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Kumar V, Barwal A, Sharma N, Mir DS, Kumar P, Kumar V. Therapeutic proteins: developments, progress, challenges, and future perspectives. 3 Biotech 2024; 14:112. [PMID: 38510462 PMCID: PMC10948735 DOI: 10.1007/s13205-024-03958-z] [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: 06/03/2023] [Accepted: 02/13/2024] [Indexed: 03/22/2024] Open
Abstract
Proteins are considered magic molecules due to their enormous applications in the health sector. Over the past few decades, therapeutic proteins have emerged as a promising treatment option for various diseases, particularly cancer, cardiovascular disease, diabetes, and others. The formulation of protein-based therapies is a major area of research, however, a few factors still hinder the large-scale production of these therapeutic products, such as stability, heterogenicity, immunogenicity, high cost of production, etc. This review provides comprehensive information on various sources and production of therapeutic proteins. The review also summarizes the challenges currently faced by scientists while developing protein-based therapeutics, along with possible solutions. It can be concluded that these proteins can be used in combination with small molecular drugs to give synergistic benefits in the future.
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Affiliation(s)
- Vimal Kumar
- University Institute of Biotechnology, Chandigarh University, Gharuan, Mohali, Punjab 140413 India
| | - Arti Barwal
- Department of Microbial Biotechnology, Panjab University, South Campus, Sector-25, Chandigarh, 160014 India
| | - Nitin Sharma
- Department of Biotechnology, Chandigarh Group of Colleges, Mohali, Punjab 140307 India
| | - Danish Shafi Mir
- University Institute of Biotechnology, Chandigarh University, Gharuan, Mohali, Punjab 140413 India
| | - Pradeep Kumar
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, 173229 India
| | - Vikas Kumar
- University Institute of Biotechnology, Chandigarh University, Gharuan, Mohali, Punjab 140413 India
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Ceylan HK. Enhanced Biomass Production of Recombinant Pfu DNA Polymerase Producer Escherichia coli BL21(DE3) by Optimization of Induction Variables Using Response Surface Methodology. Protein J 2023:10.1007/s10930-023-10122-8. [PMID: 37199865 DOI: 10.1007/s10930-023-10122-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/29/2023] [Indexed: 05/19/2023]
Abstract
Pfu DNA polymerase is one of the most preferred molecular enzymes that is isolated from the hyperthermophilic Pyrococcus furiosus and used for high-throughput DNA synthesis by the polymerase chain reaction. Therefore, an efficient Pfu DNA polymerase production method is necessary for molecular techniques. In the present study, Pfu DNA polymerase was expressed in recombinant Escherichia coli BL21(DE3) and significant parameters for the biomass production were optimized using the central composite design which is the most popular method of response surface methodology. Induction conditions including cell density prior induction (OD600nm), post-induction temperature, IPTG concentration, and post-induction time and their interactions on biomass production were investigated. The maximum biomass production (14.1 g/L) in shake flasks was achieved using the following predicted optimal conditions: OD600nm before induction of 0.4 and the induction at 32 °C for 7.7 h, with 0.6 mM IPTG. Optimized culture conditions were implemented to scale up experiments. 22% and 70% increase in biomass production was achieved in 3 L and 10 L bioreactors, respectively as compared to initial biomass production observed in unoptimized conditions. Similary, a 30% increase of Pfu DNA polymerase production was obtained after the optimization. The polymerase activity of the purifed Pfu DNA polymerase was assessed by PCR amplification and determined as 2.9 U/μl by comparison with commercial Pfu DNA polymerase. The findings of this study indicated that the proposed fermentation conditions will contribute to further scale‑up studies to enhance the biomass for the production of other recombinant proteins.
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Affiliation(s)
- Hülya Kuduğ Ceylan
- Department of Basic Pharmaceutical Sciences, Faculty of Pharmacy, Tokat Gaziosmanpaşa University, 60250, Tokat, Turkey.
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Zhang F, Fan X, Xu K, Wang S, Shi S, Yi L, Zhang G. Development of a Bacterial FhuD-Lysozyme-SsrA Mediated Autolytic (FLSA) System for Effective Release of Intracellular Products. ACS Synth Biol 2023; 12:196-202. [PMID: 36580286 DOI: 10.1021/acssynbio.2c00466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Developing effective bacterial autolytic systems for fast release of intracellular bioproducts could simplify purification procedures and help with the high throughput screening of mutant libraries in protein engineering. Here, we developed a fast and tightly regulated E. coli autolytic system, named the FhuD-lysozyme-SsrA mediated autolytic (FLSA) system, by integrating the secretion signal peptide, T7 lysozyme, and E. coli ClpX/P-SsrA protein degradation machinery. To decrease the cytotoxicity of leaky T7 lysozymes, the SsrA tag was fused to the C-terminus of T7 lysozyme to confer a tight regulation of its production. Using sfGFP as a reporter, we demonstrated that anchoring the Sec-Tat dual pathway signal peptide FhuD to the N-terminus of T7 lysozyme-SsrA could give the highest cell lysing efficiency. The optimization of the FLSA system indicated that weak alkaline conditions (pH 8.0) and 0.5% Triton X-100 could further increase the lysing efficiency by about 24%. The FLSA system was validated by efficient production of sfGFP and human growth hormone 1 (hGH1) in a shake flask, with a cell lytic efficiency of approximately 82% and 80%, respectively. Besides, the FLSA system was applied for large-scale fermentation, in which approximately 90% sGFP was released with a cell density OD600 of 110. Moreover, the FLSA system was also tested for α-amylase mutant library screening in microplates, and the results showed that intracellular α-amylase can be efficiently released out of cells for activity quantitation. In all, the FLSA system can facilitate the release of intracellular recombinant proteins into the cell culture medium, which has the potential to serve as an integrated system for large-scale production of recombinant targets and high throughput enzyme engineering in synthetic biology.
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Affiliation(s)
- Faying Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.,School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Xian Fan
- School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Ke Xu
- School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Shihui Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Shuobo Shi
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Li Yi
- School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Guimin Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.,School of Life Sciences, Hubei University, Wuhan 430062, China
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Packiam KAR, Ooi CW, Li F, Mei S, Tey BT, Fang Ong H, Song J, Ramanan RN. PERISCOPE-Opt: Machine learning-based prediction of optimal fermentation conditions and yields of recombinant periplasmic protein expressed in Escherichia coli. Comput Struct Biotechnol J 2022; 20:2909-2920. [PMID: 35765650 PMCID: PMC9201004 DOI: 10.1016/j.csbj.2022.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 06/01/2022] [Accepted: 06/01/2022] [Indexed: 11/26/2022] Open
Abstract
The ensemble model considered both fermentation conditions and protein properties. Optimal fermentation conditions and periplasmic recombinant protein yield can be predicted. Predictor’s accuracy and Pearson correlation coefficient are 75% and 0.91, respectively.
Optimization of the fermentation process for recombinant protein production (RPP) is often resource-intensive. Machine learning (ML) approaches are helpful in minimizing the experimentations and find vast applications in RPP. However, these ML-based tools primarily focus on features with respect to amino-acid-sequence, ruling out the influence of fermentation process conditions. The present study combines the features derived from fermentation process conditions with that from amino acid-sequence to construct an ML-based model that predicts the maximal protein yields and the corresponding fermentation conditions for the expression of target recombinant protein in the Escherichia coli periplasm. Two sets of XGBoost classifiers were employed in the first stage to classify the expression levels of the target protein as high (>50 mg/L), medium (between 0.5 and 50 mg/L), or low (<0.5 mg/L). The second-stage framework consisted of three regression models involving support vector machines and random forest to predict the expression yields corresponding to each expression-level-class. Independent tests showed that the predictor achieved an overall average accuracy of 75% and a Pearson coefficient correlation of 0.91 for the correctly classified instances. Therefore, our model offers a reliable substitution of numerous trial-and-error experiments to identify the optimal fermentation conditions and yield for RPP. It is also implemented as an open-access webserver, PERISCOPE-Opt (http://periscope-opt.erc.monash.edu).
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Machine learning modeling for solubility prediction of recombinant antibody fragment in four different E. coli strains. Sci Rep 2022; 12:5463. [PMID: 35361835 PMCID: PMC8971470 DOI: 10.1038/s41598-022-09500-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 03/14/2022] [Indexed: 11/08/2022] Open
Abstract
The solubility of proteins is usually a necessity for their functioning. Recently an emergence of machine learning approaches as trained alternatives to statistical models has been evidenced for empirical modeling and optimization. Here, soluble production of anti-EpCAM extracellular domain (EpEx) single chain variable fragment (scFv) antibody was modeled and optimized as a function of four literature based numerical factors (post-induction temperature, post-induction time, cell density of induction time, and inducer concentration) and one categorical variable using artificial neural network (ANN) and response surface methodology (RSM). Models were established by the CCD experimental data derived from 232 separate experiments. The concentration of soluble scFv reached 112.4 mg/L at the optimum condition and strain (induction at cell density 0.6 with 0.4 mM IPTG for 24 h at 23 °C in Origami). The predicted value obtained by ANN for the response (106.1 mg/L) was closer to the experimental result than that obtained by RSM (97.9 mg/L), which again confirmed a higher accuracy of ANN model. To the author's knowledge this is the first report on comparison of ANN and RSM in statistical optimization of fermentation conditions of E.coli for the soluble production of recombinant scFv.
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Javadian FS, Basafa M, Behravan A, Hashemi A. Solubility assessment of single-chain antibody fragment against epithelial cell adhesion molecule extracellular domain in four Escherichia coli strains. J Genet Eng Biotechnol 2021; 19:26. [PMID: 33543415 PMCID: PMC7862456 DOI: 10.1186/s43141-021-00126-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 01/25/2021] [Indexed: 12/23/2022]
Abstract
BACKGROUND Overexpression of the EpCAM (epithelial cell adhesion molecule) in malignancies makes it an attractive target for passive immunotherapy in a wide range of carcinomas. In comparison with full-length antibodies, due to the small size, the scFvs (single-chain variable fragments) are more suitable for recombinant expression in E. coli (Escherichia coli). However, the proteins expressed in large amounts in E. coli tend to form inclusion bodies that need to be refolded which may result in poor recovery of bioactive proteins. Various engineered strains were shown to be able to alleviate the insolubility problem. Here, we studied the impact of four E. coli strains on the soluble level of anti-EpEX-scFv (anti-EpCAM extracellular domain-scFv) protein. RESULTS Although results showed that the amount of soluble anti-EpEX-scFv obtained in BL21TM (DE3) (114.22 ± 3.47 mg/L) was significantly higher to those produced in the same condition in E. coli RosettaTM (DE3) (71.39 ± 0.31 mg/L), and OrigamiTM T7 (58.99 ± 0.44 mg/L) strains, it was not significantly different from that produced by E. coli SHuffleTM T7 (108.87 ± 2.71 mg/L). Furthermore, the highest volumetric productivity of protein reached 318.29 ± 26.38 mg/L in BL21TM (DE3). CONCLUSIONS Although BL21TM (DE3) can be a suitable strain for high-level production of anti-EpEX-scFv protein, due to higher solubility yield (about 55%), E. coli SHuffleTM T7 seems to be better candidate for soluble production of scfv compared to BL21TM (DE3) (solubility yield of about 30%).
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Affiliation(s)
- Fatemeh Sadat Javadian
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, ValiAsr Avenue, Niayesh Junction, PO Box 14155-6153, Tehran, Iran
| | - Majid Basafa
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, ValiAsr Avenue, Niayesh Junction, PO Box 14155-6153, Tehran, Iran
| | - Aidin Behravan
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, ValiAsr Avenue, Niayesh Junction, PO Box 14155-6153, Tehran, Iran
| | - Atieh Hashemi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, ValiAsr Avenue, Niayesh Junction, PO Box 14155-6153, Tehran, Iran.
- Protein Technology Research Center, Shahid Beheshti University of Medical Sciences, ValiAsr Avenue, Niayesh Junction, PO Box 14155-6153, Tehran, Iran.
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Papaneophytou C, Zervou ME, Theofanous A. Optimization of a Colorimetric Assay to Determine Lactate Dehydrogenase B Activity Using Design of Experiments. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2020; 26:383-399. [PMID: 32935604 DOI: 10.1177/2472555220956589] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Lactate dehydrogenase B (LDH-B) is overexpressed in lung and breast cancer, and it has been considered as a potential target to treat these types of cancer. Herein, we propose a straightforward incomplete factorial (IF) design composed of 12 combinations of two reaction buffers, three pH values, three salt (NaCl) concentrations, and three incubation times, which we called IF-BPST (Buffer/pH/Salt/Time), for the optimization of a colorimetric LDH-B assay in a final volume of 100 µL using 96-well plates. The assay is based on the absorbance change at ~570 nm and the color change of the reaction mixture due to the release of NADH that reacts with nitroblue tetrazolium (NBT) and phenazine methosulfate (PMS), resulting in the formation of a blue-purple formazan. The results obtained using the IF-BPST were comparable with those obtained by response surface methodology. Our work revealed that the NBT/PMS assay with some modifications can be used to measure the activity of LDH-B and other dehydrogenases in a high-throughput screening format at the early stages of drug discovery. LDH-B containing lysates cannot be assayed directly, however, due to the sensitivity of the method toward detergents. Thus, we suggest precipitating the proteins in the lysates to remove the interfering detergents, and then to dissolve the protein pellet in a suitable buffer and carry out the assay.
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Affiliation(s)
- Christos Papaneophytou
- Department of Life and Health Sciences, School of Sciences and Engineering, University of Nicosia, Nicosia, Cyprus
| | - Maria-Elli Zervou
- Department of Life and Health Sciences, School of Sciences and Engineering, University of Nicosia, Nicosia, Cyprus
| | - Anastasis Theofanous
- Department of Life and Health Sciences, School of Sciences and Engineering, University of Nicosia, Nicosia, Cyprus
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Singha TK, Dagar VK, Gulati P, Kumar S. Kinetic study and optimization of recombinant human tumor necrosis factor-alpha (rhTNF-α) production in Escherichia coli. Prep Biochem Biotechnol 2020; 51:267-276. [PMID: 32876507 DOI: 10.1080/10826068.2020.1815056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Tumor necrosis factor-alpha (TNF-α) is an inflammatory cytokine that plays a major role in immune regulation, homeostatic function, and cellular organization. The present study was undertaken to overproduce recombinant human TNF-α (rhTNF-α) in Escherichia coli (E.coli) in high cell density culture. The use of a codon-optimized gene and strong promoter-based (T7) expression system, choice of Terrific Broth (TB) as medium, and subsequent optimization of culture conditions in shake flasks resulted in production of 0.95 g/L insoluble rhTNF-α comprising upto 50% of total cellular protein (TCP) The protein yield further increased upto 1.26 g/L in 1 L TB medium batch culture in bioreactor with the controlled temperature, pH, and dissolved oxygen. In a series of chemostats operated at dilution rates of 0.2 h-1, 0.3 h-1, 0.4 h-1 and 0.5 h-1 the specific growth rate (μ) positively correlated with specific yield (Yp/x) and a maximum yield of 164 mg/g DCW was obtained at μ = 0.4 h-1 within 4 h post-induction. A fed-batch cultivation in TB with an exponential feeding profile (μ = ∼0.4 h-1) of concentrated feed resulted in an accumulation of 5.5 g/L of rhTNF-α within 14 h of cultivation which accounted for ∼29% of TCP.
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Affiliation(s)
| | - Vikas Kumar Dagar
- Department of Microbiology, University of Delhi South Campus, New Delhi, India
| | - Pooja Gulati
- Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Sanjay Kumar
- Department of Microbiology, Maharshi Dayanand University, Rohtak, India
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Soluble tumour necrosis factor receptor I is a promising early indicator of complicated clinical outcome in patients following severe trauma. Cent Eur J Immunol 2020; 44:423-432. [PMID: 32140055 PMCID: PMC7050055 DOI: 10.5114/ceji.2019.92804] [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: 01/29/2018] [Accepted: 01/30/2018] [Indexed: 12/20/2022] Open
Abstract
Post-traumatic mortality rates are still very high and show an increasing tendency. Early identification of patients at high risk of severe complications has a significant impact on treatment outcomes. The aim of the study was to better understand the early pathological inflammatory response to injury and infection, and to determine the usefulness of the assessment of TNF-α and sTNFR1 concentrations in the peripheral blood as early indicators of severe post-traumatic complications. The study was carried out in a group of 51 patients after trauma, treated in the ED, including 32 patients who met the inclusion criteria for immunological analysis. Patients were divided into two groups using the ISS scale (A ISS ≥ 20, B ISS < 20). The highest TNF-α and sTNFR1 concentrations in both groups were recorded at admission and were significantly higher in group A compared to group B (A vs. B TNF-α 2.46 pg/ml vs. 1.78 pg/ml; sTNFR1 1667.5 pg/ml vs. 875.2 p < 0.005). The concentration of sTNFR1 in patients with severe complications was significantly higher compared to patients without complications and preceded clinical symptoms of complications (C+ vs. C– 1561.5 pg/ml vs. 930.6 pg/ml, p < 0,005). The high diagnostic sensitivity calculated from the ROC curves was found for the concentrations of both cytokines: TNF-α (AUC = 0.91, p = 0.004) and sTNFR1 (AUC = 0.86, p = 0.011). Elevated levels of sTNFR1, determined in the peripheral blood shortly after injury, are significantly associated with the occurrence of later complications, which in some patients lead to death. In contrast, high levels of TNF-α shortly after injury are associated with mortality.
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Kanno AI, Leite LCDC, Pereira LR, de Jesus MJR, Andreata-Santos R, Alves RPDS, Durigon EL, Ferreira LCDS, Gonçalves VM. Optimization and scale-up production of Zika virus ΔNS1 in Escherichia coli: application of Response Surface Methodology. AMB Express 2019; 10:1. [PMID: 31893321 PMCID: PMC6938527 DOI: 10.1186/s13568-019-0926-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 12/03/2019] [Indexed: 02/01/2023] Open
Abstract
Diagnosing Zika virus (ZIKV) infections has been challenging due to the cross-reactivity of induced antibodies with other flavivirus. The concomitant occurrence of ZIKV and Dengue virus (DENV) in endemic regions requires diagnostic tools with the ability to distinguish these two viral infections. Recent studies demonstrated that immunoassays using the C-terminal fragment of ZIKV NS1 antigen (ΔNS1) can be used to discriminate ZIKV from DENV infections. In order to be used in serological tests, the expression/solubility of ΔNS1 and growth of recombinant E. coli strain were optimized by Response Surface Methodology. Temperature, time and IPTG concentration were evaluated. According to the model, the best condition determined in small scale cultures was 21 °C for 20 h with 0.7 mM of IPTG, which predicted 7.5 g/L of biomass and 962 mg/L of ΔNS1. These conditions were validated and used in a 6-L batch in the bioreactor, which produced 6.4 g/L of biomass and 500 mg/L of ΔNS1 in 12 h of induction. The serological ELISA test performed with purified ΔNS1 showed low cross-reactivity with antibodies from DENV-infected human subjects. Denaturation of ΔNS1 decreased the detection of anti-ZIKV antibodies, thus indicating the contribution of conformational epitopes and confirming the importance of properly folded ΔNS1 for the specificity of the serological analyses. Obtaining high yields of soluble ΔNS1 supports the viability of an effective serologic diagnostic test capable of differentiating ZIKV from other flavivirus infections.
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Tripathi NK, Shrivastava A. Recent Developments in Bioprocessing of Recombinant Proteins: Expression Hosts and Process Development. Front Bioeng Biotechnol 2019; 7:420. [PMID: 31921823 PMCID: PMC6932962 DOI: 10.3389/fbioe.2019.00420] [Citation(s) in RCA: 237] [Impact Index Per Article: 47.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Accepted: 11/29/2019] [Indexed: 12/22/2022] Open
Abstract
Infectious diseases, along with cancers, are among the main causes of death among humans worldwide. The production of therapeutic proteins for treating diseases at large scale for millions of individuals is one of the essential needs of mankind. Recent progress in the area of recombinant DNA technologies has paved the way to producing recombinant proteins that can be used as therapeutics, vaccines, and diagnostic reagents. Recombinant proteins for these applications are mainly produced using prokaryotic and eukaryotic expression host systems such as mammalian cells, bacteria, yeast, insect cells, and transgenic plants at laboratory scale as well as in large-scale settings. The development of efficient bioprocessing strategies is crucial for industrial production of recombinant proteins of therapeutic and prophylactic importance. Recently, advances have been made in the various areas of bioprocessing and are being utilized to develop effective processes for producing recombinant proteins. These include the use of high-throughput devices for effective bioprocess optimization and of disposable systems, continuous upstream processing, continuous chromatography, integrated continuous bioprocessing, Quality by Design, and process analytical technologies to achieve quality product with higher yield. This review summarizes recent developments in the bioprocessing of recombinant proteins, including in various expression systems, bioprocess development, and the upstream and downstream processing of recombinant proteins.
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Affiliation(s)
- Nagesh K. Tripathi
- Bioprocess Scale Up Facility, Defence Research and Development Establishment, Gwalior, India
| | - Ambuj Shrivastava
- Division of Virology, Defence Research and Development Establishment, Gwalior, India
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Gutiérrez-González M, Farías C, Tello S, Pérez-Etcheverry D, Romero A, Zúñiga R, Ribeiro CH, Lorenzo-Ferreiro C, Molina MC. Optimization of culture conditions for the expression of three different insoluble proteins in Escherichia coli. Sci Rep 2019; 9:16850. [PMID: 31727948 PMCID: PMC6856375 DOI: 10.1038/s41598-019-53200-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 10/12/2019] [Indexed: 02/06/2023] Open
Abstract
Recombinant protein expression for structural and therapeutic applications requires the use of systems with high expression yields. Escherichia coli is considered the workhorse for this purpose, given its fast growth rate and feasible manipulation. However, bacterial inclusion body formation remains a challenge for further protein purification. We analyzed and optimized the expression conditions for three different proteins: an anti-MICA scFv, MICA, and p19 subunit of IL-23. We used a response surface methodology based on a three-level Box-Behnken design, which included three factors: post-induction temperature, post-induction time and IPTG concentration. Comparing this information with soluble protein data in a principal component analysis revealed that insoluble and soluble proteins have different optimal conditions for post-induction temperature, post-induction time, IPTG concentration and in amino acid sequence features. Finally, we optimized the refolding conditions of the least expressed protein, anti-MICA scFv, using a fast dilution protocol with different additives, obtaining soluble and active scFv for binding assays. These results allowed us to obtain higher yields of proteins expressed in inclusion bodies. Further studies using the system proposed in this study may lead to the identification of optimal environmental factors for a given protein sequence, favoring the acceleration of bioprocess development and structural studies.
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Affiliation(s)
- Matías Gutiérrez-González
- Centro de Inmunobiotecnología, Programa Disciplinario de Inmunología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile.,Programa de Doctorado en Farmacología, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Camila Farías
- Centro de Inmunobiotecnología, Programa Disciplinario de Inmunología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Samantha Tello
- Centro de Inmunobiotecnología, Programa Disciplinario de Inmunología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Diana Pérez-Etcheverry
- Área de Biotecnología, Instituto Polo Tecnológico de Pando, Facultad de Química, Universidad de la República Oriental del Uruguay, Montevideo, Uruguay
| | - Alfonso Romero
- Centro de Inmunobiotecnología, Programa Disciplinario de Inmunología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Roberto Zúñiga
- Centro de Inmunobiotecnología, Programa Disciplinario de Inmunología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Carolina H Ribeiro
- Centro de Inmunobiotecnología, Programa Disciplinario de Inmunología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Carmen Lorenzo-Ferreiro
- Área de Biotecnología, Instituto Polo Tecnológico de Pando, Facultad de Química, Universidad de la República Oriental del Uruguay, Montevideo, Uruguay
| | - María Carmen Molina
- Centro de Inmunobiotecnología, Programa Disciplinario de Inmunología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile.
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Design of Experiments As a Tool for Optimization in Recombinant Protein Biotechnology: From Constructs to Crystals. Mol Biotechnol 2019; 61:873-891. [DOI: 10.1007/s12033-019-00218-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Optimization of recombinant maize CDKA;1 and CycD6;1 production in Escherichia coli by response surface methodology. Protein Expr Purif 2019; 165:105483. [PMID: 31479737 DOI: 10.1016/j.pep.2019.105483] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 08/30/2019] [Accepted: 08/30/2019] [Indexed: 11/24/2022]
Abstract
The complex formed by the cyclin-dependent kinase A (CDKA) and cyclin D is responsible for the G1-S transition in the plant cell cycle. Maize (Zea mays L) CDKA; 1 and CycD6; 1 were cloned and expressed in E. coli. The present study describes the optimization of both proteins production using a statistical approach known as response surface methodology (RSM). The experimental design took into account the effects of four variables: optical density of the culture (OD600) before induction, isopropyl β-d-1-thiogalactopyranoside (IPTG) concentration, post-induction temperature, and post-induction time. For each protein, a 24 full factorial central composite rotary design for these four independent variables (at five levels each) was employed to fit a polynomial model; which indicated that 30 experiments were required for this procedure. An optimization of CDKA; 1 and CycD6; 1 production levels in the soluble fraction was achieved. Protein conformation and stability were studied by circular dichroism and fluorescence spectroscopy. Finally, in vitro Cyc-CDK complex formation and its kinase activity were confirmed.
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15
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Hajihassan Z, Tilko PG, Sadat SM. Improved Production of Recombinant Human β-NGF in Escherichia coli - a Bioreactor Scale Study. Pol J Microbiol 2018; 67:355-363. [PMID: 30451453 PMCID: PMC7256796 DOI: 10.21307/pjm-2018-045] [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] [Accepted: 06/16/2018] [Indexed: 11/11/2022] Open
Abstract
Human nerve growth factor β (β-NGF) is considered a major therapeutic agent for treatment of neurodegenerative diseases. We have previously reported the optimized conditions for β-NGF overproduction in Escherichia coli in a shake-flask culture. In this study the optimal %DO (dissolved oxygen) and post induction temperature values for improved production of β-NGF were found in the bioreactor scale using response surface methodology (RSM) as the most common statistical method. Also, for further enhancement of the yield, different post-induction periods of time were selected for testing. In all experiments, the productivity level and bacterial cell growth were evaluated by western blotting technique and monitoring of absorbance at 600 nm, respectively. Our results indicated that %DO, the post-induction time and temperature have significant effects on the production of β-NGF. After 2 hours of induction, the low post induction temperature of 32°C and 20% DO were used to increase the production of β-NGF in a 5-l bioreactor. Another important result obtained in this study was that the improved β-NGF production was not achieved at highest dry cell weigh or highest cell growth. These results are definitely of importance for industrial β-NGF production.
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Affiliation(s)
- Zahra Hajihassan
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran
| | - Pouria Gholami Tilko
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran
| | - Seyedeh Mahdieh Sadat
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran
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Uhoraningoga A, Kinsella GK, Henehan GT, Ryan BJ. The Goldilocks Approach: A Review of Employing Design of Experiments in Prokaryotic Recombinant Protein Production. Bioengineering (Basel) 2018; 5:E89. [PMID: 30347746 PMCID: PMC6316313 DOI: 10.3390/bioengineering5040089] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 10/09/2018] [Accepted: 10/12/2018] [Indexed: 02/06/2023] Open
Abstract
The production of high yields of soluble recombinant protein is one of the main objectives of protein biotechnology. Several factors, such as expression system, vector, host, media composition and induction conditions can influence recombinant protein yield. Identifying the most important factors for optimum protein expression may involve significant investment of time and considerable cost. To address this problem, statistical models such as Design of Experiments (DoE) have been used to optimise recombinant protein production. This review examines the application of DoE in the production of recombinant proteins in prokaryotic expression systems with specific emphasis on media composition and culture conditions. The review examines the most commonly used DoE screening and optimisation designs. It provides examples of DoE applied to optimisation of media and culture conditions.
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Affiliation(s)
| | | | - Gary T Henehan
- Dublin Institute of Technology, Dublin D01 HV58, Ireland.
| | - Barry J Ryan
- Dublin Institute of Technology, Dublin D01 HV58, Ireland.
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17
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Batumalaie K, Khalili E, Mahat NA, Huyop FZ, Wahab RA. A statistical approach for optimizing the protocol for overexpressing lipase KV1 in Escherichia coli: purification and characterization. BIOTECHNOL BIOTEC EQ 2017. [DOI: 10.1080/13102818.2017.1407670] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Kalaivani Batumalaie
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
| | - Elham Khalili
- Department of Biotechnology and Medical Engineering, Faculty of Bioscience and Medical Engineering, Universiti Teknologi Malaysia, Johor, Malaysia
| | - Naji Arafat Mahat
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
| | - Fahrul Zaman Huyop
- Department of Biotechnology and Medical Engineering, Faculty of Bioscience and Medical Engineering, Universiti Teknologi Malaysia, Johor, Malaysia
| | - Roswanira Abdul Wahab
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
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18
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Antoniou G, Papakyriacou I, Papaneophytou C. Optimization of Soluble Expression and Purification of Recombinant Human Rhinovirus Type-14 3C Protease Using Statistically Designed Experiments: Isolation and Characterization of the Enzyme. Mol Biotechnol 2017; 59:407-424. [PMID: 28801725 DOI: 10.1007/s12033-017-0032-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Human rhinovirus (HRV) 3C protease is widely used in recombinant protein production for various applications such as biochemical characterization and structural biology projects to separate recombinant fusion proteins from their affinity tags in order to prevent interference between these tags and the target proteins. Herein, we report the optimization of expression and purification conditions of glutathione S-transferase (GST)-tagged HRV 3C protease by statistically designed experiments. Soluble expression of GST-HRV 3C protease was initially optimized by response surface methodology (RSM), and a 5.5-fold increase in enzyme yield was achieved. Subsequently, we developed a new incomplete factorial (IF) design that examines four variables (bacterial strain, expression temperature, induction time, and inducer concentration) in a single experiment. The new design called Incomplete Factorial-Strain/Temperature/Time/Inducer (IF-STTI) was validated using three GST-tagged proteins. In all cases, IF-STTI resulted in only 10% lower expression yields than those obtained by RSM. Purification of GST-HRV 3C was optimized by an IF design that examines simultaneously the effect of the amount of resin, incubation time of cell lysate with resin, and glycerol and DTT concentration in buffers, and a further 15% increase in protease recovery was achieved. Purified GST-HRV 3C protease was active at both 4 and 25 °C in a variety of buffers.
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Affiliation(s)
- Georgia Antoniou
- Department of Life and Health Sciences, School of Sciences and Engineering, University of Nicosia, 46 Makedonitissas Ave., 1700, Nicosia, Cyprus
| | - Irineos Papakyriacou
- Department of Life and Health Sciences, School of Sciences and Engineering, University of Nicosia, 46 Makedonitissas Ave., 1700, Nicosia, Cyprus
| | - Christos Papaneophytou
- Department of Life and Health Sciences, School of Sciences and Engineering, University of Nicosia, 46 Makedonitissas Ave., 1700, Nicosia, Cyprus.
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Uversky VN, El-Baky NA, El-Fakharany EM, Sabry A, Mattar EH, Uversky AV, Redwan EM. Functionality of intrinsic disorder in tumor necrosis factor-α and its receptors. FEBS J 2017; 284:3589-3618. [PMID: 28746777 DOI: 10.1111/febs.14182] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 06/15/2017] [Accepted: 07/20/2017] [Indexed: 01/02/2023]
Affiliation(s)
- Vladimir N. Uversky
- Department of Biological Sciences; Faculty of Sciences; King Abdulaziz University; Jeddah Saudi Arabia
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute; Morsani College of Medicine; University of South Florida; Tampa FL USA
- Institute for Biological Instrumentation; Russian Academy of Sciences; Pushchino, Moscow Region Russia
| | - Nawal Abd El-Baky
- Protective Proteins Laboratory; Protein Research Department; Genetic Engineering and Biotechnology Research Institute; City for Scientific Research and Technology Applications; New Borg EL-Arab, Alexandria Egypt
| | - Esmail M. El-Fakharany
- Protective Proteins Laboratory; Protein Research Department; Genetic Engineering and Biotechnology Research Institute; City for Scientific Research and Technology Applications; New Borg EL-Arab, Alexandria Egypt
| | - Amira Sabry
- Protective Proteins Laboratory; Protein Research Department; Genetic Engineering and Biotechnology Research Institute; City for Scientific Research and Technology Applications; New Borg EL-Arab, Alexandria Egypt
| | - Ehab H. Mattar
- Department of Biological Sciences; Faculty of Sciences; King Abdulaziz University; Jeddah Saudi Arabia
| | - Alexey V. Uversky
- Center for Data Analytics and Biomedical Informatics; Department of Computer and Information Sciences; College of Science and Technology; Temple University; Philadelphia PA USA
| | - Elrashdy M. Redwan
- Department of Biological Sciences; Faculty of Sciences; King Abdulaziz University; Jeddah Saudi Arabia
- Protective Proteins Laboratory; Protein Research Department; Genetic Engineering and Biotechnology Research Institute; City for Scientific Research and Technology Applications; New Borg EL-Arab, Alexandria Egypt
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20
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Sun L, Chen C, Zhu A, Huang Y, Zhu H, Yi C. TRAIL mutant membrane penetrating peptide alike-MuR6-TR enhances the antitumor effects of TRAIL in pancreatic carcinoma both in vitro and in vivo. Int J Mol Med 2017; 39:1468-1476. [PMID: 28487979 PMCID: PMC5428941 DOI: 10.3892/ijmm.2017.2968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Accepted: 04/10/2017] [Indexed: 02/05/2023] Open
Abstract
To remedy the drug resistance of natural tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) and enhance its antitumor effects, we prepared a type of TRAIL mutant membrane penetrating peptide alike (TMPPA)‑TRAIL mutant R6 (MuR6-TR) by mutating the N‑terminal of the soluble TRAIL gene sequence. The expressed MuR6‑TR protein was purified to treat pancreatic carcinoma cell lines BxPC‑3 and PANC‑1. The inhibitory effects on the proliferation of BxPC‑3 and PANC‑1 cells was assessed with CCK‑8 assay and compared with natural TRAIL. The antitumor effect of MuR6‑TR was assessed on implant tumors derived from PANC‑1 cells in nude mice and compared with gemcitabine. Finally, the soluble MuR6‑TR gene was successfully mutated with 4 amino acids in the N‑terminal of TRAIL and had a molecular size of 513 bp. The mutant MuR6‑TR was connected to pET32a and verified by enzymatic digestion and sequencing. The recombinant MuR6‑TR was transformed and expressed in Escherichia coli. The CCK‑8 assay results indicated that MuR6‑TR inhibited the growth of BxPC‑3 and PANC‑1 cells in a dose‑dependent manner, with IC50 values of 4.63 and 7.84 ng/ml, respectively, which were much lower than that of natural TRAIL. MuR6‑TR demonstrated a higher inhibitory effect on tumor growth (24.2%) than natural TRAIL (14.4%) and an effect similar to that of gemcitabine at an early period. Thus, the mutant MuR6‑TR exhibited a stronger antitumor effect than that of natural TRAIL both in vivo and in vitro and may have potential therapeutic value for pancreatic carcinoma, which requires further validation.
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Affiliation(s)
- Lei Sun
- Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan University
- No. 4 West China Teaching Hospital, Sichuan University
| | - Chen Chen
- Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan University
| | - Aijing Zhu
- Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan University
| | - Ying Huang
- Department of Pathophysiology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Hong Zhu
- Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan University
| | - Cheng Yi
- Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan University
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Gholami Tilko P, Hajihassan Z, Moghimi H. Optimization of recombinant β-NGF expression in Escherichia coli using response surface methodology. Prep Biochem Biotechnol 2017; 47:406-413. [PMID: 27813712 DOI: 10.1080/10826068.2016.1252927] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Human nerve growth factor a member of the neurotrophin family can be used to treat neurodegenerative diseases. As it has disulfide bonds in its structure, periplasmic expression of it using appropriate signal sequence is beneficial. Therefore, in this work β-nerve growth factor (β-NGF) was expressed in Escherichia coli using pET39b expression vector containing DsbA signal sequence. In an initial step, the effect of isopropyl β-D-1-thiogalactopyranoside (IPTG) and lactose concentration as inducer on protein production was investigated using response surface methodology. Then the effect of different postinduction time and temperature on protein production was studied. Our results indicated that the highest β-NGF production was achieved with 1 mM IPTG and low concentrations of lactose (0-2% w/v), low cultivation temperature of 25°C and postinduction time of 2 hr. Also following β-NGF purification, bioassay test using PC12 cell line was done. The biological activity of the purified β-NGF showed a similar cell proliferation activity with the standard recombinant human β-NGF. In conclusion, the results indicated an optimized upstream process to obtain high yields of biologically active β-NGF.
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Affiliation(s)
- Pouria Gholami Tilko
- a Department of Life Science Engineering, Faculty of New Sciences and Technologies , University of Tehran , Tehran , Iran.,b Department of Microbial Biotechnology, School of Biology, College of Science , University of Tehran , Tehran , Iran
| | - Zahra Hajihassan
- a Department of Life Science Engineering, Faculty of New Sciences and Technologies , University of Tehran , Tehran , Iran
| | - Hamid Moghimi
- b Department of Microbial Biotechnology, School of Biology, College of Science , University of Tehran , Tehran , Iran
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Cheminformatics-aided discovery of small-molecule Protein-Protein Interaction (PPI) dual inhibitors of Tumor Necrosis Factor (TNF) and Receptor Activator of NF-κB Ligand (RANKL). PLoS Comput Biol 2017; 13:e1005372. [PMID: 28426652 PMCID: PMC5398486 DOI: 10.1371/journal.pcbi.1005372] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 01/17/2017] [Indexed: 12/20/2022] Open
Abstract
We present an in silico drug discovery pipeline developed and applied for the identification and virtual screening of small-molecule Protein-Protein Interaction (PPI) compounds that act as dual inhibitors of TNF and RANKL through the trimerization interface. The cheminformatics part of the pipeline was developed by combining structure-based with ligand-based modeling using the largest available set of known TNF inhibitors in the literature (2481 small molecules). To facilitate virtual screening, the consensus predictive model was made freely available at: http://enalos.insilicotox.com/TNFPubChem/. We thus generated a priority list of nine small molecules as candidates for direct TNF function inhibition. In vitro evaluation of these compounds led to the selection of two small molecules that act as potent direct inhibitors of TNF function, with IC50 values comparable to those of a previously-described direct inhibitor (SPD304), but with significantly reduced toxicity. These molecules were also identified as RANKL inhibitors and validated in vitro with respect to this second functionality. Direct binding of the two compounds was confirmed both for TNF and RANKL, as well as their ability to inhibit the biologically-active trimer forms. Molecular dynamics calculations were also carried out for the two small molecules in each protein to offer additional insight into the interactions that govern TNF and RANKL complex formation. To our knowledge, these compounds, namely T8 and T23, constitute the second and third published examples of dual small-molecule direct function inhibitors of TNF and RANKL, and could serve as lead compounds for the development of novel treatments for inflammatory and autoimmune diseases.
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23
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Mohajeri A, Pilehvar-Soltanahmadi Y, Abdolalizadeh J, Karimi P, Zarghami N. Effect of Culture Condition Variables on Human Endostatin Gene Expression in Escherichia coli Using Response Surface Methodology. Jundishapur J Microbiol 2016; 9:e34091. [PMID: 27800134 PMCID: PMC5080621 DOI: 10.5812/jjm.34091] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 02/15/2016] [Accepted: 02/20/2016] [Indexed: 01/22/2023] Open
Abstract
Background Recombinant human endostatin (rhES) is an angiogenesis inhibitor used as a specific drug for the treatment of non-small-cell lung cancer. As mRNA concentration affects the recombinant protein expression level, any factor affecting mRNA concentration can alter the protein expression level. Response surface methodology (RSM) based on the Box-Behnken design (BBD) is a statistical tool for experimental design and for optimizing biotechnological processes. Objectives This investigation aimed to predict and develop the optimal culture conditions for mRNA expression of the synthetic human endostatin (hES) gene in Escherichia coli BL21 (DE3). Materials and Methods The hES gene was amplified, cloned, and expressed in the E. coli expression system. Three factors, including isopropyl β-D-1-thiogalactopyranoside (IPTG) concentration, post-induction time, and cell density before induction, were selected as important factors. The mRNA expression level was determined using real-time PCR. The expression levels of hES mRNA under the different growth conditions were analyzed. SDS-PAGE and western blot analyses were carried out for further confirmation of interest-gene expression. Results A maximum rhES mRNA level of 376.16% was obtained under the following conditions: 0.6 mM IPTG, 7 hours post-induction time, and 0.9 cell density before induction. The level of rhES mRNA was significantly correlated with post-induction time, IPTG concentration, and cell density before induction (P < 0.05). The expression of the hES gene was confirmed by western blot. Conclusions The obtained results indicate that RSM is an effective method for the optimization of culture conditions for hES gene expression in E. coli.
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Affiliation(s)
- Abbas Mohajeri
- Tuberculosis and Lung Disease Research Center, Tabriz University of Medical Sciences, Tabriz, IR Iran
| | - Yones Pilehvar-Soltanahmadi
- Tuberculosis and Lung Disease Research Center, Tabriz University of Medical Sciences, Tabriz, IR Iran
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, IR Iran
| | - Jalal Abdolalizadeh
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, IR Iran
| | - Pouran Karimi
- Neurosciences Research Center (NSRC), Tabriz University of Medical Sciences, Tabriz, IR Iran
| | - Nosratollah Zarghami
- Tuberculosis and Lung Disease Research Center, Tabriz University of Medical Sciences, Tabriz, IR Iran
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, IR Iran
- Corresponding author: Nosratollah Zarghami, Tuberculosis and Lung Disease Research Center, Tabriz University of Medical Sciences, Tabriz, IR Iran. Tel: +98-4113378093, E-mail:
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Papaneophytou C, Kontopidis G. A comparison of statistical approaches used for the optimization of soluble protein expression in Escherichia coli. Protein Expr Purif 2015; 120:126-37. [PMID: 26721705 DOI: 10.1016/j.pep.2015.12.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Revised: 11/16/2015] [Accepted: 12/18/2015] [Indexed: 01/30/2023]
Abstract
During a discovery project of potential inhibitors for three proteins, TNF-α, RANKL and HO-1, implicated in the pathogenesis of rheumatoid arthritis, significant amounts of purified proteins were required. The application of statistically designed experiments for screening and optimization of induction conditions allows rapid identification of the important factors and interactions between them. We have previously used response surface methodology (RSM) for the optimization of soluble expression of TNF-α and RANKL. In this work, we initially applied RSM for the optimization of recombinant HO-1 and a 91% increase of protein production was achieved. Subsequently, we slightly modified a published incomplete factorial approach (called IF1) in order to evaluate the effect of three expression variables (bacterial strains, induction temperatures and culture media) on soluble expression levels of the three tested proteins. However, soluble expression yields of TNF-α and RANKL obtained by the IF1 method were significantly lower (<50%) than those obtained by RSM. We further modified the IF1 approach by replacing the culture media with induction times and the resulted method called IF-STT (Incomplete Factorial-Stain/Temperature/Time) was validated using the three proteins. Interestingly, soluble expression levels of the three proteins obtained by IF-STT were only 1.2-fold lower than those obtained by RSM. Although RSM is probably the best approach for optimization of biological processes, the IF-STT is faster, it examines the most important factors (bacterial strain, temperature and time) influencing protein soluble expression in a single experiment, and can be used in any recombinant protein expression project as a starting point.
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Affiliation(s)
- Christos Papaneophytou
- Veterinary School, University of Thessaly, Trikalon 224, Karditsa 43100, Greece; Institute for Research and Technology of Thessaly (I.RE.TE.TH.), The Centre for Research & Technology Hellas (CE.R.TH.), Dimitriados 95 & Paulou Mela, Volos 383 33, Greece
| | - George Kontopidis
- Veterinary School, University of Thessaly, Trikalon 224, Karditsa 43100, Greece; Institute for Research and Technology of Thessaly (I.RE.TE.TH.), The Centre for Research & Technology Hellas (CE.R.TH.), Dimitriados 95 & Paulou Mela, Volos 383 33, Greece.
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Papaneophytou C, Alexiou P, Papakyriakou A, Ntougkos E, Tsiliouka K, Maranti A, Liepouri F, Strongilos A, Mettou A, Couladouros E, Eliopoulos E, Douni E, Kollias G, Kontopidis G. Synthesis and biological evaluation of potential small moleculeinhibitors of tumor necrosis factor. MEDCHEMCOMM 2015. [DOI: 10.1039/c5md00023h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A series of 39 novel SPD-304 analogs were designed synthesized and evaluated as inhibitors of TNF.
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Affiliation(s)
| | - Polyxeni Alexiou
- Laboratory of General Chemistry
- Department of Science
- Agricultural University of Athens
- Athens 11855
- Greece
| | - Athanasios Papakyriakou
- Laboratory of Genetics
- Department of Biotechnology
- Agricultural University of Athens
- Athens 11855
- Greece
| | | | | | | | | | | | - Anthi Mettou
- Department of Biochemistry
- Veterinary School
- University of Thessaly
- Karditsa 43100
- Greece
| | - Elias Couladouros
- Laboratory of General Chemistry
- Department of Science
- Agricultural University of Athens
- Athens 11855
- Greece
| | - Elias Eliopoulos
- Laboratory of Genetics
- Department of Biotechnology
- Agricultural University of Athens
- Athens 11855
- Greece
| | - Eleni Douni
- Laboratory of Genetics
- Department of Biotechnology
- Agricultural University of Athens
- Athens 11855
- Greece
| | - George Kollias
- Biomedical Sciences Research Center “Alexander Fleming”
- Vari
- Greece
| | - George Kontopidis
- Department of Biochemistry
- Veterinary School
- University of Thessaly
- Karditsa 43100
- Greece
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26
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Lee MS, Lin IF, Lai GH, Lin YC, Li KY. Statistical optimization of culture medium for the overproduction of chicken anemia virus immunogen- VP1 protein in a recombinantE. colifor vaccine application. ASIA-PAC J CHEM ENG 2014. [DOI: 10.1002/apj.1850] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Meng-Shiou Lee
- Dept. of Chinese Pharmaceutical Science and Chinese Medicine Resources; China Medical University; 91 Hsuh-shih Rd Taichung 40402 Taiwan
| | - I-Fen Lin
- Graduate Institute of Food Science; Tunghai University; No.1727, Sec.4, Taiwan Boulevard Taichung 40704 Taiwan
| | - Guan-Hua Lai
- Graduate institute of Biotechnology; National Chung Hsing University; 250 Kuo Kuang Rd. Taichung 402 Taiwan
| | - Yen-Chang Lin
- Graduate Institute of Biotechnology; Chinese Culture University; 55, Hwa-Kang Rd Taipei 111 Taiwan
| | - Ken-Yuon Li
- Graduate Institute of Food Science; Tunghai University; No.1727, Sec.4, Taiwan Boulevard Taichung 40704 Taiwan
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27
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Alexiou P, Papakyriakou A, Ntougkos E, Papaneophytou CP, Liepouri F, Mettou A, Katsoulis I, Maranti A, Tsiliouka K, Strongilos A, Chaitidou S, Douni E, Kontopidis G, Kollias G, Couladouros E, Eliopoulos E. Rationally Designed Less Toxic SPD-304 Analogs and Preliminary Evaluation of Their TNF Inhibitory Effects. Arch Pharm (Weinheim) 2014; 347:798-805. [DOI: 10.1002/ardp.201400198] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 06/26/2014] [Accepted: 07/03/2014] [Indexed: 12/11/2022]
Affiliation(s)
- Polyxeni Alexiou
- Laboratory of General Chemistry; Department of Science; Agricultural University of Athens; Athens Greece
| | - Athanasios Papakyriakou
- Laboratory of Genetics; Department of Biotechnology; Agricultural University of Athens; Athens Greece
| | | | - Christos P. Papaneophytou
- Institute for Research and Technology - Thessaly (I.RE.TE.TH.)/The Centre for Research & Technology Hellas (CE.R.TH.); Technology Park of Thessaly; Volos Greece
- Veterinary School; University of Thessaly; Karditsa Greece
| | | | - Anthi Mettou
- Institute for Research and Technology - Thessaly (I.RE.TE.TH.)/The Centre for Research & Technology Hellas (CE.R.TH.); Technology Park of Thessaly; Volos Greece
- Veterinary School; University of Thessaly; Karditsa Greece
| | | | | | | | | | | | - Eleni Douni
- Laboratory of Genetics; Department of Biotechnology; Agricultural University of Athens; Athens Greece
- Biomedical Sciences Research Center “Alexander Fleming”; Vari; Greece
| | - George Kontopidis
- Institute for Research and Technology - Thessaly (I.RE.TE.TH.)/The Centre for Research & Technology Hellas (CE.R.TH.); Technology Park of Thessaly; Volos Greece
- Veterinary School; University of Thessaly; Karditsa Greece
| | - George Kollias
- Biomedical Sciences Research Center “Alexander Fleming”; Vari; Greece
| | - Elias Couladouros
- Laboratory of General Chemistry; Department of Science; Agricultural University of Athens; Athens Greece
| | - Elias Eliopoulos
- Laboratory of Genetics; Department of Biotechnology; Agricultural University of Athens; Athens Greece
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28
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Wang Y, Ren W, Gao D, Wang L, Yang Y, Bai Q. One-step refolding and purification of recombinant human tumor necrosis factor-α (rhTNF-α) using ion-exchange chromatography. Biomed Chromatogr 2014; 29:305-11. [PMID: 24941919 DOI: 10.1002/bmc.3276] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Revised: 05/12/2014] [Accepted: 05/21/2014] [Indexed: 11/05/2022]
Abstract
Protein refolding is a key step for the production of recombinant proteins, especially at large scales, and usually their yields are very low. Chromatographic-based protein refolding techniques have proven to be superior to conventional dilution refolding methods. High refolding yield can be achieved using these methods compared with dilution refolding of proteins. In this work, recombinant human tumor necrosis factor-α (rhTNF-α) from inclusion bodies expressed in Escherichia coli was renatured with simultaneous purification by ion exchange chromatography with a DEAE Sepharose FF column. Several chromatographic parameters influencing the refolding yield of the denatured/reduced rhTNF-α, such as the urea concentration, pH value and concentration ratio of glutathione/oxidized glutathione in the mobile phase, were investigated in detail. Under optimal conditions, rhTNF-α can be renatured and purified simultaneously within 30 min by one step. Specific bioactivity of 2.18 × 10(8) IU/mg, purity of 95.2% and mass recovery of 76.8% of refolded rhTNF-α were achieved. Compared with the usual dilution method, the ion exchange chromatography method developed here is simple and more effective for rhTNF-α refolding in terms of specific bioactivity and mass recovery.
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Affiliation(s)
- Yan Wang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Institute of Modern Separation Science, Key Laboratory of Modern Separation Science in Shaanxi Province, Northwest University, Xi'an, 710069, China
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29
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Fang XJ, Tang ZX, Li ZH, Zhang ZL, Shi LE. Production of a new non-specific nuclease from Yersinia enterocolitica subsp. palearctica: optimization of induction conditions using response surface methodology. BIOTECHNOL BIOTEC EQ 2014; 28:559-566. [PMID: 26019543 PMCID: PMC4433914 DOI: 10.1080/13102818.2014.915612] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 12/27/2013] [Indexed: 01/16/2023] Open
Abstract
A new non-specific nuclease from Yersinia enterocolitica subsp. palearctica (Y. NSN) was expressed in Escherichia coli (E. coli) BL 21 StarTM (DE3)plysS. Induction conditions, including isopropyl-β-D-thiogalactoside (IPTG) concentration, cell density (OD600), induction time and induction temperature, were optimized using response surface methodology. Statistical analysis of the results revealed that induction temperature and all the quadratic terms of variables had significant effects on enzyme activity of Y. NSN. The optimal induction conditions were as follows: 1.5 mmol/L IPTG, OD600 of 0.80, induction time of 20.5 h, and induction temperature of 32 °C. Under the optimized conditions, the highest enzyme activity could be obtained.
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Affiliation(s)
- Xiu-Juan Fang
- College of Life and Environmental Sciences, Hangzhou Normal University , Hangzhou , Zhejiang , P.R. China
| | - Zhen-Xing Tang
- College of Life and Environmental Sciences, Hangzhou Normal University , Hangzhou , Zhejiang , P.R. China ; Date Palm Research Center, King Faisal University , Al-hasa , Saudi Arabia ; Department of Food Science, Anqing Vocational & Technical College , Anqing , Anhui , P.R. China
| | - Zhen-Hua Li
- College of Life and Environmental Sciences, Hangzhou Normal University , Hangzhou , Zhejiang , P.R. China
| | - Zhi-Liang Zhang
- College of Life and Environmental Sciences, Hangzhou Normal University , Hangzhou , Zhejiang , P.R. China
| | - Lu-E Shi
- College of Life and Environmental Sciences, Hangzhou Normal University , Hangzhou , Zhejiang , P.R. China
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30
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Optimizing the production of an α-(1→2) branching sucrase in Escherichia coli using statistical design. Appl Microbiol Biotechnol 2014; 98:5173-84. [DOI: 10.1007/s00253-014-5627-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 02/17/2014] [Accepted: 02/21/2014] [Indexed: 12/14/2022]
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31
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Ding L, He S, Yan X. Efficient preparation of pseudoalteromone A from marine Pseudoalteromonas rubra QD1-2 by combination of response surface methodology and high-speed counter-current chromatography: a comparison with high-performance liquid chromatography. Appl Microbiol Biotechnol 2014; 98:4369-77. [PMID: 24477384 DOI: 10.1007/s00253-014-5530-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 01/05/2014] [Accepted: 01/09/2014] [Indexed: 10/25/2022]
Abstract
Pseudoalteromone A (PA) is a cytotoxic and anti-inflammatory ubiquinone discovered recently from a marine bacterium Pseudoalteromonas sp. CGH2XX. In order to meet its sample supply for further in vivo pharmacological investigation, an efficient method was developed for the preparation of PA by combination of response surface methodology (RSM) and high-speed counter-current chromatography (HSCCC) from marine bacterium P. rubra QD1-2. First, optimization of culture conditions was studied by the RSM to enhance PA production. The results indicated that the optimal cultivation condition was peptone (2.21 g/l), yeast extract (3.125 g/l), glucose (0.125 g/l), KBr (0.02 g/l), inoculum size (6.5 %), medium volume (595 ml), initial pH value (7.0), temperature (28 °C). Under the optimized fermentation condition, PA production was 1.04 mg/l with 14.8-fold increase comparing to 0.07 mg/l under original standard fermentation condition. The PA production was further investigated using a 14-l jar fermenter. Compared to the flask culture, P. rubra QD1-2 offered 45 % increase of PA production at 1.51 mg/l. Then, a rapid and efficient method for the separation and purification of PA from crude culture extract was developed using HSCCC. The two-phase solvent system used for HSCCC separation was composed of n-hexane-ethyl acetate-methanol-water (5:5:9:5, v/v/v/v). The isolation was accomplished within 100 min, and the purity of PA was over 95 %. The recovery of the process was 93 %.
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Affiliation(s)
- Lijian Ding
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, China
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32
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Papaneophytou CP, Kontopidis G. Statistical approaches to maximize recombinant protein expression in Escherichia coli: a general review. Protein Expr Purif 2013; 94:22-32. [PMID: 24211770 DOI: 10.1016/j.pep.2013.10.016] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 10/23/2013] [Accepted: 10/25/2013] [Indexed: 11/16/2022]
Abstract
The supply of many valuable proteins that have potential clinical or industrial use is often limited by their low natural availability. With the modern advances in genomics, proteomics and bioinformatics, the number of proteins being produced using recombinant techniques is exponentially increasing and seems to guarantee an unlimited supply of recombinant proteins. The demand of recombinant proteins has increased as more applications in several fields become a commercial reality. Escherichia coli (E. coli) is the most widely used expression system for the production of recombinant proteins for structural and functional studies. However, producing soluble proteins in E. coli is still a major bottleneck for structural biology projects. One of the most challenging steps in any structural biology project is predicting which protein or protein fragment will express solubly and purify for crystallographic studies. The production of soluble and active proteins is influenced by several factors including expression host, fusion tag, induction temperature and time. Statistical designed experiments are gaining success in the production of recombinant protein because they provide information on variable interactions that escape the "one-factor-at-a-time" method. Here, we review the most important factors affecting the production of recombinant proteins in a soluble form. Moreover, we provide information about how the statistical design experiments can increase protein yield and purity as well as find conditions for crystal growth.
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Affiliation(s)
- Christos P Papaneophytou
- Veterinary School, University of Thessaly, Trikalon 224, Karditsa 43100, Greece; Institute for Research and Technology - Thessaly (I.RE.TE.TH.), The Centre for Research & Technology Hellas (CE.R.TH.), Technology Park of Thessaly, 1st Industrial Area, Volos 38500, Greece
| | - George Kontopidis
- Veterinary School, University of Thessaly, Trikalon 224, Karditsa 43100, Greece; Institute for Research and Technology - Thessaly (I.RE.TE.TH.), The Centre for Research & Technology Hellas (CE.R.TH.), Technology Park of Thessaly, 1st Industrial Area, Volos 38500, Greece.
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33
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Expression, purification and characterization of two truncated peste des petits ruminants virus matrix proteins in Escherichia coli, and production of polyclonal antibodies against this protein. Protein Expr Purif 2013; 91:1-9. [DOI: 10.1016/j.pep.2013.06.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Revised: 06/02/2013] [Accepted: 06/21/2013] [Indexed: 11/18/2022]
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34
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Papaneophytou CP, Rinotas V, Douni E, Kontopidis G. A statistical approach for optimization of RANKL overexpression in Escherichia coli: purification and characterization of the protein. Protein Expr Purif 2013; 90:9-19. [PMID: 23623854 DOI: 10.1016/j.pep.2013.04.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Revised: 04/15/2013] [Accepted: 04/16/2013] [Indexed: 12/21/2022]
Abstract
Receptor activator of nuclear factor-κB (RANK) and its cognate ligand (RANKL) is a member of the TNF superfamily of cytokines which is essential in osteobiology and its overexpression has been implicated in the pathogenesis of bone degenerative diseases such as osteoporosis. Therefore, RANKL is considered a major therapeutic target for the suppression of bone resorption in bone metabolic diseases such as rheumatoid arthritis and cancer metastasis. To evaluate the inhibitory effect of potential RANKL inhibitors a sufficient amount of protein is required. In this work RANKL was cloned for expression at high levels in Escherichia coli with the interaction of changing cultures conditions in order to produce the protein in a soluble form. In an initial step, the effect of expression host on soluble protein production was investigated and BL21(DE3) pLysS was the most efficient one found for the production of RANKL. Central composite design experiment in the following revealed that cell density before induction, IPTG concentration, post-induction temperature and time as well as their interactions had a significant influence on soluble RANKL production. An 80% increase of protein production was achieved after the determination of the optimum induction conditions: OD600nm before induction 0.55, an IPTG concentration of 0.3mM, a post-induction temperature of 25°C and a post-induction time of 6.5h. Following RANKL purification the thermal stability of the protein was studied. The interaction of RANKL with SPD304, a patented small-molecule inhibitor of TNF-α, was also studied in a fluorescence binding assay resulting in a Kd value of 14.1 ± 0.5 μM.
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Affiliation(s)
- Christos P Papaneophytou
- Institute for Research and Technology - Thessaly, The Centre for Research & Technology Hellas, Technology Park of Thessaly, 1st Industrial Area, Volos 38500, Greece
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