exist with other particles, and the cargo components of exosomes are highly heterogeneous. Thus, the isolation and molecular characterization of exosomes are still technically challenging. Microfluidics technology effectively addresses this challenge by virtue of its inherent advantages, such as precise manipulation of fluids, low consumption of samples and reagents, and a high level of integration. Recent advances in microfluidics allow in situ exosome capture and molecular detection with unprecedented selectivity and sensitivity. In this review, the state-of-the-art developments in microfluidics-based exosome research, including exosome isolation approaches and molecular detection strategies, with highlights of the characterization of exosomal biomarkers in cancer liquid biopsy is summarized. The major challenges are also discussed and some perspectives for the future directions of exosome-based liquid biopsy in microfluidic systems are presented.
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Affiliation(s)
- Bingqian Lin
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Yanmei Lei
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Junxia Wang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Lin Zhu
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Yuqi Wu
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Huimin Zhang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Lingling Wu
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Peng Zhang
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Chaoyong Yang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
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146
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Pauk JN, Raju Palanisamy J, Kager J, Koczka K, Berghammer G, Herwig C, Veiter L. Advances in monitoring and control of refolding kinetics combining PAT and modeling. Appl Microbiol Biotechnol 2021; 105:2243-2260. [PMID: 33598720 PMCID: PMC7954745 DOI: 10.1007/s00253-021-11151-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 01/19/2021] [Accepted: 01/27/2021] [Indexed: 12/21/2022]
Abstract
Overexpression of recombinant proteins in Escherichia coli results in misfolded and non-active protein aggregates in the cytoplasm, so-called inclusion bodies (IB). In recent years, a change in the mindset regarding IBs could be observed: IBs are no longer considered an unwanted waste product, but a valid alternative to produce a product with high yield, purity, and stability in short process times. However, solubilization of IBs and subsequent refolding is necessary to obtain a correctly folded and active product. This protein refolding process is a crucial downstream unit operation-commonly done as a dilution in batch or fed-batch mode. Drawbacks of the state-of-the-art include the following: the large volume of buffers and capacities of refolding tanks, issues with uniform mixing, challenging analytics at low protein concentrations, reaction kinetics in non-usable aggregates, and generally low re-folding yields. There is no generic platform procedure available and a lack of robust control strategies. The introduction of Quality by Design (QbD) is the method-of-choice to provide a controlled and reproducible refolding environment. However, reliable online monitoring techniques to describe the refolding kinetics in real-time are scarce. In our view, only monitoring and control of re-folding kinetics can ensure a productive, scalable, and versatile platform technology for re-folding processes. For this review, we screened the current literature for a combination of online process analytical technology (PAT) and modeling techniques to ensure a controlled refolding process. Based on our research, we propose an integrated approach based on the idea that all aspects that cannot be monitored directly are estimated via digital twins and used in real-time for process control. KEY POINTS: • Monitoring and a thorough understanding of refolding kinetics are essential for model-based control of refolding processes. • The introduction of Quality by Design combining Process Analytical Technology and modeling ensures a robust platform for inclusion body refolding.
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Affiliation(s)
- Jan Niklas Pauk
- Research Area Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, Vienna University of Technology, Gumpendorferstrasse 1a/166, 1060, Vienna, Austria
- Competence Center CHASE GmbH, Altenbergerstraße 69, 4040, Linz, Austria
| | - Janani Raju Palanisamy
- Research Area Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, Vienna University of Technology, Gumpendorferstrasse 1a/166, 1060, Vienna, Austria
| | - Julian Kager
- Research Area Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, Vienna University of Technology, Gumpendorferstrasse 1a/166, 1060, Vienna, Austria
| | - Krisztina Koczka
- Bilfinger Industrietechnik Salzburg GmbH, Mooslackengasse 17, 1190, Vienna, Austria
| | - Gerald Berghammer
- Bilfinger Industrietechnik Salzburg GmbH, Mooslackengasse 17, 1190, Vienna, Austria
| | - Christoph Herwig
- Research Area Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, Vienna University of Technology, Gumpendorferstrasse 1a/166, 1060, Vienna, Austria.
| | - Lukas Veiter
- Research Area Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, Vienna University of Technology, Gumpendorferstrasse 1a/166, 1060, Vienna, Austria
- Competence Center CHASE GmbH, Altenbergerstraße 69, 4040, Linz, Austria
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147
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Greer T, O'Brien Johnson R, Cejkov M, Zheng X, Li N. Integration of liquid chromatography mass spectrometry with a heavy peptide response curve accurately measures unprocessed C-terminal lysine during peptide mapping analysis of therapeutic antibodies in a single run. J Pharm Biomed Anal 2021; 197:113963. [PMID: 33626446 DOI: 10.1016/j.jpba.2021.113963] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 01/29/2021] [Accepted: 02/06/2021] [Indexed: 11/24/2022]
Abstract
Therapeutic monoclonal and bispecific antibodies are susceptible to modification after protein biosynthesis. These post-translational modifications (PTMs) not only contribute to mass and charge heterogeneity, but they can also negatively impact the molecule's activity, half-life, and immunogenicity. Therefore, identification and quantification of PTMs are critical to ensure the safety and efficacy of an antibody therapeutic as well as demonstrate product consistency and process control. Unprocessed C-terminal lysine on the heavy chain (HC) is a prevalent modification that contributes to this charge heterogeneity in antibodies. Peptide mapping through liquid chromatography tandem mass spectrometry (LC-MS2) enjoys higher selectivity and sensitivity for measuring this PTM relative to global PTM methods, but differences in the ionization efficiencies of the unprocessed C-terminal K peptide and the truncated C-terminal K peptide result in its overestimation. Consequently, large discrepancies in this PTM's measured abundance may exist between different characterization assays used in regulatory filings, which can be further compounded by large variability when multiple mass spectrometers are used to quantify C-terminal K during a therapeutic's lifespan. In this study, we propose a simple new method to quantify unprocessed C-terminal K in antibodies in a single LC-MS2 run that incorporates heavy isotopic standards for both the unprocessed and truncated C-terminal K peptide to build a response curve and correct for the disparity in ionization efficiency between these two different peptide sequences. The approach was evaluated across two different Orbitrap-based mass spectrometers using multiple monoclonal and bispecific therapeutic antibodies, resulting in accurate (<10% error, as determined with peptide standards) and precise C-terminal K quantification during peptide mapping analysis.
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Affiliation(s)
- Tyler Greer
- Analytical Chemistry, Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591-6707, United States
| | - Reid O'Brien Johnson
- Analytical Chemistry, Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591-6707, United States
| | - Milos Cejkov
- Analytical Chemistry, Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591-6707, United States
| | - Xiaojing Zheng
- Analytical Chemistry, Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591-6707, United States.
| | - Ning Li
- Analytical Chemistry, Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591-6707, United States
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148
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Sunderhaus A, Imran R, Goudelock A, Nassar M, Cooper K, Patterson D, Abdel Aziz MH. Engineering soluble artificial epidermal growth factor receptor mimics capable of spontaneous in vitro dimerization. Biotechnol Bioeng 2021; 118:1466-1475. [PMID: 33331661 DOI: 10.1002/bit.27659] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/08/2020] [Accepted: 12/12/2020] [Indexed: 12/11/2022]
Abstract
Epidermal growth factor receptor (EGFR) is a clinically validated target for a multitude of human cancers. The receptor is activated upon ligand binding through a critical dimerization step. Dimerization can be replicated in vitro by locally concentrating the receptor kinase domains on the surface of lipid-based vesicles. In this study we investigated the use of coiled coils to induce spontaneous receptor kinase domain dimerization in vitro to form non-membrane-bound artificial receptor mimics in solution. Two engineered forms of EGFR kinase domain fused to coiled coil complementary peptides were designed to self-associate upon mixing. Two fusion protein species (P3-EGFR and P4-EGFR) independently showed the same activity and polymerization profile known to exist with EGFR kinase domains. Upon mixing the two species, coiled coil heterodimers were formed that induced EGFR association to form dimers of the kinase domains. This was accompanied by 11.5-fold increase in the phosphorylation rate indicative of kinase domain activation equivalent to the levels achieved using vesicle localization and mimicking in vivo ligand-induced activation. This study presents a soluble tyrosine kinase receptor mimic capable of spontaneous in vitro activation that can facilitate functional and drug discovery studies for this clinically important receptor class.
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Affiliation(s)
- Allison Sunderhaus
- Fisch College of Pharmacy, The University of Texas at Tyler, Tyler, Texas, USA
| | - Ramsha Imran
- Fisch College of Pharmacy, The University of Texas at Tyler, Tyler, Texas, USA
| | - Amanda Goudelock
- Fisch College of Pharmacy, The University of Texas at Tyler, Tyler, Texas, USA
| | - Manon Nassar
- Department of Chemistry and Biochemistry, The University of Texas at Tyler, Tyler, Texas, USA
| | - Kendall Cooper
- Department of Chemistry and Biochemistry, The University of Texas at Tyler, Tyler, Texas, USA
| | - Dustin Patterson
- Department of Chemistry and Biochemistry, The University of Texas at Tyler, Tyler, Texas, USA
| | - May H Abdel Aziz
- Fisch College of Pharmacy, The University of Texas at Tyler, Tyler, Texas, USA
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149
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Abstract
The conjugation of cytotoxic drugs to monoclonal antibodies (mAbs) generates heterogeneous drug load distribution. Antibody-drug conjugates (ADC) are physically less stable as compared to their parent molecule due to modifications made in order to link drugs to the interchain sulfhydryl groups of monoclonal antibodies. The conjugation of small molecule drugs to mAbs alters the physicochemical properties of mAbs and also impacts their degradation profile. The use of appropriate analytical tools to monitor physical stability changes is necessary to identify key product quality attributes such as aggregation. This chapter discusses suitable stress conditions and the use of stability indicating analytical methods to detect degradation products.
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150
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LI J, ZHUO Y, ZHANG Y, LI N, WU J. [Size exclusion-reverse liquid column chromatography-mass spectrometry and its application in the identification of post-translationally modified proteins in rat kidney]. Se Pu 2021; 39:87-95. [PMID: 34227362 PMCID: PMC9274831 DOI: 10.3724/sp.j.1123.2020.05028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Indexed: 11/25/2022] Open
Abstract
Proteomics is an emerging field that has been shown to play a crucial role in unveiling the mechanisms underlying physiological and pathological processes, and liquid chromatography-mass spectrometry (LC-MS) is one of the most important methods employed in this field. However, in complex biological systems, such as eukaryotes, it is challenging to perform a comprehensive and unbiased proteome analysis due to the high complexity of biological samples and enormous differences in sample contents. For example, post-translational modifications (PTMs) in proteins are imperative for cell signaling, but post-translationally modified proteins account for about 1% of the total proteins in a single cell, making their identification extremely difficult. Therefore, chromatographic separation methods based on different principles are generally applied to reduce the complexity of biological samples and enrich trace proteins for their identification through mass spectrometry (MS). In this study, we developed a new proteomics method by combining size exclusion chromatography (SEC) and reversed-phase chromatography (RPLC), to separate and identify trace proteins in complex systems. SEC was used to separate and enrich kidney-specific proteins. After optimization of the method, it was found that 30 mmol/L of ammonium acetate could efficiently separate rat kidney proteins from the total protein fraction so that they could be eluted based on their relative molecular mass. Sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis and LC-MS results showed that our SEC separation method not only refined the protein composition of the biological sample but also enhanced the relative contents of trace proteins through multiple injections. The collected protein fractions were further concentrated through ultrafiltration centrifugation followed by freeze-drying, which further improved the recovery of trace proteins by approximately 90% and largely decreased the time required with the use of freeze-drying alone. Thereafter, five protein fractions were separately digested using trypsin, and the resultant peptides were further analyzed by reverse phase chromatography-MS analysis. In the RPLC column, the peptides were isolated mainly based on their hydrophobicity. As a result, by combining SEC and RPLC, 23621 peptides and 1345 proteins were identified from the kidney, with an increase in numbers by 69% and 27%, respectively, when compared to those obtained using the common 2D strong cation exchange (SCX)-RPLC-MS method. However, no significant difference was observed in the pI and grand average of hydropathicity (GRAVY) values. Gene ontology (GO) analysis revealed an increase in the number of proteins in each cell component, especially the membrane. Furthermore, identification of a higher rate of identified peptides than proteins suggested that the protein coverage was also improved, thereby facilitating the detection of PTM proteins. Consequently, five common PTMs in biological processes, including methylation, acetylation, carbamylation, oxidation, and phosphorylation, were examined and compared between the two methods. As expected, the number of post-translationally modified peptides identified using SEC-RPLC-MS were 1.7-1.9 times more than those determined using the SCX-RPLC-MS method. Especially for the identification of phosphorylated peptides, we could achieve the level of the targeted enrichment strategy; however no significant difference was observed in the extents of phosphorylation among serine, threonine, and tyrosine. These results further indicate that upon combining SEC and RPLC, high efficiency could be achieved by decreasing the complexity of the protein sample, and the identification was unbiased. Finally, the phosphorylation of some kidney proteins, such as spectrin, L-lactate dehydrogenase, and ATPases, was found, which is critical for their functions. In summary, the SEC-RPLC-MS approach was developed for the identification of rat kidney proteins and is especially applicable for the identification of PTM proteins. Using this method, the identification efficiency for PTM peptides increased significantly. Therefore, this method has potential for better understanding the impact of PTM on kidney proteins and further elucidating the potential mechanisms underlying its physiological and pathological functions.
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Affiliation(s)
- Jianmin LI
- 澳门科技大学中医药学院, 中药质量研究国家重点实验室, 澳门 999078
- Faculty of Chinese Medicine, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China
| | - Yue ZHUO
- 澳门科技大学中医药学院, 中药质量研究国家重点实验室, 澳门 999078
- Faculty of Chinese Medicine, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China
| | - Yida ZHANG
- 澳门科技大学中医药学院, 中药质量研究国家重点实验室, 澳门 999078
- Faculty of Chinese Medicine, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China
| | - Na LI
- 澳门科技大学中医药学院, 中药质量研究国家重点实验室, 澳门 999078
- Faculty of Chinese Medicine, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China
| | - Jianlin WU
- 澳门科技大学中医药学院, 中药质量研究国家重点实验室, 澳门 999078
- Faculty of Chinese Medicine, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China
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