1
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Shi W, Zhang TY, Fang CY, Zhang SQ, Li KB, Zhang XB, Han DM. Transforming waste into valuables: Preparation and evaluation of dual-ligand hydrophobic charge-induction chromatography using two poor performing ligands. J Chromatogr A 2024; 1726:464975. [PMID: 38735118 DOI: 10.1016/j.chroma.2024.464975] [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: 03/06/2024] [Revised: 04/28/2024] [Accepted: 05/06/2024] [Indexed: 05/14/2024]
Abstract
In conventional chromatographic ligand screening, underperforming ligands are often dismissed. However, this practice may inadvertently overlook potential opportunities. This study aims to investigate whether these underperforming ligands can be repurposed as valuable assets. Hydrophobic charge-induction chromatography (HCIC) is chosen as the validation target for its potential as an innovative chromatographic mode. A novel dual-ligand approach is employed, combining two suboptimal ligands (5-Aminobenzimidazole and Tryptamine) to explore enhanced performance and optimization prospects. Various dual-ligand HCIC resins with different ligand densities were synthesized by adjusting the ligand ratio and concentration. The resins were characterized to assess appearance, functional groups, and pore features using SEM, FTIR, and ISEC techniques. Performance assessments were conducted using single-ligand mode resins as controls, evaluating the selectivity against human immunoglobulin G and human serum albumin. Static adsorption experiments were performed to understand pH and salt influence on adsorption. Breakthrough experiments were conducted to assess dynamic adsorption capacity of the novel resin. Finally, chromatographic separation using human serum was performed to evaluate the purity and yield of the resin. Results indicated that the dual-ligand HCIC resin designed for human antibodies demonstrates exceptional selectivity, surpassing not only single ligand states but also outperforming certain high-performing ligand types, particularly under specific salt and pH conditions. Ultimately, a high yield of 83.9 % and purity of 96.7 % were achieved in the separation of hIgG from human serum with the dual-ligand HCIC, significantly superior to the single-ligand resins. In conclusion, through rational design and proper operational conditions, the dual-ligand mode can revitalize underutilized ligands, potentially introducing novel and promising chromatographic modes.
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Affiliation(s)
- Wei Shi
- School of Pharmaceutical and Chemical Engineering, Taizhou University, Jiaojiang 318000, China; Taizhou Research Institute of Bio-Medical and Chemical Industry CO., LTD, Jiaojiang 318000, China
| | - Tian-Yi Zhang
- School of Pharmaceutical and Chemical Engineering, Taizhou University, Jiaojiang 318000, China
| | - Chao-Ying Fang
- School of Pharmaceutical and Chemical Engineering, Taizhou University, Jiaojiang 318000, China
| | - Si-Qi Zhang
- School of Pharmaceutical and Chemical Engineering, Taizhou University, Jiaojiang 318000, China
| | - Kai-Bin Li
- School of Pharmaceutical and Chemical Engineering, Taizhou University, Jiaojiang 318000, China
| | - Xiao-Bin Zhang
- School of Pharmaceutical and Chemical Engineering, Taizhou University, Jiaojiang 318000, China
| | - De-Man Han
- School of Pharmaceutical and Chemical Engineering, Taizhou University, Jiaojiang 318000, China.
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2
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Yu L, Yang D, Chu M, Sun Y. Advances and challenges in the purification of recombinant coagulation factors: A review. J Chromatogr A 2024; 1716:464662. [PMID: 38244305 DOI: 10.1016/j.chroma.2024.464662] [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: 01/02/2024] [Revised: 01/12/2024] [Accepted: 01/14/2024] [Indexed: 01/22/2024]
Abstract
Hemostasis is a complex process for the cessation of bleeding from an injured blood vessel, involving the interplay of 12 coagulation factors in the coagulation cascade with activated blood platelets and the vessel wall. Hence, the coagulation factors are important to control hemorrhage. However, the low abundance of many coagulation factors in human plasma proteins limited their production in therapeutic drugs and their clinical applications. With the development of modern biotechnology, commercially manufactured recombinant coagulation factors became available as hemostatic therapeutics, emerging a huge potential in pharmaceutical manufacturing market. Unlike antibodies, whose standard operation unit or platform purification processes in the industrial-scale downstream processing has been well-established, the complexity in post-translational modification and differences in structures of the coagulation factors posed specific challenges with respect to the downstream processing, which have long been limiting their industrial-scale production. This review presents a comprehensive overview of the technological development of commercially manufactured recombinant coagulation factors, with emphasis on their advances and challenges in the separation and purification processes. Firstly, the licensed products of the plasma derived and recombinant coagulation factors are summarized. Then, typical recombinant coagulation factors, i.e. factors VII, VIII and IX, are introduced with detailed discussion on their preparative separation procedures for both the licensed products of industrial-scale and the experimental cases of laboratory-scale. Finally, perspectives and challenges in the future development of the purification technology of recombinant coagulation factors are highlighted to provide new insight into the design of cost-effective purification processes of recombinant coagulation factors.
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Affiliation(s)
- Linling Yu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
| | - Dongmei Yang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
| | - Mengyao Chu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
| | - Yan Sun
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China.
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3
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Barbieri E, Mollica GN, Moore BD, Sripada SA, Shastry S, Kilgore RE, Loudermilk CM, Whitacre ZH, Kilgour KM, Wuestenhagen E, Aldinger A, Graalfs H, Rammo O, Schulte MM, Johnson TF, Daniele MA, Menegatti S. Peptide ligands targeting the vesicular stomatitis virus G (VSV-G) protein for the affinity purification of lentivirus particles. Biotechnol Bioeng 2024; 121:618-639. [PMID: 37947118 DOI: 10.1002/bit.28594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/17/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023]
Abstract
The recent uptick in the approval of ex vivo cell therapies highlights the relevance of lentivirus (LV) as an enabling viral vector of modern medicine. As labile biologics, however, LVs pose critical challenges to industrial biomanufacturing. In particular, LV purification-currently reliant on filtration and anion-exchange or size-exclusion chromatography-suffers from long process times and low yield of transducing particles, which translate into high waiting time and cost to patients. Seeking to improve LV downstream processing, this study introduces peptides targeting the enveloped protein Vesicular stomatitis virus G (VSV-G) to serve as affinity ligands for the chromatographic purification of LV particles. An ensemble of candidate ligands was initially discovered by implementing a dual-fluorescence screening technology and a targeted in silico approach designed to identify sequences with high selectivity and tunable affinity. The selected peptides were conjugated on Poros resin and their LV binding-and-release performance was optimized by adjusting the flow rate, composition, and pH of the chromatographic buffers. Ligands GKEAAFAA and SRAFVGDADRD were selected for their high product yield (50%-60% of viral genomes; 40%-50% of HT1080 cell-transducing particles) upon elution in PIPES buffer with 0.65 M NaCl at pH 7.4. The peptide-based adsorbents also presented remarkable values of binding capacity (up to 3·109 TU per mL of resin, or 5·1011 vp per mL of resin, at the residence time of 1 min) and clearance of host cell proteins (up to a 220-fold reduction of HEK293 HCPs). Additionally, GKEAAFAA demonstrated high resistance to caustic cleaning-in-place (0.5 M NaOH, 30 min) with no observable loss in product yield and quality.
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Affiliation(s)
- Eduardo Barbieri
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Gina N Mollica
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Brandyn D Moore
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Sobhana A Sripada
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Shriarjun Shastry
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, North Carolina, USA
| | - Ryan E Kilgore
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Casee M Loudermilk
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Zachary H Whitacre
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Katie M Kilgour
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | | | | | | | | | | | - Thomas F Johnson
- Department of Biochemical Engineering, University College London, London, UK
| | - Michael A Daniele
- North Carolina Viral Vector Initiative in Research and Learning (NC-VVIRAL), North Carolina State University, Raleigh, North Carolina, USA
- Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, Raleigh, North Carolina, USA
| | - Stefano Menegatti
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, North Carolina, USA
- North Carolina Viral Vector Initiative in Research and Learning (NC-VVIRAL), North Carolina State University, Raleigh, North Carolina, USA
- LigaTrap Technologies LLC, Raleigh, North Carolina, USA
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4
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Shastry S, Chu W, Barbieri E, Greback-Clarke P, Smith WK, Cummings C, Minzoni A, Pancorbo J, Gilleskie G, Ritola K, Daniele MA, Johnson TF, Menegatti S. Rational design and experimental evaluation of peptide ligands for the purification of adeno-associated viruses via affinity chromatography. Biotechnol J 2024; 19:e2300230. [PMID: 37728197 DOI: 10.1002/biot.202300230] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 09/12/2023] [Accepted: 09/14/2023] [Indexed: 09/21/2023]
Abstract
Adeno-associated viruses (AAVs) have acquired a central role in modern medicine as delivery agents for gene therapies targeting rare diseases. While new AAVs with improved tissue targeting, potency, and safety are being introduced, their biomanufacturing technology is lagging. In particular, the AAV purification pipeline hinges on protein ligands for the affinity-based capture step. While featuring excellent AAV binding capacity and selectivity, these ligands require strong acid (pH <3) elution conditions, which can compromise the product's activity and stability. Additionally, their high cost and limited lifetime has a significant impact on the price tag of AAV-based therapies. Seeking to introduce a more robust and affordable affinity technology, this study introduces a cohort of peptide ligands that (i) mimic the biorecognition activity of the AAV receptor (AAVR) and anti-AAV antibody A20, (ii) enable product elution under near-physiological conditions (pH 6.0), and (iii) grant extended reusability by withstanding multiple regenerations. A20-mimetic CYIHFSGYTNYNPSLKSC and AAVR-mimetic CVIDGSQSTDDDKIC demonstrated excellent capture of serotypes belonging to distinct clones/clades - namely, AAV1, AAV2, AAV5, AAV6, AAV8, and AAV9. This corroborates the in silico models documenting their ability to target regions of the viral capsid that are conserved across all serotypes. CVIDGSQSTDDDKIC-Toyopearl resin features binding capacity (≈1014 vp mL-1 ) and product yields (≈60%-80%) on par with commercial adsorbents, and purifies AAV2 from HEK293 and Sf9 cell lysates with high recovery (up to 78%), reduction of host cell proteins (up to 700-fold), and high transduction activity (up to 65%).
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Affiliation(s)
- Shriarjun Shastry
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, North Carolina, USA
| | - Wenning Chu
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Eduardo Barbieri
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Paul Greback-Clarke
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, North Carolina, USA
| | - William K Smith
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, North Carolina, USA
| | - Christopher Cummings
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, North Carolina, USA
| | - Arianna Minzoni
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Jennifer Pancorbo
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, North Carolina, USA
| | - Gary Gilleskie
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, North Carolina, USA
| | - Kimberly Ritola
- Neuroscience Center, Brain Initiative Neurotools Vector Core, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- North Carolina Viral Vector Initiative in Research and Learning (NC-VVIRAL), North Carolina State University, Raleigh, North Carolina, USA
| | - Michael A Daniele
- North Carolina Viral Vector Initiative in Research and Learning (NC-VVIRAL), North Carolina State University, Raleigh, North Carolina, USA
- Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, Raleigh, North Carolina, USA
| | - Thomas F Johnson
- Department of Biochemical Engineering, University College London, London, UK
| | - Stefano Menegatti
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, North Carolina, USA
- North Carolina Viral Vector Initiative in Research and Learning (NC-VVIRAL), North Carolina State University, Raleigh, North Carolina, USA
- LigaTrap Technologies LLC, Raleigh, North Carolina, USA
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5
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Suderman RJ, Gibson SD, Strecker M, Bonner AM, Chao DM. Protein engineering of a nanoCLAMP antibody mimetic scaffold as a platform for producing bioprocess-compatible affinity capture ligands. J Biol Chem 2023; 299:104910. [PMID: 37315789 PMCID: PMC10404686 DOI: 10.1016/j.jbc.2023.104910] [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: 12/23/2022] [Revised: 05/17/2023] [Accepted: 06/06/2023] [Indexed: 06/16/2023] Open
Abstract
Protein A affinity chromatography is widely used for the large-scale purification of antibodies because of its high yield, selectivity, and compatibility with NaOH sanitation. A general platform to produce robust affinity capture ligands for proteins beyond antibodies would improve bioprocessing efficiency. We previously developed nanoCLAMPs (nano Clostridial Antibody Mimetic Proteins), a class of antibody mimetic proteins useful as lab-scale affinity capture reagents. This work describes a protein engineering campaign to develop a more robust nanoCLAMP scaffold compatible with harsh bioprocessing conditions. The campaign generated an improved scaffold with dramatically improved resistance to heat, proteases, and NaOH. To isolate additional nanoCLAMPs based on this scaffold, we constructed a randomized library of 1 × 1010 clones and isolated binders to several targets. We then performed an in-depth characterization of nanoCLAMPs recognizing yeast SUMO, a fusion partner used for the purification of recombinant proteins. These second-generation nanoCLAMPs typically had a Kd of <80 nM, a Tm of >70 °C, and a t1/2 in 0.1 mg/ml trypsin of >20 h. Affinity chromatography resins bearing these next-generation nanoCLAMPs enabled single-step purifications of SUMO fusions. Bound target proteins could be eluted at neutral or acidic pH. These affinity resins maintained binding capacity and selectivity over 20 purification cycles, each including 10 min of cleaning-in-place with 0.1 M NaOH, and remained functional after exposure to 100% DMF and autoclaving. The improved nanoCLAMP scaffold will enable the development of robust, high-performance affinity chromatography resins against a wide range of protein targets.
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Affiliation(s)
| | - Shane D Gibson
- Nectagen, Inc, Kansas City, Kansas, USA; University of Washington, Seattle, Washington, USA
| | - Mary Strecker
- Nectagen, Inc, Kansas City, Kansas, USA; Two Dot Consulting, Arvada, Colorado, USA
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6
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Sorour AA, Olama ZA, El-Naggar MY, Ali SM. Bioprocess development for extraction and purification of cellulases from Aspergillus niger 3ASZ using statistical experimental design techniques. Int J Biol Macromol 2023; 242:124759. [PMID: 37150365 DOI: 10.1016/j.ijbiomac.2023.124759] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 05/01/2023] [Accepted: 05/02/2023] [Indexed: 05/09/2023]
Abstract
The amount of cellulosic materials is large and may lead to environmental pollution, so they can be converted into useful materials for use in food or energy. Statistical design (Plackett-Burman and Box-Behnken) was the main topic of this study and was used to optimize the effect of environmental factors on cellulase production by Aspergillus niger. Cellulase production using Plackett-Burman was 6.86-fold higher than the production of cellulase using the basal medium. B0X-Benken showed an increase in the cellulase production equal to 18 times compared to the basal medium, where the cellulase produced had an activity equal to 79.4 U/mL/min. Ammonium sulfate precipitation was applied to the crude enzyme, followed by sequential fractionation with an Amicon system. The Amicon was used to demonstrate the final volume, total enzyme activity, specific activity, purification fold, and yield of cellulase (partially purified enzyme). Numerous cellulolytic enzymes are abundant in Aspergillus species. All of the data showed that Aspergillus sp. might be a reliable source of industrially and economically useful cellulases. By statistically calculating the relevance of a large number of elements in one experiment using a multifactorial statistical design, time may be saved while still maintaining the validity of each component.
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Affiliation(s)
- Aman A Sorour
- Botany and Microbiology Department, Faculty of Science, Alexandria University, Egypt
| | - Zakia A Olama
- Botany and Microbiology Department, Faculty of Science, Alexandria University, Egypt
| | - Moustafa Y El-Naggar
- Botany and Microbiology Department, Faculty of Science, Alexandria University, Egypt
| | - Safaa M Ali
- Nucleic Acid Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications, Alexandria, Egypt.
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7
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Prodromou R, Moore B, Chu W, Deal H, Miguel AS, Brown AC, Daniele MA, Pozdin V, Menegatti S. Molecular engineering of cyclic azobenzene-peptide hybrid ligands for the purification of human blood Factor VIII via photo-affinity chromatography. ADVANCED FUNCTIONAL MATERIALS 2023; 33:2213881. [PMID: 37576949 PMCID: PMC10421628 DOI: 10.1002/adfm.202213881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Indexed: 08/15/2023]
Abstract
The use of benign stimuli to control the binding and release of labile biologics for their isolation from complex feedstocks is a key goal of modern biopharmaceutical technology. This study introduces cyclic azobenzene-peptide (CAP) hybrid ligands for the rapid and discrete photo-responsive capture and release of blood coagulation Factor VIII (FVIII). A predictive method - based on amino acid sequence and molecular architecture of CAPs - was developed to correlate the conformation of cis/trans CAP photo-isomers to FVIII binding and release. The combined in silico and in vitro analysis of FVIII:peptide interactions guided the design of a rational approach to optimize isomerization kinetics and biorecognition of CAPs. A photoaffinity adsorbent, prepared by conjugating selected CAP G-cycloAZOB[Lys-YYKHLYN-Lys]-G on translucent chromatographic beads, featured high binding capacity (> 6 mg of FVIII per mL of resin) and rapid photo-isomerization kinetics (τ < 30s) when exposed to 420-450 nm light at the intensity of 0.1 W·cm-2. The adsorbent purified FVIII from a recombinant harvest using a single mobile phase, affording high product yield (>90%), purity (>95%), and blood clotting activity. The CAPs introduced in this report demonstrate a novel route integrating gentle operational conditions in a rapid and efficient bioprocess for the purification of life-saving biotherapeutics.
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Affiliation(s)
- Raphael Prodromou
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC 27695, USA
| | - Brandyn Moore
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC 27695, USA
| | - Wenning Chu
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC 27695, USA
| | - Halston Deal
- Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, 911 Oval Drive, Raleigh, NC 27695, USA
| | - Adriana San Miguel
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC 27695, USA
| | - Ashley C. Brown
- Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, 911 Oval Drive, Raleigh, NC 27695, USA
| | - Michael A. Daniele
- Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, 911 Oval Drive, Raleigh, NC 27695, USA
- Department of Electrical and Computer Engineering, North Carolina State University, 890 Oval Drive, Raleigh, NC 27695, USA
| | - Vladimir Pozdin
- Department of Electrical and Computer Engineering, Florida International University, 10555 West Flagler St., Miami, FL 33174, USA
- Department of Mechanical and Materials Engineering, Florida International University, 10555 West Flagler St., Miami, FL 33174, USA
| | - Stefano Menegatti
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC 27695, USA
- Biomanufacturing Training and Education Center (BTEC), 850 Oval Drive, Raleigh, NC 27606, USA
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8
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Shi W, Zhu SN, Xu H, Li KB, Zhang SQ, Zhang TY, Fang CY, Zhang XB, Han DM. Simultaneous Recovery of Bovine Serum Albumin and Bovine Immunoglobulin G with Dual-Ligand Hydrophobic Charge-Induction Chromatography. Ind Eng Chem Res 2023. [DOI: 10.1021/acs.iecr.3c00503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
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9
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Sripada SA, Chu W, Williams TI, Teten MA, Mosley BJ, Carbonell RG, Lenhoff AM, Cramer SM, Bill J, Yigzaw Y, Roush D, Menegatti S. Towards continuous mAb purification: clearance of host cell proteins from CHO cell culture harvests via "flow-through affinity chromatography" using peptide-based adsorbents. Biotechnol Bioeng 2022; 119:1873-1889. [PMID: 35377460 DOI: 10.1002/bit.28096] [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] [Received: 11/17/2021] [Revised: 03/22/2022] [Accepted: 03/27/2022] [Indexed: 11/12/2022]
Abstract
The growth of advanced analytics in manufacturing monoclonal antibodies (mAb) has highlighted the challenges associated with the clearance of host cell proteins (HCPs). Of special concern is the removal of "persistent" HCPs, including immunogenic and mAb-degrading proteins, that co-elute from the Protein A resin and can escape the polishing steps. Responding to this challenge, we introduced an ensemble of peptide ligands that target the HCPs in Chinese hamster ovary (CHO) cell culture fluids and enable mAb purification via flow-through affinity chromatography. This work describes their integration into LigaGuardTM, an affinity adsorbent featuring an equilibrium binding capacity of ~30 mg of HCPs per mL of resin as well as dynamic capacities up to 16 and 22 mg/mL at 1- and 2-minute residence times, respectively. When evaluated against cell culture harvests with different mAb and HCP titers and properties, LigaGuardTM afforded high HCP clearance, with logarithmic removal values (LRVs) up to 1.5, and mAb yield above 90%. Proteomic analysis of the effluents confirmed the removal of high-risk HCPs, including cathepsins, histones, glutathione-S transferase, and lipoprotein lipases. Finally, combining LigaGuardTM for HCP removal with affinity adsorbents for product capture afforded a global mAb yield of 85%, and HCP and DNA LRVs > 4. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Sobhana A Sripada
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC, 27695, USA
| | - Wenning Chu
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC, 27695, USA
| | - Taufika Islam Williams
- Molecular Education, Technology, and Research Innovation Center (METRIC), North Carolina State University, 2620 Yarbrough Dr., Raleigh, NC, 27607, USA.,Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC, 27695, USA
| | - Matthew A Teten
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, 850 Oval Dr, Raleigh, NC, 27606, USA
| | - Brian J Mosley
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, 850 Oval Dr, Raleigh, NC, 27606, USA
| | - Ruben G Carbonell
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC, 27695, USA.,Biomanufacturing Training and Education Center (BTEC), North Carolina State University, 850 Oval Dr, Raleigh, NC, 27606, USA
| | - Abraham M Lenhoff
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street Colburn Laboratory Newark, DE, 19716, USA
| | - Steven M Cramer
- The Howard P. Isermann Department of Chemical and Biological Engineering and the Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th St, Troy, NY, 12180, USA
| | - Jerome Bill
- Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Yinges Yigzaw
- Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - David Roush
- Merck & Co., 2000 Galloping Hill Rd, Kenilworth, NJ, 07033, USA
| | - Stefano Menegatti
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC, 27695, USA.,Biomanufacturing Training and Education Center (BTEC), North Carolina State University, 850 Oval Dr, Raleigh, NC, 27606, USA
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10
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Bacon K, Menegatti S, Rao BM. Discovery of Cyclic Peptide Binders from Chemically Constrained Yeast Display Libraries. Methods Mol Biol 2022; 2491:387-415. [PMID: 35482201 DOI: 10.1007/978-1-0716-2285-8_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Cyclic peptides with engineered protein-binding activity have great potential as therapeutic and diagnostic reagents owing to their favorable properties, including high affinity and selectivity. Cyclic peptide binders have generally been isolated from phage display combinatorial libraries utilizing panning based selections. As an alternative, we have developed a yeast surface display platform to identify and characterize cyclic peptide binders from genetically encoded combinatorial libraries. Through a combination of magnetic selection and fluorescence-activated cell sorting (FACS), high-affinity cyclic peptide binders can be efficiently isolated from yeast display libraries. In this platform, linear peptide precursors are expressed as yeast surface fusions. To achieve cyclization of the linear precursors, the cells are incubated with disuccinimidyl glutarate, which crosslinks amine groups within the displayed linear peptide sequence. Here, we detail protocols for cyclizing linear peptides expressed as yeast surface fusions. We also discuss how to synthesize a yeast display library of linear peptide precursors. Subsequently, we provide suggestions on how to utilize magnetic selections and FACS to isolate cyclic peptide binders for target proteins of interest from a peptide combinatorial library. Lastly, we detail how yeast surface displayed cyclic peptides can be used to obtain efficient estimates of binding affinity, eliminating the need for chemically synthesized peptides when performing mutant characterization.
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Affiliation(s)
- Kaitlyn Bacon
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Stefano Menegatti
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, NC, USA
| | - Balaji M Rao
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA.
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, NC, USA.
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Krishnan M, Choi J, Jang A, Yoon YK, Kim Y. Antiseptic 9-Meric Peptide with Potency against Carbapenem-Resistant Acinetobacter baumannii Infection. Int J Mol Sci 2021; 22:12520. [PMID: 34830401 PMCID: PMC8621208 DOI: 10.3390/ijms222212520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 11/17/2021] [Accepted: 11/17/2021] [Indexed: 11/18/2022] Open
Abstract
Carbapenem-resistant A. baumannii (CRAB) infection can cause acute host reactions that lead to high-fatality sepsis, making it important to develop new therapeutic options. Previously, we developed a short 9-meric peptide, Pro9-3D, with significant antibacterial and cytotoxic effects. In this study, we attempted to produce safer peptide antibiotics against CRAB by reversing the parent sequence to generate R-Pro9-3 and R-Pro9-3D. Among the tested peptides, R-Pro9-3D had the most rapid and effective antibacterial activity against Gram-negative bacteria, particularly clinical CRAB isolates. Analyses of antimicrobial mechanisms based on lipopolysaccharide (LPS)-neutralization, LPS binding, and membrane depolarization, as well as SEM ultrastructural investigations, revealed that R-Pro9-3D binds strongly to LPS and impairs the membrane integrity of CRAB by effectively permeabilizing its outer membrane. R-Pro9-3D was also less cytotoxic and had better proteolytic stability than Pro9-3D and killed biofilm forming CRAB. As an LPS-neutralizing peptide, R-Pro9-3D effectively reduced LPS-induced pro-inflammatory cytokine levels in RAW 264.7 cells. The antiseptic abilities of R-Pro9-3D were also investigated using a mouse model of CRAB-induced sepsis, which revealed that R-Pro9-3D reduced multiple organ damage and attenuated systemic infection by acting as an antibacterial and immunosuppressive agent. Thus, R-Pro9-3D displays potential as a novel antiseptic peptide for treating Gram-negative CRAB infections.
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Affiliation(s)
- Manigandan Krishnan
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Korea; (M.K.); (J.C.); (A.J.)
| | - Joonhyeok Choi
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Korea; (M.K.); (J.C.); (A.J.)
| | - Ahjin Jang
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Korea; (M.K.); (J.C.); (A.J.)
| | - Young Kyung Yoon
- Department of Internal Medicine, Division of Infectious Diseases, College of Medicine, Korea University Anam Hospital, Korea University, Seoul 02841, Korea;
| | - Yangmee Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Korea; (M.K.); (J.C.); (A.J.)
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Kurnia D, Kelutur FJ, Mustarichie R. Potential anti-alopecia constituents from Theobroma cacao: An in silico study. J Adv Pharm Technol Res 2021; 12:169-174. [PMID: 34159149 PMCID: PMC8177142 DOI: 10.4103/japtr.japtr_329_20] [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: 12/16/2020] [Revised: 02/17/2021] [Accepted: 03/03/2021] [Indexed: 11/06/2022] Open
Abstract
Tinea capitis is local alopecia caused by a dermatophyte infection of the scalp. Trichophyton rubrum produces the squalene epoxidase enzyme, which has a crucial role in prolonged dermatophyte infection, as well as in synthesizing fatty acids in this dermatophyte group. This study analyzes Trichophyton cacao compounds as anti-alopecia by inhibiting the squalene epoxidase enzyme formation, in silico. The structure of T. cacao compounds was prepared using the MolView Web application. The compound docked to squalene epoxidase using AutoDock Vina in PyRx 0.8, followed by PyMOL for visualization, and the Proteins Plus program to analyze the complexity. The binding affinity value of catechin, epicatechin (−8.0 kcal/mol), and anthocyanin (−7.8 kcal/mol) compounds was higher than the positive control (terbinafine, −6.7 kcal/mol). Pre-ADMET demonstrated that catechin and epicatechin had moderate Human Intestinal Absorption (66.71%), but anthocyanin was very good (100%). Caco-2 parameters for catechin and epicatechin were relatively low (<4 nm s − 1), while anthocyanin, theobromine, and terbinafine were within 4–70 nm s − 1. Plasma protein binding shows catechin, epicatechin, and anthocyanin diffuse through the plasma membrane and interact with plasma proteins. The toxicity results for all compounds are mutagenic, and only terbinafine is carcinogenic. Based on the Lipinski's “Rule of Five,” compounds from T. Cacao can be given orally. Catechin and epicatechin compounds have the potential to act as anti-alopecia. These two compounds can diffuse and interact with plasma proteins so they are directly on the target when given orally.
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Affiliation(s)
- Dikdik Kurnia
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Padjadjaran University, Sumedang, West Java, Indonesia
| | - Faruk Jayanto Kelutur
- Department of Pharmaceutical Analysis and Medicinal Chemistry, Faculty of Pharmacy, Universitas Padjadjaran, Sumedang, West Java, Indonesia
| | - Resmi Mustarichie
- Department of Pharmaceutical Analysis and Medicinal Chemistry, Faculty of Pharmacy, Universitas Padjadjaran, Sumedang, West Java, Indonesia
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Focused peptide library screening as a route to a superior affinity ligand for antibody purification. Sci Rep 2021; 11:11650. [PMID: 34079028 PMCID: PMC8173005 DOI: 10.1038/s41598-021-91208-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 05/24/2021] [Indexed: 12/18/2022] Open
Abstract
Affinity chromatography is the linchpin of antibody downstream processing and typically relies on bacterial immunoglobulin (Ig)-binding proteins, epitomized by staphylococcal protein A-based ligands. However, such affinity ligands are fairly costly and suffer from chemical instability, leading to ligand denaturation and leaching from chromatographic support. Innovations in this area are aimed at developing robust and highly selective antibody ligands capable of withstanding harsh column sanitization conditions. We report the development and first-stage characterization of a selective short linear peptide ligand of the IgG Fc region capable of capturing all four IgG subclasses. The ligand was discovered through in vitro directed evolution. A focused phage-display library based on a previously identified peptide lead was subjected to a single-round screen against a pool of human IgG. The hits were identified with next-generation sequencing and ranked according to the enrichment ratio relative to their frequency in the pre-screened library. The top enriched peptide GSYWYNVWF displaying highest affinity for IgG was coupled to bromohydrin-activated agarose beads via a branched linker. The resulting affinity matrix was characterized with a dynamic binding capacity of approx. 43 mg/mL, on par with commercially employed protein A-based resin.
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