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Kamstrup Sell D, Sinkjaer AW, Bakhshinejad B, Kjaer A. Propagation Capacity of Phage Display Peptide Libraries Is Affected by the Length and Conformation of Displayed Peptide. Molecules 2023; 28:5318. [PMID: 37513190 PMCID: PMC10386350 DOI: 10.3390/molecules28145318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/30/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
The larger size and diversity of phage display peptide libraries enhance the probability of finding clinically valuable ligands. A simple way of increasing the throughput of selection is to mix multiple peptide libraries with different characteristics of displayed peptides and use it as biopanning input. In phage display, the peptide is genetically coupled with a biological entity (the phage), and the representation of peptides in the selection system is dependent on the propagation capacity of phages. Little is known about how the characteristics of displayed peptides affect the propagation capacity of the pooled library. In this work, next-generation sequencing (NGS) was used to investigate the amplification capacity of three widely used commercial phage display peptide libraries (Ph.D.™-7, Ph.D.™-12, and Ph.D.™-C7C from New England Biolabs). The three libraries were pooled and subjected to competitive propagation, and the proportion of each library in the pool was quantitated at two time points during propagation. The results of the inter-library competitive propagation assay led to the conclusion that the propagation capacity of phage libraries on a population level is decreased with increasing length and cyclic conformation of displayed peptides. Moreover, the enrichment factor (EF) analysis of the phage population revealed a higher propagation capacity of the Ph.D.TM-7 library. Our findings provide evidence for the contribution of the length and structural conformation of displayed peptides to the unequal propagation rates of phage display libraries and suggest that it is important to take peptide characteristics into account once pooling multiple combinatorial libraries for phage display selection through biopanning.
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Affiliation(s)
- Danna Kamstrup Sell
- Department of Clinical Physiology and Nuclear Medicine & Cluster for Molecular Imaging, Copenhagen University Hospital-Rigshospitalet & Department of Biomedical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Anders Wilgaard Sinkjaer
- Department of Clinical Physiology and Nuclear Medicine & Cluster for Molecular Imaging, Copenhagen University Hospital-Rigshospitalet & Department of Biomedical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Babak Bakhshinejad
- Department of Clinical Physiology and Nuclear Medicine & Cluster for Molecular Imaging, Copenhagen University Hospital-Rigshospitalet & Department of Biomedical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Andreas Kjaer
- Department of Clinical Physiology and Nuclear Medicine & Cluster for Molecular Imaging, Copenhagen University Hospital-Rigshospitalet & Department of Biomedical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
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2
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Hou L, Hou Y, Liang Y, Chen B, Zhang X, Wang Y, Zhou K, Zhong T, Long B, Pang W, Wang L, Han X, Li L, Xu C, Gross I, Gaiddon C, Fu W, Yao H, Meng X. Anti-tumor effects of P-LPK-CPT, a peptide-camptothecin conjugate, in colorectal cancer. Commun Biol 2022; 5:1248. [PMID: 36376440 PMCID: PMC9663589 DOI: 10.1038/s42003-022-04191-1] [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: 01/11/2022] [Accepted: 10/31/2022] [Indexed: 11/16/2022] Open
Abstract
To explore highly selective targeting molecules of colorectal cancer (CRC) is a challenge. We previously identified a twelve-amino acid peptide (LPKTVSSDMSLN, namely P-LPK) by phage display technique which may specifically binds to CRC cells. Here we show that P-LPK selectively bind to a panel of human CRC cell lines and CRC tissues. In vivo, Gallium-68 (68Ga) labeled P-LPK exhibits selective accumulation at tumor sites. Then, we designed a peptide-conjugated drug comprising P-LPK and camptothecin (CPT) (namely P-LPK-CPT), and found P-LPK-CPT significantly inhibits tumor growth with fewer side effects in vitro and in vivo. Furthermore, through co-immunoprecipitation and molecular docking experiment, the glutamine transporter solute carrier 1 family member 5 (SLC1A5) was identified as the possible target of P-LPK. The binding ability of P-LPK and SLC1A5 is verified by surface plasmon resonance and immunofluorescence. Taken together, P-LPK-CPT is highly effective for CRC and deserves further development as a promising anti-tumor therapeutic for CRC, especially SLC1A5-high expression type. A peptide that specifically targets amino acid transporter SLC1A5 in colorectal cancer cells is identified and conjugated with camptothecin to show selective cytotoxicity to colorectal cancer cells in preclinical models.
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Pereira AC, Ferreira D, Santos-Pereira C, Vieira TF, Sousa SF, Sales G, Rodrigues LR. Selection of a new peptide homing SK-BR-3 breast cancer cells. Chem Biol Drug Des 2020; 97:893-903. [PMID: 33314617 DOI: 10.1111/cbdd.13816] [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: 10/01/2020] [Revised: 11/23/2020] [Accepted: 12/05/2020] [Indexed: 11/28/2022]
Abstract
Breast cancer diagnosis remains a challenge, mostly due to its heterogeneity. This reality translates in delayed treatments, increasing treatment aggressiveness and lower chances of overall survival. The conventional detection techniques, although becoming increasingly sophisticated each year, still lack the ability to provide reliable conclusions without being time consuming, expensive, and uncomfortable for the patients. The identification of novel biomarkers for breast cancer research is therefore of utmost relevance for an early diagnosis. Moreover, breast cancer-specific peptide moieties can be used to develop novel targeted drug delivery systems. In this work, we used phage display to identify a novel peptide with specificity to the SK-BR-3 breast cancer cell line. Cytometry assays confirmed its specificity, while bioinformatics and docking studies predicted the potential biomarkers at the SK-BR-3 cells' surface. These findings can be potentially useful in the clinical context, contributing to more specific and targeted therapeutic solutions against HER2-positive breast cancer subtypes.
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Affiliation(s)
- Ana Cláudia Pereira
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal.,MIT-Portugal Program, Lisbon, Portugal.,Biomark - Sensor Research, Superior Institute of Engineering of Porto, Porto, Portugal
| | - Débora Ferreira
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal.,MIT-Portugal Program, Lisbon, Portugal
| | - Cátia Santos-Pereira
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal.,UCIBIO@REQUIMTE - BioSIM, Department of Biomedicine, Faculty of Medicine University of Porto, Alameda Professor Hernâni Monteiro, Porto, Portugal.,CBMA - Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Braga, Portugal
| | - Tatiana F Vieira
- UCIBIO@REQUIMTE - BioSIM, Department of Biomedicine, Faculty of Medicine University of Porto, Alameda Professor Hernâni Monteiro, Porto, Portugal
| | - Sérgio F Sousa
- UCIBIO@REQUIMTE - BioSIM, Department of Biomedicine, Faculty of Medicine University of Porto, Alameda Professor Hernâni Monteiro, Porto, Portugal
| | - Goreti Sales
- Biomark - Sensor Research, Superior Institute of Engineering of Porto, Porto, Portugal
| | - Lígia R Rodrigues
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal.,MIT-Portugal Program, Lisbon, Portugal
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Xu H, Cao B, Li Y, Mao C. Phage nanofibers in nanomedicine: Biopanning for early diagnosis, targeted therapy, and proteomics analysis. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2020; 12:e1623. [PMID: 32147974 DOI: 10.1002/wnan.1623] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 01/02/2020] [Accepted: 02/04/2020] [Indexed: 12/16/2022]
Abstract
Display of a peptide or protein of interest on the filamentous phage (also known as bacteriophage), a biological nanofiber, has opened a new route for disease diagnosis and therapy as well as proteomics. Earlier phage display was widely used in protein-protein or antigen-antibody studies. In recent years, its application in nanomedicine is becoming increasingly popular and encouraging. We aim to review the current status in this research direction. For better understanding, we start with a brief introduction of basic biology and structure of the filamentous phage. We present the principle of phage display and library construction method on the basis of the filamentous phage. We summarize the use of the phage displayed peptide library for selecting peptides with high affinity against cells or tissues. We then review the recent applications of the selected cell or tissue targeting peptides in developing new targeting probes and therapeutics to advance the early diagnosis and targeted therapy of different diseases in nanomedicine. We also discuss the integration of antibody phage display and modern proteomics in discovering new biomarkers or target proteins for disease diagnosis and therapy. Finally, we propose an outlook for further advancing the potential impact of phage display on future nanomedicine. This article is categorized under: Biology-Inspired Nanomaterials > Protein and Virus-Based Structures.
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Affiliation(s)
- Hong Xu
- Department of Chemistry & Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
| | - Binrui Cao
- Department of Chemistry & Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
| | - Yan Li
- Department of Chemistry & Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
| | - Chuanbin Mao
- Department of Chemistry & Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
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Ferreira D, Silva AP, Nobrega FL, Martins IM, Barbosa-Matos C, Granja S, Martins SF, Baltazar F, Rodrigues LR. Rational Identification of a Colorectal Cancer Targeting Peptide through Phage Display. Sci Rep 2019; 9:3958. [PMID: 30850705 PMCID: PMC6408488 DOI: 10.1038/s41598-019-40562-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 02/19/2019] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer is frequently diagnosed at an advanced stage due to the absence of early clinical indicators. Hence, the identification of new targeting molecules is crucial for an early detection and development of targeted therapies. This study aimed to identify and characterize novel peptides specific for the colorectal cancer cell line RKO using a phage-displayed peptide library. After four rounds of selection plus a negative step with normal colorectal cells, CCD-841-CoN, there was an obvious phage enrichment that specifically bound to RKO cells. Cell-based enzyme-linked immunosorbent assay (ELISA) was performed to assess the most specific peptides leading to the selection of the peptide sequence CPKSNNGVC. Through fluorescence microscopy and cytometry, the synthetic peptide RKOpep was shown to specifically bind to RKO cells, as well as to other human colorectal cancer cells including Caco-2, HCT 116 and HCT-15, but not to the normal non-cancer cells. Moreover, it was shown that RKOpep specifically targeted human colorectal cancer cell tissues. A bioinformatics analysis suggested that the RKOpep targets the monocarboxylate transporter 1, which has been implicated in colorectal cancer progression and prognosis, proven through gene knockdown approaches and shown by immunocytochemistry co-localization studies. The peptide herein identified can be a potential candidate for targeted therapies for colorectal cancer.
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Affiliation(s)
- Débora Ferreira
- Centre of Biological Engineering, University of Minho (CEB), Campus de Gualtar, 4710-057, Braga, Portugal.,MIT-Portugal Program, Lisbon, Portugal
| | - Ana P Silva
- Centre of Biological Engineering, University of Minho (CEB), Campus de Gualtar, 4710-057, Braga, Portugal
| | - Franklin L Nobrega
- Centre of Biological Engineering, University of Minho (CEB), Campus de Gualtar, 4710-057, Braga, Portugal.,Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, Netherlands
| | - Ivone M Martins
- Centre of Biological Engineering, University of Minho (CEB), Campus de Gualtar, 4710-057, Braga, Portugal
| | - Catarina Barbosa-Matos
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Sara Granja
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Sandra F Martins
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal.,Surgery Department, Coloproctology Unit, Braga Hospital, Braga, Portugal
| | - Fátima Baltazar
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Ligia R Rodrigues
- Centre of Biological Engineering, University of Minho (CEB), Campus de Gualtar, 4710-057, Braga, Portugal. .,MIT-Portugal Program, Lisbon, Portugal.
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Saueressig S, Tessmann J, Mastelari R, da Silva LP, Buss J, Segatto NV, Begnini KR, Pacheco B, de Pereira CMP, Collares T, Seixas FK. Synergistic effect of pyrazoles derivatives and doxorubicin in claudin-low breast cancer subtype. Biomed Pharmacother 2017; 98:390-398. [PMID: 29276967 DOI: 10.1016/j.biopha.2017.12.062] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 11/20/2017] [Accepted: 12/14/2017] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Breast cancer is a global public health problem. For some subtypes, such as Claudin-low, the prognosis is poorer and the treatment is still a challenge. Pyrazoles are an important class of heterocyclic compounds and are promising anticancer agents based on their chemical properties. The present study was aimed not only at testing pyrazoles previously prepared by our research group in two breast cancer cell lines characterized by intermediated response to conventional chemotherapy but also at analyzing the possible synergistic effect of these pyrazoles associated with doxorubicin. METHODS Four 1-thiocarbamoyl-3,5-diaryl-4,5-dihydro-1H pyrazoles were tested for the first time in MCF-7 and MDA-MB-231 culture cells. The pyrazoles with best results in cytotoxicity were used in combination with doxorubicin and compared with this drug alone as standard. The synergic effect was analyzed using Combination Index method. In addition, cell death and apoptosis assays were carried out. RESULTS Two pyrazoles with cytotoxic effect in MCF-7 and especially in MDA-MB-231 were identified. This activity was markedly higher in pyrazoles containing bromine and chlorine substituents. The combination of these pyrazoles with doxorubicin had a significant synergic effect in both cells tested and mainly in MDA-MB-231. These data were confirmed with apoptosis and cell death analysis. CONCLUSIONS The synergic effect observed with combination of these pyrazoles and doxorubicin deserves special attention in Claudin-low breast cancer subtype. This should be explored in order to improve treatment results and minimize side effects.
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Affiliation(s)
- Silvia Saueressig
- Programa de Pós-Graduação Em Biotecnologia (PPGB), Biotecnologia/Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil; Grupo de Pesquisa Em Oncologia Celular E Molecular (GPO), Laboratório de Biotecnologia Do Câncer, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Josiane Tessmann
- Programa de Pós-Graduação Em Biotecnologia (PPGB), Biotecnologia/Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil; Grupo de Pesquisa Em Oncologia Celular E Molecular (GPO), Laboratório de Biotecnologia Do Câncer, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Rosiane Mastelari
- Programa de Pós-Graduação Em Biotecnologia (PPGB), Biotecnologia/Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil; Grupo de Pesquisa Em Oncologia Celular E Molecular (GPO), Laboratório de Biotecnologia Do Câncer, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Liziane Pereira da Silva
- Programa de Pós-Graduação Em Biotecnologia (PPGB), Biotecnologia/Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil; Grupo de Pesquisa Em Oncologia Celular E Molecular (GPO), Laboratório de Biotecnologia Do Câncer, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Julieti Buss
- Grupo de Pesquisa Em Oncologia Celular E Molecular (GPO), Laboratório de Biotecnologia Do Câncer, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Natalia Vieira Segatto
- Grupo de Pesquisa Em Oncologia Celular E Molecular (GPO), Laboratório de Biotecnologia Do Câncer, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Karine Rech Begnini
- Programa de Pós-Graduação Em Biotecnologia (PPGB), Biotecnologia/Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil; Grupo de Pesquisa Em Oncologia Celular E Molecular (GPO), Laboratório de Biotecnologia Do Câncer, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Bruna Pacheco
- Grupo de Pesquisa Em Oncologia Celular E Molecular (GPO), Laboratório de Biotecnologia Do Câncer, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | | | - Tiago Collares
- Programa de Pós-Graduação Em Biotecnologia (PPGB), Biotecnologia/Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil; Grupo de Pesquisa Em Oncologia Celular E Molecular (GPO), Laboratório de Biotecnologia Do Câncer, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil; Programa de Pós-Graduação Em Bioquímica E Bioprospecção, UFPel, Pelotas, Brazil
| | - Fabiana Kömmling Seixas
- Programa de Pós-Graduação Em Biotecnologia (PPGB), Biotecnologia/Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil; Grupo de Pesquisa Em Oncologia Celular E Molecular (GPO), Laboratório de Biotecnologia Do Câncer, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil.
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