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Muslihati A, Septiani NLW, Gumilar G, Nugraha N, Wasisto HS, Yuliarto B. Peptide-Based Flavivirus Biosensors: From Cell Structure to Virological and Serological Detection Methods. ACS Biomater Sci Eng 2024; 10:2041-2061. [PMID: 38526408 DOI: 10.1021/acsbiomaterials.3c01965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
In tropical and developing countries, mosquito-borne diseases by flaviviruses pose a serious threat to public health. Early detection is critical for preventing their spread, but conventional methods are time-consuming and require skilled technicians. Biosensors have been developed to address this issue, but cross-reactivity with other flaviviruses remains a challenge. Peptides are essentially biomaterials used in diagnostics that allow virological and serological techniques to identify flavivirus selectively. This biomaterial originated as a small protein consisting of two to 50 amino acid chains. They offer flexibility in chemical modification and can be easily synthesized and applied to living cells in the engineering process. Peptides could potentially be developed as robust, low-cost, sensitive, and selective receptors for detecting flaviviruses. However, modification and selection of the receptor agents are crucial to determine the effectiveness of binding between the targets and the receptors. This paper addresses two potential peptide nucleic acids (PNAs) and affinity peptides that can detect flavivirus from another target-based biosensor as well as the potential peptide behaviors of flaviviruses. The PNAs detect flaviviruses based on the nucleotide base sequence of the target's virological profile via Watson-Crick base pairing, while the affinity peptides sense the epitope or immunological profile of the targets. Recent developments in the functionalization of peptides for flavivirus biosensors are explored in this Review by division into electrochemical, optical, and other detection methods.
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Affiliation(s)
- Atqiya Muslihati
- Doctoral Program of Engineering Physics, Faculty of Industrial Technology, Institut Teknologi Bandung, Ganesha 10, Bandung 40132, Indonesia
- Advanced Functional Material Laboratory, Faculty of Industrial Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung 41032, Indonesia
- PT Biostark Analitika Inovasi, Bandung 40375, Indonesia
| | - Ni Luh Wulan Septiani
- Advanced Functional Material Laboratory, Faculty of Industrial Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung 41032, Indonesia
- Research Center for Nanotechnology Systems, National Research and Innovation Agency (BRIN), Kawasan Puspiptek, South Tangerang 15134, Indonesia
| | - Gilang Gumilar
- Research Center for Electronics, National Research and Innovation Agency (BRIN), Bandung 40135, Indonesia
| | - Nugraha Nugraha
- Advanced Functional Material Laboratory, Faculty of Industrial Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung 41032, Indonesia
- Research Center for Nanosciences and Nanotechnology (RCNN), Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung 41032, Indonesia
| | | | - Brian Yuliarto
- Advanced Functional Material Laboratory, Faculty of Industrial Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung 41032, Indonesia
- Research Center for Nanosciences and Nanotechnology (RCNN), Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung 41032, Indonesia
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2
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Functional Peptides from One-bead One-compound High-throughput Screening Technique. Chem Res Chin Univ 2023. [DOI: 10.1007/s40242-023-2356-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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3
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Puumala LS, Grist SM, Morales JM, Bickford JR, Chrostowski L, Shekhar S, Cheung KC. Biofunctionalization of Multiplexed Silicon Photonic Biosensors. BIOSENSORS 2022; 13:bios13010053. [PMID: 36671887 PMCID: PMC9855810 DOI: 10.3390/bios13010053] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/10/2022] [Accepted: 12/23/2022] [Indexed: 05/28/2023]
Abstract
Silicon photonic (SiP) sensors offer a promising platform for robust and low-cost decentralized diagnostics due to their high scalability, low limit of detection, and ability to integrate multiple sensors for multiplexed analyte detection. Their CMOS-compatible fabrication enables chip-scale miniaturization, high scalability, and low-cost mass production. Sensitive, specific detection with silicon photonic sensors is afforded through biofunctionalization of the sensor surface; consequently, this functionalization chemistry is inextricably linked to sensor performance. In this review, we first highlight the biofunctionalization needs for SiP biosensors, including sensitivity, specificity, cost, shelf-stability, and replicability and establish a set of performance criteria. We then benchmark biofunctionalization strategies for SiP biosensors against these criteria, organizing the review around three key aspects: bioreceptor selection, immobilization strategies, and patterning techniques. First, we evaluate bioreceptors, including antibodies, aptamers, nucleic acid probes, molecularly imprinted polymers, peptides, glycans, and lectins. We then compare adsorption, bioaffinity, and covalent chemistries for immobilizing bioreceptors on SiP surfaces. Finally, we compare biopatterning techniques for spatially controlling and multiplexing the biofunctionalization of SiP sensors, including microcontact printing, pin- and pipette-based spotting, microfluidic patterning in channels, inkjet printing, and microfluidic probes.
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Affiliation(s)
- Lauren S. Puumala
- School of Biomedical Engineering, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
- Centre for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Samantha M. Grist
- School of Biomedical Engineering, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
- Centre for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
- Dream Photonics Inc., Vancouver, BC V6T 0A7, Canada
| | - Jennifer M. Morales
- Army Research Laboratory, US Army Combat Capabilities Development Command, 2800 Powder Mill Rd., Adelphi, MD 20783, USA
| | - Justin R. Bickford
- Army Research Laboratory, US Army Combat Capabilities Development Command, 2800 Powder Mill Rd., Adelphi, MD 20783, USA
| | - Lukas Chrostowski
- Dream Photonics Inc., Vancouver, BC V6T 0A7, Canada
- Department of Electrical and Computer Engineering, University of British Columbia, 2332 Main Mall, Vancouver, BC V6T 1Z4, Canada
- Stewart Blusson Quantum Matter Institute, University of British Columbia, 2355 East Mall, Vancouver, BC V6T 1Z4, Canada
| | - Sudip Shekhar
- Dream Photonics Inc., Vancouver, BC V6T 0A7, Canada
- Department of Electrical and Computer Engineering, University of British Columbia, 2332 Main Mall, Vancouver, BC V6T 1Z4, Canada
| | - Karen C. Cheung
- School of Biomedical Engineering, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
- Centre for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
- Department of Electrical and Computer Engineering, University of British Columbia, 2332 Main Mall, Vancouver, BC V6T 1Z4, Canada
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4
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Layouni R, Cao T, Coppock MB, Laibinis PE, Weiss SM. Peptide-Based Capture of Chikungunya Virus E2 Protein Using Porous Silicon Biosensor. SENSORS (BASEL, SWITZERLAND) 2021; 21:8248. [PMID: 34960341 PMCID: PMC8708774 DOI: 10.3390/s21248248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/02/2021] [Accepted: 12/08/2021] [Indexed: 12/04/2022]
Abstract
The detection of pathogens presents specific challenges in ensuring that biosensors remain operable despite exposure to elevated temperatures or other extreme conditions. The most vulnerable component of a biosensor is typically the bioreceptor. Accordingly, the robustness of peptides as bioreceptors offers improved stability and reliability toward harsh environments compared to monoclonal antibodies that may lose their ability to bind target molecules after such exposures. Here, we demonstrate peptide-based capture of the Chikungunya virus E2 protein in a porous silicon microcavity biosensor at room temperature and after exposure of the peptide-functionalized biosensor to high temperature. Contact angle measurements, attenuated total reflectance-Fourier transform infrared spectra, and optical reflectance measurements confirm peptide functionalization and selective E2 protein capture. This work opens the door for other pathogenic biomarker detection using peptide-based capture agents on porous silicon and other surface-based sensor platforms.
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Affiliation(s)
- Rabeb Layouni
- Department of Chemical & Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235, USA; (R.L.); (P.E.L.)
| | - Tengfei Cao
- Interdisciplinary Material Science Program, Vanderbilt University, Nashville, TN 37235, USA;
| | - Matthew B. Coppock
- Human Research and Engineering Directorate, DEVCOM Army Research Laboratory, Adelphi, MD 20783, USA;
| | - Paul E. Laibinis
- Department of Chemical & Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235, USA; (R.L.); (P.E.L.)
- Interdisciplinary Material Science Program, Vanderbilt University, Nashville, TN 37235, USA;
| | - Sharon M. Weiss
- Interdisciplinary Material Science Program, Vanderbilt University, Nashville, TN 37235, USA;
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN 37235, USA
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Ye X, Gaucher JF, Vidal M, Broussy S. A Structural Overview of Vascular Endothelial Growth Factors Pharmacological Ligands: From Macromolecules to Designed Peptidomimetics. Molecules 2021; 26:6759. [PMID: 34833851 PMCID: PMC8625919 DOI: 10.3390/molecules26226759] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/02/2021] [Accepted: 11/03/2021] [Indexed: 12/27/2022] Open
Abstract
The vascular endothelial growth factor (VEGF) family of cytokines plays a key role in vasculogenesis, angiogenesis, and lymphangiogenesis. VEGF-A is the main member of this family, alongside placental growth factor (PlGF), VEGF-B/C/D in mammals, and VEGF-E/F in other organisms. To study the activities of these growth factors under physiological and pathological conditions, resulting in therapeutic applications in cancer and age-related macular degeneration, blocking ligands have been developed. These have mostly been large biomolecules like antibodies. Ligands with high affinities, at least in the nanomolar range, and accurate structural data from X-ray crystallography and NMR spectroscopy have been described. They constitute the main focus of this overview, which evidences similarities and differences in their binding modes. For VEGF-A ligands, and to a limited extent also for PlGF, a transition is now observed towards developing smaller ligands like nanobodies and peptides. These include unnatural amino acids and chemical modifications for designed and improved properties, such as serum stability and greater affinity. However, this review also highlights the scarcity of such small molecular entities and the striking lack of small organic molecule ligands. It also shows the gap between the rather large array of ligands targeting VEGF-A and the general absence of ligands binding other VEGF members, besides some antibodies. Future developments in these directions are expected in the upcoming years, and the study of these growth factors and their promising therapeutic applications will be welcomed.
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Affiliation(s)
- Xiaoqing Ye
- Faculté de Pharmacie de Paris, Université de Paris, CiTCoM, 8038 CNRS, U 1268 INSERM, 75006 Paris, France; (X.Y.); (M.V.)
| | - Jean-François Gaucher
- Laboratoire de Cristallographie et RMN Biologiques, Faculté de Pharmacie de Paris, Université de Paris, CiTCoM, 8038 CNRS, 75006 Paris, France;
| | - Michel Vidal
- Faculté de Pharmacie de Paris, Université de Paris, CiTCoM, 8038 CNRS, U 1268 INSERM, 75006 Paris, France; (X.Y.); (M.V.)
- Service Biologie du Médicament, Toxicologie, AP-HP, Hôpital Cochin, 75014 Paris, France
| | - Sylvain Broussy
- Faculté de Pharmacie de Paris, Université de Paris, CiTCoM, 8038 CNRS, U 1268 INSERM, 75006 Paris, France; (X.Y.); (M.V.)
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6
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Protein Catalyzed Capture (PCC) Agents for Antigen Targeting. Methods Mol Biol 2021. [PMID: 34596849 DOI: 10.1007/978-1-0716-1689-5_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The protein catalyzed capture agent (PCC) method is a powerful combinatorial screening strategy for discovering synthetic macrocyclic peptide ligands, called PCCs, to designated protein epitopes. The foundational concept of the PCC method is the use of in situ click chemistry to survey large combinatorial libraries of peptides for ligands to designated biological targets. State-of-the-art PCC screens integrate synthetic libraries of constrained macrocyclic peptides with epitope-specific targeting strategies to identify high-affinity (<100 nM) binders de novo. Automated instrumentation can accelerate PCC discovery to a rapid 2-week timeframe. Here, we describe methods to perform combinatorial screens that yield epitope-targeted PCCs.
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7
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Narayanam MK, Lai BT, Loredo JM, Wilson JA, Eliasen AM, LaBerge NA, Nason M, Cantu AL, Luton BK, Xu S, Agnew HD, Murphy JM. Positron Emission Tomography Tracer Design of Targeted Synthetic Peptides via 18F-Sydnone Alkyne Cycloaddition. Bioconjug Chem 2021; 32:2073-2082. [PMID: 34415731 DOI: 10.1021/acs.bioconjchem.1c00379] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Chemically synthesized, small peptides that bind with high affinity and specificity to CD8-expressing (CD8+) tumor-infiltrating T cells, yet retain the desirable characteristics of small molecules, hold valuable potential for diagnostic molecular imaging of immune response. Here, we report the development of 18F-labeled peptides targeting human CD8α with nanomolar affinity via the strain-promoted sydnone-alkyne cycloaddition with 4-[18F]fluorophenyl sydnone. The 18F-sydnone is produced in one step, in high radiochemical yield, and the peptide labeling proceeds rapidly. A hydrophilic chemical linker results in a tracer with favorable pharmacokinetic properties and improved image contrast, as demonstrated by in vivo PET imaging studies.
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Affiliation(s)
- Maruthi Kumar Narayanam
- Department of Molecular and Medical Pharmacology and Crump Institute for Molecular Imaging, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Bert T Lai
- Indi Molecular, Inc., 6162 Bristol Parkway, Culver City, California 90230, United States
| | - Jacquie Malette Loredo
- Indi Molecular, Inc., 6162 Bristol Parkway, Culver City, California 90230, United States
| | - Jeré A Wilson
- Indi Molecular, Inc., 6162 Bristol Parkway, Culver City, California 90230, United States
| | - Anders M Eliasen
- Indi Molecular, Inc., 6162 Bristol Parkway, Culver City, California 90230, United States
| | - Nicole A LaBerge
- Indi Molecular, Inc., 6162 Bristol Parkway, Culver City, California 90230, United States
| | - Malley Nason
- Indi Molecular, Inc., 6162 Bristol Parkway, Culver City, California 90230, United States
| | - Annabelle L Cantu
- Indi Molecular, Inc., 6162 Bristol Parkway, Culver City, California 90230, United States
| | - Breanna K Luton
- Indi Molecular, Inc., 6162 Bristol Parkway, Culver City, California 90230, United States
| | - Shili Xu
- Department of Molecular and Medical Pharmacology and Crump Institute for Molecular Imaging, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Heather D Agnew
- Indi Molecular, Inc., 6162 Bristol Parkway, Culver City, California 90230, United States
| | - Jennifer M Murphy
- Department of Molecular and Medical Pharmacology and Crump Institute for Molecular Imaging, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, United States
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8
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Peptide Inhibitors of Vascular Endothelial Growth Factor A: Current Situation and Perspectives. Pharmaceutics 2021; 13:pharmaceutics13091337. [PMID: 34575413 PMCID: PMC8467741 DOI: 10.3390/pharmaceutics13091337] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/18/2021] [Accepted: 08/24/2021] [Indexed: 12/11/2022] Open
Abstract
Vascular endothelial growth factors (VEGFs) are the family of extracellular signaling proteins involved in the processes of angiogenesis. VEGFA overexpression and altered regulation of VEGFA signaling pathways lead to pathological angiogenesis, which contributes to the progression of various diseases, such as age-related macular degeneration and cancer. Monoclonal antibodies and decoy receptors have been extensively used in the anti-angiogenic therapies for the neutralization of VEGFA. However, multiple side effects, solubility and aggregation issues, and the involvement of compensatory VEGFA-independent pro-angiogenic mechanisms limit the use of the existing VEGFA inhibitors. Short chemically synthesized VEGFA binding peptides are a promising alternative to these full-length proteins. In this review, we summarize anti-VEGFA peptides identified so far and discuss the molecular basis of their inhibitory activity to highlight their pharmacological potential as anti-angiogenic drugs.
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9
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Agnew HD, Coppock MB, Idso MN, Lai BT, Liang J, McCarthy-Torrens AM, Warren CM, Heath JR. Protein-Catalyzed Capture Agents. Chem Rev 2019; 119:9950-9970. [PMID: 30838853 DOI: 10.1021/acs.chemrev.8b00660] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Protein-catalyzed capture agents (PCCs) are synthetic and modular peptide-based affinity agents that are developed through the use of single-generation in situ click chemistry screens against large peptide libraries. In such screens, the target protein, or a synthetic epitope fragment of that protein, provides a template for selectively promoting the noncopper catalyzed azide-alkyne dipolar cycloaddition click reaction between either a library peptide and a known ligand or a library peptide and the synthetic epitope. The development of epitope-targeted PCCs was motivated by the desire to fully generalize pioneering work from the Sharpless and Finn groups in which in situ click screens were used to develop potent, divalent enzymatic inhibitors. In fact, a large degree of generality has now been achieved. Various PCCs have demonstrated utility for selective protein detection, as allosteric or direct inhibitors, as modulators of protein folding, and as tools for in vivo tumor imaging. We provide a historical context for PCCs and place them within the broader scope of biological and synthetic aptamers. The development of PCCs is presented as (i) Generation I PCCs, which are branched ligands engineered through an iterative, nonepitope-targeted process, and (ii) Generation II PCCs, which are typically developed from macrocyclic peptide libraries and are precisely epitope-targeted. We provide statistical comparisons of Generation II PCCs relative to monoclonal antibodies in which the protein target is the same. Finally, we discuss current challenges and future opportunities of PCCs.
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Affiliation(s)
- Heather D Agnew
- Indi Molecular, Inc. , 6162 Bristol Parkway , Culver City , California 90230 , United States
| | - Matthew B Coppock
- Sensors and Electron Devices Directorate , U.S. Army Research Laboratory , Adelphi , Maryland 20783 , United States
| | - Matthew N Idso
- Institute for Systems Biology , 401 Terry Avenue North , Seattle , Washington 98109-5234 , United States
| | - Bert T Lai
- Indi Molecular, Inc. , 6162 Bristol Parkway , Culver City , California 90230 , United States
| | - JingXin Liang
- Institute for Systems Biology , 401 Terry Avenue North , Seattle , Washington 98109-5234 , United States
| | - Amy M McCarthy-Torrens
- Institute for Systems Biology , 401 Terry Avenue North , Seattle , Washington 98109-5234 , United States
| | - Carmen M Warren
- Indi Molecular, Inc. , 6162 Bristol Parkway , Culver City , California 90230 , United States
| | - James R Heath
- Institute for Systems Biology , 401 Terry Avenue North , Seattle , Washington 98109-5234 , United States
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10
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Mertz L. On the Cusp of a Healthcare Revolution: BME Technologies Have the Potential to ?Transform Our World? IEEE Pulse 2018; 9:4-7. [PMID: 29373848 DOI: 10.1109/mpul.2017.2772684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Of the key technologies listed as "ready to propel industries and transform our world" in the 2017 report Top 50 Emerging Technologies: Growth Opportunities of Strategic Imperative, most fall under the scope of biomedical engineering (BME). Issued by the major market research and analysis company Frost and Sullivan [1], the report's findings are no surprise to the researchers, clinicians, and others who are heavily invested in this field.
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11
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Sarkes DA, Jahnke JP, Stratis-Cullum DN. Semi-automated Biopanning of Bacterial Display Libraries for Peptide Affinity Reagent Discovery and Analysis of Resulting Isolates. J Vis Exp 2017. [PMID: 29286465 PMCID: PMC5755526 DOI: 10.3791/56061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Biopanning bacterial display libraries is a proven technique for peptide affinity reagent discovery for recognition of both biotic and abiotic targets. Peptide affinity reagents can be used for similar applications to antibodies, including sensing and therapeutics, but are more robust and able to perform in more extreme environments. Specific enrichment of peptide capture agents to a protein target of interest is enhanced using semi-automated sorting methods which improve binding and wash steps and therefore decrease the occurrence of false positive binders. A semi-automated sorting method is described herein for use with a commercial automated magnetic-activated cell sorting device with an unconstrained bacterial display sorting library expressing random 15-mer peptides. With slight modifications, these methods are extendable to other automated devices, other sorting libraries, and other organisms. A primary goal of this work is to provide a comprehensive methodology and expound the thought process applied in analyzing and minimizing the resulting pool of candidates. These techniques include analysis of on-cell binding using fluorescence-activated cell sorting (FACS), to assess affinity and specificity during sorting and in comparing individual candidates, and the analysis of peptide sequences to identify trends and consensus sequences for understanding and potentially improving the affinity to and specificity for the target of interest.
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Affiliation(s)
- Deborah A Sarkes
- Sensors and Electron Devices Directorate, US Army Research Laboratory;
| | - Justin P Jahnke
- Sensors and Electron Devices Directorate, US Army Research Laboratory
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12
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Xiong Y, Ford NR, Hecht KA, Roesijadi G, Squier TC. Hydrogel Tethering Enhances Interdomain Stabilization of Single-Chain Antibodies. Bioconjug Chem 2017; 28:2804-2814. [DOI: 10.1021/acs.bioconjchem.7b00512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yijia Xiong
- Department
of Basic Medical Sciences, Western University of Health Sciences, Lebanon, Oregon 97355, United States
| | - Nicole R. Ford
- Marine
Biotechnology, Pacific Northwest National Laboratory, Sequim, Washington 98382, United States
| | - Karen A. Hecht
- Marine
Biotechnology, Pacific Northwest National Laboratory, Sequim, Washington 98382, United States
| | - Guritno Roesijadi
- Marine
Biotechnology, Pacific Northwest National Laboratory, Sequim, Washington 98382, United States
- Department
of Microbiology, Oregon State University, Corvallis, Oregon 97331, United States
| | - Thomas C. Squier
- Department
of Basic Medical Sciences, Western University of Health Sciences, Lebanon, Oregon 97355, United States
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13
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Coppock MB, Warner CR, Dorsey B, Orlicki JA, Sarkes DA, Lai BT, Pitram SM, Rohde RD, Malette J, Wilson JA, Kearney P, Fang KC, Law SM, Candelario SL, Farrow B, Finch AS, Agnew HD, Heath JR, Stratis‐Cullum DN. Protein catalyzed capture agents with tailored performance for in vitro and in vivo applications. Biopolymers 2017; 108:e22934. [PMID: 27539157 PMCID: PMC6585716 DOI: 10.1002/bip.22934] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 07/25/2016] [Accepted: 08/17/2016] [Indexed: 12/12/2022]
Abstract
We report on peptide-based ligands matured through the protein catalyzed capture (PCC) agent method to tailor molecular binders for in vitro sensing/diagnostics and in vivo pharmacokinetics parameters. A vascular endothelial growth factor (VEGF) binding peptide and a peptide against the protective antigen (PA) protein of Bacillus anthracis discovered through phage and bacterial display panning technologies, respectively, were modified with click handles and subjected to iterative in situ click chemistry screens using synthetic peptide libraries. Each azide-alkyne cycloaddition iteration, promoted by the respective target proteins, yielded improvements in metrics for the application of interest. The anti-VEGF PCC was explored as a stable in vivo imaging probe. It exhibited excellent stability against proteases and a mean elimination in vivo half-life (T1/2 ) of 36 min. Intraperitoneal injection of the reagent results in slow clearance from the peritoneal cavity and kidney retention at extended times, while intravenous injection translates to rapid renal clearance. The ligand competed with the commercial antibody for binding to VEGF in vivo. The anti-PA ligand was developed for detection assays that perform in demanding physical environments. The matured anti-PA PCC exhibited no solution aggregation, no fragmentation when heated to 100°C, and > 81% binding activity for PA after heating at 90°C for 1 h. We discuss the potential of the PCC agent screening process for the discovery and enrichment of next generation antibody alternatives.
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Affiliation(s)
- Matthew B. Coppock
- Sensors and Electron Devices DirectorateU.S. Army Research LaboratoryAdelphiMD20783
| | - Candice R. Warner
- Excet, SpringfieldVA 22151 supporting USA Edgewood Chemical Biological CenterAberdeen Proving GroundMD21010
| | - Brandi Dorsey
- Federal Staffing Resources, Annapolis, MD supporting U.S. Army Research LaboratoryAdelphiMD20783
| | - Joshua A. Orlicki
- Weapons and Materials Research DirectorateU.S. Army Research LaboratoryAberdeen Proving GroundMD21005
| | - Deborah A. Sarkes
- Sensors and Electron Devices DirectorateU.S. Army Research LaboratoryAdelphiMD20783
| | - Bert T. Lai
- Indi Molecular6162 Bristol ParkwayCulver CityCA90230
| | | | | | | | | | | | | | | | | | - Blake Farrow
- Division of Chemistry and Chemical EngineeringCalifornia Institute of Technology1200 East California BoulevardPasadenaCA91125
| | - Amethist S. Finch
- Sensors and Electron Devices DirectorateU.S. Army Research LaboratoryAdelphiMD20783
| | | | - James R. Heath
- Division of Chemistry and Chemical EngineeringCalifornia Institute of Technology1200 East California BoulevardPasadenaCA91125
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14
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Sarkes DA, Hurley MM, Stratis-Cullum DN. Unraveling the Roots of Selectivity of Peptide Affinity Reagents for Structurally Similar Ribosomal Inactivating Protein Derivatives. Molecules 2016; 21:E1504. [PMID: 27834872 PMCID: PMC6272918 DOI: 10.3390/molecules21111504] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 11/02/2016] [Accepted: 11/04/2016] [Indexed: 11/17/2022] Open
Abstract
Peptide capture agents have become increasingly useful tools for a variety of sensing applications due to their ease of discovery, stability, and robustness. Despite the ability to rapidly discover candidates through biopanning bacterial display libraries and easily mature them to Protein Catalyzed Capture (PCC) agents with even higher affinity and selectivity, an ongoing challenge and critical selection criteria is that the peptide candidates and final reagent be selective enough to replace antibodies, the gold-standard across immunoassay platforms. Here, we have discovered peptide affinity reagents against abrax, a derivative of abrin with reduced toxicity. Using on-cell Fluorescence Activated Cell Sorting (FACS) assays, we show that the peptides are highly selective for abrax over RiVax, a similar derivative of ricin originally designed as a vaccine, with significant structural homology to abrax. We rank the newly discovered peptides for strongest affinity and analyze three observed consensus sequences with varying affinity and specificity. The strongest (Tier 1) consensus was FWDTWF, which is highly aromatic and hydrophobic. To better understand the observed selectivity, we use the XPairIt peptide-protein docking protocol to analyze binding location predictions of the individual Tier 1 peptides and consensus on abrax and RiVax. The binding location profiles on the two proteins are quite distinct, which we determine is due to differences in pocket size, pocket environment (including hydrophobicity and electronegativity), and steric hindrance. This study provides a model system to show that peptide capture candidates can be quite selective for a structurally similar protein system, even without further maturation, and offers an in silico method of analysis for understanding binding and down-selecting candidates.
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Affiliation(s)
- Deborah A Sarkes
- Biotechnology Branch, Sensors and Electron Devices Directorate, US Army Research Laboratory, Adelphi, MD 20783, USA.
| | - Margaret M Hurley
- Biotechnology Branch, Sensors and Electron Devices Directorate, US Army Research Laboratory, Adelphi, MD 20783, USA.
| | - Dimitra N Stratis-Cullum
- Biotechnology Branch, Sensors and Electron Devices Directorate, US Army Research Laboratory, Adelphi, MD 20783, USA.
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