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Stamm SM, Wagner R, Lang DA, Skerra A, Gebauer M. Development of a Clonal and High-Yield Mammalian Cell Line for the Manufacturing of a Hyperactive Human DNase I with Extended Plasma Half-Life Using PASylation ® Technology. Pharmaceutics 2024; 16:967. [PMID: 39065664 PMCID: PMC11280007 DOI: 10.3390/pharmaceutics16070967] [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: 05/30/2024] [Revised: 06/27/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
Cumulative evidence from several pre-clinical studies suggests that restoration of plasma DNase activity in a thrombo-inflammatory state may improve clinical outcomes. Following injury, hyperactivated immune cells release large amounts of granular proteins together with DNA, which often accumulate in the surrounding environment in so-called neutrophil extracellular traps (NETs). Degradation of excess NETs by systemic DNase administration offers a promising therapeutic approach to ameliorate inflammation and dissolve intravascular clots. In order to expand the therapeutic utility of human DNase I, a variant of the enzyme was developed that has both a prolonged systemic half-life and a higher catalytic activity compared to Dornase alfa (Pulmozyme®), the recombinant form of DNase I approved for inhaled therapy of cystic fibrosis. The hyperactive enzyme was "PASylated" by genetic fusion with a strongly hydrophilic and biodegradable PAS-polypeptide to increase its hydrodynamic volume and retard kidney filtration. A stable TurboCell™ CHO-K1-based cell line was generated which is suitable for the future production of PASylated DNase I according to good manufacturing practice (GMP). Furthermore, a robust bioprocess strategy was devised and an effective downstream process was developed. The final protein product is characterized by excellent purity, favorable physicochemical properties, a 14-fold higher DNA-degrading activity than Dornase alfa and a sustained pharmacokinetic profile, with a 22-fold slower clearance in rats.
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Affiliation(s)
- Serge M. Stamm
- Rentschler Biopharma SE, Erwin-Rentschler-Str. 21, 88471 Laupheim, Germany; (S.M.S.); (R.W.)
| | - Roland Wagner
- Rentschler Biopharma SE, Erwin-Rentschler-Str. 21, 88471 Laupheim, Germany; (S.M.S.); (R.W.)
| | - Dietmar A. Lang
- Rentschler Biopharma SE, Erwin-Rentschler-Str. 21, 88471 Laupheim, Germany; (S.M.S.); (R.W.)
| | - Arne Skerra
- XL-Protein GmbH, Lise-Meitner-Str. 30, 85354 Freising, Germany
- Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising, Germany
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Zeng X, Bai G, Sun C, Ma B. Recent Progress in Antibody Epitope Prediction. Antibodies (Basel) 2023; 12:52. [PMID: 37606436 PMCID: PMC10443277 DOI: 10.3390/antib12030052] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 08/23/2023] Open
Abstract
Recent progress in epitope prediction has shown promising results in the development of vaccines and therapeutics against various diseases. However, the overall accuracy and success rate need to be improved greatly to gain practical application significance, especially conformational epitope prediction. In this review, we examined the general features of antibody-antigen recognition, highlighting the conformation selection mechanism in flexible antibody-antigen binding. We recently highlighted the success and warning signs of antibody epitope predictions, including linear and conformation epitope predictions. While deep learning-based models gradually outperform traditional feature-based machine learning, sequence and structure features still provide insight into antibody-antigen recognition problems.
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Affiliation(s)
- Xincheng Zeng
- Engineering Research Center of Cell & Therapeutic Antibody (MOE), School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China; (X.Z.); (C.S.)
| | - Ganggang Bai
- Engineering Research Center of Cell & Therapeutic Antibody (MOE), School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China; (X.Z.); (C.S.)
| | - Chuance Sun
- Engineering Research Center of Cell & Therapeutic Antibody (MOE), School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China; (X.Z.); (C.S.)
| | - Buyong Ma
- Engineering Research Center of Cell & Therapeutic Antibody (MOE), School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China; (X.Z.); (C.S.)
- Shanghai Digiwiser Biological, Inc., Shanghai 200131, China
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Ruffolo JA, Chu LS, Mahajan SP, Gray JJ. Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies. Nat Commun 2023; 14:2389. [PMID: 37185622 PMCID: PMC10129313 DOI: 10.1038/s41467-023-38063-x] [Citation(s) in RCA: 59] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 04/14/2023] [Indexed: 05/17/2023] Open
Abstract
Antibodies have the capacity to bind a diverse set of antigens, and they have become critical therapeutics and diagnostic molecules. The binding of antibodies is facilitated by a set of six hypervariable loops that are diversified through genetic recombination and mutation. Even with recent advances, accurate structural prediction of these loops remains a challenge. Here, we present IgFold, a fast deep learning method for antibody structure prediction. IgFold consists of a pre-trained language model trained on 558 million natural antibody sequences followed by graph networks that directly predict backbone atom coordinates. IgFold predicts structures of similar or better quality than alternative methods (including AlphaFold) in significantly less time (under 25 s). Accurate structure prediction on this timescale makes possible avenues of investigation that were previously infeasible. As a demonstration of IgFold's capabilities, we predicted structures for 1.4 million paired antibody sequences, providing structural insights to 500-fold more antibodies than have experimentally determined structures.
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Affiliation(s)
- Jeffrey A Ruffolo
- Program in Molecular Biophysics, The Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Lee-Shin Chu
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Sai Pooja Mahajan
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Jeffrey J Gray
- Program in Molecular Biophysics, The Johns Hopkins University, Baltimore, MD, 21218, USA.
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, MD, 21218, USA.
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Najjari A, Shahbazmohammadi H, Nojoumi SA, Omidinia E. PASylated Urate Oxidase Enzyme: Enhancing Biocatalytic Activity, Physicochemical Properties, and Plasma Half-Life. ACS OMEGA 2022; 7:46118-46130. [PMID: 36570261 PMCID: PMC9773812 DOI: 10.1021/acsomega.2c04071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 11/18/2022] [Indexed: 05/02/2023]
Abstract
Recombinant urate oxidase (UOX, E.C.1.7.3.3) is an important therapeutic enzyme used in preventing and treating chemotherapy-induced hyperuricemia and severe gout. However, UOX use is limited due to the poor stability and short plasma half-life. To solve this problem, we designed three PASylated variants of Aspergillus flavus UOX with different PAS sequences at the C- or N-terminus. The genes of native and PASylated variants (UOX-PAS20, PAS24-UOX, and UOX-PAS100) were designed and produced in Escherichia coli strain BL21 (DE3). The expressed recombinant native and PASylated enzymes were compared in terms of biophysical properties, kinetics parameters, and pharmacokinetics behavior using standard methods. PASylation of UOX with PAS100 polymer caused a 1.24-fold reduction in K m to 52.61 μM, and a 3.87-fold increase in K cat/K m for uric acid compared to the native variant. UOX-PAS100 retained its activity in different temperatures (20-55 °C); however, other variants lost nearly 50% of their original activity at 55 °C. UOX-PAS100 exhibited a 1.78-fold increase in hydrodynamic radius and a 1.64-fold larger apparent molecular size in comparison to the native UOX. Circular dichroism (CD) spectroscopy demonstrated that the addition of the PAS tag does not change the secondary structure of the fusion enzyme. The tryptophan fluorescence emission spectra for PASylated enzymes showed a significant modification in the conformational state of UOX by the PAS polymer presence. UOX-PAS100 retained 89.0% of the original activity following 72 h incubation in the presence of plasma at 37 °C. However, only about 61.0%, 57.0%, 50.0%, and 52.0% of activity from PAS24-UOX, UOX-PAS20, native UOX, and rasburicase (Fasturtec, Italy) remained, respectively, at the identical time. UOX-PAS100 had an increased biological half-life (8.21 h) when compared with the rasburicase (3.12 h) and native UOX (2.87 h) after being injected into a rat. Having considering everything, our results suggest that the UOX-PAS100, an A. flavus UOX fused with a C-terminally 100 amino acid PAS-residue, is a proper candidate with enhanced biological activity and extended plasma half-life for clinical therapy in patients suffering from hyperuricemia.
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Affiliation(s)
- Abbas Najjari
- Enzyme
Technology Laboratory, Department of Biochemistry, Genetic and Metabolism
Research Group, Pasteur Institute of Iran, Tehran 1316943551, Iran
| | - Hamid Shahbazmohammadi
- Cellular
and Molecular Research Center, Research Institute for Prevention of
Non-Communicable Diseases, Qazvin University
of Medical Sciences, Qazvin 15315-34199, Iran
- Emails
for H.S.: ;
| | - Seyed Ali Nojoumi
- Microbiology
Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran
| | - Eskandar Omidinia
- Enzyme
Technology Laboratory, Department of Biochemistry, Genetic and Metabolism
Research Group, Pasteur Institute of Iran, Tehran 1316943551, Iran
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Goncalves AG, Hartzell EJ, Sullivan MO, Chen W. Recombinant protein polymer-antibody conjugates for applications in nanotechnology and biomedicine. Adv Drug Deliv Rev 2022; 191:114570. [PMID: 36228897 DOI: 10.1016/j.addr.2022.114570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 09/03/2022] [Accepted: 10/04/2022] [Indexed: 01/24/2023]
Abstract
Currently, there are over 100 antibody-based therapeutics on the market for the treatment of various diseases. The increasing importance of antibody treatment is further highlighted by the recent FDA emergency use authorization of certain antibody therapies for COVID-19 treatment. Protein-based materials have gained momentum for antibody delivery due to their biocompatibility, tunable chemistry, monodispersity, and straightforward synthesis and purification. In this review, we discuss progress in engineering the molecular features of protein-based biomaterials, in particular recombinant protein polymers, for introducing novel functionalities and enhancing the delivery properties of antibodies and related binding protein domains.
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Affiliation(s)
- Antonio G Goncalves
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, DE 19716, United States
| | - Emily J Hartzell
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, DE 19716, United States
| | - Millicent O Sullivan
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, DE 19716, United States.
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, DE 19716, United States.
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Friedrich L, Kikuchi Y, Matsuda Y, Binder U, Skerra A. Efficient secretory production of proline/alanine/serine (PAS) biopolymers in Corynebacterium glutamicum yielding a monodisperse biological alternative to polyethylene glycol (PEG). Microb Cell Fact 2022; 21:227. [PMID: 36307781 PMCID: PMC9616612 DOI: 10.1186/s12934-022-01948-5] [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: 06/10/2022] [Accepted: 10/12/2022] [Indexed: 11/10/2022] Open
Abstract
Background PAS biopolymers are recombinant polypeptides comprising the small uncharged l-amino acids Pro, Ala and/or Ser which resemble the widely used poly-ethylene glycol (PEG) in terms of pronounced hydrophilicity. Likewise, their random chain behaviour in physiological solution results in a strongly expanded hydrodynamic volume. Thus, apart from their use as fusion partner for biopharmaceuticals to achieve prolonged half-life in vivo, PAS biopolymers appear attractive as substitute for PEG—or other poorly degradable chemical polymers—in many areas. As a prerequisite for the wide application of PAS biopolymers at affordable cost, we have established their highly efficient biotechnological production in Corynebacterium glutamicum serving as a well characterized bacterial host organism. Results Using the CspA signal sequence, we have secreted two representative PAS biopolymers as polypeptides with ~ 600 and ~ 1200 amino acid residues, respectively. Both PAS biopolymers were purified from the culture supernatant by means of a simple downstream process in a truly monodisperse state as evidenced by ESI–MS. Yields after purification were up to ≥ 4 g per liter culture, with potential for further increase by strain optimization as well as fermentation and bioprocess development. Beyond direct application as hydrocolloids or to exploit their rheological properties, such PAS biopolymers are suitable for site-specific chemical conjugation with pharmacologically active molecules via their unique terminal amino or carboxyl groups. To enable the specific activation of the carboxylate, without interference by the free amino group, we generated a blocked N-terminus for the PAS(1200) polypeptide simply by introducing an N-terminal Gln residue which, after processing of the signal peptide, was cyclised to a chemically inert pyroglutamyl group upon acid treatment. The fact that PAS biopolymers are genetically encoded offers further conjugation strategies via incorporation of amino acids with reactive side chains (e.g., Cys, Lys, Glu/Asp) at defined positions. Conclusions Our new PAS expression platform using Corynex® technology opens the way to applications of PASylation® technology in multiple areas such as the pharmaceutical industry, cosmetics and food technology.
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Affiliation(s)
- L Friedrich
- XL-protein GmbH, Lise-Meitner-Strasse 30, 85354, Freising, Germany
| | - Y Kikuchi
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki-ku, Kawasaki, 210-8681, Japan
| | - Y Matsuda
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki-ku, Kawasaki, 210-8681, Japan
| | - U Binder
- XL-protein GmbH, Lise-Meitner-Strasse 30, 85354, Freising, Germany
| | - A Skerra
- XL-protein GmbH, Lise-Meitner-Strasse 30, 85354, Freising, Germany. .,Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354, Freising, Germany.
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Schilz J, Clement C, Greiner F, Skerra A. Direct Affinity Purification of Long‐Acting PASylated Proteins with Therapeutic Potential Using L‐Prolinamide for Mild Elution. Angew Chem Int Ed Engl 2022; 61:e202200079. [PMID: 35325504 PMCID: PMC9320812 DOI: 10.1002/anie.202200079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Jonas Schilz
- Lehrstuhl für Biologische Chemie Technische Universität München Emil-Erlenmeyer-Forum 5 85354 Freising (Weihenstephan) Germany
| | - Charlotte Clement
- Lehrstuhl für Biologische Chemie Technische Universität München Emil-Erlenmeyer-Forum 5 85354 Freising (Weihenstephan) Germany
| | - Franziska Greiner
- Lehrstuhl für Biologische Chemie Technische Universität München Emil-Erlenmeyer-Forum 5 85354 Freising (Weihenstephan) Germany
| | - Arne Skerra
- Lehrstuhl für Biologische Chemie Technische Universität München Emil-Erlenmeyer-Forum 5 85354 Freising (Weihenstephan) Germany
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Schilz J, Clement C, Greiner F, Skerra A. Direct Affinity Purification of Long‐Acting PASylated Proteins with Therapeutic Potential Using L‐Prolinamide for Mild Elution. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202200079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Jonas Schilz
- TUM: Technische Universitat Munchen Biological Chemistry GERMANY
| | | | | | - Arne Skerra
- Technische Universität München Lehrstuhl für Biologische Chemie Emil-Erlenmeyer-Forum 5 85354 Freising GERMANY
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