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Nadal-Bufi F, Mason JM, Chan LY, Craik DJ, Kaas Q, Troeira Henriques S. Designed β-Hairpins Inhibit LDH5 Oligomerization and Enzymatic Activity. J Med Chem 2021; 64:3767-3779. [PMID: 33765386 DOI: 10.1021/acs.jmedchem.0c01898] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Lactate dehydrogenase 5 (LDH5) is overexpressed in metastatic tumors and is an attractive target for anticancer therapy. Small-molecule drugs have been developed to target the substrate/cofactor sites of LDH5, but none has reached the clinic to date, and alternative strategies remain almost unexplored. Combining rational and computer-based approaches, we identified peptidic sequences with high affinity toward a β-sheet region that is involved in protein-protein interactions (PPIs) required for the activity of LDH5. To improve stability and potency, these sequences were grafted into a cyclic cell-penetrating β-hairpin peptide scaffold. The lead grafted peptide, cGmC9, inhibited LDH5 activity in vitro in low micromolar range and more efficiently than the small-molecule inhibitor GNE-140. cGmC9 inhibits LDH5 by targeting an interface unlikely to be inhibited by small-molecule drugs. This lead will guide the development of new LDH5 inhibitors and challenges the landscape of drug discovery programs exclusively dedicated to small molecules.
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Affiliation(s)
- Ferran Nadal-Bufi
- School of Biomedical Sciences, Translational Research Institute, Queensland University of Technology, Brisbane, Queensland 4102, Australia
| | - Jody M Mason
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom
| | - Lai Yue Chan
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Quentin Kaas
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Sónia Troeira Henriques
- School of Biomedical Sciences, Translational Research Institute, Queensland University of Technology, Brisbane, Queensland 4102, Australia
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
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Lin MW, Shen CC, Lin YJ, Chou MY, Pham NN, Chang YH, Chang CW, Hwu JR, Nguyen MTT, Hu YC. Enhancing the yield and activity of defucosylated antibody produced by CHO-K1 cells using Cas13d-mediated multiplex gene targeting. J Taiwan Inst Chem Eng 2021. [DOI: 10.1016/j.jtice.2021.03.040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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O'Brien CM, Mulukutla BC, Mashek DG, Hu WS. Regulation of Metabolic Homeostasis in Cell Culture Bioprocesses. Trends Biotechnol 2020; 38:1113-1127. [PMID: 32941791 DOI: 10.1016/j.tibtech.2020.02.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 02/11/2020] [Accepted: 02/12/2020] [Indexed: 12/26/2022]
Abstract
Mammalian cells are the main tool for the production of therapeutic proteins, viruses for gene therapy, and cells for cell therapy. In production processes cell metabolism is the main driver that causes changes in the growth environment and affects productivity and product quality. Of all nutrients, glucose has the most prominent impact on bioprocesses. We summarize recent findings on the regulation of glucose and energy metabolism in cultured cells. Local allosteric regulations and post-translational modifications of enzymes in metabolic networks interplay with global signaling and transcriptional regulation. These regulatory networks sustain homeostasis across the cytosolic and mitochondrial compartments. Understanding the regulation of glucose metabolism and metabolic state is crucial for enhancing process productivity and product quality.
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Affiliation(s)
- Conor M O'Brien
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA
| | | | - Douglas G Mashek
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Wei-Shou Hu
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA.
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Chandrawanshi V, Kulkarni R, Prabhu A, Mehra S. Enhancing titers and productivity of rCHO clones with a combination of an optimized fed-batch process and ER-stress adaptation. J Biotechnol 2020; 311:49-58. [PMID: 32070675 DOI: 10.1016/j.jbiotec.2020.02.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 01/24/2020] [Accepted: 02/14/2020] [Indexed: 01/01/2023]
Abstract
To increase the productivity of rCHO cells, many cell engineering approaches have been demonstrated that over-express or knockout a specific gene to achieve increased titers. In this work, we present an alternate approach, based on the concept of evolutionary adaptation, to achieve cells with higher titers. rCHO cells, producing a monoclonal antibody, are adapted to ER-stress, by continuous culturing under increasing concentration of tunicamycin. A sustained higher productivity of at-least 2-fold was achieved in all the clones, in a concentration-dependent manner. Similarly, a 1.5-2 fold increase in final titers was also achieved in the batch culture. Based on metabolic analysis of the adapted cells, a fed-batch process was designed where significantly higher titersare achieved as compared to control. Metabolic flux analysis is employed in addition with gene expression analysis of key genes to understand the basis of increased performance of the adapted cells. Overall, this work illustrates how process modifications and cellular adaptation can be used in synergy to drive up product titers.
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Affiliation(s)
- Vikas Chandrawanshi
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Rohan Kulkarni
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Anuja Prabhu
- CSIR-National Chemical Laboratory, Pune, India; Academyof Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sarika Mehra
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India; Wadhwani Research Center for Bioengineering, Indian Institute of Technology Bombay, Mumbai, India.
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Schweickert PG, Cheng Z. Application of Genetic Engineering in Biotherapeutics Development. J Pharm Innov 2019. [DOI: 10.1007/s12247-019-09411-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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O'Brien C, Allman A, Daoutidis P, Hu WS. Kinetic model optimization and its application to mitigating the Warburg effect through multiple enzyme alterations. Metab Eng 2019; 56:154-164. [PMID: 31400493 DOI: 10.1016/j.ymben.2019.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/05/2019] [Accepted: 08/06/2019] [Indexed: 12/17/2022]
Abstract
Pathway engineering is a powerful tool in biotechnological and clinical applications. However, many phenomena cannot be rewired with a single enzyme change, and in a complex network like energy metabolism, the selection of combinations of targets to engineer is a daunting task. To facilitate this process, we have developed an optimization framework and applied it to a mechanistic kinetic model of energy metabolism. We then identified combinations of enzyme alternations that led to the elimination of the Warburg effect seen in the metabolism of cancer cells and cell lines, a phenomenon coupling rapid proliferation to lactate production. Typically, optimization approaches use integer variables to achieve the desired flux redistribution with a minimum number of altered genes. This framework uses convex penalty terms to replace these integer variables and improve computational tractability. Optimal solutions are identified which substantially reduce or eliminate lactate production while maintaining the requirements for cellular proliferation using three or more enzymes.
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Affiliation(s)
- Conor O'Brien
- Department of Chemical Engineering and Materials Science, University of Minnesota, 421 Washington Avenue SE, Minneapolis, MN, 55455-0132, USA
| | - Andrew Allman
- Department of Chemical Engineering and Materials Science, University of Minnesota, 421 Washington Avenue SE, Minneapolis, MN, 55455-0132, USA
| | - Prodromos Daoutidis
- Department of Chemical Engineering and Materials Science, University of Minnesota, 421 Washington Avenue SE, Minneapolis, MN, 55455-0132, USA
| | - Wei-Shou Hu
- Department of Chemical Engineering and Materials Science, University of Minnesota, 421 Washington Avenue SE, Minneapolis, MN, 55455-0132, USA.
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Buchsteiner M, Quek LE, Gray P, Nielsen LK. Improving culture performance and antibody production in CHO cell culture processes by reducing the Warburg effect. Biotechnol Bioeng 2018; 115:2315-2327. [PMID: 29704441 DOI: 10.1002/bit.26724] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 04/08/2018] [Accepted: 04/25/2018] [Indexed: 12/14/2022]
Abstract
Lactate is one of the key waste metabolites of mammalian cell culture. High lactate levels are caused by high aerobic glycolysis, also known as the Warburg effect, and are usually associated with adverse culture performance. Therefore, reducing lactate accumulation has been an ongoing challenge in the cell culture development to improve growth, productivity, and process robustness. The pyruvate dehydrogenase complex (PDC) plays a crucial role for the fate of pyruvate, as it converts pyruvate to acetyl coenzyme A (acetyl-CoA). The PDC activity can be indirectly increased by inhibiting the PDC inhibitor, pyruvate dehydrogenase kinase, using dichloroacetate (DCA), resulting in less pyruvate being available for lactate formation. Here, Chinese hamster ovary cells were cultivated either with 5 mM DCA or without DCA in various batch and fed-batch bioreactor processes. In all cultures, DCA increased peak viable cell density (VCD), culture length and final antibody titer. The strongest effect was observed in a fed batch with media and glucose feeding in which peak VCD was increased by more than 50%, culture length was extended by more than 3 days, and the final antibody titer increased by more than twofold. In cultures with DCA, lactate production and glucose consumption during exponential growth were on average reduced by approximately 40% and 35%, respectively. Metabolic flux analysis showed reduced glycolytic fluxes, whereas fluxes in the tricarboxylic acid (TCA) cycle were not affected, suggesting that cultures with DCA use glucose more efficiently. In a proteomics analysis, only few proteins were identified as being differentially expressed, indicating that DCA acts on a posttranslational level. Antibody quality in terms of aggregation, charge variant, and glycosylation pattern was unaffected. Subsequent bioreactor experiments with sodium lactate and sodium chloride feeding indicated that lower osmolality, rather than lower lactate concentration itself, improved culture performance in DCA cultures. In conclusion, the addition of DCA to the cell culture improved culture performance and increased antibody titers without any disadvantages for cell-specific productivity or antibody quality.
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Affiliation(s)
- Maria Buchsteiner
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland, Australia
| | - Lake-Ee Quek
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
| | - Peter Gray
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland, Australia
| | - Lars K Nielsen
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland, Australia.,Novo Nordisk Foundation Center for Biosustainability, The Technical University of Denmark, Kongens Lyngby, Denmark
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Zepeda AB, Figueroa CA, Pessoa A, Farías JG. Free fatty acids reduce metabolic stress and favor a stable production of heterologous proteins in Pichia pastoris. Braz J Microbiol 2018; 49:856-864. [PMID: 29705163 PMCID: PMC6175731 DOI: 10.1016/j.bjm.2018.03.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 02/19/2018] [Accepted: 03/21/2018] [Indexed: 12/20/2022] Open
Abstract
The growth of yeasts in culture media can be affected by many factors. For example, methanol can be metabolized by other pathways to produce ethanol, which acts as an inhibitor of the heterologous protein production pathway; oxygen concentration can generate aerobic or anaerobic environments and affects the fermentation rate; and temperature affects the central carbon metabolism and stress response protein folding. The main goal of this study was determine the implication of free fatty acids on the production of heterologous proteins in different culture conditions in cultures of Pichia pastoris. We evaluated cell viability using propidium iodide by flow cytometry and thiobarbituric acid reactive substances to measure cell membrane damage. The results indicate that the use of low temperatures and low methanol concentrations favors the decrease in lipid peroxidation in the transition phase from glycerol to methanol. In addition, a temperature of 14 °C + 1%M provided the most stable viability. By contrast, the temperature of 18 °C + 1.5%M favored the production of a higher antibody fragment concentration. In summary, these results demonstrate that the decrease in lipid peroxidation is related to an increased production of free fatty acids.
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Affiliation(s)
- Andrea B Zepeda
- Universidad de La Frontera, Facultad de Ingeniería, Ciencias y Administración, Departamento de Ingeniería Química, Temuco, Chile; Universidade de São Paulo, Faculdade de Ciências Farmacêuticas, Departamento de Tecnologia Bioquímico-Farmacêutica, São Paulo, SP, Brazil
| | - Carolina A Figueroa
- Universidad de La Frontera, Facultad de Ingeniería, Ciencias y Administración, Departamento de Ingeniería Química, Temuco, Chile; Universidade de São Paulo, Faculdade de Ciências Farmacêuticas, Departamento de Tecnologia Bioquímico-Farmacêutica, São Paulo, SP, Brazil
| | - Adalberto Pessoa
- Universidade de São Paulo, Faculdade de Ciências Farmacêuticas, Departamento de Tecnologia Bioquímico-Farmacêutica, São Paulo, SP, Brazil
| | - Jorge G Farías
- Universidad de La Frontera, Facultad de Ingeniería, Ciencias y Administración, Departamento de Ingeniería Química, Temuco, Chile.
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Pereira S, Kildegaard HF, Andersen MR. Impact of CHO Metabolism on Cell Growth and Protein Production: An Overview of Toxic and Inhibiting Metabolites and Nutrients. Biotechnol J 2018; 13:e1700499. [DOI: 10.1002/biot.201700499] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 12/21/2017] [Indexed: 12/19/2022]
Affiliation(s)
- Sara Pereira
- The Novo Nordisk Foundation Center for Biosustainability; Technical University of Denmark; 2800 Kgs. Lyngby Denmark
- Department of Biotechnology and Biomedicine Technical University of Denmark; 2800 Kgs. Lyngby Denmark
| | - Helene Faustrup Kildegaard
- The Novo Nordisk Foundation Center for Biosustainability; Technical University of Denmark; 2800 Kgs. Lyngby Denmark
| | - Mikael Rørdam Andersen
- Department of Biotechnology and Biomedicine Technical University of Denmark; 2800 Kgs. Lyngby Denmark
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Reduction of ammonia and lactate through the coupling of glutamine synthetase selection and downregulation of lactate dehydrogenase-A in CHO cells. Appl Microbiol Biotechnol 2016; 101:1035-1045. [DOI: 10.1007/s00253-016-7876-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Revised: 09/06/2016] [Accepted: 09/16/2016] [Indexed: 01/17/2023]
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11
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The art of CHO cell engineering: A comprehensive retrospect and future perspectives. Biotechnol Adv 2015; 33:1878-96. [DOI: 10.1016/j.biotechadv.2015.10.015] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 10/21/2015] [Accepted: 10/30/2015] [Indexed: 12/14/2022]
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