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Production and optimization of a vasostatin-30 and vasoinhibin fusion protein that inhibits tumor angiogenesis and dissemination of breast cancer cells in a zebrafish model. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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2
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Triebel J, Robles JP, Zamora M, Martínez de la Escalera G, Bertsch T, Clapp C. Regulator of Angiogenesis and Vascular Function: A 2019 Update of the Vasoinhibin Nomenclature. Front Endocrinol (Lausanne) 2019; 10:214. [PMID: 31024452 PMCID: PMC6467929 DOI: 10.3389/fendo.2019.00214] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 03/18/2019] [Indexed: 02/02/2023] Open
Affiliation(s)
- Jakob Triebel
- Institute for Clinical Chemistry, Laboratory Medicine and Transfusion Medicine, General Hospital Nuremberg and Paracelsus Medical University Nuremberg, Nuremberg, Germany
- *Correspondence: Jakob Triebel
| | - Juan Pablo Robles
- Instituto de Neurobiología, Universidad Nacional Autónoma de México, Querétaro, Mexico
| | - Magdalena Zamora
- Instituto de Neurobiología, Universidad Nacional Autónoma de México, Querétaro, Mexico
| | | | - Thomas Bertsch
- Institute for Clinical Chemistry, Laboratory Medicine and Transfusion Medicine, General Hospital Nuremberg and Paracelsus Medical University Nuremberg, Nuremberg, Germany
| | - Carmen Clapp
- Instituto de Neurobiología, Universidad Nacional Autónoma de México, Querétaro, Mexico
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3
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Blanco JL, Porto-Pazos AB, Pazos A, Fernandez-Lozano C. Prediction of high anti-angiogenic activity peptides in silico using a generalized linear model and feature selection. Sci Rep 2018; 8:15688. [PMID: 30356060 PMCID: PMC6200741 DOI: 10.1038/s41598-018-33911-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 10/06/2018] [Indexed: 12/22/2022] Open
Abstract
Screening and in silico modeling are critical activities for the reduction of experimental costs. They also speed up research notably and strengthen the theoretical framework, thus allowing researchers to numerically quantify the importance of a particular subset of information. For example, in fields such as cancer and other highly prevalent diseases, having a reliable prediction method is crucial. The objective of this paper is to classify peptide sequences according to their anti-angiogenic activity to understand the underlying principles via machine learning. First, the peptide sequences were converted into three types of numerical molecular descriptors based on the amino acid composition. We performed different experiments with the descriptors and merged them to obtain baseline results for the performance of the models, particularly of each molecular descriptor subset. A feature selection process was applied to reduce the dimensionality of the problem and remove noisy features – which are highly present in biological problems. After a robust machine learning experimental design under equal conditions (nested resampling, cross-validation, hyperparameter tuning and different runs), we statistically and significantly outperformed the best previously published anti-angiogenic model with a generalized linear model via coordinate descent (glmnet), achieving a mean AUC value greater than 0.96 and with an accuracy of 0.86 with 200 molecular descriptors, mixed from the three groups. A final analysis with the top-40 discriminative anti-angiogenic activity peptides is presented along with a discussion of the feature selection process and the individual importance of each molecular descriptors According to our findings, anti-angiogenic activity peptides are strongly associated with amino acid sequences SP, LSL, PF, DIT, PC, GH, RQ, QD, TC, SC, AS, CLD, ST, MF, GRE, IQ, CQ and HG.
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Affiliation(s)
- Jose Liñares Blanco
- Department of Computer Science, Faculty of Computer Science, University of A Coruña, A Coruña, 15071, Spain
| | - Ana B Porto-Pazos
- Department of Computer Science, Faculty of Computer Science, University of A Coruña, A Coruña, 15071, Spain.,Instituto de Investigación Biomédica de A Coruña (INIBIC). Complexo Hospitalario Universitario de A Coruña, A Coruña, Spain
| | - Alejandro Pazos
- Department of Computer Science, Faculty of Computer Science, University of A Coruña, A Coruña, 15071, Spain.,Instituto de Investigación Biomédica de A Coruña (INIBIC). Complexo Hospitalario Universitario de A Coruña, A Coruña, Spain
| | - Carlos Fernandez-Lozano
- Department of Computer Science, Faculty of Computer Science, University of A Coruña, A Coruña, 15071, Spain. .,Instituto de Investigación Biomédica de A Coruña (INIBIC). Complexo Hospitalario Universitario de A Coruña, A Coruña, Spain.
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Calderon-Salais S, Velazquez-Bernardino P, Balderas-Hernandez VE, Barba de la Rosa AP, De Leon-Rodriguez A. Constitutive expression of the active fragment of human vasostatin Vs30 in Pichia pastoris SMD1168H. Protein Expr Purif 2017; 144:40-45. [PMID: 29221829 DOI: 10.1016/j.pep.2017.12.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 10/25/2017] [Accepted: 12/04/2017] [Indexed: 11/26/2022]
Abstract
Vasostatin 30 (Vs30) is an active fragment derived from the N-terminal region (135-164 aa) of human calreticulin and has the ability to inhibit angiogenesis. In this work, the expression of Vs30 was performed using a protease-deficient strain of the methylotrophic yeast Pichia pastoris. The vs30 gene was optimized for P. pastoris preferential codon usage and inserted into constitutive expression vector pGAPZαA. In addition, a plasmid with four copies of the expression cassette was obtained and transformed into P. pastoris. The flask fermentation conditions were: culture volume of 25 mL in 250 mL baffled flasks at 28 °C, pH 6 and harvest time of 48 h. Up to 21.07 mg/L Vs30 were attained and purified by ultrafiltration with a 30-kDa cut-off membrane and the recovery was 49.7%. Bioactivity of Vs30 was confirmed by the inhibition of cell proliferation, as well as the inhibition of the capillary-like structures formation of EA.hy926 cells in vitro. This work constitutes the first report on the expression of Vs30 in Pichia pastoris using a constitutive promoter and multi-copy approach such as strategies to improve the recombinant Vs30 expression.
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Affiliation(s)
- Sergio Calderon-Salais
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C., Camino a la Presa San José 2055, Col. Lomas 4(a) Sección, C.P. 78216 San Luis Potosí, SLP, Mexico
| | - Prisiliana Velazquez-Bernardino
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C., Camino a la Presa San José 2055, Col. Lomas 4(a) Sección, C.P. 78216 San Luis Potosí, SLP, Mexico
| | - Victor E Balderas-Hernandez
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C., Camino a la Presa San José 2055, Col. Lomas 4(a) Sección, C.P. 78216 San Luis Potosí, SLP, Mexico
| | - Ana P Barba de la Rosa
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C., Camino a la Presa San José 2055, Col. Lomas 4(a) Sección, C.P. 78216 San Luis Potosí, SLP, Mexico
| | - Antonio De Leon-Rodriguez
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C., Camino a la Presa San José 2055, Col. Lomas 4(a) Sección, C.P. 78216 San Luis Potosí, SLP, Mexico.
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Chura-Chambi RM, Arcuri HA, Lino F, Versati N, Palma MS, Favaro DC, Morganti L. Structural studies of the protein endostatin in fusion with BAX BH3 death domain, a hybrid that presents enhanced antitumoral activity. Biotechnol Appl Biochem 2016; 64:356-363. [PMID: 27144384 DOI: 10.1002/bab.1503] [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: 01/05/2016] [Accepted: 04/28/2016] [Indexed: 11/12/2022]
Abstract
Endostatin (ES) is an antiangiogenic protein that exhibits antitumor activity in animal models. However, the activity observed in animals was not observed in human clinical trials. ES-BAX is a fusion protein composed of two functional domains: ES, which presents specificity and is internalized by activated endothelial cells and the proapoptotic BH3 domain of the protein BAX, a peptide inductor of cellular death when internalized. We have previously shown (Chura-Chambi et al., Cell Death Dis, 5, e1371, 2014) that ES-BAX presents improved antitumor activity in relation to wild-type ES. Secondary and tertiary structures of ES-BAX are similar to ES, as indicated by homology-modeling studies and molecular dynamics simulations. Tryptophan intrinsic fluorescence and circular dichroism spectroscopy corroborate these data. 15 N HSQC NMR indicates that ES-BAX is structured, but some ES residues have suffered chemical shift perturbations, suggesting that the BH3 peptide interacts with some parts of the ES protein. ES and ES-BAX present similar stability to thermal denaturation. The production of stable hybrid proteins can be a new approach to the development of therapeutic agents presenting specificity for tumoral endothelium and improved antitumor effect.
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Affiliation(s)
- Rosa Maria Chura-Chambi
- Centro de Biotecnologia, Instituto de Pesquisas Energéticas e Nucleares, IPEN-CNEN/SP, São Paulo, Brazil
| | - Helen Andrade Arcuri
- Departamento de Imunologia Clínica e Alergia da Faculdade de Medicina da USP, São Paulo, Brazil
| | - Felipe Lino
- Centro de Biotecnologia, Instituto de Pesquisas Energéticas e Nucleares, IPEN-CNEN/SP, São Paulo, Brazil
| | - Natan Versati
- Centro de Biotecnologia, Instituto de Pesquisas Energéticas e Nucleares, IPEN-CNEN/SP, São Paulo, Brazil
| | - Mario Sergio Palma
- Centro de Estudos de Insetos Sociais, Instituto de Biociências de Rio Claro, UNESP, Rio Claro, São Paulo, Brazil
| | - Denize C Favaro
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ligia Morganti
- Centro de Biotecnologia, Instituto de Pesquisas Energéticas e Nucleares, IPEN-CNEN/SP, São Paulo, Brazil
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Fan J, Wang Z, Huang L, Shen Y. Efficient refolding of the bifunctional therapeutic fusion protein VAS-TRAIL by a triple agent solution. Protein Expr Purif 2015; 125:68-73. [PMID: 26358405 DOI: 10.1016/j.pep.2015.09.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 09/04/2015] [Accepted: 09/05/2015] [Indexed: 11/15/2022]
Abstract
VAS-TRAIL is a bifunctional fusion protein that combines anti-angiogenic activity with tumor-selective apoptotic activity for enhanced anti-tumor efficacy. VAS-TRAIL is expressed as inclusion body in Escherichia coli, but protein refolding is difficult to achieve and results in low yields of bioactive protein. In this study, we describe an efficient method for VAS-TRAIL refolding. The solubilization of aggregated VAS-TRAIL was achieved by a triple agent solution, which consists of an alkaline solution (pH 11.5) containing 0.4M l-arginine and 2M urea. The solubilized protein showed high purity and preserved secondary structure according to fluorescence properties. VAS-TRAIL refolding was performed through stepwise dialysis and resulted in more than 50% recovery of the soluble protein. The function of l-arginine was additive with alkaline pH, as shown by the significant improvement in refolding yield (≈30%) by l-arginine-containing solubilization solutions compared with alkaline solubilization solutions without l-arginine. The refolded VAS-TRAIL also showed β-sheet structures and the propensity for oligomerization. Bioassays showed that the refolded fusion protein exhibited the expected activities, including its apoptotic activities toward tumor and endothelial cells, which proposed its promising therapeutic potential.
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Affiliation(s)
- Jiying Fan
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai 200237, China
| | - Zhanqing Wang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai 200237, China
| | - Liying Huang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai 200237, China
| | - Yaling Shen
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai 200237, China.
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Fan J, Huang L, Sun J, Qiu Y, Zhou J, Shen Y. Strategy for linker selection to enhance refolding and bioactivity of VAS-TRAIL fusion protein based on inclusion body conformation and activity. J Biotechnol 2015; 209:16-22. [PMID: 26072465 DOI: 10.1016/j.jbiotec.2015.06.383] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Accepted: 06/06/2015] [Indexed: 11/25/2022]
Abstract
A bifunctional fusion protein, VAS-TRAIL, was designed for superior therapeutic efficacy by combining anti-angiogenesis activity with tumor-selective apoptosis activity. The protein was expressed as inclusion body (IB) in Escherichia coli. To enhance refolding yield and bioactivity, four fusions were constructed with different linkers (no linker, flexible linker, rigid linker, and helix-forming linker). A novel linker selection strategy based on IB conformational quality and activity was applied to predict the suitable linker. The conformational quality and activity of VAS-TRAIL IBs were analyzed by ATR-FTIR and cytotoxicity assay, respectively. Results demonstrated that aggregated VRT (fusion with rigid linker) contained the highest native-like β structure content and retained part of the expected activity, namely, cytotoxicity activity on tumor cells. This finding suggested that the rigid linker was the most suitable candidate. Further results of in vitro refolding and subsequent circular dichroism and activity assay of four refolded fusions were significantly correlated with the predictions. Refolding of VRT yielded more soluble proteins containing the expected secondary structure and the highest bioactivity compared with that of other fusions. Our research may offer an efficient method for the high-throughput design of aggregated-prone therapeutic fusion protein.
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Affiliation(s)
- Jiying Fan
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai 200237, China
| | - Liying Huang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai 200237, China
| | - Jing Sun
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai 200237, China
| | - Yi Qiu
- Shanghai Gebaide Biotechnical Co., Ltd., Shanghai 201403, China
| | - Jinsong Zhou
- Shanghai Gebaide Biotechnical Co., Ltd., Shanghai 201403, China
| | - Yaling Shen
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai 200237, China.
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Triebel J, Bertsch T, Martínez de la Escalera G, Clapp C. On the Path toward Classifying Hormones of the Vasoinhibin-Family. Front Endocrinol (Lausanne) 2015; 6:16. [PMID: 25713559 PMCID: PMC4322836 DOI: 10.3389/fendo.2015.00016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 01/26/2015] [Indexed: 11/21/2022] Open
Affiliation(s)
- Jakob Triebel
- Institute for Clinical Chemistry, Laboratory Medicine and Transfusion Medicine, Paracelsus Medical University, Nuremberg, Germany
- *Correspondence:
| | - Thomas Bertsch
- Institute for Clinical Chemistry, Laboratory Medicine and Transfusion Medicine, Paracelsus Medical University, Nuremberg, Germany
| | | | - Carmen Clapp
- Instituto de Neurobiología, Universidad Nacional Autónoma de México (UNAM), Campus UNAM-Juriquilla, Querétaro, México
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