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D'Atri V, Imiołek M, Quinn C, Finny A, Lauber M, Fekete S, Guillarme D. Size exclusion chromatography of biopharmaceutical products: From current practices for proteins to emerging trends for viral vectors, nucleic acids and lipid nanoparticles. J Chromatogr A 2024; 1722:464862. [PMID: 38581978 DOI: 10.1016/j.chroma.2024.464862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 03/29/2024] [Accepted: 03/31/2024] [Indexed: 04/08/2024]
Abstract
The 21st century has been particularly productive for the biopharmaceutical industry, with the introduction of several classes of innovative therapeutics, such as monoclonal antibodies and related compounds, gene therapy products, and RNA-based modalities. All these new molecules are susceptible to aggregation and fragmentation, which necessitates a size variant analysis for their comprehensive characterization. Size exclusion chromatography (SEC) is one of the reference techniques that can be applied. The analytical techniques for mAbs are now well established and some of them are now emerging for the newer modalities. In this context, the objective of this review article is: i) to provide a short historical background on SEC, ii) to suggest some clear guidelines on the selection of packing material and mobile phase for successful method development in modern SEC; and iii) to highlight recent advances in SEC, such as the use of narrow-bore and micro-bore columns, ultra-wide pore columns, and low-adsorption column hardware. Some important innovations, such as recycling SEC, the coupling of SEC with mass spectrometry, and the use of alternative detectors such as charge detection mass spectrometry and mass photometry are also described. In addition, this review discusses the use of SEC in multidimensional setups and shows some of the most recent advances at the preparative scale. In the third part of the article, the possibility of SEC for the characterization of new modalities is also reviewed. The final objective of this review is to provide a clear summary of opportunities and limitations of SEC for the analysis of different biopharmaceutical products.
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Affiliation(s)
- Valentina D'Atri
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU - Rue Michel Servet 1,4, 1211 Geneva, Switzerland; School of Pharmaceutical Sciences, University of Geneva, CMU - Rue Michel Servet 1,4, 1211 Geneva, Switzerland
| | | | | | - Abraham Finny
- Waters Corporation, Wyatt Technology, Santa Barbara, CA, USA
| | - Matthew Lauber
- Waters Corporation, Wyatt Technology, Santa Barbara, CA, USA
| | | | - Davy Guillarme
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU - Rue Michel Servet 1,4, 1211 Geneva, Switzerland; School of Pharmaceutical Sciences, University of Geneva, CMU - Rue Michel Servet 1,4, 1211 Geneva, Switzerland.
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Ewonde Ewonde R, Böttinger K, De Vos J, Lingg N, Jungbauer A, Pohl CA, Huber CG, Desmet G, Eeltink S. Selectivity and Resolving Power of Hydrophobic Interaction Chromatography Targeting the Separation of Monoclonal Antibody Variants. Anal Chem 2024; 96:1121-1128. [PMID: 38190620 PMCID: PMC10809212 DOI: 10.1021/acs.analchem.3c04011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/21/2023] [Accepted: 12/21/2023] [Indexed: 01/10/2024]
Abstract
This study presents a comprehensive investigation of the mechanistic understanding of retention and selectivity in hydrophobic interaction chromatography. It provides valuable insights into crucial method-development parameters involved in achieving chromatographic resolution for profiling molecular variants of trastuzumab. Retention characteristics have been assessed for three column chemistries, i.e., butyl, alkylamide, and long-stranded multialkylamide ligands, while distinguishing column hydrophobicity and surface area. Salt type and specifically chloride ions proved to be the key driver for improving chromatographic selectivity, and this was attributed to the spatial distribution of ions at the protein surface, which is ion-specific. The effect was notably more pronounced on the multialkylamide column, as proteins intercalated between the multiamide polymer strands, enabling steric effects. Column coupling proved to be an effective approach for maximizing resolution between molecular variants present in the trastuzumab reference sample and trastuzumab variants induced by forced oxidation. Liquid chromatography-mass spectrometry (LC-MS)/MS peptide mapping experiments after fraction collection indicate that the presence of chloride in the mobile phase enables the selectivity of site-specific deamidation (N30) situated at the heavy chain. Moreover, site-specific oxidation of peptides (M255, W420, and M431) was observed for peptides situated at the Fc region close to the CH2-CH3 interface, previously reported to activate unfolding of trastuzumab, increasing the accessible surface area and hence resulting in an increase in chromatographic retention.
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Affiliation(s)
- Raphael Ewonde Ewonde
- Department
of Chemical Engineering, Vrije Universiteit
Brussel (VUB), Pleinlaan 2, 1050 Brussels, Belgium
| | - Katharina Böttinger
- Department
of Biosciences and Medical Biology, Bioanalytical Research Laboratories, University of Salzburg, Hellbrunner Strasse 34, 5020 Salzburg, Austria
| | - Jelle De Vos
- Department
of Chemical Engineering, Vrije Universiteit
Brussel (VUB), Pleinlaan 2, 1050 Brussels, Belgium
| | - Nico Lingg
- Department
of Biotechnology, Institute of Bioprocess
Science and Engineering, University of Natural Resources and Life
Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Alois Jungbauer
- Department
of Biotechnology, Institute of Bioprocess
Science and Engineering, University of Natural Resources and Life
Sciences, Muthgasse 18, 1190 Vienna, Austria
| | | | - Christian G. Huber
- Department
of Biosciences and Medical Biology, Bioanalytical Research Laboratories, University of Salzburg, Hellbrunner Strasse 34, 5020 Salzburg, Austria
| | - Gert Desmet
- Department
of Chemical Engineering, Vrije Universiteit
Brussel (VUB), Pleinlaan 2, 1050 Brussels, Belgium
| | - Sebastiaan Eeltink
- Department
of Chemical Engineering, Vrije Universiteit
Brussel (VUB), Pleinlaan 2, 1050 Brussels, Belgium
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Sadeghi A, PourEskandar S, Askari E, Akbari M. Polymeric Nanoparticles and Nanogels: How Do They Interact with Proteins? Gels 2023; 9:632. [PMID: 37623087 PMCID: PMC10453451 DOI: 10.3390/gels9080632] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/21/2023] [Accepted: 07/27/2023] [Indexed: 08/26/2023] Open
Abstract
Polymeric nanomaterials, nanogels, and solid nanoparticles can be fabricated using single or double emulsion methods. These materials hold great promise for various biomedical applications due to their biocompatibility, biodegradability, and their ability to control interactions with body fluids and cells. Despite the increasing use of nanoparticles in biomedicine and the plethora of publications on the topic, the biological behavior and efficacy of polymeric nanoparticles (PNPs) have not been as extensively studied as those of other nanoparticles. The gap between the potential of PNPs and their applications can mainly be attributed to the incomplete understanding of their biological identity. Under physiological conditions, such as specific temperatures and adequate protein concentrations, PNPs become coated with a "protein corona" (PC), rendering them potent tools for proteomics studies. In this review, we initially investigate the synthesis routes and chemical composition of conventional PNPs to better comprehend how they interact with proteins. Subsequently, we comprehensively explore the effects of material and biological parameters on the interactions between nanoparticles and proteins, encompassing reactions such as hydrophobic bonding and electrostatic interactions. Moreover, we delve into recent advances in PNP-based models that can be applied to nanoproteomics, discussing the new opportunities they offer for the clinical translation of nanoparticles and early prediction of diseases. By addressing these essential aspects, we aim to shed light on the potential of polymeric nanoparticles for biomedical applications and foster further research in this critical area.
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Affiliation(s)
- Amirhossein Sadeghi
- Polymer Laboratory, School of Chemistry, College of Science, University of Tehran, Tehran P.O. Box 141556455, Iran
| | - Shadi PourEskandar
- Department of Chemical Engineering, Razi University, Kermanshah P.O. Box 6718773654, Iran
| | - Esfandyar Askari
- Biomaterials and Tissue Engineering Research Group, Department of Interdisciplinary Technologies, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran P.O. Box 1684613114, Iran
| | - Mohsen Akbari
- Mechanical Engineering Department, University of Victoria, 3800 Finnerty Rd., Victoria, BC V8P 5C2, Canada
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Sato R, Tomioka Y, Sakuma C, Nakagawa M, Kurosawa Y, Shiba K, Arakawa T, Akuta T. Detection of concentration-dependent conformational changes in SARS-CoV-2 nucleoprotein by agarose native gel electrophoresis. Anal Biochem 2023; 662:114995. [PMID: 36427555 PMCID: PMC9681993 DOI: 10.1016/j.ab.2022.114995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/02/2022] [Accepted: 11/14/2022] [Indexed: 11/24/2022]
Abstract
The nucleoprotein (NP) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is abundantly expressed during infection, making it a diagnostic target protein. We analyzed the structure of the NP in solution using a recombinant protein produced in E. coli. A codon-optimized Profinity eXact™-tagged NP cDNA was cloned into pET-3d vector and transformed into E. coli T7 Express. The recombinant protein was first purified via chromatographic step using an affinity tag-based system that was followed by tag cleavage with sodium fluoride, resulting in proteolytic removal of the N-terminal tag sequence. The digested sample was then loaded directly onto a size exclusion chromatography run in the presence of L-Arg-HCl, resulting in removal of host nucleic acids and endotoxin. The molecular mass of the main NP fraction was determined by mass photometry as a dimeric form of NP, consistent with the blue native PAGE results. Interestingly, analysis of the purified NP by our newly developed agarose native gel electrophoresis revealed that it behaved like an acidic protein at low concentration despite its alkaline isoelectric point (theoretical pI = 10) and displayed a unique character of concentration-dependent charge and shape changes. This study should shed light into the behavior of NP in the viral life cycle.
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Affiliation(s)
- Ryo Sato
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-shi, Ibaraki, 318-0004, Japan.
| | - Yui Tomioka
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-shi, Ibaraki, 318-0004, Japan.
| | - Chiaki Sakuma
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-shi, Ibaraki, 318-0004, Japan.
| | - Masataka Nakagawa
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-shi, Ibaraki, 318-0004, Japan.
| | - Yasunori Kurosawa
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-shi, Ibaraki, 318-0004, Japan; Abwiz Bio Inc., 9823 Pacific Heights Blvd., Suite J, San Diego, CA, 92121, USA.
| | - Kohei Shiba
- Refeyn Japan, K.K., 1-1-14, Sakuraguchi-cho, Nada-ku, Kobe, Hyogo, 6570036, Japan.
| | - Tsutomu Arakawa
- Alliance Protein Laboratories, 13380 Pantera Rd, San Diego, CA, 92130, USA.
| | - Teruo Akuta
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-shi, Ibaraki, 318-0004, Japan.
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CASPON platform technology: Ultrafast circularly permuted caspase-2 cleaves tagged fusion proteins before all 20 natural amino acids at the N-terminus. N Biotechnol 2022; 71:37-46. [DOI: 10.1016/j.nbt.2022.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/13/2022] [Accepted: 07/30/2022] [Indexed: 11/21/2022]
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Fusion Tag Design Influences Soluble Recombinant Protein Production in Escherichia coli. Int J Mol Sci 2022; 23:ijms23147678. [PMID: 35887026 PMCID: PMC9321918 DOI: 10.3390/ijms23147678] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/30/2022] [Accepted: 07/09/2022] [Indexed: 02/01/2023] Open
Abstract
Fusion protein technologies to facilitate soluble expression, detection, or subsequent affinity purification in Escherichia coli are widely used but may also be associated with negative consequences. Although commonly employed solubility tags have a positive influence on titers, their large molecular mass inherently results in stochiometric losses of product yield. Furthermore, the introduction of affinity tags, especially the polyhistidine tag, has been associated with undesirable changes in expression levels. Fusion tags are also known to influence the functionality of the protein of interest due to conformational changes. Therefore, particularly for biopharmaceutical applications, the removal of the fusion tag is a requirement to ensure the safety and efficacy of the therapeutic protein. The design of suitable fusion tags enabling the efficient manufacturing of the recombinant protein remains a challenge. Here, we evaluated several N-terminal fusion tag combinations and their influence on product titer and cell growth to find an ideal design for a generic fusion tag. For enhancing soluble expression, a negatively charged peptide tag derived from the T7 bacteriophage was combined with affinity tags and a caspase-2 cleavage site applicable for CASPase-based fusiON (CASPON) platform technology. The effects of each combinatorial tag element were investigated in an integrated manner using human fibroblast growth factor 2 as a model protein in fed-batch lab-scale bioreactor cultivations. To confirm the generic applicability for manufacturing, seven additional pharmaceutically relevant proteins were produced using the best performing tag of this study, named CASPON-tag, and tag removal was demonstrated.
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