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Özdemir Bahadir A, Balcioğlu BK, Serhatli M, Işik Ş, Erdağ B. Identifying specific matrix metalloproteinase-2-inhibiting peptides through phage display-based subtractive screening. Turk J Biol 2022; 45:674-682. [PMID: 35068948 PMCID: PMC8733953 DOI: 10.3906/biy-2105-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 09/27/2021] [Indexed: 11/03/2022] Open
Abstract
Gelatinases A and B, which are members of the matrix metalloproteinase (MMP) family, play essential roles in cancer development and metastasis, as they can break down basal membranes. Therefore, the determination and inhibition of gelatinases is essential for cancer treatment. Peptides that can specifically block each gelatinase may, therefore, be useful for cancer treatment. In this study, subtractive panning was carried out using a 12-mer peptide library to identify peptides that block gelatinase A activity (MMP-2), which is a key pharmacological target. Using this method, 17 unique peptide sequences were determined. MMP-2 inhibition by these peptides was evaluated through zymogram analyses, which revealed that four peptides inhibited MMP-2 activity by at least 65%. These four peptides were synthesized and used for in vitro wound healing using human umbilical vein endothelial cells, and two peptides, AOMP12 and AOMP29, were found to inhibit wound healing by 40%. These peptides are, thus, potential candidates for MMP-2 inhibition for cancer treatment. Furthermore, our findings suggest that our substractive biopanning screening method is a suitable strategy for identifying peptides that selectively inhibit MMP-2.
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Affiliation(s)
- Aylin Özdemir Bahadir
- Genetic Engineering and Biotechnology Institute, Marmara Research Center, TÜBİTAK, Kocaeli Turkey
| | - Bertan Koray Balcioğlu
- Genetic Engineering and Biotechnology Institute, Marmara Research Center, TÜBİTAK, Kocaeli Turkey
| | - Müge Serhatli
- Genetic Engineering and Biotechnology Institute, Marmara Research Center, TÜBİTAK, Kocaeli Turkey
| | - Şeyma Işik
- Department of Medical Biotechnology Institute of Health Sciences Acıbadem Mehmet Ali Aydınlar University, İstanbul Turkey
| | - Berrin Erdağ
- Department of Medical Biology, Basic Medical Sciences, İstanbul Aydın University, İs-tanbul Turkey
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Denizci Öncü M, Balcıoğlu BK, Özgür B, Öztürk HÜ, Serhatlı M, Işık Ş, Erdağ B, Dinler Doğanay G, Özdemir Bahadır A. Structure-based engineering of an antiangiogenic scFv antibody for soluble production in E. coli without loss of activity. Biotechnol Appl Biochem 2021; 69:2122-2137. [PMID: 34694021 DOI: 10.1002/bab.2273] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 10/18/2021] [Indexed: 11/09/2022]
Abstract
Development of monoclonal antibody therapeutics against vascular endothelial growth factor receptor 2 (VEGFR-2) protein, which is the main regulator in angiogenesis, has been a major challenge for years. In the current study, we engineer an inclusion body forming single-chain variable fragment (scFv) against VEGFR-2 by using complementarity determining regions (CDR) grafting technique to improve its solubility and investigate the activity of the engineered molecule. CDR sequences of the target scFv were grafted into the framework of another intrinsically soluble scFv molecule. Based on the computational results, CDR grafting has increased the solubility of the grafted scFv molecule. Results confirmed that the grafting approach increased in vivo folding properties of the target scFv molecule compared with the original scFv molecule. Similar binding affinities to the VEGFR-2 were observed for the original and the grafted scFv by surface plasmon resonance assays. Biological activity assays, including human umbilical vein endothelial cells proliferation and wound healing assays, showed that grafted scFv molecule has an antiangiogenic property. This study suggests that an antiangiogenic scFv fully expressed as an inclusion body can be rescued by grafting its CDR regions to a scFv expressed in a soluble form without any loss in its binding property and its activity.
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Affiliation(s)
- Melis Denizci Öncü
- Genetic Engineering and Biotechnology Institute, Marmara Research Center, The Scientific and Technological Research Council of Turkey, Kocaeli, Turkey.,Molecular Biology and Genetics Department, İstanbul Technical University, Istanbul, Turkey
| | - Bertan Koray Balcıoğlu
- Genetic Engineering and Biotechnology Institute, Marmara Research Center, The Scientific and Technological Research Council of Turkey, Kocaeli, Turkey
| | - Beytullah Özgür
- Genetic Engineering and Biotechnology Institute, Marmara Research Center, The Scientific and Technological Research Council of Turkey, Kocaeli, Turkey
| | - Hasan Ümit Öztürk
- Genetic Engineering and Biotechnology Institute, Marmara Research Center, The Scientific and Technological Research Council of Turkey, Kocaeli, Turkey
| | - Müge Serhatlı
- Genetic Engineering and Biotechnology Institute, Marmara Research Center, The Scientific and Technological Research Council of Turkey, Kocaeli, Turkey
| | - Şeyma Işık
- Medical Biotechnology Department, Acıbadem University, Istanbul, Turkey
| | - Berrin Erdağ
- Health Sciences Department, İstanbul Aydın University, Istanbul, Turkey
| | - Gizem Dinler Doğanay
- Molecular Biology and Genetics Department, İstanbul Technical University, Istanbul, Turkey
| | - Aylin Özdemir Bahadır
- Genetic Engineering and Biotechnology Institute, Marmara Research Center, The Scientific and Technological Research Council of Turkey, Kocaeli, Turkey
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BalcioĞlu BK, Denİzcİ ÖncÜ M, ÖztÜrk HÜ, YÜcel F, Kaya F, Serhatli M, ÜlbeĞİ Polat H, Tekİn Ş, Özdemİr Bahadir A. SARS-CoV-2 neutralizing antibody development strategies. Turk J Biol 2020; 44:203-214. [PMID: 32595357 PMCID: PMC7314503 DOI: 10.3906/biy-2005-91] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
In December 2019 a novel coronavirus was detected in Wuhan City of Hubei Province-China. Owing to a high rate of transmission from human to human, the new virus called SARS-CoV-2 differed from others by its unexpectedly rapid spread. The World Health Organization (WHO) described the most recent coronavirus epidemic as a global pandemic in March 2020. The virus spread triggered a health crisis (the COVID-19 disease) within three months, with socioeconomic implications. No approved targeted-therapies are available for COVID-19, yet. However, it is foreseen that antibody-based treatments may provide an immediate cure for patients. Current neutralizing antibody development studies primarily target the S protein among the structural elements of SARS-CoV-2, which mediates the cell entry of the virus through the angiotensin converting enzyme 2 (ACE2) receptor of host cells. This review aims to provide some of the neutralizing antibody development strategies for SARS-CoV-2 and in vitro and in vivo neutralization assays.
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Affiliation(s)
- Bertan Koray BalcioĞlu
- Genetic Engineering and Biotechnology Institute, Marmara Research Center, TÜBİTAK, Kocaeli Turkey
| | - Melis Denİzcİ ÖncÜ
- Genetic Engineering and Biotechnology Institute, Marmara Research Center, TÜBİTAK, Kocaeli Turkey
| | - Hasan Ümit ÖztÜrk
- Genetic Engineering and Biotechnology Institute, Marmara Research Center, TÜBİTAK, Kocaeli Turkey
| | - Fatıma YÜcel
- Genetic Engineering and Biotechnology Institute, Marmara Research Center, TÜBİTAK, Kocaeli Turkey
| | - Filiz Kaya
- Genetic Engineering and Biotechnology Institute, Marmara Research Center, TÜBİTAK, Kocaeli Turkey
| | - Müge Serhatli
- Genetic Engineering and Biotechnology Institute, Marmara Research Center, TÜBİTAK, Kocaeli Turkey
| | - Hivda ÜlbeĞİ Polat
- Genetic Engineering and Biotechnology Institute, Marmara Research Center, TÜBİTAK, Kocaeli Turkey
| | - Şaban Tekİn
- Genetic Engineering and Biotechnology Institute, Marmara Research Center, TÜBİTAK, Kocaeli Turkey
- Department of Basic Medical Sciences, Faculty of Medicine, University of Health Sciences, İstanbul Turkey
| | - Aylin Özdemİr Bahadir
- Genetic Engineering and Biotechnology Institute, Marmara Research Center, TÜBİTAK, Kocaeli Turkey
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QbD Based Media Development for the Production of Fab Fragments in E. coli. Bioengineering (Basel) 2019; 6:bioengineering6020029. [PMID: 30925730 PMCID: PMC6631317 DOI: 10.3390/bioengineering6020029] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 03/20/2019] [Accepted: 03/23/2019] [Indexed: 11/29/2022] Open
Abstract
Ranibizumab is a biotherapeutic Fab fragment used for the treatment of age-related macular degeneration and macular oedema. It is currently expressed in the gram-negative bacterium, Escherichia coli. However, low expression levels result in a high manufacturing cost. The protein expression can be increased by manipulating nutritional requirements (carbon source, nitrogen source, buffering agent), process parameters (pH, inducer concentration, agitation, temperature), and the genetic make-up of the producing strain. Further, understanding the impact of these factors on product quality is a requirement as per the principles of Quality by Design (QbD). In this paper, we examine the effect of various media components and process parameters on the expression level and quality of the biotherapeutic. First, risk analysis was performed to shortlist different media components based on the literature. Next, experiments were performed to screen these components. Eight components were identified for further investigation and were examined for their effect and interactions using a Fractional Factorial experimental design. Sucrose, biotin, and pantothenate were found to have the maximum effect during Fab production. Furthermore, cyanocobalamin glutathione and biotin-glutathione were the most significant interactions observed. Product identification was performed with Liquid Chromatography–Mass Spectrometry (LC-MS), the expression level was quantified using Bio-layer Interferometry, Reverse Phase-HPLC, and SDS-PAGE, and product quality were measured by RP-HPLC. Overall, a five-fold enhancement of the target protein titer was obtained (from 5 mg/L to 25 mg/L) using the screened medium components vis-a-vis the basal medium, thereby demonstrating the efficacy of the systematic approach purported by QbD.
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Erdag B, Balcioglu KB, Bahadir AO, Hinc D, Ibrahimoglu O, Bahar A, Basalp A, Yucel F. Cloning of anti-HBsAg single-chain variable fragments from hybridoma cells for one-step ELISA. BIOTECHNOL BIOTEC EQ 2017. [DOI: 10.1080/13102818.2017.1348256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Berrin Erdag
- TUBITAK Marmara Research Center, Genetic Engineering and Biotechnology Institute, Gebze, Kocaeli, Turkey
| | - Koray Bertan Balcioglu
- TUBITAK Marmara Research Center, Genetic Engineering and Biotechnology Institute, Gebze, Kocaeli, Turkey
| | - Aylin Ozdemir Bahadir
- TUBITAK Marmara Research Center, Genetic Engineering and Biotechnology Institute, Gebze, Kocaeli, Turkey
| | - Duygu Hinc
- TUBITAK Marmara Research Center, Genetic Engineering and Biotechnology Institute, Gebze, Kocaeli, Turkey
| | - Ozlem Ibrahimoglu
- TUBITAK Marmara Research Center, Genetic Engineering and Biotechnology Institute, Gebze, Kocaeli, Turkey
| | - Aydin Bahar
- TUBITAK Marmara Research Center, Genetic Engineering and Biotechnology Institute, Gebze, Kocaeli, Turkey
| | - Aynur Basalp
- Sağlık Yüksekokulu, Mehmet Akif Ersoy Üniversitesi, Department of Health Managment, İstiklal Yerleşkesi, Burdur, Turkey
| | - Fatima Yucel
- TUBITAK Marmara Research Center, Genetic Engineering and Biotechnology Institute, Gebze, Kocaeli, Turkey
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Angiogenic growth factors interactome and drug discovery: The contribution of surface plasmon resonance. Cytokine Growth Factor Rev 2014; 26:293-310. [PMID: 25465594 DOI: 10.1016/j.cytogfr.2014.11.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 11/10/2014] [Accepted: 11/11/2014] [Indexed: 11/21/2022]
Abstract
Angiogenesis is implicated in several pathological conditions, including cancer, and in regenerative processes, including the formation of collateral blood vessels after stroke. Physiological angiogenesis is the outcome of a fine balance between the action of angiogenic growth factors (AGFs) and anti-angiogenic molecules, while pathological angiogenesis occurs when this balance is pushed toward AGFs. AGFs interact with multiple endothelial cell (EC) surface receptors inducing cell proliferation, migration and proteases upregulation. On the contrary, free or extracellular matrix-associated molecules inhibit angiogenesis by sequestering AGFs (thus hampering EC stimulation) or by interacting with specific EC receptors inducing apoptosis or decreasing responsiveness to AGFs. Thus, angiogenesis results from an intricate network of interactions among pro- and anti-angiogenic molecules, EC receptors and various modulators. All these interactions represent targets for the development of pro- or anti-angiogenic therapies. These aims call for suitable technologies to study the countless interactions occurring during neovascularization. Surface plasmon resonance (SPR) is a label-free optical technique to study biomolecular interactions in real time. It has become the golden standard technology for interaction analysis in biomedical research, including angiogenesis. From a survey of the literature it emerges that SPR has already contributed substantially to the better understanding of the neovascularization process, laying the basis for the decoding of the angiogenesis "interactome" and the identification of "hub molecules" that may represent preferential targets for an efficacious modulation of angiogenesis. Here, the still unexploited full potential of SPR is enlightened, pointing to improvements in its use for a deeper understanding of the mechanisms of neovascularization and the identification of novel anti-angiogenic drugs.
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Koray Balcioglu B, Ozdemir-Bahadir A, Ozlem Ibrahimoglu O, Burak Caliskan H, Hinc D, Tamerler C, Erdag B. Genetically engineered bifunctional molecular biosensing probes: recombinant antibody against hepatitis B virus surface antigen on Gold Chips. N Biotechnol 2012. [DOI: 10.1016/j.nbt.2012.08.083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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da Silva FA, Li M, Rato S, Maia S, Malhó R, Warren K, Harrich D, Craigie R, Barbas C, Goncalves J. Recombinant rabbit single-chain antibodies bind to the catalytic and C-terminal domains of HIV-1 integrase protein and strongly inhibit HIV-1 replication. Biotechnol Appl Biochem 2012; 59:353-66. [PMID: 23586912 PMCID: PMC3917493 DOI: 10.1002/bab.1034] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 07/26/2012] [Indexed: 11/11/2022]
Abstract
The human immunodeficiency virus type 1 (HIV-1) integrase (IN) protein plays an important role during the early stages of the retroviral life cycle and therefore is an attractive target for therapeutic intervention. We immunized rabbits with HIV-1 IN protein and developed a combinatorial single-chain variable fragment (scFv) library against IN. Five different scFv antibodies with high binding activity and specificity for IN were identified. These scFvs recognize the catalytic and C-terminal domains of IN and block the strand-transfer process. Cells expressing anti-IN-scFvs were highly resistant to HIV-1 replication due to an inhibition of the integration process itself. These results provide proof-of-concept that rabbit anti-IN-scFv intrabodies can be designed to block the early stages of HIV-1 replication without causing cellular toxicity. Therefore, these anti-IN-scFvs may be useful agents for "intracellular immunization"-based gene therapy strategies. Furthermore, because of their epitope binding characteristics, these scFvs can be used also as new tools to study the structure and function of HIV-1 IN protein.
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Affiliation(s)
- Frederico Aires da Silva
- URIA—Centro de Patogénese Molecular, Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
- IMM—Instituto de Medicina Molecular, Lisbon, Portugal
| | - Min Li
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sylvie Rato
- URIA—Centro de Patogénese Molecular, Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
- IMM—Instituto de Medicina Molecular, Lisbon, Portugal
| | - Sara Maia
- URIA—Centro de Patogénese Molecular, Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
- IMM—Instituto de Medicina Molecular, Lisbon, Portugal
| | - Rui Malhó
- Faculdade de Ciências de Lisboa, Universidade de Lisboa, BioFIG, Lisbon, Portugal
| | - Kylie Warren
- Division of Immunology and Infectious Disease, Queensland Institute of Medical Research, Brisbane, Australia
| | - David Harrich
- Division of Immunology and Infectious Disease, Queensland Institute of Medical Research, Brisbane, Australia
| | - Robert Craigie
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Carlos Barbas
- Skaggs Institute for Chemical Biology and Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Joao Goncalves
- URIA—Centro de Patogénese Molecular, Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
- IMM—Instituto de Medicina Molecular, Lisbon, Portugal
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Zhang J, Li H, Wang X, Qi H, Miao X, Zhang T, Chen G, Wang M. Phage-derived fully human antibody scFv fragment directed against human vascular endothelial growth factor receptor 2 blocked its interaction with VEGF. Biotechnol Prog 2012; 28:981-9. [DOI: 10.1002/btpr.1559] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Revised: 04/12/2012] [Indexed: 11/10/2022]
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Phage displayed peptides/antibodies recognizing growth factors and their tyrosine kinase receptors as tools for anti-cancer therapeutics. Int J Mol Sci 2012; 13:5254-5277. [PMID: 22606042 PMCID: PMC3344278 DOI: 10.3390/ijms13045254] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 04/09/2012] [Accepted: 04/20/2012] [Indexed: 12/21/2022] Open
Abstract
The basic idea of displaying peptides on a phage, introduced by George P. Smith in 1985, was greatly developed and improved by McCafferty and colleagues at the MRC Laboratory of Molecular Biology and, later, by Barbas and colleagues at the Scripps Research Institute. Their approach was dedicated to building a system for the production of antibodies, similar to a naïve B cell repertoire, in order to by-pass the standard hybridoma technology that requires animal immunization. Both groups merged the phage display technology with an antibody library to obtain a huge number of phage variants, each of them carrying a specific antibody ready to bind its target molecule, allowing, later on, rare phage (one in a million) to be isolated by affinity chromatography. Here, we will briefly review the basis of the technology and the therapeutic application of phage-derived bioactive molecules when addressed against key players in tumor development and progression: growth factors and their tyrosine kinase receptors.
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