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Uko SO, Malami I, Ibrahim KG, Lawal N, Bello MB, Abubakar MB, Imam MU. Revolutionizing snakebite care with novel antivenoms: Breakthroughs and barriers. Heliyon 2024; 10:e25531. [PMID: 38333815 PMCID: PMC10850593 DOI: 10.1016/j.heliyon.2024.e25531] [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: 12/24/2023] [Revised: 01/27/2024] [Accepted: 01/29/2024] [Indexed: 02/10/2024] Open
Abstract
Snakebite envenoming (SBE) is a global public health concern, primarily due to the lack of effective antivenom for treating snakebites inflicted by medically significant venomous snakes prevalent across various geographic locations. The rising demand for safe, cost-effective, and potent snakebite treatments highlights the urgent need to develop alternative therapeutics targeting relevant toxins. This development could provide promising discoveries to create novel recombinant solutions, leveraging human monoclonal antibodies, synthetic peptides and nanobodies. Such technologies as recombinant DNA, peptide and epitope mapping phage display etc) have the potential to exceed the traditional use of equine polyclonal antibodies, which have long been used in antivenom production. Recombinant antivenom can be engineered to target certain toxins that play a critical role in snakebite pathology. This approach has the potential to produce antivenom with improved efficacy and safety profiles. However, there are limitations and challenges associated with these emerging technologies. Therefore, identifying the limitations is critical for overcoming the associated challenges and optimizing the development of recombinant antivenoms. This review is aimed at presenting a thorough overview of diverse technologies used in the development of recombinant antivenom, emphasizing their limitations and offering insights into prospects for advancing recombinant antivenoms.
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Affiliation(s)
- Samuel Odo Uko
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University Sokoto, Nigeria
- Department of Biochemistry and Molecular Biology, Faculty of Chemical and Life Sciecnes, Usmanu Danfodiyo University Sokoto, Nigeria
| | - Ibrahim Malami
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University Sokoto, Nigeria
- Department of Pharmacognosy and Ethnopharmacy, Faculty of Pharmaceutical Sciences, Usmanu Danfodiyo University Sokoto, Nigeria
| | - Kasimu Ghandi Ibrahim
- Department of Basic Medical and Dental Sciences, Faculty of Dentistry, Zarqa University, P. O. Box 2000, Zarqa, 13110, Jordan
| | - Nafiu Lawal
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University Sokoto, Nigeria
- Department of Veterinary Microbiology, Faculty of Veterinary Medicine, Usmanu Danfodiyo University Sokoto, Nigeria
| | - Muhammad Bashir Bello
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University Sokoto, Nigeria
- Department of Veterinary Microbiology, Faculty of Veterinary Medicine, Usmanu Danfodiyo University Sokoto, Nigeria
- Vaccine Development Unit, Infectious Disease Research Department, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | - Murtala Bello Abubakar
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University Sokoto, Nigeria
- Department of Physiology, College of Health Sciences, Usmanu Danfodiyo University Sokoto, Nigeria
- Department of Physiology, College of Medicine and Health Sciences, Baze University, Abuja, Nigeria
| | - Mustapha Umar Imam
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University Sokoto, Nigeria
- Department of Medical Biochemistry, College of Health Sciences, Usmanu Danfodiyo University Sokoto, Nigeria
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2
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Cheng L, Deng Z, Tao H, Song W, Xing B, Liu W, Kong L, Yuan S, Ma Y, Wu Y, Huang X, Peng Y, Wong NK, Liu Y, Wang Y, Shen Y, Li J, Xiao M. Harnessing stepping-stone hosts to engineer, select, and reboot synthetic bacteriophages in one pot. CELL REPORTS METHODS 2022; 2:100217. [PMID: 35637913 PMCID: PMC9142689 DOI: 10.1016/j.crmeth.2022.100217] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 03/07/2022] [Accepted: 04/25/2022] [Indexed: 11/24/2022]
Abstract
Advances in synthetic genomics have led to a great demand for genetic manipulation. Trimming any process to simplify and accelerate streamlining of genetic code into life holds great promise for synthesizing and studying organisms. Here, we develop a simple but powerful stepping-stone strategy to promote genome refactoring of viruses in one pot, validated by successful cross-genus and cross-order rebooting of 90 phages infecting 4 orders of popular pathogens. Genomic sequencing suggests that rebooting outcome is associated with gene number and DNA polymerase availability within phage genomes. We integrate recombineering, screening, and rebooting processes in one pot and demonstrate genome assembly and genome editing of phages by stepping-stone hosts in an efficient and economic manner. Under this framework, in vitro assembly, yeast-based assembly, or genetic manipulation of native hosts are not required. As additional stepping-stone hosts are being developed, this framework will open doors for synthetic phages targeting more pathogens and commensals.
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Affiliation(s)
- Li Cheng
- BGI-Shenzhen, Shenzhen 518083, China
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China
| | - Ziqing Deng
- BGI-Shenzhen, Shenzhen 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China
- BGI-Beijing, Beijing 100101, China
| | - Haoran Tao
- BGI-Shenzhen, Shenzhen 518083, China
- University of the Chinese Academy of Sciences, Beijing 101408, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China
| | - Wenchen Song
- BGI-Shenzhen, Shenzhen 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China
| | - Bo Xing
- BGI-Shenzhen, Shenzhen 518083, China
- University of the Chinese Academy of Sciences, Beijing 101408, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China
| | - Wenfeng Liu
- BGI-Shenzhen, Shenzhen 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China
| | - Lingxin Kong
- BGI-Shenzhen, Shenzhen 518083, China
- University of the Chinese Academy of Sciences, Beijing 101408, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China
| | - Shengjian Yuan
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yingfei Ma
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yayun Wu
- Infection Control Center, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Xun Huang
- Infection Control Center, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Yun Peng
- Shenzhen Key Laboratory of Pathogen and Immunity, Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, State Key Discipline of Infectious Disease, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen Third People's Hospital, 518112 Shenzhen, China
| | - Nai-Kei Wong
- Shenzhen Key Laboratory of Pathogen and Immunity, Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, State Key Discipline of Infectious Disease, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen Third People's Hospital, 518112 Shenzhen, China
| | - Yingxia Liu
- Shenzhen Key Laboratory of Pathogen and Immunity, Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, State Key Discipline of Infectious Disease, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen Third People's Hospital, 518112 Shenzhen, China
| | - Yun Wang
- BGI-Shenzhen, Shenzhen 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
- Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Shenzhen 518120, China
| | - Yue Shen
- BGI-Shenzhen, Shenzhen 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
- Shenzhen Engineering Laboratory for Innovative Molecular Diagnostics, BGI-Shenzhen, Shenzhen 518120, China
| | - Junhua Li
- BGI-Shenzhen, Shenzhen 518083, China
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China
| | - Minfeng Xiao
- BGI-Shenzhen, Shenzhen 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China
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3
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Sun X, Li L, Pan L, Wang Z, Chen H, Shao C, Yu J, Ren Y, Wang X, Huang X, Zhang R, Li G. Infectious bronchitis virus: Identification of Gallus gallus APN high-affinity ligands with antiviral effects. Antiviral Res 2020; 186:104998. [PMID: 33340637 DOI: 10.1016/j.antiviral.2020.104998] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 12/12/2020] [Accepted: 12/14/2020] [Indexed: 12/12/2022]
Abstract
Infectious bronchitis virus (IBV) is a coronavirus, causes infectious bronchitis (IB) with high morbidity and mortality, and gives rise to huge economic losses for the poultry industry. Aminopeptidase N (APN) may be one of the IBV functional receptors. In this study, Gallus gallus APN (gAPN) protein was screened by phage-displayed 12-mer peptide library. Two high-affinity peptides H (HDYLYYTFTGNP) and T (TKFSPPSFWYLH) to gAPN protein were selected for in depth characterization of their anti-IBV effects. In vitro, indirect ELISA showed that these two high-affinity ligands could bind IBV S1 antibodies. Quantitative real-time PCR (qRT-PCR) assay, virus yield reduction assay and indirect immunofluorescence assay results revealed 3.125-50 μg/ml of peptide H and 6.25-50 μg/ml of peptide T reduced IBV proliferation in chicken embryo kidney cells (CEKs). In vivo, high-affinity phage-vaccinated chickens were able to induce specific IBV S1 antibodies and IBV neutralizing antibodies. QRT-PCR results confirmed that high-affinity phages reduced virus proliferation in chicken tracheas, lungs and kidneys, and alleviated IBV-induced lesions. By multiple sequence alignment, motif 'YxYY' and 'FxPPxxWxLH' of high-affinity peptides were identified in IBV S1-NTD, while another motif 'YxFxGN' located in S2. These results indicated that high affinity peptides of gAPN could present an alternative approach to IB prevention or treatment.
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Affiliation(s)
- Xiaoqi Sun
- College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Lanlan Li
- College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Long Pan
- College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Zheng Wang
- College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Huijie Chen
- College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Changhao Shao
- College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Jia Yu
- College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Yudong Ren
- College of Electrical and Information Technology, Northeast Agricultural University, Harbin, 150030, China
| | - Xiurong Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Science, Harbin, 150069, China
| | - Xiaodan Huang
- College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Ruili Zhang
- College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Guangxing Li
- College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin, 150030, China.
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4
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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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5
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Bansal R, Care A, Lord MS, Walsh TR, Sunna A. Experimental and theoretical tools to elucidate the binding mechanisms of solid-binding peptides. N Biotechnol 2019; 52:9-18. [PMID: 30954671 DOI: 10.1016/j.nbt.2019.04.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 03/31/2019] [Accepted: 04/01/2019] [Indexed: 12/19/2022]
Abstract
The interactions between biomolecules and solid surfaces play an important role in designing new materials and applications which mimic nature. Recently, solid-binding peptides (SBPs) have emerged as potential molecular building blocks in nanobiotechnology. SBPs exhibit high selectivity and binding affinity towards a wide range of inorganic and organic materials. Although these peptides have been widely used in various applications, there is a need to understand the interaction mechanism between the peptide and its material substrate, which is challenging both experimentally and theoretically. This review describes the main characterisation techniques currently available to study SBP-surface interactions and their contribution to gain a better insight for designing new peptides for tailored binding.
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Affiliation(s)
- Rachit Bansal
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia; ARC Centre of Excellence for Nanoscale Biophotonics, Macquarie University, Sydney, NSW 2109, Australia
| | - Andrew Care
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia; ARC Centre of Excellence for Nanoscale Biophotonics, Macquarie University, Sydney, NSW 2109, Australia
| | - Megan S Lord
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, NSW 2052, Australia
| | - Tiffany R Walsh
- Institute for Frontier Materials, Deakin University, Geelong, Victoria 3216, Australia
| | - Anwar Sunna
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia; ARC Centre of Excellence for Nanoscale Biophotonics, Macquarie University, Sydney, NSW 2109, Australia; Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, NSW 2109, Australia.
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6
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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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7
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He B, Tjhung KF, Bennett NJ, Chou Y, Rau A, Huang J, Derda R. Compositional Bias in Naïve and Chemically-modified Phage-Displayed Libraries uncovered by Paired-end Deep Sequencing. Sci Rep 2018; 8:1214. [PMID: 29352178 PMCID: PMC5775325 DOI: 10.1038/s41598-018-19439-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 01/02/2018] [Indexed: 01/09/2023] Open
Abstract
Understanding the composition of a genetically-encoded (GE) library is instrumental to the success of ligand discovery. In this manuscript, we investigate the bias in GE-libraries of linear, macrocyclic and chemically post-translationally modified (cPTM) tetrapeptides displayed on the M13KE platform, which are produced via trinucleotide cassette synthesis (19 codons) and NNK-randomized codon. Differential enrichment of synthetic DNA {S}, ligated vector {L} (extension and ligation of synthetic DNA into the vector), naïve libraries {N} (transformation of the ligated vector into the bacteria followed by expression of the library for 4.5 hours to yield a "naïve" library), and libraries chemically modified by aldehyde ligation and cysteine macrocyclization {M} characterized by paired-end deep sequencing, detected a significant drop in diversity in {L} → {N}, but only a minor compositional difference in {S} → {L} and {N} → {M}. Libraries expressed at the N-terminus of phage protein pIII censored positively charged amino acids Arg and Lys; libraries expressed between pIII domains N1 and N2 overcame Arg/Lys-censorship but introduced new bias towards Gly and Ser. Interrogation of biases arising from cPTM by aldehyde ligation and cysteine macrocyclization unveiled censorship of sequences with Ser/Phe. Analogous analysis can be used to explore library diversity in new display platforms and optimize cPTM of these libraries.
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Affiliation(s)
- Bifang He
- Department of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, AB T6G 2G2, Canada
- Key Laboratory for NeuroInformation of Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Katrina F Tjhung
- Department of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, AB T6G 2G2, Canada
- The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA, 92037, USA
- The Salk Institute, 10010 N. Torrey Pines Rd., La Jolla, CA, 92037, USA
| | - Nicholas J Bennett
- Department of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Ying Chou
- Department of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Andrea Rau
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Jian Huang
- Key Laboratory for NeuroInformation of Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China
- Center for Information in Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Ratmir Derda
- Department of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, AB T6G 2G2, Canada.
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8
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Zade HM, Keshavarz R, Shekarabi HSZ, Bakhshinejad B. Biased selection of propagation-related TUPs from phage display peptide libraries. Amino Acids 2017; 49:1293-1308. [DOI: 10.1007/s00726-017-2452-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 06/09/2017] [Indexed: 10/19/2022]
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9
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Care A, Bergquist PL, Sunna A. Solid-Binding Peptides in Biomedicine. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1030:21-36. [PMID: 29081048 DOI: 10.1007/978-3-319-66095-0_2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Some peptides are able to bind to inorganic materials such as silica and gold. Over the past decade, Solid-binding peptides (SBPs) have been used increasingly as molecular building blocks in nanobiotechnology. These peptides show selectivity and bind with high affinity to a diverse range of inorganic surfaces e.g. metals, metal oxides, metal compounds, magnetic materials, semiconductors, carbon materials, polymers and minerals. They can be used in applications such as protein purification and synthesis, assembly and the functionalization of nanomaterials. They offer simple and versatile bioconjugation methods that can increase biocompatibility and also direct the immobilization and orientation of nanoscale entities onto solid supports without impeding their functionality. SBPs have been employed in numerous nanobiotechnological applications such as the controlled synthesis of nanomaterials and nanostructures, formation of hybrid biomaterials, immobilization of functional proteins and improved nanomaterial biocompatibility. With advances in nanotechnology, a multitude of novel nanomaterials have been designed and synthesized for diagnostic and therapeutic applications. New approaches have been developed recently to exert a greater control over bioconjugation and eventually, over the optimal and functional display of biomolecules on the surfaces of many types of solid materials. In this chapter we describe SBPs and highlight some selected examples of their potential applications in biomedicine.
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Affiliation(s)
- Andrew Care
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Peter L Bergquist
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), Macquarie University, North Ryde, NSW, Australia.,Biomolecular Discovery and Design Research Centre, Macquarie University, North Ryde, NSW, Australia.,Department of Molecular Medicine & Pathology, Medical School, University of Auckland, Auckland, New Zealand
| | - Anwar Sunna
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), Macquarie University, North Ryde, NSW, Australia. .,Department of Molecular Medicine & Pathology, Medical School, University of Auckland, Auckland, New Zealand.
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10
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Laustsen AH, Lauridsen LP, Lomonte B, Andersen MR, Lohse B. Pitfalls to avoid when using phage display for snake toxins. Toxicon 2016; 126:79-89. [PMID: 28017694 DOI: 10.1016/j.toxicon.2016.12.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 12/12/2016] [Accepted: 12/21/2016] [Indexed: 10/20/2022]
Abstract
Antivenoms against bites and stings from snakes, spiders, and scorpions are associated with immunological side effects and high cost of production, since these therapies are still derived from the serum of hyper-immunized production animals. Biotechnological innovations within envenoming therapies are thus warranted, and phage display technology may be a promising avenue for bringing antivenoms into the modern era of biologics. Although phage display technology represents a robust and high-throughput approach for the discovery of antibody-based antitoxins, several pitfalls may present themselves when animal toxins are used as targets for phage display selection. Here, we report selected critical challenges from our own phage display experiments associated with biotinylation of antigens, clone picking, and the presence of amber codons within antibody fragment structures in some phage display libraries. These challenges may be detrimental to the outcome of phage display experiments, and we aim to help other researchers avoiding these pitfalls by presenting their solutions.
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Affiliation(s)
- Andreas Hougaard Laustsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Denmark; Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Line Præst Lauridsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Denmark
| | - Bruno Lomonte
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | | | - Brian Lohse
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark.
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11
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Hsiao YH, Huang CY, Hu CY, Wu YY, Wu CH, Hsu CH, Chen C. Continuous microfluidic assortment of interactive ligands (CMAIL). Sci Rep 2016; 6:32454. [PMID: 27578501 PMCID: PMC5006012 DOI: 10.1038/srep32454] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 08/09/2016] [Indexed: 01/15/2023] Open
Abstract
Finding an interactive ligand-receptor pair is crucial to many applications, including the development of monoclonal antibodies. Biopanning, a commonly used technique for affinity screening, involves a series of washing steps and is lengthy and tedious. Here we present an approach termed continuous microfluidic assortment of interactive ligands, or CMAIL, for the screening and sorting of antigen-binding single-chain variable antibody fragments (scFv) displayed on bacteriophages (phages). Phages carrying native negative charges on their coat proteins were electrophoresed through a hydrogel matrix functionalized with target antigens under two alternating orthogonal electric fields. During the weak horizontal electric field phase, phages were differentially swept laterally depending on their affinity for the antigen, and all phages were electrophoresed down to be collected during the strong vertical electric field phase. Phages of different affinity were spatially separated, allowing the continuous operation. More than 105 CFU (colony forming unit) antigen-interacting phages were isolated with ~100% specificity from a phage library containing 3 × 109 individual members within 40 minutes of sorting using CMAIL. CMAIL is rapid, sensitive, specific, and does not employ washing, elution or magnetic beads. In conclusion, we have developed an efficient and cost-effective method for isolating and sorting affinity reagents involving phage display.
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Affiliation(s)
- Yi-Hsing Hsiao
- Institute of Nanoengineering and Microsystems, National Tsing Hua University, Hsinchu 30013, Taiwan.,Institute of Biomedical Engineering and Nanomedicine, National Health Research Institutes, Miaoli 35053, Taiwan
| | - Chao-Yang Huang
- Development Center for Biotechnology, New Taipei City 22180, Taiwan
| | - Chih-Yung Hu
- Development Center for Biotechnology, New Taipei City 22180, Taiwan
| | - Yen-Yu Wu
- Development Center for Biotechnology, New Taipei City 22180, Taiwan
| | - Chung-Hsiun Wu
- Development Center for Biotechnology, New Taipei City 22180, Taiwan
| | - Chia-Hsien Hsu
- Institute of Nanoengineering and Microsystems, National Tsing Hua University, Hsinchu 30013, Taiwan.,Institute of Biomedical Engineering and Nanomedicine, National Health Research Institutes, Miaoli 35053, Taiwan
| | - Chihchen Chen
- Institute of Nanoengineering and Microsystems, National Tsing Hua University, Hsinchu 30013, Taiwan.,Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
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12
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Silva VL, Ferreira D, Nobrega FL, Martins IM, Kluskens LD, Rodrigues LR. Selection of Novel Peptides Homing the 4T1 CELL Line: Exploring Alternative Targets for Triple Negative Breast Cancer. PLoS One 2016; 11:e0161290. [PMID: 27548261 PMCID: PMC4993384 DOI: 10.1371/journal.pone.0161290] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 06/27/2016] [Indexed: 11/30/2022] Open
Abstract
The use of bacteriophages to select novel ligands has been widely explored for cancer therapy. Their application is most warranted in cancer subtypes lacking knowledge on how to target the cancer cells in question, such as the triple negative breast cancer, eventually leading to the development of alternative nanomedicines for cancer therapeutics. Therefore, the following study aimed to select and characterize novel peptides for a triple negative breast cancer murine mammary carcinoma cell line– 4T1. Using phage display, 7 and 12 amino acid random peptide libraries were screened against the 4T1 cell line. A total of four rounds, plus a counter-selection round using the 3T3 murine fibroblast cell line, was performed. The enriched selective peptides were characterized and their binding capacity towards 4T1 tissue samples was confirmed by immunofluorescence and flow cytometry analysis. The selected peptides (4T1pep1 –CPTASNTSC and 4T1pep2—EVQSSKFPAHVS) were enriched over few rounds of selection and exhibited specific binding to the 4T1 cell line. Interestingly, affinity to the human MDA-MB-231 cell line was also observed for both peptides, promoting the translational application of these novel ligands between species. Additionally, bioinformatics analysis suggested that both peptides target human Mucin-16. This protein has been implicated in different types of cancer, as it is involved in many important cellular functions. This study strongly supports the need of finding alternative targeting systems for TNBC and the peptides herein selected exhibit promising future application as novel homing peptides for breast cancer therapy.
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Affiliation(s)
- Vera L. Silva
- CEB—Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, Braga, Portugal
| | - Debora Ferreira
- CEB—Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, Braga, Portugal
| | - Franklin L. Nobrega
- CEB—Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, Braga, Portugal
| | - Ivone M. Martins
- CEB—Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, Braga, Portugal
| | - Leon D. Kluskens
- CEB—Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, Braga, Portugal
| | - Ligia R. Rodrigues
- CEB—Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, Braga, Portugal
- * E-mail:
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13
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Solid-binding peptides: smart tools for nanobiotechnology. Trends Biotechnol 2015; 33:259-68. [PMID: 25796487 DOI: 10.1016/j.tibtech.2015.02.005] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 02/15/2015] [Accepted: 02/23/2015] [Indexed: 12/12/2022]
Abstract
Over the past decade, solid-binding peptides (SBPs) have been used increasingly as molecular building blocks in nanobiotechnology. These peptides show selectivity and bind with high affinity to the surfaces of a diverse range of solid materials including metals, metal oxides, metal compounds, magnetic materials, semiconductors, carbon materials, polymers, and minerals. They can direct the assembly and functionalisation of materials, and have the ability to mediate the synthesis and construction of nanoparticles and complex nanostructures. As the availability of newly synthesised nanomaterials expands rapidly, so too do the potential applications for SBPs.
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